key: cord-331421-rioeke67 authors: valentowitsch, johann title: flattening the covid-19 curve: the impact of contact restrictions on the infection curve in germany date: 2020-07-22 journal: gesundheitswesen doi: 10.1055/a-1194-4967 sha: doc_id: 331421 cord_uid: rioeke67 although germany is coping well with the coronavirus crisis, many voices are currently being raised that fundamentally question the success of the contact restriction strategy to contain the virus. i show in this study that there is no justification for such criticism. in fact, contact restrictions have flattened the infection curve and were possibly decisive for the good german performance in the crisis. in many parts of the world, germany is seen as a model and exemplary country in the fight against the new cornavirus. compared to the rest of the world, germany has one of the lowest case fatality rates and handles the coronavirus crisis very well [2] . germany also seems to have got the infection rate under control relatively quickly. according to estimates by the robert koch institute, the effective basic reproductive number dropped below the critical mark just a few weeks after the outbreak of the disease [6] . in addition to the good german health care system, the massive political crackdown of social life is held responsible for the rapid success in disease control. in order to stop the spread of the coronavirus, german politics has largely shut down large parts of public and cultural life. schools and daycare centers were closed, companies were asked to send their employees home, and extensive contact restrictions were put in place -in short: public life was torn out of normality and, wher ever possible, put into an artificial deep sleep. however, from an economic point of view, the consequences of the social lockdown are gigantic and cannot be compared to any other crisis in the post-war period. economists recently predicted a drop in german gross domestic product up to 10 % this year [3] . in the end, the social lockdown will most likely rob many people of their economic existence and drive many companies into bankruptcy. against this background, voices were rasied early, just like in other countries that pursue a strategy similar to germany, which called for a rapid end to the drastic measures or even questioned the usefulness of the contact restriction strategy as a whole. thus, given the current situation, it is important to know how effectively the lockdown actually helps to contain the epidemic. based on this question, i will show that the contact restriction strategy has fundamentally not missed its target. even if many people question the success of the strategy, social distancing has actually led to a massive reduction in the infection rate and thus made it possible to flatten the infection curve. according to the results of my estimate, the infection rate in germany would be many times higher without contact restrictions. the temporary lockdown of social life was therefore an important and correct step to contain the disease. in this study, i look at the daily infection rate in germany and, based on a set of plausible basic reproduction numbers, estimate how the infection rate would have developed had the social lockdown not occurred. i therefore estimate a counterfactual scenario based on the actual infection dynamics that could be observed in the first weeks before the first political interventions. for the calibration of the estimate i use the number of cases documented by the robert koch institute, an independent german fe-deral authority for infectious diseases and non-communicable diseases. in my study, the calibration sample began at the end of february with the appearance of the first local outbreaks, which, unlike in january, could no longer be completely controlled by the authorities through quarantine measures. the end of the calibration sample marks march 30 th . the first political decisions that worked towards a comprehensive restriction of social contacts in germany can be dated back to march 16 [3] . for my investigation, i assumed that the effects of the corona regulations on the case number statistics will manifest themselves about 2 weeks later. i am guided by the official assessment of the robert koch institute, according to which the case statistics in germany document the situation around 2 weeks later [6] . the robert koch institute gives 2 main reasons for the delay in statistics. on the one hand, in most cases it takes about 5-7 days between being infected and going to the doctor, and on the other hand, another 7 days pass from the laboratory detection of the infection to the notification of the illness to the robert koch institute. in germany, the federal organization of health authorities can be held responsible for the comparatively long transmission of infection numbers. the german health authorities first aggregate the data at the level of individual regional districts and only then report the case numbers to the robert koch institute in berlin [6] . for the counterfactual simulation of the disease development from march 30 th , i used a branching process model based on the renewal equation [1] . the methodological approach used in this study builds on nouvellet et al. [4] . the model simulation is based on the estimation of the serial interval, which represents the duration between symptom onset of a secondary case and that of its primary case, and the estimation of the basic reproduction number, which describes the expected number of cases directly generated by one case in a population where all individuals are susceptible to infection. the serial interval was assumed to be gamma distributed with parameters taken from the literature. initial studies indicate a serial interval between 4 and 8 days for the novel coronavirus [5] . the basic reproduction number for the simulation estimates was also borrowed from the literature. the world health organization estimates that the basic reproductive count for the new type of coronavirus would be between 2 and 2.5 without state intervention [7] . based on this, each infected person would have to infect about 2 more people with the virus on average, which would lead to an exponential increase in the number of cases. simulation results are summarized in ▶ fig. 1 . as can be seen from the illustration, the social lockdown broke the infection line and greatly weakened the exponential increase in the number of infections. without political intervention, the number of infections should have been 20 to 50 times higher than at the current level. these days, not only in germany, there is much controversy about the usefulness of government interventions in social life. the debate is often emotional and is much more based on guesswork than fact. i have shown that there is currently no reason to doubt the effectiveness of the social lockdown measures. based on the results of my analysis, it is obvious that contact restrictions are contributing to the slowing down of the virus epidemic. nevertheless, the question must be asked how long such measures can be maintained without the economy collapsing or acceptance of the population disappearing. moreover, the social lockdown effect may not prove to be sustainable because people do not want to stick to the strict rules for long and neglect the risk of infection over time. however, since the disease is not yet completely contained, such negligence can overturn the positive development of infection dynamics at any time and quickly bring the development of case numbers back to the point of exponential increase. germany is currently well positioned in the coronavirus crisis, which can be attributed not least to the effect of the official contact restriction measures. other countries that decided social distancing too late or simply did not consider it as a real option for action are now much worse off and have significantly increased mortality rates. while the utilization of intensive care beds did not yet reach its capacity limit in german hospitals even at the height of the crisis, triage decisions had to be made elsewhere and patients had to be ventilated selectively [2] . the german special route, of which the rest of the world often speaks with admiration, is actually not very puzzling in itself. rather, the current situation in germany testifies to the effectiveness of the measures taken at an early stage, the success of which, however, is fragile and prone to setbacks. estimating individual and household reproduction numbers in an emerging epidemic predicting the prevalence of covid-19 pandemic in germany an economic policy exit strategy from the corona lockdown a simple approach to measure transmissibility and forecast incidence a systematic review of covid-19 epidemiology based on current evidence lagebericht des rki zur coronavirus-krankheit-2019 (covid-19) report of the who-china joint mission on coronavirus disease 2019 (covid-19) the authors declare that they have no conflict of interest. key: cord-027027-2vxnmiyj authors: schartau, patricia; kirby, mike title: male mortality and the german response: lessons from covid‐19 date: 2020-06-04 journal: nan doi: 10.1002/tre.752 sha: doc_id: 27027 cord_uid: 2vxnmiyj the current covid‐19 outbreak has raised many questions, amongst them the higher mortality rates in men and the low overall mortality rates in germany compared to other european countries. here the authors explore some of the reasons behind both these phenomena and outline what we can learn from them for the future. o n average, men die younger and are at higher risk of life-threatening ailments, including heart disease and many forms of cancer. the sars-cov-2 coronavirus appears to be following suit. in all six of the countries that, up to 20th march, had sex-specific records of deaths from covid-19, the proportion of men was higher than women. over time this was confirmed by data collected by global health 50/50 (may 6th) in countries that had a high covid-19 caseload; with death rates of 62% men and 38% women in italy, 58% and 42% (respectively) in spain, and 80% and 20% (respectively) in greece. 1 in a very recent (29th april) preliminary study published in frontiers in public health, 2 beijing researchers explored the role of gender in morbidity and mortality of a small sample of 43 patients with a covid-19 diagnosis. they concluded that while men and women have the same prevalence of infection, men with covid-19 are at higher risk for worse outcomes and death, independent of their age. the authors further investigated the data of 37 patients who had died of covid-19 from the chinese public health science data centre and found that the number of men who died was 2.4 times that of women. given the small sample sizes, no generalisation of the results is possible at this stage; however, the widely noted tendency that men are more severely affected by covid-19 and have a higher mortality rate than women holds. 2 uk data collected and analysed from 1st february-25th april 2020 confirmed (amongst other factors) a male hazard ratio of 1.99 in covid-19 related deaths when compared to females. 3 there are possible biological and behavioural explanations for this trend, as discussed in this issue's 'journal watch', which include: hormones, the immune system, genetics and the fact that older men have more (severe) comorbidities than their female counterparts. male lifestyle factors, such as a higher ratio of smoking and alcohol intake, lower compliance with handwashing advice, and delays in presentation, may play a role in explaining the above findings. evidently, poor hand hygiene in men could expose them more frequently to the virus, and to a higher viral load, which in turn can affect severity of the infection. a uk survey of >2000 adults from march 2020 found that both men and women had taken steps to protect themselves from the virus by improving their personal hygiene such as hand washing; however, fewer men (67%) than women (74%) had up-scaled their hand washing routine. 4 more research is required in order to fully explore why men are more vulnerable to covid-19. a greater in-depth understanding of the underlying biological and behavioural processes will help to inform targeted measures -a form of precision medicine where the goal is to better understand sex and gender differences in disease and drug response in order to tailor preventive measures and treatment. however, it must be remembered that covid-19 affects all of us significantly, regardless of sex and gender. in the next section, we will move to discuss how governmental and public the current covid-19 outbreak has raised many questions, amongst them the higher mortality rates in men and the low overall mortality rates in germany compared to other european countries. here the authors explore some of the reasons behind both these phenomena and outline what we can learn from them for the future. no there has been much debate about why germany has one of the lowest fatality rates in europe. as per the 11th may 2020, 171 879 cases of covid-19 have been identified and 7569 deaths registered, giving a fatality rate of 4.4%. as shown in figure 1 , this compares with, for example, fatality rates of the uk (14.53%) and france (15.04%). 5 as it happens, one of the authors (ps) of this article was in the small town of landsberg for a meeting on the day when germany's first covid-19 case was recorded there: the patient was a male who worked for a company that has two car plants in wuhan in china. the author spent the following days in munich and was particularly struck by the speed at which the local health department and federal authorities acted. within a couple of days of the first case being recorded, contacts had been identified and quarantined, and the company closed its bavarian plant in addition to the ones based in china in order to contain the outbreak. the public was informed locally and nationally about the case and measures were taken without any delay. this early action is an example of the coordinated and rapid response that defines how the german authorities have dealt with the current covid-19 situation. the german healthcare system has been persistently modernised over the last 20 years, which certainly put germany in a good position to deal with the covid-19 pandemic. the result of this was more hospital beds, more ventilators, more intensive care unit (icu) beds and more hospital doctors per capita than any other comparable country in europe. 6, 7, 8 in addition, community specialist practices and a dense network of primary care physicians provided a strong backbone to support hospital care during the outbreak. germany was one of the first countries to initiate so-called social distancing measures. this allowed the early shielding of the elderly population while a meticulous tracing of the chain of infections was undertaken in order to suppress spread. the government made optimal use of the time available after the first cases emerged in southern germany, upscaling bed capacity, joining the ppe eu procurement scheme, and mobilising the diagnostics industry that was already well established. furthermore, the government listened to scientific advisors and drew them in early to the decision-making process. as mentioned, in germany the diagnostics infrastructure was readily in place and scaled up upon the emergence of covid-19 cases. this allowed germany to become one of the first countries to develop a reliable covid-19 test as early as january, and to initiate widespread testing. from early on, for example, germany tested >20 people per thousand (as compared to the uk, which tested 5.54 per 1000). 9 in the bmj, 10 christian drosten, virologist at the berlin university hospital charité, highlighted that in germany testing is done across an array of quality-controlled labs rather than relying on a central lab for all processing and testing. as a result, early widespread testing resulted in up-to-date analysis of current infection trends and timely countermeasures, increased identification of mild cases and, therefore, a lower overall case fatality rate. in germany, regular national updates were held where the current situation was summarised, scientific evidence discussed, and the rationale for decisions laid open to the public. 11, 12 broader society, possibly as a result of the transparent communication strategy, mostly followed the measures implemented or recommended by the government. however, there is admittedly no reliable source of data to suggest that this was adhered to more (or less) in germany as compared to other european countries. an additional reason for the robust management of the covid-19 crisis by the german healthcare system up to this point is the digitalisation that has taken place, particularly over the past two years and more rapidly over the past weeks and months. this has started to move germany to a partially digitalised system. at the end of last year, the german government passed the digital care act (dca). 13 this enables, amongst others, an expansion of telemedicine to all medical specialties and affiliated healthcare professionals -offered free of charge in the covid-19 related context. the german government developed strategies to encourage production and widespread usage of ce-certified covid-19 chatbots and triage apps by established authorities (for example, the robert-koch-institut), all of which happened within days and weeks. digital prescribing is following suit. in light of the dca and covid-19, a vibrant german digital health ecosystem has emerged rapidly, covering anything from screening, prevention and diagnosis to treatment and rehabilitation. and many of these companies have switched to a free service in covid-19 times. 13 the german national health innovation hub that was formed a couple of years ago by the ministry of health has incorporated an up-to-date covid-19 section on their website that summarises, signposts and evaluates digital applications relating specifically to covid-19 and distributes this in a daily newsletter. 14 furthermore, in search for covid-19 solutions, the german government organised a covid-19related hackathon (an event where people collaborate to try and initiate solutions to technical problems within a certain time frame, in this case within 48 hours) in march. this led to the selection of 20 out of 1500 projects aiming, for example, to optimise national ppe distribution, the delivery of food and medicines, communication relating to infection control, and local business support, to name but a few. 15 over the last months, germany has been catching up fast with other countries, such as the uk, where digital healthcare solutions such as telemedicine and digital prescribing were already well embedded prior to covid-19. in addition to developing digital health interventions and system optimisations, researchers and developers in the uk and across europe have been working to determine whether existing technologies can be given new applications to assist with the pandemic. examples of such innovation include: mobile phone location data to predict disease spread and the impact of interventions such as social distancing; robots designed to clean hospitals; drones to deliver food to patients; health tracker apps to monitor for potential covid-19 symptoms; new equipment designs, such as the ventilator challenge uk consortium to provide more than 10 000 ventilators; the involvement of private industry experts from formula one, dyson, and 3d printer companies to develop new devices in record time; and the use of ai algorithms for speedy drug development. 16, 17, 18 the successful management of covid-19 is clearly multifactorial and will change as more deaths across europe are unfortunately inevitable. nevertheless, we can conclude that up to this point, germany's covid-19 management has been exemplary and there is a lot to learn from the country's healthcare, communication and policy strategies. across the world, once the pandemic starts to subside, further comparative and collaborative analysis of strategies and policies is required in order to better prepare us globally for future pandemics. what is evident from the current situation is that an effective future response requires the sharing of information and collaboration across nations. mike kirby has received funding from the pharmaceutical industry for research, travel and educational initiatives; however, no funding was directly related to the writing of this article. gender differences in patients with covid-19: focus on severity and mortality gender differences in patients with covid-19: focus on severity and mortality opensafely: factors associated with covid-19-related hospital death in the linked electronic health records of 17 million adult nhs patients most americans are worried about covid-19-but not republicans covid-19) death rate in countries with confirmed deaths and over 1,000 reported cases as of the countries with the most critical care beds per capita leads europe in hospital bed capacity. statista germany has a low coronavirus mortality rate: here's why what can data on testing tell us about the pandemic covid-19: why germany's case fatality rate seems so low the leader of the free world gives a speech, and she nails it making the fight against the coronavirus pandemic sustainable here to stay: digital health in times of covid-19 -a german deep dive corona -sars cov 2 -covid-19 the #wirvsvirus hackathon. wirvsvirus china's tech fights back ventilator challenge uk to start production in covid-19 fight ai-designed drug to enter human clinical trial for first time key: cord-337037-xpj17vn4 authors: weigel, ralf; krüger, carsten title: global child health in germany time for action date: 2020-10-09 journal: global health action doi: 10.1080/16549716.2020.1829401 sha: doc_id: 337037 cord_uid: xpj17vn4 child health is central to the sdg agenda. universities in the uk and other european countries provide leadership in research and education for global child health to inform related policy and practice, but the german contribution is inadequate. german paediatricians and other child health professionals could make more substantial contributions to the debate at home and internationally, but lack opportunities for scholarship and research. we argue, that there is a momentum to advance global child health in academia and call on german universities to realise this potential. 'viruses don't need visas, pathogens don't need passports' -the world health organization (who) director-general's urgent message to the participants of the world health summit in berlin in 2017 is more relevant today than ever [1] . the impact of the sars-cov-2 pandemic on children is a powerful reminder in this regard [2] and other threats are looming [3, 4] . germany, like other highincome countries, is a beneficiary of globalisation. however, benefits come with responsibilities: as a signatory of the sustainable development goals (sdg) 2016-2030, germany committed to advance health globally [5] . child health and well-being are central to the sdg agenda illustrating our responsibility for future generations [6, 7] . unfortunately, global child health in germany is somewhat neglected in research and education. we need a major effort to improve the situation. in germany, global child health institutions and the scientific debate are still in their infancy compared to other european countries. in the uk (uk), the centres at the university college london, the london school of hygiene and tropical medicine, the liverpool school of tropical medicine, and other universities have active research groups in global child health as an integral part of maternal, newborn, child and adolescent health. the royal college of paediatrics and child health annual meetings regularly devote entire days to global child health research and training. global child health topics regularly feature in the college's scientific journal. universities in italy, the netherlands, norway and sweden have institutes dedicated to international maternal and child health. at the universities in utrecht, london and liverpool, under-and postgraduates can attend various courses on global child health. in sweden, the institute for global health transformation initiated a multidisciplinary forum hosted by the royal swedish academy of sciences, which resulted in a roadmap on global child health with five priority areas in the context of the sdgs [8] . although germany has successful research groups in maternal and child public health that collaborate internationally, for example at the universities in hamburg, heidelberg and munich, there is no such overarching forum to share ideas, to develop strategies and to provide direction. it is the private witten/ herdecke university that has the only professorship for global child health, funded by the friede springer foundation [9] . the german society for tropical paediatrics and international child health (gtp) is a professional society established almost 40 years ago with about 400 current members which brings together paediatricians with different backgrounds at its annual meetings and offers a range of trainings, but its mandate for research is limited [10] . the academic global child health landscape in germany is fragmented, without a dedicated chair at a statefunded university and with little collaboration between different actors. however, there are also deeper and more systemic reasons why german global health research and education as a whole are underdeveloped [11, 12] . for contact ralf weigel ralf.weigel@uni-wh.de friede springer endowed professorship for global child health, witten/herdecke university, witten 58448, germany example, the abuse of public health by the nazi regime for their racial hygiene policies and atrocities descredited the field and left a stain that still affects perceptions today [13, 14] . currently, public health research is concentrated at several federal institutions, such as the robert koch institute (rki) and the federal centre for health education (bzga). but, compared with universities, their scholarly role is limited. at the local level, public health interventions are implemented by public health offices that have no formal academic role [15] . furthermore, global health policy programmes in germany are distributed over six ministries and international health programmes are funded to a large degree not by the ministry of health but the federal ministry for economic cooperation and development. its main implementers, the society for international cooperation (giz) and the kreditanstalt für wiederaufbau (kfw), a promotional bank owned by the state, have little focus on academic research and education. thus, the historical heritage, and the policy and funding structure appear to be barriers that may have contributed to the slow development of an academic base in global health in general [16] and global child health specifically. within this historical and structural context and with weakly organised public or global health institutions, it is not surprising that german paediatricians are hard to find in scientific landmark publications, guidelines and reports of global relevance. in the 108page global strategy 2016-2030 for the health of women, children and adolescents [17] , a groundbreaking document for the global health of mothers and children, no german name is found in the recognition and author lists, similar to the 16 review articles in the bmj special issue 2015, which provides the scientific background for the strategy [18] . of the 471 organisations that contributed to the development process of the strategy, only five came from germany [19] . the same applies to the who publications 'standards to improve the quality of care for mothers and newborn babies in health care institutions' from 2016 [20] and 'standards to improve the quality of care for children and adolescents in health care institutions' from 2018 [21] . among the authors from more than 100 institutions, only three and seven, respectively, are from germany, and only in one case from a paediatric professional society. similarly, of the institutions involved in 'the 2019 report of the lancet countdown on health and climate change: ensuring that the health of a child born today is not defined by a changing climate', 10 come from the us, 11 from the uk, five from other european countries, including one from germany, and five from other, non-european countries [4] . although this lack of representation is not necessarily a sign of a lack of participation in the international scientific debate, the few opportunities german researchers have to engage in global child health research and education at universities suggest that this is, in fact, the case. without academic leadership, a lively exchange of ideas, a research agenda and funding, it is hard to participate and to be heard. without global child health institutes, students and young researchers have few opportunities and academic career prospects, preventing them from engaging in research and applying for funding. our research and educational institutions need to provide a better environment for child health professionals that they can move the global scientific and policy debate forward and contribute more substantially to the global research agenda. many opportunities exist for paediatricians and other health workers caring for children to engage with the realities of global child health in research and education. for example, in 2015/2016, some 350,000 children and their families came to germany to seek refuge, many of them vulnerable with multiple risks and in urgent need of health care [22, 23] . their physical and mental health needs and strategies to meet them are important to share [24, 25] . what are the enablers and barriers to their integration in the health care and education system, viewed from a child rights perspective [26] ? germany's development cooperation focus on health systems strenghtening offers further opportunities. the initiative 'hospital partnerships -partners strengthen health' financed by the federal ministry for economic cooperation and development and the else kröner-fresenius foundation, supports 181 projects with institutions from 51 low-and middle-income countries, several of them focusing on mother and child health [27] . the german academic exchange service (daad) has helped to establish 28 cooperations between universities in germany and low-and middle-income countries with its 'partnership for health care in developing countries' programme [28] , some addressing maternal and child health. rigorous evaluation of the short and long term effects of interventions implemented within these partnerships, for example on human resources or on child health outcomes, would also make a substantial contribution to the field. it is time for german universities to use this potential to strengthen research and education in global child health -there is momentum to realise this. the sars-cov-2 pandemic has fuelled a debate of how social determinants, such as access to education, affect health, well-being and development of children in germany and elsewhere [29, 30] . children are leading in advocacy for their own for their right to health in the context of climate change, holding world leaders accountable in the fridays-for-future movement. the experiences of families while educating their children at home during lock-downs due to the pandemic as well as the voices of children concerned about climate change are making headlines in the media [31, 32] . this may represent an opportunity to leverage global child health concepts, such as social and environmental determinants of health and child rights, higher on the policy and research agenda. as germany is updating its global health strategy, receiving valuable advice from various professional organisations [33, 34] , global child health has to become a core element of this strategy, building on and developing further existing initiatives. a recent discussion paper, published by the commission for global child health of the german academy for child and adolescent medicine (dakj), listed several recommendations for improving the landscape of global child health research and education [35] . in addition, the german society of tropical paediatrics and international child health and the named dakj commission will continue to lobby for the inclusion of global child health into the planned german centre for child health, funded by the federal ministry of education and research [36] . and the recently founded global health hub germany [37] and the german alliance for global health research [38] are also prime opportunities for building institutional capacity. to date, the global child health agenda has had limited visibility in germany. we call on the academic leadership of paediatric professional societies in germany to provide a forum for the scientific and political aspects of global child health, to provide leadership and to lobby for funding from the government. paediatric researchers should respond more actively to calls from multilateral agencies like who [39, 40] and make public their positions on issues such as child rights [41] . medical faculties need to strenghten their academic base by offering under-and postgraduate education in global child health through institutes and chairs so that students and young researchers see a path for their careers. we must now seize the opportunities unfolding for urgently needed engagement in this important field in research and education. german universities can and should play a much more active part in advancing the health and well-being of children throughout the world. viruses don't need visas, pathogens don't need passports early estimates of the indirect effects of the covid-19 pandemic on maternal and child mortality in low-income and middle-income countries: a modelling study climate change and global child health: what can paediatricians do? the 2019 report of the lancet countdown on health and climate change: ensuring that the health of a child born today is not defined by a changing climate united nations department of economic and social affairs. the sustainable development goals report placing children and adolescents at the centre of the sustainable development goals will deliver for current and future generations a future for the world's children? a who-unicef-lancet commission swedish institute fo global health transformation. a new roadmap on global child health germany's expanding role in global health german society for tropical paediatrics and international child health global health education in germany: an analysis of current capacity, needs and barriers global health research and education at medical faculties in germany results presented of the research project confronting the past: contemporary german paediatric response to medical practice in the third reich statutory health insurance in germany: a health system shaped by 135 years of solidarity, self-governance, and competition germany's expanding role in global health every women every child. the global strategy for women's, children's and adolescents health towards a new global strategy for women's, children's and adolescents' health participating organizations: fhi360 standards for improving quality of maternal and newborn care in health facilities geneva standards for improving the quality of care for children and young adolescents in health facilities accumulated environmental risk in young refugees-a prospective evaluation recommendations for the diagnosis and prevention of infectious diseases in pediatric and adolescent refugees in germany: statement of the german society of pediatric infectious diseases, the society of tropical pediatrics and international child health mental health needs of refugee children in specialized early education and care programs in germany immunization coverage among refugee children in berlin unaccompanied refugee minors in germany: attitudes of the general population towards a vulnerable group else kröner fresenius-stiftung. initiative hospital partnerships pagel -partnerships for the health sector in developing countries covid-19 and its impact on child and adolescent psychiatry -a german and personal perspective children and adolescents in the covid-19 pandemic: schools and daycare centers are to be opened again without restrictions. the protection of teachers, educators, carers and parents and the general hygiene rules do not conflict with this after two years of school strikes, the world is still in a state of climate crisis denial we swallowed our misgivings'; 2020 statement of the international advisory board on global health: global health centre, the graduate institute of international and development studies deutsche gesellschaft für public health deutschland und sein engagement für die gesundheit der kinder weltweit federal ministry of education and research. startschuss für zwei neue deutsche zentren der gesundheitsforschung deutsche gesellschaft für internationale zusammenarbeit (giz) gmbh. global health hub germany berlin charité global health. german alliance for global health research berlin who hospital care for children guidelines: what do users need? new who standards for improving the quality of healthcare for children and adolescents the budapest declaration for children and youth on the move-comment in the lancet child and adolescent health we thank william christopher buck for proofreading the manuscript. rw wrote the draft manuscript, which ck reviewed. both authors read and approved the final version. rw holds the friede springer endowed professorship for global child health at the witten/herdecke university. ck is currently the chairperson of the german society of tropical paediatrics and international child health and the spokesperson of the committee of global child health of the german academy of child and adolescent medicine. not applicable. the authors have no funding to report. this call to action addresses child health professionals and stakeholders to engage in research and education for global child health at germany's higher education institutions. universities should realise the momentum and recognise the importance of global child health to enable substantial contributions to the scientific and policy debate at the national and global levels. http://orcid.org/0000-0001-9034-2634 carsten krüger http://orcid.org/0000-0001-7936-7689 key: cord-028201-x57bhyhr authors: platz, thomas; bender, andreas; dohle, christian; gorsler, anna; knecht, stefan; liepert, joachim; mokrusch, thomas; sailer, michael title: german hospital capacities for prolonged mechanical ventilator weaning in neurorehabilitation – results of a representative survey date: 2020-07-01 journal: neurol res pract doi: 10.1186/s42466-020-00065-1 sha: doc_id: 28201 cord_uid: x57bhyhr a brief survey among members of the german neurorehabilitation society aimed to document the hospital capacities (“beds”) for prolonged weaning from a mechanical ventilator for patients with neuro-disabilities that require simultaneous multi-professional neurorehabilitation treatment. sixty-eight institutions declared to have capacities with a broad distribution across germany and its federal states. overall, 1094 “beds” for prolonged weaning (and neurorehabilitation) were reported, 871 together with further information regarding their identification and hence regional location. these units had on average 16.1 beds for prolonged weaning (95% confidence interval 12.6 to 19.6) with a range from 2 to 68 beds per organization. the data indicate substantial capacities for the combined prolonged weaning and neurorehabilitation treatment in germany. for most “beds” included in this analysis a basic validation was possible. while a reasonable coverage of these specialized service capacities by the survey is likely, the number reported could still be biased by underreporting by non-response. both the broad variation of number of “beds” for prolonged weaning per unit and their unequal geographical distribution across federal states (per capita rate) warrant a more refined follow-up survey that will provide insights into reasons for the observed pattern of variation for these specialized hospital capacities. weaning is the medical process of withdrawing ventilator support. prolonged weaning describes a situation of initial weaning failure, i.e. when more than three spontaneous breathing trials (sbt) or 7 days from the first sbt are required, and hence prolonged weaning care [1] . in specialized pulmonologic weaning centers, about 50% of all patients with initial weaning failure can be liberated from mechanical ventilation [2] . however, a substantial subset of patients in need for prolonged weaning treatment is also affected by neurodisabilities and requires the combination of prolonged weaning treatment and multi-professional neurorehabilitation to address their various needs for improving both their health, body functions, and autonomy with activities of daily living [5] . in a german cohort, 26% of 754 patients admitted for "early neurorehabilitation" were on mechanical ventilation commencing their neurological rehabilitation; their weaning rate from mechanical ventilation was 65% during their stay [4] . while there is a considerable need for such a specialized combined service with proven effectiveness, there is a lack of knowledge about such hospital capacities that are currently available in germany. the german neurorehabilitation society (deutsche gesellschaft für neurorehabilitation, dgnr e.v.) conducted a survey among its members to document hospital capacities ("beds") for prolonged weaning for patients with neuro-disabilities that require simultaneous multiprofessional neurorehabilitation treatment ("neuro-weaning beds"). by email invitation end of december 2019 and a repeated invitation at the beginning of january 2020, 381 members of the dgnr were invited to participate in a short online survey. they were asked to answer two questions hosted on the platform invote.de (provided by netzmanufaktur gmbh, theaterstraße 4, 01067 dresden): 1. number of "neuro-weaning beds" in their hospital 2. combined question to indicate number of "neuroweaning beds", organizational background (acute care hospital versus rehabilitation facility), name of the hospital, and name of head of department. by repeating the question for number of beds and by asking for more detailed (identifying) information, the validation of entries was sought to be promoted. in addition, society members were encouraged to make sure within their hospital by contact with their head of department that data entry was provided only once per hospital to prevent reporting in duplicate. all entries were screened for validity. based on hospital name and head of department name the location of each unit within one of 16 german federal states was coded. the number of "neuro-weaning beds" per federal state was divided by population statistics for that state as published by the german federal agency for statistics [7] to obtain the rate of "neuro-weaning beds" per 1.000.000 inhabitants. descriptive statistics were generated using the software package sas. sixty-nine of a total of 123 survey respondents indicated that their hospital provides capacities for combined prolonged weaning and neurorehabilitation ("neuro-weaning beds"). one entry was regarded as "invalid entry": the entry stated "135" (beds) without further information and was not used for the descriptive statistics (as stated below). the 68 remaining units had a total of 1094 "neuroweaning beds", on average 16.1 beds (95% confidence interval 12.6 to 19.6) with a range from 2 to 68 beds per organization. given a total population of 82.792 thousand inhabitants in germany [7] this statistic would imply a capacity of 13.2 "neuro-weaning beds" per 10 6 inhabitants. as a sensitivity analysis we further analyzed the subset of data from units that gave more detailed (identifying) information (n = 57). collectively these units reported 871 "neuro-weaning beds" with on average 15.3 beds for prolonged weaning (95% confidence interval 11.7 to 18.8) and a range from 2 to 68 beds per organization. three of these units were specialized for health care in children and adolescents (22 beds), two units for people with spinal cord injury (12 beds). the (subset of) units that reported "neuro-weaning beds" together with their identification served as basis to describe their distribution across federal states in germany (see table 1 ). this representative survey indicated substantial hospital capacities for combined prolonged weaning and neurorehabilitation with a total of 1094 "neuro-weaning beds" in germany. for 871 of these "neuro-weaning beds" identifying information was available supporting the survey's validity. as with any voluntary survey, there is a relevant risk of underreporting. thus, the true number of "neuroweaning beds" in germany is likely to be higher than the one reported here. the number of "neuro-weaning beds" within individual reporting hospitals varies considerably (from 2 to 68 beds) with an average of 16 beds and a 95% confidence interval ranging from 12 to 19. this indicates both a central tendency for organizational size and substantial differences in organizational settings. the analysis of the geographical distribution across federal states of germany was based on the 80% of "neuro-weaning beds" reported with identifying information. hence, this analysis suffers from an "incomplete data" bias and absolute numbers should be interpreted with great caution. the data nevertheless points to a huge variability of population-based density of "neuroweaning beds" (per 10 6 inhabitants for german federal states) in germany. the survey generated a crude estimate of hospital capacities ("beds") for prolonged weaning from a mechanical ventilator for patients with neuro-disabilities that require simultaneous multi-professional neurorehabilitation treatment. the substantial variability in size of units and their geographical distribution warrants a more refined follow-up survey to learn about the setting and organizational structures of such units before further conclusions can be drawn. however, this survey already confirms the high relevance of these "neuro-weaning" capacities for the recovery from breathing failure and hence the avoidance of long-term intensive home care. the number of people in need for invasive long-term ventilation in germany dramatically increased over the past 15 years to an estimate of currently 20.000 patients, implying additional health care costs of around 4 billion euros per year [3] . it is estimated that approximately 10.000 patients with neuro-disabilities in need for weaning from mechanical ventilation can be taken care of each year with the capacity of 1094 "neuro-weaning beds" of this survey. given a success rate of 65 to 75% [4, 6] , they collectively might prevent an estimated 7000 new cases of long-term ventilation per year, let alone the other neurorehabilitation achievements in terms of disability reduction and re-gaining autonomy with activities of daily living. weaning from mechanical ventilation s2k guideline "prolongiertes weaning tremendous increase of home care in ventilated and tracheostomized patients -reasons, consequences, solutions rehabilitationsverlauf von patienten in der neurologisch-neurochirurgischen frührehabilitation: ergebnisse einer multizentrischen erfassung im jahr 2014 in deutschland. nervenarzt prolonged weaning during early neurological and neurosurgical rehabilitation: s2k guideline published by the weaning committee of the german neurorehabilitation society (dgnr) factors influencing weaning from mechani-cal ventilation in neurological and neurosurgical early rehabilitation patients kapitel 2 bevölkerung, familien springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations the help of katherina rupp, medical documentation assistance is gratefully acknowledged. authors' contributions tp collected, analyzed, and interpreted the data regarding "neuro-weaning beds" and wrote a first draft of the manuscript. all authors read and edited the manuscript, and approved the final manuscript.authors' information thomas platz acts as president of the dgnr, christian dohle as president elect, thomas mokrusch as past president. this work was supported by the bdh bundesverband rehabilitation e.v. (charity for neuro-disabilities) by a non-restricted personal grant to tp. the sponsors had no role in the decision to publish or any content of the publication. the datasets generated during this survey are not publicly available, since no consent to share the hospital-based information has been obtained. confidential inspection of the data is possible at the site of the corresponding author on reasonable request.ethics approval and consent to participate not applicable. not applicable. the authors declare that they have no competing interests. key: cord-252343-a85wz2hs authors: skoda, eva-maria; teufel, martin; stang, andreas; jöckel, karl-heinz; junne, florian; weismüller, benjamin; hetkamp, madeleine; musche, venja; kohler, hannah; dörrie, nora; schweda, adam; bäuerle, alexander title: psychological burden of healthcare professionals in germany during the acute phase of the covid-19 pandemic: differences and similarities in the international context date: 2020-08-07 journal: j public health (oxf) doi: 10.1093/pubmed/fdaa124 sha: doc_id: 252343 cord_uid: a85wz2hs background: healthcare professionals (hps) are the key figures to keep up the healthcare system during the covid-19 pandemic and thus are one of the most vulnerable groups in this. to this point, the extent of this psychological burden, especially in europe and germany, remains unclear. this is the first study investigating german hps after the covid-19 outbreak. methods: we performed an online-based cross-sectional study after the covid-19 outbreak in germany (10–31 march 2020). in total, 2224 hps (physicians n = 492, nursing staff n = 1511, paramedics n = 221) and 10 639 non-healthcare professionals (nhps) were assessed including generalized anxiety (generalized anxiety disorder-7), depression (patient health questionnaire-2), current health status (eq-5d-3l), covid-19-related fear, subjective level of information regarding covid-19. results: hps showed less generalized anxiety, depression and covid-19-related fear and higher health status and subjective level of information regarding covid-19 than the nhps. within the hp groups, nursing staff were the most psychologically burdened. subjective levels of information regarding covid-19 correlated negatively with generalized anxiety levels across all groups. among hps, nursing staff showed the highest and paramedics the lowest generalized anxiety levels. conclusions: in the context of covid-19, german hps seem to be less psychological burdened than nhps, and also less burdened compared with existing international data. the covid 19 pandemic reached germany in late february 2020. it brought not only objective medical challenges for healthcare professionals (hps), but also reports and findings from other more affected countries. due to exponentially increasing case numbers and large numbers of patients requiring intensive care, those more affected countries are facing unexpected challenges. countries such as china, italy, spain, brasil and the usa were and are currently reaching the limits of their healthcare systems in the context of this pandemic: something that was previously unimaginable in industrialized countries. 1 such a development seems to have been avoided in germany but is not completely ruled out for the future. in the face of an ever-renewing european and a further worldwide escalation, there is no shortage of uncertainty and concern among hps. it is already known from countries other than germany that hps are under elevated psychological stress during the covid-19 pandemic and show increased levels of various psychometric values, including anxiety and depression. 2-5 existing evidence, e.g. from china, already shows the extent of the psychological burden on hps. front-line healthcare workers were identified as bearing a particularly heavy psychological burden. 2,6 however, these studies were conducted during the extreme stress phase of the covid-19 epidemic in china. only few data in the context of other studies suggest that, e.g. in the uk, a heightened psychological burden for the hps may exist. 7 there is, as yet no comparable data, especially from a time when the health system is still mainly coping normally, alongside already population-wide uncertainty, particularly in europe. the german situation to this point is 2-fold: continuing and past restrictions in public life, contact restrictions, empty supermarket shelves and daily updated increasing case numbers are still coupled with a hospital system that is and was largely still able to cope normally. this is combined with mortality rates, which are, for the moment, low when compared internationally. 8, 9 though, the german population shows itself already burdened in terms of generalized anxiety, depression and distress, which is in line with evidence from other countries, 10,11 customized low-threshold interventions, offline as well as online, are needed and already implemented. [12] [13] [14] the aim of this study was to close the research gap and provide initial findings on psychological burden of german hps after the covid-19 outbreak. it is hypothesized that the group of hp in germany will mirror the existing, population-wide elevated psychological burden 15 to an even greater extend by being in the 'front line', as already could be observed in previous studies in other countries. 2,3 a nationwide, online-supported cross-sectional survey was conducted. participants were recruited via online channels and official channels e.g. websites of clinics. the survey period was from the 10-31 march 2020. it was during this period that the first increased numbers of covid-19 cases in germany, increasingly restrictive government regulations, the closure of european borders and the restriction of individual freedoms occurred. in total, 12 863 people completed the questionnaire, of which we identified 2224 people in the medical sector as hps and 10 639 as non-healthcare professionals (nhps). hps were from three different groups: physicians, nursing staff and paramedics. the sample description can be seen in table 1 . all participants gave their written consent to participate in the survey and the evaluation of the collected data. the study was conducted in accordance with the ethical guidelines from the declaration of helsinki and was approved by the local ethics committee of the faculty of medicine. details of general socio-demographic variables were asked. validated psychometric instruments were used to assess psychological burden. the generalized anxiety disorder-7 (gad-7) to measure generalized anxiety symptoms over the course of the last 2 weeks (gad-7, 7 items, 4-point likert scale meaning 0 = never to 3 = nearly every day), 16 the patient health questionnaire-2 (phq-2) to screen for depression symptoms over the course of the last 4 weeks (phq-2, 2 items, 4-point likert scale meaning 0 = never to 3 = nearly every day) 17 and the visual analogous scale of the euroqol eq-5d-3l scale to assess current health status (ranging from 0 [worst imaginable health status] to 100 [best imaginable health status]). 18 additionally, based on scientific and media reports, multiple items and item scales were formed in expert consensus with regard to 'covid-19-related fear' (one item, 7-point likert scale meaning 1 = very low to 7 = extremely high), 'the subjective level of information regarding covid-19' (3 items: i feel informed about covid-19; i feel informed about measures to avoid an infection with covid-19; i understand the health authorities' advice regarding covid-19. seven-point likert scale, meaning 1 = complete disagreement to 7 = complete agreement). scale reliability for was tested using cronbach's α for internal consistency. 'the subjective level of information regarding covid-19' showed high internal consistency (cronbach's α = 0.801). the descriptive and inferential statistics were performed with r3.6.1 (r core team, 2019). sum scores for the gad-7 and phq-2 and mean scores for all other scales were calculated. to assess the hypotheses, the 95% confidence of the association measures are reported; for each difference between the groups after having assessed the global mean difference in the respective scale. hence, the assumptions were assessed based on their precision. [19] [20] [21] generally, test statistics and p values are not reported given that at this sample size even the slightest deviation from equivalence results in extremely low p values. when the confidence interval (ci) of the effect size covers 0, we assume there is no effect. as soon as this is the case, we use the guidelines by sawilowsky 22 to evaluate the importance of the effect; a cohen's d ∼0.2 is considered a small, a d ∼0.5 is considered medium-sized and d ∼0.8 is regarded as large effects. due to the large sample size and the intuitive and common interpretation of the effect sizes, parametric methods were also used for violation of the normality assumption. 23 for mean comparisons welch's t-test with the cohen's d association measure was used, for multiple mean comparisons and between-subject analysis of variance with the association measure η 2 with subsequent t-tests for post hoc comparisons with tukey error correction. a complete summary of all post hoc group comparisons after calculation of the variance analyses and post hoc tests can be assessed in the supplementary materials. to clear the association of subjective level of information regarding covid-19 and other variables, spearman correlations between variables were performed. to subsequently test the interdependence of variables a robust linear mestimator regression was performed (rlm from the r package mass, 2002). all spearman correlations including confidence between the measures are provided in the supplemental material. following the results of the correlation analyses, prevalence ratios for the amount of participants with moderate generalized anxiety in relation to the subjective level of information regarding covid-19 were explored. levels of generalized anxiety were divided by using the gad-7 sum score of ≥10 24 as a split into low levels of generalized anxiety (<10) and moderate to high levels of generalized anxiety (≥10). this was compared with a pre-covid-19 standard population, where 5.9% of the population scored above ≥10. 25 the subjective level of information regarding covid-19 was split by the median into high (≥median) and low ( 0. this means we can restrict analysis for example to t c = 1 and vary only d · p and x 0 . the other scale invariance is described by "x(·) solution of ode(dp, t c , n, instead of a further analytical proceeding, the above equation's evolution was examined via computer simulation, for various parameter choices d · p and initial values. the purpose is first to explore the general (i.e. not real-data matched) behaviour of equation (2) (next subsection), then to fit the parameters to observed real data (section 4). throughout it was used n = 1.0, t c = 1 and a (forward euler) discretization step size of 0.01 (corresponding to resolution=100 in code). the below discusses general features of the model and its behaviour under parameter variations. this is for demonstration only, and arguments on the proliferation phenomena should be taken as schematic. (whether the phenomena occur in the real parametrization is to be discussed in section 4.) fig 1a shows the evolution behaviour for some arbitrary but temporally constant parameter set. the most striking feature at this graph is that the number of infections asymptotically does not reach the total number n of agents. rather, the limit is a value x(∞) < n which depends on the d · p and the initial value. for comparison, the evolution of the number of infections as would arise when observing eqn. (1) [with same d · p parameter] is depicted as grey dashed line; in it, the x(t) converges to n independent of the choice of d · p. (in subsequent text, this will be referred to as "bounded exponential growth".) the reason for including this curve here and in following graphs is that it can give a hint on trajectories of future viruses that may have a much more extended infectiousness interval. in fact, this curve would result if infected individuals remained infinitely long infectious and were not quarantined. in simulations, the dependence of the limit x(∞) on d · p appeared to be generally overproportional (see fig 1b) . this is well-known behaviour also in the instantaneous-state models. on the other hand, the dependence of the limit on x 0 was linear or sub-linear. in instantaneous-state models, the limit does not depend on the size of the initiating jump of noteworthy is (in both cases) that even though the same number of exogenously infected was used as initially, the contagion effect is much smaller. the reason for this is that already about one fifth of the population had been infected (thus was immune in this model). 6 all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in the copyright holder for this this version posted august 22, 2020. . https://doi.org/10.1101/2020.08.20.20178301 doi: medrxiv preprint we use here the number of reported covid-19 cases (as aggregated by the robert-koch-institut [1]) as a proxy for the number of infections in germany. 4 we fit parameters for the interval until beginning of may 2020, assuming that the evolution proceeded within two different parameter regimes: first a d · p corresponding to no restrictions, then a d · p corresponding to the restrictions posed by contact disencouragement and store closure. (the observational interval used for parameter estimation does cover only a few days of the time of obligatory indoor face mask wearing.) we can derive parameters and based on them predict the trajectory of infections way forward. because of the simplicity of the examined model, there is the risk of a high model error existing. therefore, at the present state of this text, such estimation can only serve to determine reasonable bounds on the parameters of the model, rather than to give a reliable forecast of expect number of eventual infections. fitting of parameters is here conducted manually, focussing on moments in the time series that are indicative of parameter changes. at the beginning of april 2020, the number of weekly new covid-19 cases stood at about 40000 in germany. if we regard the modelling time unit to correspond to a real duration of 2 weeks (implying that each individual newly infected is non-contagious two weeks after and onwards), then we have a new-infections rate of 80000 individuals per such time unit which corresponds to an increment of approximately ∆x = 0.001 per unit time after normalizing to n = 1.0. identifying the moment which was one week after the initial wider lock-down in germany (i.e. around 29th march) as moment t = 3 in the modelling, parameters consequently need to be fitted such thatẋ(3.0+) = 0.001 (green line). (the t = 3.0 also implies that the model assumes around 6 weeks of initial evolution under a low-restrictions scenario, which matches the timeline of the outbreak in germany approximately.) fig 3a shows the trajectory of the system evolution using initially d·p = 1.42 and switching to d·p = 0.7 afterwards. fig 3b shows the evolution if no parameter switch (i.e. no intervention) had happened at t = 3.0. note: the matching is overly simplified for the interval t ∈ [0, 3.0], leading to an overestimated x(t), since for example x(3.0) = 0.0025 -corresponding to 200000 individuals-, while the actually reported number was around 52550. in reality, the d · p must have been larger than 1.42 at the beginning of the interval, but on the other hand closer to (but above) 1.0 in the second half of [0, 3.0]. assuming an infected individual occupies an intensive-care bed with ventilator (icu) for one to two weeks, the icu capacity in germany currently is about 12500 to 25000 icu cases per week. this allows for a maximum of 87500 to 175000 reported infections per week (assuming share of cases needing intensive care around 14.28%), i.e. 175000 to 350000 reported infections per two weeks. this in turn corresponds to a normalized increment of 0.0021875 to 0.0043750 per time unit (a horizontal line somewhere in the upper half of the graphs in fig 3) . it is necessary to remark that the conclusion drawn in connection with fig 2e and 2f i.e. that a second outbreak of similar magnitude as initially would not effect a substantial increase in the accumulated number of infected individuals -cannot be affirmed for the current scenario (in germany and elsewhere), since that number is rather about 0.25% to 0.5% of total population currently, rather than the 1/5 prevailing in the demo scenario in fig 2e and 2f at the onset of the second outbreak. the challenge with lockdown measures for the current corona virus is the following: when imposing them, they will show effect only if the basic reproduction number is pushed below 1 sufficiently enough. then, after the number of infected individuals has eventually dwindled, a lift of the lockdown is tempting -however even a slight increase of r 0 above one opens the way to renewed catastrophic infections increase. one therefore has a binary evolution characteristic; to control r 0 by policy such that a steady stream of just managable new infections is maintained is daunting, and likely impossible (in practice) if a policy requiring a constant set of restrictions is targetted. the natural answer, at least from a theoretical point of view, is to consider phases of lifted restrictions interleft with repeated adaptively switched phases of more stringent restrictions or more stringent enforcement of existing restrictions. the need for such strategy is not in principle altered by the local aspect of transmission, except that switched lockdowns only need to be local and thus do not affect the whole population. another point that needs to be mentioned is that the graphs suggest that a future virus having infectiousness lasting much longer than the about two to three weeks for sars-cov-2 and also being as highly infectious would pose serious challenges for containment, because of resource exhaustion in the mid-stages of the pandemic. 8 all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in in this study a novel model for virus proliferation dynamics was developed and with it the sars-cov-2 outbreak in germany retraced on an aggregate level, using covid-19 case count data by the robert-koch institute in berlin. elementary properties of the model were identified. predictions by the model for different levels of mitigation measures were hinted at or stated in approximate manner, and put into context of available health care resources in germany. future policy oriented work would need to address better understanding of fine-grained and adaptively activated mitigation measures, for which a spacial model should be favoured over purely aggregate models as the present one. further, for purpose of improving parameter and state estimates, the issue of underreporting (i.e. #actual > #reported cases) must be taken into account appropriately. ideally, one can develop an estimate for the factor of underreporting from more exact spacial analyses. on the mathematical side, a more rigorous formulation of the instantaneous proliferation dynamics is desirable, which allows to link parameters of the aggregate model to well-defined elementary parameters and results in more systematic parameter estimation. the ultimate goal is to be able to estimate more local structure from the observed time series. 10 all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in the copyright holder for this this version posted august 22, 2020. . https://doi.org/10.1101/2020.08.20.20178301 doi: medrxiv preprint a additional graphs a.1 data series on daily newly reported covid-19 cases figure 5 : a "smoothed" derivate of numbers of daily newly reported covid-19 cases in germany published by [rob] . the blue squares and green triangles series show (for comparison) the sum of daily new cases over a moving 7-day window. orange diamonds and triangles show daily new cases after scaled with a weekday-specific weight factor to remove the weekly pattern seen in the original data. the weight factors were estimated from data corresponding to the squares and diamonds series, i.e. from the interval from 1st april until 6th may 2020. germany imposed face-mask wearing in stores starting from 27th april and allowed certain (moderate) shop reopening starting from 4th may 2020. the "bend" at around 14th april is remarkable because no changes in measures were effected at that time or within the preceding one week. b refinement of the infectiousness mechanism, including a model generalization so far, a crude specification of the infectiousness has been used, putting focus on the main infectiousness interval of a few days. an additional aspect in the virus transmission which should be accounted for in a refinement is the transmission from longer lived remnants of the virus in otherwise cured individuals. for this, we imagine that individuals infected at time t 0 remain contagious until t 0 + t c2 with reduced probability, additionally to the previously used interval [0, t c ]. concretely, let p 2 be the probability that an individual which has been infected for a duration exceeding t c but not exceeding t c2 , will transmit the virus in a unit time step. withp 2 := p 2 /p the adjusted model equation then readṡ x(t) = d · p · (x(t) − x(t − t c )) +p 2 (x(t − t c ) − x(t − t c2 )) · (1 − x(t)/n ), 11 all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in the copyright holder for this this version posted august 22, 2020. . mathematical epidemiology: past, present, and future temporal dynamics in viral shedding and transmissibility of covid-19 deterministic and stochastic epidemics in closed populations a contribution to the mathematical theory of epidemics effective containment explains subexponential growth in recent confirmed covid-19 cases in china covid-19: fallzahlen in deutschland und weltweit temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov-2: an observational cohort study katrin zwirglmaier, christian drosten, and clemens wendtner. clinical presentation and virological assessment of hospitalized cases of coronavirus disease 2019 in a travel-associated transmission cluster early prediction of the 2019 novel coronavirus outbreak in the mainland china based on simple mathematical model since those individuals must be added to the instantaneous reservoir from which infections are generated. the equation is better written aṡif we denote by i(t) the infectiousness profile, which shall describe the relative infectiousness of an infected individual 5 at time increment +t after the infection moment (relative to infectiousness at t = 0), then the above used specification for sars-cov-2 is expressed asits derivative is (with dirac notation) i = δ 0 − (1 −p 2 ) · δ tc −p 2 · δ t c2 . we therefore find that the model equation (6) in fact is generally best written aṡwhere " * " denotes the function convolution. a dirac notation-free representation deriveshere the last integral signifies the well-known stieltjes integral.note: the infection from contaminated surfaces of objects can be represented in the same framework. this is because initially and during the evolution of the spread, viruses are on surfaces mostly there where infected individuals previously had been. key: cord-299988-jaekryq5 authors: karte, claudia; platje, nadine; bullermann, johannes; beer, martin; höper, dirk; blome, sandra title: re-emergence of porcine epidemic diarrhea virus in a piglet-producing farm in northwestern germany in 2019 date: 2020-09-10 journal: bmc vet res doi: 10.1186/s12917-020-02548-4 sha: doc_id: 299988 cord_uid: jaekryq5 background: porcine epidemic diarrhea (ped) is a viral enteric disease of pigs. it affects all age classes of animals but lethality is mainly seen in suckling piglets. after its first appearance in england in 1971, porcine epidemic diarrhea virus (pedv) has spread worldwide. while sporadic outbreaks prevailed in europe, the disease had high impact in asia. following particularly severe outbreaks in 2011, high impact cases were also reported in the united states and neighboring countries in 2013. subsequently, outbreaks were also reported in several european countries including germany. these outbreaks were less severe. this case report describes a recent case of ped re-emergence in germany and the sequence analyses of the causative pedv. case presentation: in spring 2019 5 years after re-introduction of ped into central europe, a piglet-producer in northwestern germany experienced an outbreak that affected sows, their suckling piglets, and weaners. after initial confirmation of pedv by real-time rt-pcr, fecal material and small intestine samples from affected pigs were subjected to metagenomic analyses employing next-generation sequencing. phylogenetic analyses showed high identities among the pedv sequences obtained from samples of different animals and a close relation to recent strains from hungary and france. compared to the pedv strains analyzed in 2014, genetic drift could be confirmed. changes were mainly observed in the spike protein encoding s gene segment. in addition, metagenomic analyses showed multiple picobirnavirus reads in all investigated samples. conclusion: this case report shows that pedv is still circulating in europe. the causative strains are moderately virulent and are still closely related to the so-called indel strains reported previously in europe, including germany. however, a genetic drift has taken place that can be seen in a novel cluster comprising strains from germany, hungary and france in 2019. relevance and impact of the detected picobirna sequences need further investigations. porcine epidemic diarrhea (ped) is an acute and highly contagious enteric disease of swine that results in severe enteritis, diarrhea, vomiting, and dehydration. especially in suckling pigs, lethality can be very high [1] [2] [3] . the causative agent, porcine epidemic diarrhea virus (pedv), is an enveloped positive single-stranded rna virus that belongs to the family coronaviridae, genus alphacoronavirus [4] . the complex coronavirus particles are pleomorphic and possess club-shaped surface projectors [5] . the length of the genome ranges from 27 to 31 kilobases [6] . coronaviruses have a low tenacity [7] but are shed in high amounts and are thus easily transmitted by the fecal-oral route [8] . after its first recognition in the 1970s in europe [7, 9] , the disease caused considerable economic losses especially in asia, where the disease remains endemic [10, 11] . in europe, the disease disappeared quickly, and from most countries, only very sporadic cases were reported over the last three decades. after reports from asia, that a new pedv variant caused considerable losses [12, 13] , that highly virulent pedv variant emerged also in the united states (us) in 2013, with swine farms experiencing explosive epidemics affecting all age classes of animals, with up to 95% mortality in suckling pigs [2, 14] . in 2014, several cases of ped were also reported from southern and western germany. in most cases, fattening pigs were affected showing high morbidity with almost non-existent mortality [15] . however, some breeding herds reported high mortality rates with up to 85% losses in suckling piglets [1] . similar outbreaks were observed in several other central european countries including france, the netherlands, italy, slovenia, belgium, romania, portugal, spain, and austria [16] [17] [18] [19] [20] [21] [22] [23] . the characterization of the involved virus strains revealed that so-called s-indel variants of the virus were involved in central europe, which, in contrast to the highly virulent non-indel strains from asia and the usa, are characterized by deletions and insertions in the spike protein encoding s gene [23] . in the majority of cases, the s-indel variants are associated with milder ped courses. in the absence of reporting obligations, and following the confirmation that the pedv strains in the eu did not belong to the highly virulent non-inde l type, notification and broader follow-up of cases decreased. however, sporadic outbreaks, sometimes with severe problems to get rid of the disease, were still reported from all production systems from different regions of germany and other countries (personal communications and unpublished data). from this time, pedv sequence information is largely missing. when a new wave of ped struck a piglet producer in northwestern germany in 2019, questions were raised to what extent the virus might have changed and if a new emerging variant was causing the clinical case in sows, piglets and weaners. here, we report on the clinical presentation and the whole-genome sequencing of the causative 2019 pedv strain. the affected piglet producer is located in northwestern germany. the farm keeps approximately 350 sows in seven groups (50 sows each), and has a total of 2200 piglet rearing places (1000 on site and 1200 in a leased farm). on the premise, sows and piglets are kept in the same building complex. the farm also includes a fattening unit with 1500 fattening slots. this unit is in close proximity to the above-mentioned units but has its own building with a hygiene lock. three other pig farms are in the radius of 500 m around the holding. prior to the disease event, the farm recorded 33 weaned piglets per sow and year with suckling losses below 10%. loss in piglet rearing and fattening was < 2%. the animals were routinely screened for enteric pathogens and only rotavirus types a and c were detected every now and again (rotavirus type c only very sporadically). the farm was unsuspicious for dysentery and was tested negative for tgev and pdcov prior, during and after the disease event. the routinely applied immunization scheme included maternal vaccinations against colibacillosis, oedema disease, and necrotic enteritis. depending on the infection pressure, rotavirus a vaccines were used in gilts. piglets received vaccinations against porcine circovirus type 2 (pcv-2), mycoplasma, and shiga toxin producing e. coli. sows in integration and reproduction received additional vaccination e.g. against porcine respiratory and reproductive syndrome virus, influenza virus, and parvovirus. in spring 2019, massive diarrhea occurred in sows and suckling pigs. at first, nursing sows (60% of the sows in the unit) in the farrowing unit showed inappetence and shortly afterwards mushy diarrhoea. fever or increased temperature were not detected. the sows recovered completely after three to 4 days. the suckling piglets, which were about 14 days old, showed the first signs of diarrhea two to 3 days after the mothers. about 70% of the litters of this first affected farrowing group showed diarrhea and losses rose to 10% (see table 1 ). immediate investigations confirmed pedv (rt-qpcr from fecal samples and organs). sick piglets were treated with commercial electrolyte solution and additional water supply was given to sows. to increase maternal immunity, infection was enforced in the waiting area. weaned piglets with secondary infections received antibiotic treatment. in total, three farrowing groups (sows and suckling pigs) showed clinical signs of ped and increased loss rates in suckling pigs (10 to 30%). morbidity reached 60 to 90% in sows and 70 to 100% in piglets (see table 1 ). some of the weaned piglets also showed diarrhea, wasting, and growth retardation. the overall losses in piglet rearing rose to 5 to 10% (details see table 1 ). in the fourth farrowing group (approx. eight weeks after the first clinical signs) no clinical signs indicative for ped were recorded and up to now no further ped suspicions arose. in autumn, five suckling piglets were randomly selected and subjected to necropsy and ped screening. all samples were negative for pedv. in the connected fattening unit, no ped signs were recorded at any time. serological checks in the sow rearing unit (separate building) gave negative results. during the disease event, intensive cleaning and disinfection was carried out in the farrowing unit, on driveways, in the waiting areas, and all related stables. disinfectants were chosen in accordance with the list recommended by the germany veterinary society (dvg) for enveloped viruses. purchase of gilts was stopped and replaced by self-remounting. follow-up investigations showed that neighboring farms were also affected by ped shortly before the onset in the described farm. upon initial confirmation of ped by a private laboratory, fecal samples from five sows and feces and intestines from two affected piglets were sent to the friedrich-loeffler-institut (fli) for further analyses and nextgeneration sequencing. ribonucleic acids were extracted from fecal samples or supernatants from homogenized intestines using trizol reagent (lifetechnologies, darmstadt, germany) in combination with the rneasy mini kit (qiagen, hilden, germany) and dnase digestion on the spin column. all rnas were confirmed to be pedv positive by rt-qpcr [24, 25] . subsequently, all samples were subjected to whole genome sequencing and metagenomic analyses using the illumina miseq platform as previously described [26] . in brief, nucleic acids were processed into shotgun dna libraries and then deep-sequenced. the resulting raw data was taxonomically classified using the software pipeline riems [27] . the obtained sequence reads were assembled to determine the genomes in full length. all sequences are available from the insdc databases under study accession prjeb38314. with the help of the geneious prime software suite (v. 2019.2.3; biomatters ltd., auckland, new zealand), phylogenetic analyses were performed (for details see legend fig. 1 ). the genomes originating from the reported german case form a new and distinct cluster within the s-indel strains (see fig. 1 ). close relatives are three virus strains reported in 2019, two from hungary [16] (accessions mh593900 and kx289955) and one from france (accession mn056942). identity among the new german pedv strains was almost 100% (> 99.9%) whereas identities of > 98.8% were found with regard to the hungarian and french sequences. comparing the german strains from 2014 with the german strains detected in 2019, identities are higher than 99.5%. comparisons between german prototype strains from 2014 (the first reported strain, bh76/14-01_l00719_ farm a) and 2019 (894_3_l03204_ger) show high similarities in the nucleotide sequence (see supplementary figure 1 ). in total, 135 nucleotides exchanges are the rna-shotgun sequencing approach allowed metagenomic analyses using riems. in this analysis, several reads were classified taxonomically as picobirnaviridae sequences. multiple reads of the rna-dependent rnapolymerase gene as well as the gene segment encoding the capsid were found in the fecal but not the intestine samples. porcine epidemic diarrhea can have a tremendous impact on the pig industry as was seen in the us following the introduction of pedv in 2013 [2, 29] . critical losses occurred especially in piglet rearing companies and the losses impacted the whole pork industry [15, 29] . following the devastating outbreaks on the american continent, re-emergence of pedv was also reported from europe after intensified surveillance [23] . however, here, strains of lower virulence were circulating and the reporting and follow-up of cases abated quickly despite ongoing cases. one reason for the subsiding of official follow-up is that ped is neither notifiable nor reportable but still has impact on trade and reputation. against this background, most farmers had no interest to make their cases public. thus, official and published information on the german ped situation in general and viral evolution in particular is missing roughly from 2016 onwards. when pedv was introduced in a piglet-producing farm in northwestern germany in 2019, clinical disease and losses were rather disturbing and the farmer and responsible veterinarian initiated a closer follow-up. one hypothesis for the observed impact was a change in virulence and thus, next-generation sequencing was employed to test this hypothesis. our data show that the causative virus strains are still s-indel variants with close relationship to those found in 2014 and the following years. however, viral evolution has taken place and the drift gave rise to a new cluster that comprises recent fig. 1 phylogenetic tree of current pedv strains. phylogenetic tree of 2019 pedv strains from germany, hungary, and france as well as 2014 pedv strains from germany, usa, and china. the complete genome sequences were aligned using mafft and a phylogenetic analysis was performed using phyml, with a gtr substitution model and tree reconstruction supported by 1000 bootstrapping replicas [28, 29] . green branches show the 2019 pedv isolates from germany, blue branches highlight the isolates from hungary and france and red branches are the highly virulent non-indel strains from the usa and china strains from germany, hungary, and france. given the accordant drift, one can speculate that pedv is still circulating in europe. there is no indication that these variants have a higher virulence per se. the previously observed variation seems still present. the affected farm described in this report was finally able to control the outbreak by forced infection in the waiting unit of sows, biosecurity and strict cleaning and disinfection. yet, the history of ped in neighboring fattening farms also shows that the virus was able to enter the farm and room for improvement was given in veterinary hygiene and biosafety. the exact route of introduction remained unclear. supplementary studies into the metagenomic data set showed picobirnaviral sequences in the fecal material. picobirnaviruses are non-enveloped double-stranded rna viruses. they are bisegmented with segment one consisting of 2.3 to 2.6 kilobases and segment two of 1.5 to 1.9 kilobases [30] . picobirnaviruses are often associated with cases of gastroenteritis or infections in the respiratory tract [31] . the role in diarrhea diseases in piglets is unclear, since picobirnaviruses were found in piglets with and without diarrhea [32] . the transmission is fecal-oral [33] and these viruses have so far been detected mainly in feces in various species [30, 33] . impact and relevance of these findings remains to be clarified by future studies. in conclusion, ped re-emerged in northwestern germany in 2019 leading to high morbidity and substantial impact in a piglet-producing farm. the causative virus strains are still s-indel variants but a genetic drift occurred since 2014. this drift is accordant with the evolution in other european countries. the relevance of picobirnavirus detections in fecal samples from pedvpositive animals remains unclear. supplementary information accompanies this paper at https://doi.org/10. 1186/s12917-020-02548-4. emergence of porcine epidemic diarrhea virus in southern germany emergence of porcine epidemic diarrhea virus in the united states: clinical signs, lesions, and viral genomic sequences genetic properties of endemic chinese porcine epidemic diarrhea virus strains isolated since 2010 the springer index of viruses a new coronavirus-like partiele assoeiated with diarrhea in swine diagnostic notes: update on porcine epidemic diarrhea verlaufsuntersuchung über die ausscheidung von porcine epidemic diarrhea virus (pedv) und die serokonversion nach feldinfektion bei saugferkeln und mastschweinen porcine epidemic diarrhoea (ped) -neuausbrüche in deutschen mastschweinebeständen chinese-like strain of porcine epidemic diarrhea virus pig farming. letter to the editor new variant of porcine epidemic diarrhea virus the prevalence of intestinal trichomonads in chinese pigs isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the united states comparison of porcine epidemic diarrhea viruses from germany and the united states isolation and characterisation of porcine epidemic diarrhoea virus in hungary -short communication complete genome sequence of a porcine epidemic diarrhea s gene indel strain isolated in france in complete genome sequence of a porcine epidemic diarrhea virus from a novel outbreak in belgium porcine epidemic diarrhea virus (pedv) introduction into a naive dutch pig population in 2014 outbreak of porcine epidemic diarrhea virus in portugal first detection, clinical presentation and phylogenetic characterization of porcine epidemic diarrhea virus in austria porcine epidemic diarrhoea virus in italy: disease spread and the role of transportation porcine epidemic diarrhea in europe: in-detail analyses of disease dynamics and molecular epidemiology genomnachweis des porzinen epidemischen diarrhoe virus (pedv) mittels real-time rt-pcr. avid-methodensammlung: avid-methode vir03 evidence of infectivity of airborne porcine epidemic diarrhea virus and detection of airborne viral rna at long distances from infected herds a versatile sample processing workflow for metagenomic pathogen detection riems: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets mafft: a novel method for rapid multiple sequence alignment based on fast fourier transform factors associated with time to elimination of porcine epidemic diarrhea virus in individual ontario swine herds based on surveillance data molecular detection and characterization of picobirnaviruses in piglets with diarrhea in thailand detection and molecular characterization of porcine picobirnavirus in feces of domestic pigs from kolkata, india publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations the authors thank patrick zitzow, robin brandt and ulrike kleinert for technical assistance. authors' contributions ck performed next-generation sequencing and was a major contributor in writing the manuscript, np and jb collected and analyzed clinical data, mb interpreted the overall dataset and critically revised the manuscript, sb conceived the study, assisted in interpreting the data and contributed in writing the manuscript, dh analyzed and interpreted whole-genome data and contributed to the manuscript. all authors read and approved the final manuscript. this study was funded by federal excellence initiative of mecklenburg western pomerania and european social fund (esf) grant koinfekt (esf_14-bm-a55-00xx_16). the excellence initiative covered consumables for next-generation sequencing and the personnel costs of the major contributor (ck). open access funding provided by projekt deal.availability of data and materials sequence information was deposited at the european nucleotide archive (ena) under study id prjeb38314 (accessions lr812928; lr812932; lr812927; lr812929, lr812930, lr812926, and lr812931). additional metadata are available from the authors upon reasonable request. the sample material was submitted to the friedrich-loeffler-institut for enhanced diagnostics and was taken by the responsible farm veterinarian in the context of the health monitoring program of the respective farm (in accordance with the regulation on hygiene requirements for the keeping of pigs; online available at http://www.gesetze-im-internet.de/schhalthygv/). in germany, every keeper of pigs must have his herd supervised by a veterinarian as part of the on-farm inspections, this includes clinical and laboratory checks to maintain and improve the health status of the herd. no permissions were necessary to collect the mainly non-invasive specimens. the farmer approved in-detail analyses of the ped case and shipment of samples (verbal agreement with the responsible veterinarian). all procedures were carried out in accordance with the relevant regulations. the owner of the case farm approved submission of the report. all authors have approved submission of the manuscript. the authors declare that they have no competing interests. key: cord-298469-0sny9dit authors: schlickeiser, reinhard; schlickeiser, frank title: a gaussian model for the time development of the sars-cov-2 corona pandemic disease. predictions for germany made on march 30, 2020 date: 2020-04-02 journal: nan doi: 10.1101/2020.03.31.20048942 sha: doc_id: 298469 cord_uid: 0sny9dit for germany it is predicted that the first wave of the corona pandemic disease reaches its maximum of new infections on april 11th, 2020 +5.4-3.4 days with 90 percent confidence. with a delay of about 7 days the maximum demand on breathing machines in hospitals occurs on april 18th, 2020 +5.4-3.4 days. the first pandemic wave ends in germany end of may 2020. the predictions are based on the assumption of a gaussian time evolution well justified by the central limit theorem of statistics. the width and the maximum time and thus the duration of this gaussian distribution are determined from a statistical ξ2-fit to the observed doubling times before march 28, 2020. in these days there is a very high interest in the societal, economical and political world to understand the time evolution of the first wave of infections of the population by the current sars-cov-2 (corona) virus. the most important issues are the total duration and the peak time of the infection evolution as well as the maximum number of daily infections. it would be most helpful for many people to have a reproducable, crude, but reliable estimate when this pandemic wave is over. it is the purpose of this manuscript to provide such an estimate based on a simplified gaussian model for the time development of the pandemic outburst. the best justification for the gaussian or normal distribution for the virus time evolution is given by the central limit theorem of statistics 1 . the central limit theorem states that in situations, when many n 1 independent random variables are added, their properly normalized sum tends toward a normal or gaussian distribution function of the form (1) even if the original variables themselves are not normally distributed. the spread of the virus infection of populations with high number of persons certainly is such a random process to which the central limit theorem ia applicable. each person in a given population has a probability distribution (normalized to unity) as a function of time of being infected: it is a very noncontinuous distribution being 1 at the day of infection and 0 on all other days. if one adds up these discrete distributions of persons living in villages and districts of towns of typical size of about 1000 persons one obtains quasi-continous probability distributions for be* rsch@tp4.rub.de, schlickeiser@gmail.com ing infected which certainly will be different in hotspots of the disease and isolated rural areas. if we then add up a large number of these village probability distributions for all of germany we obtain the daily infection rate distribution which according to the central limit is close to a gaussian distribution. the analysis of gaussian distribution functions plays a central role in many problems of statistical physics and plasma physics. e.g. in plasma kinetic theory they are referred to as drift-maxwellian 2 or counterstreaming bi-maxwellian 3,4 velocity distribution functions. both authors of this manuscript are not virologists but theoretical physicists in plasma physics and astrophysics (rs) and solid state physics (fs) with past experience in analyzing normal or gaussian distribution functions. apart from consulting several reviews 5-7 , as nonvirologists we are not familiar with the recent relevant virology literature. nevertheless, it is our hope that in these hard times an estimate by unbiased non-experts might be welcomed by specialists as well as the broad population, especially if some positive information and outlook is provided. we base our parameter estimates on publicly available information, especially by the excellent podcast by prof. c. drosten 8 and the recent sophisticated modelling study for germany 7 . numerical simulations and the empirical data of earlier epidemies 8 indicate that the time evolution of epidemic waves is characterized by an early exponential rise until a pronounced maximum is reached followed by a rapid decrease. as argued above we adopt a simple gaussian model for the time evolution of infections and explore its consequences. if i(t) denotes the number of infections . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20048942 doi: medrxiv preprint per day, we assume that its time evolution is given by the gaussian function shown in fig. 1 , where i 0 denotes the maximum value at time e and ∆ denotes the width of the gaussian. by monitoring the new daily infections one easily derives the relative change in the infections per day where we used the distribution (1). the monitored data are often given in terms of the doubling time d of the corresponding exponential function at any time using the distribution (3) in equation (2) provides for the relative change in daily infection rate equating the two results (2) ans (4) leads to the timedependent gaussian doubling time figure 2 shows the monitored doubling times for germany 9 starting on march 15, 2020 until march 28,2020. we assume that every value has an error of 15 percent. it starts at d(t = 0) = 2.6 days and increases to d(t = 12) = 4.8 ± 0.24 on march 28, 2020. the gaussian doubling time modeling then provides d(t = 0) = a/e = 2.6 days, corresponding to moreover, eq. (5) reduces to we determine the value of the only free parameter e in equation (7) by performing a χ 2 -fit to the data shown in fig. 2 . if m(t i ) denote the observed doubling times at days t i , δm(t i ) = 0.15m(t i ) its error and d(e, t i ) the theoretical doubling time for given values of e, we calculate the best fit with the minimum value of χ 2 min = 9.51 is provided for e = 27.5 days. the χ 2 min,p.d.f = 9.51/13 = . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint correponding to april 11, 2020 +5.4 −3.4 days. consequently, the best fit gaussian doubling time for germany is given by as an aside we note that the variation (10) becomes infinitely large as t → 27.5. moreover, for times t > e the doubling times becomes a decay half-life approaching 0 for very large times t e. moreover, after inserting the values (9) equation (6) yields with 90 percent confidence in fig. 3 we show the prediction of the doubling times in germany until day 25 corresponding to april 8th, 2020. fig. 3. the same as in fig. 2 but now the predicted doubling times until day 25 corresponding to april 8, 2020. it is known that during the whole duration of the first wave of the virus evolution 70 percent of the total population are infected 8 , if nothing is done to reduce the number of infections. scaling the total population in units of 10 5 n 5 , we estimate that 0.7q10 5 n 5 are infected during the whole duration of the first virus wave, where the quarantaning factor q accounts for the currently taken political actions such as quarantining of elder and infected people, social distancing actions in the society as well as the closure of schools and daycare facilities. integrating the gaussian (1) over all times we then obtain where we used the integral ∞ −∞ dx e −x 2 = √ π. equation (12) yields for the maximum value with the 90 percent confidence value for ∆ from equation (11) we obtain with the same confidence level for the maximum value (13) we assume as typical medical parameters those suggested by the recent modeling by the robert-koch-institute 7 (see their fig. 1 ): only about 20 percent of the infected people are seriously infected, 5 percent have to be hospitalized and 1α percent need access to breathing apparati for typically 1w week, corresponding to 7w days. we refer to the latter as nssps standing for new seriously sick persons per day. as these numbers are uncertain we keep their scalings with the typically adopted numbers. in germany there are at most 56000 breathing apparati in total available, corresponding for a population of 80 million people to 70b 70 breathing apparati available per 10 5 n 5 people. as a consequence, every day the hospitals can handle i n nssps with the infections are handable by hospitals for all times if at the maximum of the virus evolution 0.01αi 0 , denoting the maximum number of seriously sick persons per day needing access to breathing apparati, is less or equal to i n , i.e. . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20048942 doi: medrxiv preprint inserting the value (14) for the maximum value i 0 , the quantity n 5 cancels out and we obtain with 90 percent confidence the condition which is equivalent to in order to handle all serious infections in german hospitals the condition (18) has to be fulfilled. it seems that german hospitals can only ensure the best treatment of all nssps at the maximum of first wave if either (1) the number of available breathing apparati can be increased by a factor of 3, corresponding to b = 210 per day. or (2) the quarantaining factor q can be reduced to q = 0.36 +0.03 −0.02 1/3. the first option is unrealistic on short time scales. to achieve the second option of the reducing the quarantaining factor q to about 0.3 by the currently taken social distancing and quarantaining activities seems to be realistically achievable in germany. we therefore will adopt this optimistic value q = 0.3q 0.3 in our further predictions. however we note that with such a small quarantaining factor only 21000n 5 will be infected during the whole first wave of the virus, so that additionally waves are likely to occur in the future. it is important to notice that the outbreak of serious sickness syndroms of nssps is delayed to the infection time by about τ = 7 days 8 . this delay time has to be added to the above derived maximum time scale e, so that e + τ = 34.5 +5.4 −3.4 days, corresponding to april 18, 2020 +5.4 −3.4 is the predicted day in germany when the maximum number of nssps has to be treated. the number of infections are signifantly reduced by a factor 10 3 compared to the maximum i 0 at the time with 90 percent confidence. consequently, the first pandemic wave will be over in germany not before 65 days or about 2 months with the indicated uncertainty. this corresponds to 38 ± 4 days after the time of maximum. according to our predictions, the first pandemic wave in germany will reach its maximum by april 18, 2020 when about about (8.3 ± 0.78)q 0.3 n 5 nssps have to be treated in the hospitals. the wave has a broad distribution from april 6 to april 30, 2020 with more more than (4.2 ± 0.39)q 0.3 n 5 but less than (8.3 ± 0.78)q 0.3 n 5 nssps per day. the number of nssps needed to be treated at hospitals will sharply drop to less than (0.0083 ± 0.00078)q 0.30 n 5 nssps by may 26th, 2020. as germany has a population of about 80 million persons we have n 5 = 800. therefore in absolute numbers german hospitals will have to cope with (6640 ± 624)q 0.3 nssps at the maximum of the outburst on april 18th, 2020, more than (3360±312)q 0.3 but less than 6640±624 nssps per day between april 6 and april 30, 2020, before the total number per day drops below (6.64 ± 0.63)q 0.3 nssps after the end of may 2020. all errors have 90 percent confidence. our analysis can be applied to other countries too if reliable information on the early doubling times are available. we plan to test our modeling with the data from the past first corona wave in china. we end with a sentence of caution: although the central limit theorem provides us with a very good justification of the adopted gaussian time distribution function it is not guaranteed that the actual virus time evolution follows this behavior. we will only know for sure after the first pandemic wave is over. so it is possible that our estimates and we are wrong. we take this risk because we are convinced that many persons will welcome our optimistic estimate that the first wave is over by end of may 2020. there is light at the end of a long tunnel. our estimate might also help decision makers when to lift the current societal and economical lockdown. die erste welle wird gegen ende mai 2020 in deutschland enden mit einem tausendstel kleineren neuinfektionsraten. diese vorhersagen basieren auf der annahme einer gauss-förmigen zeitverteilung der infizierungsrate, die gut durch den zentralen grenzwertsatz der statistik begründet ist. die breite und die zeit des maximums der gauss-verteilung und damit deren gesamtdauer werden durch einen statistischen χ 2 -fit an die in deutschland beobachteten verdopplungszeiten vor dem 28.märz 2020 bestimmt. die behandlung aller schwer erkrankten patienten mit beatmungsgeräten ist gewährleistet, wenn es durch die andauernden quarantäne-und soziale distanzierungs-massnahmen gelingt, die anzahl der infizierten personen in der bevölkerung durch die erste welle unter 30 prozent zu halten. . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20048942 doi: medrxiv preprint an introduction to probability theory and its ppplications infectious diseases of humans: dynamics and control modellierung von beispielszenarien an der sars-cov-2 epidemie 2020 in deutschland coronavirusupdate (ndr.de/coronaupdate, 2020) süddeutsche zeitung online key: cord-331336-4kf2jn8c authors: aravindakshan, a.; boehnke, j.; gholami, e.; nayak, a. title: restarting after covid-19: a data-driven evaluation of opening scenarios date: 2020-05-30 journal: nan doi: 10.1101/2020.05.28.20115980 sha: doc_id: 331336 cord_uid: 4kf2jn8c to contain the covid-19 pandemic, several governments introduced strict non-pharmaceutical interventions (npi) that restricted movement, public gatherings, national and international travel, and shut down large parts of the economy. yet, the impact of the enforcement and subsequent loosening of these policies on the spread of covid-19 is not well understood. accordingly, we measure the impact of npi on mitigating disease spread by exploiting the spatio-temporal variations in policy measures across the 16 states of germany. this quasi-experiment identifies each policy's effect on reducing disease spread. we adapt the seir (susceptible-exposed-infected-recovered) model for disease propagation to include data on daily confirmed cases, intraand inter-state movement, and social distancing. by combining the model with measures of policy contributions on mobility reduction, we forecast scenarios for relaxing various types of npis. our model finds that, in germany, policies that mandated contact restrictions (e.g., movement in public space limited to two persons or people co-living), initial business closures (e.g., restaurant closures), stay-at-home orders (e.g., prohibition of non-essential trips), non-essential services (e.g., florists, museums) and retail outlet closures led to the sharpest drops in movement within and across states. contact restrictions were the most effective at lowering infection rates, while border closures had only minimal effects at mitigating the spread of the disease, even though cross-border travel might have played a role in seeding the disease in the population. we believe that a deeper understanding of the policy effects on mitigating the spread of covid-19 allows a more accurate forecast of the disease spread when npis are (partially) loosened, and thus also better informs policymakers towards making appropriate decisions. in response to the covid-19 pandemic, governments around the world implemented varying degrees of non-pharmaceutical interventions (npis) to control the spread of the disease (1,2,3,4). these policies severely restricted movement, public gatherings, national and international travel, and shut down large parts of the economy including schools and non-essential businesses. while the shutdowns helped delay the spread and reduce the severity of the epidemic, they also created tremendous hardships for individuals and businesses (5, 6, 7) . as the spread of covid-19 decelerated across countries, governments have started relaxing npis to help balance the need for economic security and the risk of growing infection numbers (8). nevertheless, there is limited understanding of the effect that loosening policies might have on the spread of the disease. to determine this effect, we quantify each npi's contribution to disease mitigation, permitting the forecasting of disease spread under different policy scenarios. the proposed model, then, will allow policymakers to forecast the impacts of the removal of different types of restrictions. initial analysis of the impact of policy restrictions in china suggests that npis that significantly affected human mobility (e.g., household quarantine) reduced the spread of the disease (7, 10) , even more than restrictions that limited national and international travel (11) . additionally, simulations of npis in wuhan (6) show that maintaining restrictions helped delay the epidemic peak. the results also imply that an early end to such interventions leads to an earlier secondary peak, which can be flattened by relaxing the social mixing at varying rates (6) . nevertheless, to the best of our knowledge, no study quantifies the effects of the types and timings of the implementation and relaxation of government policy interventions in reducing mobility and in turn decreasing the spread of covid-19. our estimates allow for projections of the impact of easing individual interventions on disease spread. these predictions act as decision aids for policy makers to judge how lifting certain policies changes social mobility rates and in turn the number of new covid-19 cases. using data from the 16 states of germany, we explore the effectiveness of different npis ( figure 3 ) in reducing social mobility, and in turn affecting the spread of the disease. because german states enforced (and relaxed) policies to varying degrees and at different points in time, the variations in implementation allow us to capture the incremental effectiveness of these policies at reducing social mobility amongst the general population. to determine how policy enforcement impacted mobility and disease spread, we associate the type and timing of the policy intervention to actual social mobility as recorded in the data released by google (14) . next, using our predictions of social mobility based on the policy interventions, we predict the spread of covid-19 by modifying the seir model presented in (9) to include social distancing and other forms of mobility data (e.g., travel by air, bus, rail, and road). finally, we project the impact of relaxing a policy on the number of new cases across germany and compare how differences in start times for policy relaxations alter the cumulative number of expected cases over a six-week time span. we find that not implementing social distancing in germany, would have resulted in a 37.8-fold (iqr: 27 to 52-fold) increase in cumulative infected case counts as of may 7, 2020. in other words social distancing reduced case counts by about 97.3% (iqr: 96.3-98.07%). we also find that policies are not equal in their effectiveness at reducing new cases. contact restrictions were the most effective at lowering infection rates in germany (51%, iqr: 50.7-51.2), while border closures had only minimal effects at mitigating the spread of the disease (2%, iqr: 0 -4%), even though they might have played a role in seeding the disease in the population. interconnected air, land, and sea transportation networks led to the spreading of covid-19 from wuhan, china to the rest of china and eventually to most countries around the world (12, 13). to accurately model the spatial spread of the disease into germany, we collected three types of daily mobility data: (i) daily air transportation data to capture the movement within and between germany and 142 other countries; (ii) daily ground transportation data between the nine countries that share borders with germany; and (iii) daily inter-state ground transportation. the daily covid-19 case data were obtained from the johns hopkins coronavirus resource center (15) and robert koch institute (16) for all countries in our dataset as well as the 16 german states (see figure 1 ). figure 2 shows the cumulative case numbers for all states in germany and globally. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. to encourage and enforce physical distancing, governments across all 16 states introduced a variety of npis at different points in time ( figure 3 ). data for these policies were collected from (17, 18). . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may 30, 2020. . https://doi.org/10.1101/2020.05.28.20115980 doi: medrxiv preprint figure 3 . timeline for implementation of npis across states. these policies include border closures (closing international borders), contact restriction (movement in public space is limited to two persons or people co-living), educational institutes closure (e.g. schools and . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 30, 2020. . https://doi.org/10.1101/2020.05.28.20115980 doi: medrxiv preprint universities), initial business closure (e.g. restaurants), non-essential business closure (e.g. trade shows), stay at home order and retail store closure. border closure applies to 10 states sharing international borders. we use data from march 1, 2020 to april 30, 2020 in our study. every policy was not implemented by every state as of april 26, 2020. also, none of the implemented policies were relaxed until april 20. state governments start relaxing these policies from april 20, 2020. google's covid-19 community mobility reports (14) detail how movement trends change over time as public awareness increases and npis are introduced ( figure 4 ). the report tracks movement trends over time by geography, across different categories of places such as retail and recreation, groceries and pharmacies, parks, transit stations, workplaces, and residential. we consider community mobility trends in retail and recreation as a measure of social distancing. we define social distancing as sdi = -ci/100 where ci is the community mobility trend in state i. while the community mobility data provides information on changes in local movement, it does not provide information on inter-state movement and international travel. ground transportation accounts for the vast majority of the movement, with cars accounting for 85% of total ground transportation in germany (19). we collected detailed traffic data from jan 1, 2013 to dec 31, 2018 from the german bundesanstalt für straßenwesen (federal institute for roadways). the dataset contains the hourly count of the number of vehicles crossing different checkpoints along highways. the institute used sensors to identify the type of vehicle, which we include in our analysis to estimate the number of individuals. we construct a linear regression model to predict . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 30, 2020. . https://doi.org/10.1101/2020.05.28.20115980 doi: medrxiv preprint hourly traffic for jan 1, 2020 to april 30, 2020 (details in supplementary material). the model includes year, public holidays, day of the week, and state population as control variables. to control for changes in car movement during the period of the study, we adjust the predicted daily traffic using google's community mobility data for workplaces ( figure 5 ). we used deutsche bahn's timetables (www.bahn.com) to estimate the number of daily rail travelers moving across states in germany and arriving from neighboring countries. to account for the changes in movement due to covid-19 and cancelations of several trains, we adjust the number of passengers moving across states by using the community mobility data for transit stations ( figure 6 ). is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 30, 2020. . https://doi.org/10.1101/2020.05.28.20115980 doi: medrxiv preprint we obtained the search history of a large european bus and train comparison platform to estimate the number of passengers moving across cities (states) in germany and passengers traveling to germany from neighboring countries. we set bus transport to zero after march 16, 2020 as all bus movement in germany stopped on that day. last, we obtained flight transportation information from the opensky network (20) . this database utilizes automatic dependent surveillance broadcast (ads-b) flight trajectories to identify the departure and arrival airport of a flight (figure 7) . is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 30, 2020. finally, we use additional controls to isolate the effect of individual policies. we use cumulative google trends data for the search term "covid-19 in deutschland" to control for increased awareness over time (figure 7(c) ). severe movement restrictions due to increased enforcement of these policy restrictions led to a greater sense of unease and dissatisfaction amongst some sections of the population (e.g. (21)). while such protests are small, prolonged enforcement of restrictions could increase dissatisfaction. we use weather data (max temperature in degree celsius) from wetterkontor.de as a control to account for the propensity of the population to leave their home as summer peaks. we also include an index that measures the propensity to violate (ptv) npis using the arctan function. as the policy enforcement prolongs, the ptv index increases, in turn potentially increasing social mobility (figure 7(d) ). to determine the impact of different state policies, we use a penalized linear regression (lasso regression) model to predict changes in community mobility, sdi due to a policy p that is active in state i on a given day. we explain the regression model in detail in the supplementary material. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 30, 2020. figure 8 (b) shows the predictions of mobility in a sample state (bavaria) from our model. based on these results, we note the policies that significantly affect changes in mobility to project the number of new cases when the policy is relaxed. from the graph, we see that educational facilities closures have a very large negative effect on mobility (29.26 percentage point drop in mobility, iqr: 29.25 to 29.95). even though it is plausible that the closure of educational facilities precipitates this drop (for example, children staying home without caregivers forces parents to work from home), we do not include this variable when projecting the lifting of policy restrictions scenarios. this is due to the potential confounding between initial awareness of the disease, population preparedness for a shutdown, and the closure of the educational facilities. the estimates for the other policy restrictions capture the average incremental effect of these policies across the 16 the model also finds that the longer the policies remain in place and restrict movement, the likelier it is for ptv to grow, which can lead to individuals breaking the policy restrictions on their own. we use the predicted mobility from the linear regression to determine the impact of social distancing on new case counts. we investigate the contribution of each policy to the mitigation of disease spread by determining the role of social distancing in the estimation of the number of susceptible and exposed individuals in a given population. we modify the seir model (equations 1 -5 in the supplementary material) used in (9) to include different transportation networks and predicted mobility for each state. using the estimation procedure in (9), we find the model parameters that we use to predict disease spread for all 16 states and for germany. we note that the model accounts for documented as well as undocumented infected cases. as shown in supplementary material figure s14 , the proportion of documented infected (i d ) as a function of total cases increases over time. this finding comports with expectations because of the rapid increase in testing across germany (22). figure 9 (a) shows the actual disease progression in germany, the disease spread as predicted by our model in the presence of predicted social distancing, as well as disease spread as predicted by our model when mobility remained unchanged with no social distancing measures. similar predictions for the states are provided in figure 9 (c). we use the time period of feb 18, 2020 -apr 20, 2020 to infer model parameters. this period includes early stages of the covid-19 . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 30, 2020. . epidemic in germany and the time that state policies are enacted. we use these parameters to estimate the number of daily documented cases during the time interval of feb 18, 2020 -may 7, 2020, which corresponds to 17 days out of sample forecasts. the model finds 179,487 (iqr: 144,590 -211,771) cumulative documented cases in germany as of may 7, 2020 (actual reported cases: 165,991) with the estimated average error rate of 8%. figure 9 (b) shows the amount of expected increase in the number of cases across the states of germany and the nation, if no social distancing was observed. across germany one would expect a 37.8-fold (iqr: 27 to 52) increase in the number of cases without any social distancing (i.e., # = 0), the effect varying significantly by states from a low of 13.7-fold (iqr: 7 to 21) in berlin to a high of 45.2fold (iqr: 31 to 63) in bavaria. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 30, 2020. we simulate what-if scenarios to determine the impact of lifting restriction on new cases in each state. under the scenario that a restriction has been relaxed while others remained operational, we forecast mobility using equation (11) in the supplementary material. we subsequently project the new case count using the predicted mobility. this step is repeated across all restrictions, each relaxed individually. due to the confounding noted earlier, we do not report the case of educational facilities being reopened. in scenario 1, we project all changes from april 21, 2020 to june 2, 2020, assuming that the restriction was relaxed on april 21, 2020. figures 10 (a) and (c) shows the projections of case counts over a six-week period if a restriction was relaxed exclusively. figures 10 (b) and (d) show scenario 2, which projects all changes from april 21, 2020 to june 2, 2020, assuming that the restriction was relaxed on april 28, 2020. because the two scenarios are exactly one week apart, it allows us to determine the impact of delaying the lifting of a restriction by one week. from the analysis, the lifting of contact restrictions, i.e., the rule limiting movement in public . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 30, 2020. . https://doi.org/10.1101/2020.05.28.20115980 doi: medrxiv preprint spaces, had the biggest impact on new case counts. compared to keeping the restrictions in place, lifting contact restrictions will result in a 51.5% (iqr: 51.0-52.1%) increase in daily case numbers in scenario 1 and a 27.4% (iqr: 26.8-27.8%) increase in scenario 2. however, lifting restrictions on initial business closures leads to a 29.2% (iqr: 28.6-29.7%) increase in daily case numbers in scenario 1 and a 15.8% (iqr: 15.4-16.3%) increase in scenario 2. easing nonessential service closures increases daily case numbers by 6.6% (iqr: 6.2-7.0%) in scenario 1 and 3.7% (iqr: 3.2-4.0%) in scenario 2, and the opening of retail outlets increases daily case numbers by 5.6% (iqr: 5.1-6.0%) in scenario 1 and 3.4% (iqr: 3.0-3.8%) in scenario 2. these results show that npis have differential impacts on lowering disease spread, and suggest a measured approach to lifting restrictions. for example, the opening of retail outlets could be balanced by maintaining the restrictions around limiting the number of individuals in a given place or store (e.g., controlling entry) -thereby allowing for the resumption of economic activity while limiting the risk of contagion. figure 10 (e) shows the increases in the expected number of cases if a restriction was lifted on april 21 versus on april 28. delaying the lifting of certain restrictions by one week could also have a significant impact on the total case counts. this occurs not only due to the delay, but also because the number of infected individuals that a person could come in contact with decreases over the week. for example, delaying the lifting of contact restrictions by one week reduces the number of new cases over the six-week forecast by on average 19% (iqr: 16% to 21%). we also observe that lifting restrictions on the opening of retail outlets and non-essential services leads to an average 2% (iqr: 0% to 6%) and 3% (iqr: 0% to 4%) increase in total case numbers over the six-week forecast period. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 30, 2020. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 30, 2020. this study explores the role of npis in reducing the spread of covid-19. we extend the spatiotemporal seir model in (9) by incorporating daily social distancing numbers from transportation data and mobility patterns. our model finds that without npis in place, covid-19 cases would likely have shown a 37.8-fold increase across germany. we also investigate the marginal impact of each of the various npis implemented by state governments in germany by determining the differential impacts of the policies on reducing social mobility. we relate these reductions to disease spread, reconstructing patterns of spread across the 16 states. finally, we forecast new cases when policies are relaxed, one-at-a-time. we find that certain policies have a larger impact on disease spread than others. our model forecasts find that early relaxation of some npis could lead to an increase in the number of cases, potentially leading to a second wave. this observation is confirmed by an estimated increase in the effective reproduction number ' (supplementary material). we also compare case counts if the policies were relaxed with a oneweek delay. keeping some npis in place for an extra week could reduce total covid-19 cases by up to 19% (as of june 2, 2020). the results confirm that policy restrictions are not all equal in their ability to affect disease spread. the policy of restricting mass gatherings (contact restriction) is estimated to be the most effective npi to contain covid-19, followed by closures of various businesses and stay-at-home orders. due to this variation in effect, it is advisable to lift restrictions with minimal effects first, gradually easing restrictions that potentially lead to higher case numbers. this study presents a comprehensive quantitative analysis that includes individual effects of npis on the transmission of covid-19. to the best of . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may 30, 2020. . https://doi.org/10.1101/2020.05.28.20115980 doi: medrxiv preprint our knowledge, this is the first study that uses variations in policy interventions by governments to discover their differential impacts at reducing mobility that in turn reduces disease spread. prolonged lockdowns and restrictive policies can have devastating social and economic consequences. however, opening too soon could result in rapid disease spread. therefore, governments need to develop cautious approaches to lifting restrictions in a bid to return to normalcy (23). the approach presented in this paper allows for a deeper understanding of the policy effects on mitigating the spread of covid-19. the forecasts of disease spread when npis are (partially) loosened guide policymakers towards the appropriate strategy when reversing the interventions. early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia a novel coronavirus from patients with pneumonia in china how will country-based mitigation measures influence the course of the covid-19 epidemic? the effect of control strategies to reduce social mixing on outcomes of the covid-19 epidemic in wuhan, china: a modelling study effect of non-pharmaceutical interventions to contain covid-19 in china substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov2) the effect of human mobility and control measures on the covid-19 epidemic in china the effect of travel restrictions on the spread of the 2019 novel coronavirus (covid-19) outbreak google covid-19 community mobility reports current situation report of the rki to covid-19 bringing up opensky: a large-scale ads-b sensor network for research key: cord-318766-vx0dnnxh authors: wendt, ralph; nagel, stephan; nickel, olaf; wolf, johannes; kalbitz, sven; kaiser, thorsten; borte, stephan; lübbert, christoph title: comprehensive investigation of an in-hospital transmission cluster of a symptomatic sars-cov-2–positive physician among patients and healthcare workers in germany date: 2020-06-03 journal: infection control and hospital epidemiology doi: 10.1017/ice.2020.268 sha: doc_id: 318766 cord_uid: vx0dnnxh we investigated potential transmissions of a symptomatic sars-cov-2–positive physician in a tertiary-care hospital who worked for 15 cumulative hours without wearing a face mask. no in-hospital transmissions occurred, despite 254 contacts among patients and healthcare workers. in conclusion, exposed hospital staff continued work, accompanied by close clinical and virologic monitoring. on january 27, 2020, the first infection with severe acute respiratory syndrome coronavirus 2 (sars-cov-2) was diagnosed in germany. 1 by may 20, 2020, the number of cases had increased to 176,000. 2 to address the large number of patients at a given time, hospital capacity, especially the availability of intensive care facilities and the number of healthcare workers (hcws), particularly doctors and nurses, are cornerstones and essential pillars in the struggle against the covid-19 pandemic. disease transmission among infected hcws is a major threat that could adversely affect the capacity of hospitals to care for patients and might even endanger patients. 3 we report on a symptomatic sars-cov-2-infected physician who worked in a large 1,030-bed municipal hospital in leipzig, germany. at the time of the report, coronavirus disease 2019 (covid-19) cases in germany were rapidly increasing. the index case physician had traveled to the part of germany with the highest covid-19 rates at that time, thereby visiting pubs and restaurants in the city of stuttgart (federal state of baden-wuerttemberg) on march 12-13, 2020. after returning home, she felt unwell for 2 days and had a sore throat, cough, and fever. despite these symptoms, she went to work at the hospital without wearing a face mask or other protective devices. she remained symptomatic, particularly with subfebrile temperature and frequent coughing. on march 16, 2020, she was working an 8-hour shift in addition to a 4-hour on-call shift. she was making rounds at the hospital, caring for patients, doing admissions, discussing treatments with colleagues, having frequent contact with nurses and other healthcare staff, having lunch and coffee breaks in a small lounge area, and even sitting in a crowded lecture room along with other hcws (supplemental fig. 1 online), as well as listening to employee information on the management of covid-19 patients. during the on-call shift, she saw patients all over the hospital. the next day, she stayed at home, but she returned the following day for another 3 hours of hospital work, still coughing heavily and apparently ill. when noticed, she was immediately sent home after undergoing coronavirus testing (combined nose and throat swab), which was positive for sars-cov-2. to assess sars-cov-2 infection, either copan liquid amies swabs (copan, brescia, italy) or pharyngeal lavage (10 ml saline solution) was used for sampling the nasopharyngeal material of the index physician and all contacts. rna extraction and real-time to further investigate potentially missed transmissions, we attempted to detect iga and igg antibodies against sars-cov-2 in sera, withdrawn on days 15 or16 and 22 or 23 after exposure, by an in vitro diagnostic labeled anti-sars-cov-2 enzyme-linked immunosorbent assay (elisa, euroimmun, lübeck, germany), following the manufacturer's instructions. only descriptive statistics were applied. numerical variables were summarized as means, and categorical variables were given as frequencies or proportions. ethical approval was not required for this study because only anonymous aggregated data were used, and no medical interventions were made on human subjects. sampling of hcws or patients was part of hospital policy. we identified 187 contacts with hcws and 67 contacts with patients. of these, 23 were identified as high-risk contacts, as defined by the world health organization guidance document on covid-19 global surveillance. 4 table 1 summarizes the characteristics of each high-risk contact. all high-risk contacts were subject to active symptommonitoring and committed to wearing a face mask during work. we tested all 254 potential contacts of the symptomatic sars-cov-2-positive index physician, including 67 patients, and 187 nurses and doctors, technical and medical assistants, and other healthcare staff, on day 5 after the exposure by specific rt-pcr from nose and throat swabs or pharyngeal lavage, irrespective of reported symptoms. of 187 tested hcws, 30 (16%) reported minor unspecific symptoms of upper airway infection (sore throat, coughing, sniffing). all tested persons turned out to be sars-cov-2 negative. the 23 high-risk contacts were investigated again 10 days after exposure by specific rt-pcr from nose and throat swabs. test results were negative, again. additionally, all high-risk contacts and the index physician were examined serologically on days 15 or 16 and days 22 or 23 after exposure. despite some iga positive-to-inconclusive ratios, none showed positivity for sars-cov-2 igg antibodies at follow-up except the index physician featuring seroconversion (table 2 ). we tested a large number of possible contact persons of a symptomatic sars-cov-2-infected physician among hcws and patients on day 5 after exposure; all were negative. after a comprehensive investigation of all contact clusters, we identified 23 highrisk contacts (22 hcws and 1 patient) and tested them again on day 10 after exposure. all rt-pcr tests remained negative for sars-cov-2, confirming that there was no transmission of the virus. extensive investigation and testing were performed because viral shedding of sars-cov-2 has been shown in completely asymptomatic individuals, prompting the hypothesis that clinical status is not reliable for triage and further testing. 5 sars-cov-2 has frequently been detected in asymptomatic carriers, for instance, during a cruise ship outbreak in which most of the passengers and staff were tested irrespective of symptoms: 51% of the laboratory-confirmed cases were asymptomatic at the time of confirmation. 6 for further analysis and confirmation of our results, we investigated the serum of all high-risk contacts (n = 23) on days 15 or 16 and 22 or 23 for sars-cov-2-specific antibodies. we found positive iga antibodies at both times but no igg antibodies, confirming the rt-pcr results of zero transmission. the specificities for iga and igg against sars-cov-2 were 91.3% and 100%, respectively. although the calculated performance values were obtained in a small study cohort (n = 24), the specificities were similar to those reported in a previous study and in accordance with the manufacturer's specifications. 7 these results are unexpected. considering an active sars-cov-2 transmission source with a presumably high viral burden and many high-risk contacts inside a hospital, massive spread was anticipated, particularly since a protective face mask was not in use. sars-cov-2 has been shown to persist (at least under experimental circumstances) for up to 72 hours depending on the surface type. 8 in hospitals, surfaces are frequently cleaned and disinfected, and all hcws reported regular handwashing, disinfection, and strict adherence to hygiene rules. recently, the importance of presymptomatic transmission (r p ) has been stressed (r p = 0.9 of an r 0 of 2), and the proportion of symptomatic transmission (r s ) to the basic reproduction number r 0 was calculated to be only 0.8 of an r 0 of 2. 9 a low percentage of transmission to high-risk contacts (5%) has been reported in nonhousehold members. 10 another study in the united states investigated the high-risk contacts of a patient among healthcare personnel (n = 32) and did not find any transmission, confirming our results. however, testing was only done in symptomatic persons after clinical monitoring, and asymptomatic transmission could have been missed. 11 importantly, not every infected person with sars-cov-2 is a super spreader, and not every infected individual in a closed room triggers a superspreading event, although this situation has the potential to do so and therefore must be dealt with as such. 12 in this context, our data support the recommendation to keep high-risk contacts among the hospital staff at work (especially in these difficult times with personnel shortages) when strictly using a protective mask, accompanied by close clinical and virologic monitoring. transmission of 2019-ncov infection from an asymptomatic contact in germany covid-19). world health organization website strengthening icu health security for a coronavirus pandemic global surveillance for human infection with coronavirus disease (covid-2019)-interim guidance. world health organization website evidence of sars-cov-2 infection in returning travelers from wuhan, china japan national institute of infectious diseases website severe acute respiratory syndrome coronavirus 2-specific antibody responses in coronavirus disease 2019 patients aerosol and surface stability of sars-cov-2 as compared with sars-cov-1 quantifying sars-cov-2 transmission suggests epidemic control with digital contact tracing investigation of a covid-19 outbreak in germany resulting from a single travel-associated primary case: a case series first known person-to-person transmission of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) in the usa the role of superspreaders in infectious disease acknowledgments. we kindly acknowledge the enormous personal commitment of ulrike schmidt (study department), and ines geßner as well as gerit görisch, md (both from hospital hygiene department).financial support. no financial support was provided relevant to this article. all authors report no conflicts of interest relevant to this article. key: cord-326223-q6e60nf8 authors: gembardt, florian; sterner-kock, anja; imboden, hans; spalteholz, matthias; reibitz, franziska; schultheiss, heinz-peter; siems, wolf-eberhard; walther, thomas title: organ-specific distribution of ace2 mrna and correlating peptidase activity in rodents date: 2005-02-16 journal: peptides doi: 10.1016/j.peptides.2005.01.009 sha: doc_id: 326223 cord_uid: q6e60nf8 biochemical analysis revealed that angiotensin-converting enzyme related carboxy-peptidase (ace2) cleaves angiotensin (ang) ii to ang-(1–7), a heptapeptide identified as an endogenous ligand for the g protein-coupled receptor mas. no data are currently available that systematically describe ace2 distribution and activity in rodents. therefore, we analyzed the ace2 expression in different tissues of mice and rats on mrna (rnase protection assay) and protein levels (immunohistochemistry, ace2 activity, western blot). although ace2 mrna in both investigated species showed the highest expression in the ileum, the mouse organ exceeded rat ace2, as also demonstrated in the kidney and colon. corresponding to mrna, ace2 activity was highest in the ileum and mouse kidney but weak in the rat kidney, which was also confirmed by immunohistochemistry. contrary to mrna, we found weak activity in the lung of both species. our data demonstrate a tissueand species-specific pattern for ace2 under physiological conditions. in the regulation of heart function and blood pressure, different peptide systems are involved, e.g. the renin-angiotensin system (ras), the kallikrein-kinin system, and the natriuretic peptide system. in these systems, proteases like angiotensin-converting enzyme (ace) or neutral endopeptidase (nep) have the distinction of generating or catabolizing biologically active peptides [10, 39, 42] . the newly discovered angiotensin-converting enzyme-related carboxypeptidase (ace2) has considerable sequence homology to ace (40% identity and 61% similarity), contains a hexxh zinc-binding domain, and conserves other critical residues typical of the ace family [12, 37] . the first step in generating angiotensin peptides is the cleavage of angiotensinogen to angiotensin (ang) i by renin. ang i is hydrolyzed by either ace or chymase to ang ii, which mediates its biological actions via the at1 and at2 receptors [15, 21] . ang i is also metabolized by nep to ang-(1-7) [15] , which mediates distinct effects through its receptor mas [35] . importantly, ang-(1-7) can also be directly metabolized from ang ii by ace2, whereas aminopeptidase a converts ang ii to ang iii [18] . ace2 also hydrolyzes ang i to ang-(1-9), although there is no hydrolysis of ang-(1-9), ang-(1-7), and ang(1) (2) (3) (4) (5) . moreover, ace2 hydrolysis is also specific for des-arg [9] bradykinin and its shorter fragments, although it cleaves neither bradykinin nor bradykinin-(1-7) [40] . ace2 mrna is expressed in many tissues but shows a less ubiquitous profile than ace. first studies in mice detected the highest expression in the ileum by quantitative reverse transcriptase polymerase chain reaction (qrt-pcr) [23] . ace2 is an important part of the ras, which counteracts the function of ace. it was also shown that ace2 expression can be upregulated by blockade of at 1 -receptors [27] . the importance of ace2 in cardiovascular regulation was confirmed by targeted disruption of ace2 in mice. the absence of ace2 in mice leads to a severe cardiac contractility defect, increased ang ii levels, and upregulation of hypoxia-induced genes in the heart [11] . in addition to its peptidolytic function, recent investigations have discovered that ace2 is a functional receptor for the coronavirus, which causes the severe acute respiratory syndrome (sars) [30] . in this investigation, we (i) measured the mrna distribution of ace2 through different tissues in both species. moreover, we (ii) quantified ace2 protein by western blot using a commercial polyclonal antibody to ace2. we (iii) measured ace2 activity in different tissues of mice and rats. we (iv) established a monoclonal antibody against ace2 to complete the investigation of tissue distribution by immunohistochemistry. finally, we compared (v) the distribution of ace2 in both species on the mrna and protein level. all experiments were done according to the guidelines of the federal law on the use of experimental animals in germany and were approved by the local authorities. for this investigation we used c57bl/6 mice and sprague-dawley (sd) rats in an age of 3-5 months. animals were killed by cervical dislocation. for rnase protection assay (rpa), ace2 activity assay and western blot, the tissues were snap frozen in liquid nitrogen. the samples were stored at −80 • c until further processing (all organs in total, heart divided into atria and ventricles). the tissues for immunohistochemistry were put in 4% formalin. after 24 h they were embedded and processed to paraffin sections. the polymerase chain reaction (pcr) amplified a 358 bp fragment (probe: mmace2) from mouse kidney cdna using the 5 -primer ctc agt gga tgg gat ctt gg (mmace25) and the 3 -primer tgt agc cat ctg ctc cct ct (mmace23), respectively a 342 bp fragment (probe: rnace2) from rat lung cdna using the 5 -primer cgg gga aag atg tca agc tcc tgc (rnace25) and the 3 -primer ctt gtc tgg tga cag cgc (rnace23), which were subcloned in a t-vector (promega gmbh, mannheim, germany). a sp6 polymerase transcribed a radioactive probe complementary to mmace2 (resp. rnace2) mrna, and a rna complementary to 127 nucleotides of the rl32 mrna was used as positive control [2] . ace2-specific mrna for mouse and rat were identified by rnase protection assay (rpa) using the ambion rpa ii kit (ambion (europe) ltd., huntingdon, uk). total rna was isolated from tissues using the trizol reagent (invitrogen gmbh, karlsruhe, germany) with subsequent chloroform-isopropanol extraction according to the manufacturer's instructions. a 15 g total rna fraction of each sample was hybridized with approximately 50 000 cpm for ace2 and 50 000 cpm for rl32 of the radiolabeled antisense probes in the same assay. equal loading has been insured by mrna measurements and mrna gel electrophoresis using 1 g of each sample (not shown). the hybridized fragments protected from rnase a + t1 digestion were separated by electrophoresis on a denaturing gel (5%, w/v polyacrylamide, 8 m urea) and analyzed using a fujix bas 2000 phospho-imager system (raytest gmbh, straubenhardt, germany) to perform quantitative analysis by measuring the intensity of the ace2 bands. the blots of each species were calculated to ace2 mrna expression in kidney, which was present on both blots of each species. the expression level in the lung was set to 100%. ace2 activity was measured similar to the method by vickers et al. [40] . tissue was homogenized in assay buffer (50 mm 2-morpholinoethanesulfonic acid, 300 mm nacl, 10 m zncl 2 , 0.01% brij-35, ph 6.5). protein concentration was determined using roti-quant (carl roth gmbh and co. kg, karlsruhe, germany) by the manufacturers instruction. we used mca-apk(dnp) (biosynthan gmbh, berlin, germany) dissolved in dmso (50 m, final concentration) as the ace2 substrate. the assay was performed in assay buffer and was started by adding 10 l of tissue homogenate. after 2 h incubation at ambient temperature (24 • c), the reaction was suppressed by adding 100 m o-phenanthrolin (final concentration). parallel control tests were performed in the presence of 1 m dx 600 (data not shown) [25] . after centrifugation (10 min, 10 000 × g) the fluorescence was measured at 320 nm (excitation) and 405 nm (emission) with the perkin-elmer fluorescence reader lambda 5 (perkin-elmer las gmbh, rodgau, germany). the molecular standardization was performed with mca-ap (biosynthan gmbh, berlin, germany) and calculated per mg protein. the functionality of the assay was proven by a standardized solution with defined, recombinant ace2 activity (r&d systems gmbh, wiesbaden, germany). tissue was homogenized in phosphate-buffered solution (pbs) containing protease inhibitor mixture (complete, roche diagnostics gmbh, mannheim, germany). protein concentration was determined with bca protein assay kit (perbio science gmbh, bonn, germany). sample proteins (10 g/lane) and a prestained protein-weight marker (amersham biosciences gmbh, freiburg, germany) were size fractionated by sds-polyacrylamide gels (10%) and transferred to pvdf membranes with a pegasus semidry-blotter (phase gmbh, lübeck, germany). equal loading has been insured by staining control gels with simply-blue safe stain (invitrogen gmbh, karlsruhe, germany) using 10 g of each sample (not shown). the membranes were blocked at room temperature in 5% dry milk powder (blotting grade, non-fat dry milk, bio-rad laboratories gmbh, munich, germany) prepared with tris-buffered saline containing 0.1% tween 20 (ttbs) for 1 h, incubated with goat polyclonal antibody against ace2 (santa cruz biotechnology inc., heidelberg, germany, 1:250 diluted in 5% dry milk powder ttbs, 1 h), and then washed three times with ttbs (15 min each). subsequently, the membranes were incubated with horseradish peroxidase-conjugated antigoat igg (dakocytomation a/s, glostrup, denmark, 1:1000, 1 h) and washed three times. specific immunoreactive proteins were detected by enhanced chemiluminescence (amersham biosciences gmbh, freiburg, germany). the bands on the x-ray film were quantified by densitometry scanning and expressed as percentage of the kidney protein signal. monoclonal antibodies against the synthetic peptide avgeimslsaat (aa 403-414 of murine ace2) have been raised. for immunization of the mice peptide was cross-linked with glutaraldehyde to albumin fraction v from bovine serum. balb/cj female mice were injected with the conjugate. following four booster injections the spleen lymphocytes were fused with fo myeloma cells by using polyethylene glycol 1500 (roche diagnostics gmbh, mannheim, germany) following the manufacturers instructions. the different hybridoma supernatants were screened for specific antibodies by using the synthetic peptide in the nctest [26] . for production of monoclonal antibodies, positive hybridoma cells were grown in celline incubators (integra biosciences gmbh, fernwald, germany). the mouse monoclonal antibodies were affinity purified on a mabtrap g ii column (amersham-pharmacia gmbh, otelfingen, switzerland) from cell culture supernatants. immunoglobulin class and subclasses were determined with the immuno type kit (sigma-aldrich chemie gmbh, taufkirchen, germany). paraffin sections of mouse tissues were prepared and stained using standard histology procedures. for immunostainings, deparaffinized and rehydrated tissue slides were first treated for 30 min with 30% h 2 o 2 to block the endogenous peroxidase. after rinsing in ddh 2 o and soaking in pbs for 5-10 min, slides were treated with 10% (w/v) bsa in pbs to eliminate non-specific protein binding sites. the slides were then exposed (overnight, 4 • c) to the monoclonal ace 2 antibodies (clone 7e7, 1d3) at concentrations of 1 and 4 g/ml, respectively. after removing excess antibody, slides were treated with biotin-labeled anti-mouse (dianova gmbh, hamburg, germany) antibody for 30 min at 37 • c and finally with horse-radish peroxidase (hrp) labeled streptavidine (zymed laboratories inc., san francisco, usa) for 20 min at 37 • c. after washing, slides were incubated in aminoethylcarbazol (sigma-aldrich co., st. louis, usa) for 10 min at room temperature. slides were counterstained with hematoxylin, and cover slipped according to conventional procedures. slides were examined under a conventional microscope after removing the excess substrate in ddh 2 o. negative controls were performed without the primary antibody, just applying dilution buffer of the primary antibody. data were analyzed by t-test using spss11 software (spss benelux bv, gorinchem, the netherlands). each value was expressed as the mean ± s.e.m., and statistical significance was accepted for p < 0.05. ace2 mrna could be detected in all investigated organs, but with profound distinction between different organs. in both species, only a low amount was found in ventricle, liver, testis, forebrain, and spleen ( figs. 1 and 2) , whereas in the lungs a moderate and comparable expression of ace2 mrna was found and set to 100%. the highest levels were found in the ileum of both species (fig. 3) . between the species several differences in tissue specific expression of ace2 mrna were found. the expression in mouse was most pronounced higher than in rat in kidney (∼31.9-fold), colon (∼18.6-fold), and ileum (∼12.0-fold) (fig. 3) , whereas in bladder (∼2.5-fold) and ventricle (∼2.1-fold) ace2 expression in rat exceeded the mouse. in accordance with the rna expression data, highest activity for ace2 was found in the ileum of mouse and rat (table 1) , whereas the activity in the mouse was 3.2fold higher. lowest ace2 activity was found for both species in spleen. low activity was also found for liver of mice and thymus of rats. corresponding to the differences on mrna levels in the kidney the ace2 activity fig. 3 . quantification of the rpas of mice (white columns) and rats (black columns). the mrna amount of the lungs is set to 100% (n ≤ 4) . the values are shown as mean + s.e.m. 1. ventricle, 2. kidney, 3. lung, 4. liver, 5. testis, 6. bladder, 7. forebrain, 8. spleen, 9. thymus, 10. stomach, 11. ileum, 12. colon, 13. brainstem, 14. atrium, 15. adipose tissue. * p < 0.05, ** p < 0.01, *** p < 0.0001 compared mouse vs. rat. was much higher in mice than in rats (∼13.9-fold). the activity of ace2 in the lung was different to mrna and 2.6-fold higher in rats than in mice. in contrast to rpa data the activity in colon was comparable between both species. using a commercial polyclonal antibody in western blot for the quantification of protein levels in mouse and rat tissues (fig. 4) a pattern completely different from rna expression and ace2 activity was found. a moderate and comparable expression could be detected in the kidney of both species and was set to 100%. thus, the highest amount of protein could be detected in atrium of both species (mouse: 124.5%; rat: 131.5%) and ventricle (mouse: 131.7%; rat: 143.3%). for the mouse less ace2 protein was found in lung (19.7%) and testis (28.7%), whereas no protein was detectable in these two tissues in rat. in thymus (mouse: 44.4%; rat: 50.6%) and forebrain (mouse: 87.9%; rat: 80.7%) of both species a moderate expression was detectable, whereas no ace2 protein was found in spleen of mouse and rat. to further clarify the discrepancy between rpa and activity on one side and western blot on the other, immunohistochemistry was performed in lung, kidney (fig. 5) , and testis (data not shown) of mice and rat with new monoclonal ace2 antibodies (clones 7e7 and 1d3), we generated. the antibodies were determined to belong to the igg1 subclass. in the lungs of both species alveolar macrophages and type 2 cells (fig. 5 , upper row) were stained with both monoclonal ace2 antibodies (data for clone 1d3 not shown). the epithelium of the renal tubuli was strongly stained (fig. 5 , lower row, left) in the kidney of mice. in rats only a weak signal, but the same pattern as in mouse, was detected, what aligned with mrna and ace2 activity (fig. 5, lower row, right) . in recent investigations it was shown that peptidases like ace and nep are important regulators of cardiovascular and endothelial function as well as myocardial remodelling [1, 7, 36, 41] . consequently, after its discovery in 2000, ace2 became an enzyme of interest for scientific investigation of its impact in cardiovascular physiology and pathophysiology [11, 12, 37] . to elucidate some of its physiological functions we investigated the tissue distribution of mrna and protein in a variety of tissues of c57bl/6 mice and sprague-dawley rats. while we could see correlating patterns of mrna and ace2 activity in most of the examined tissues, we also found significant divergences between the investigated species. the huge difference between mrna and protein levels in the lung may be due to shedding as demonstrated for ace [4, 12, 32] . this shedding leads to an increased secretion of ace2 and lowered its protein content in the lung by even high mrna expression. the significant differences that we found between the species on ace2 protein and mrna levels in kidney could be explained by the varying interspecies regulation and expression of peptidases, as shown in the literature for nep activity in rat and rabbit kidneys [14] . comparing our mrna and activity data with the western blot pattern, we have to conclude that the commercial polyclonal antibody is not detecting ace2 protein in organ homogenates and is not suitable for ace2 staining. in contrast, using immunohistochemistry our new monoclonal ace2 antibodies produce staining patterns comparable to our mrna and activity data. we have shown that ace2 expression in rodents is highest in ileum among the examined organs. it was shown for other peptidases of ras like ace and nep that they are also present at high levels in the intestine [29] . however, the distinct function of these peptidases in the ileum is not yet known. further investigations have to clarify the physiological and pathophysiological functions of the peptidases in the gastrointestinal tract. beside its physiological function as a peptidase, ace2 is used by coronavirus as a co-receptor in severe acute respiratory syndrome (sars) [30] . it was shown that the sars coronavirus only can enter cells which express ace2 [24] . ace2 distribution in the small intestine, lung and vascular endothelium may offer a point of entry for the sars coronavirus, but does not reflect its basic function [22, 30, 38] . interestingly, the distribution patterns we found for mrna and ace2 activity contradict investigations using a commercial northern blot for detecting mrna [12, 37] but have been confirmed by recent papers using rt-pcr [23] . this discrepancy may be a species-specific alteration of tissue distribution, since they used human tissue for northern blot, or it may be due to technique differences (commercial northern versus rpa and activity assay). the first possibility is at least supported by our finding that significant differences in ace2 expression patterns exist between the close relatives mouse and rat. recent investigations revealed biological activity for angiotensin peptides other than angii, like ang-(1-7) [16, 33, 34] . ace2 can generate ang-(1-7) by cleaving the cterminal amino acid from angii [40] . ace2 is also involved in another pathway leading to the generation of ang-(1-7). it cleaves angi to ang-(1-9) [12] . ang-(1-9) is then hydrolyzed by ace to ang-(1-7) . we demonstrated that ang-(1-7) is an endogenous ligand for the g protein-coupled receptor (gpcr) mas [35] . mrna of the gpcr mas was found at high levels in testis and certain brain regions and at fig. 5 . immunohistochemical visualization of ace2 positive cells. sections of lungs (upper row) and kidneys (lower row) from mouse (left panel) and rat (right panel). in the lungs of both species alveolar macrophages and type 2 cells were stained positive. the tubulus epithelium in mouse kidney was stained positive, whereas in the rat kidney only weak staining was seen. moderate levels in kidney and heart [2, 3, 31] . it was shown that high concentrations of ang-(1-7) were present in heart, kidney, and brain [5, 6, 8, 28] . in recent investigations, it was demonstrated that ace2, mas, and its endogenous ligand ang-(1-7) are present in the same cells of the kidney [9] . as we recently postulated, this indicates a relevant impact of the ace2/ang-(1-7)/mas axis on blood pressure regulation and cardioprotection. actual investigations indicate an upregulation of ace2 in heart failure, pointing to the relevance of ace2 in cardiac function [20, 32, 43] . however, there was a high incidence of sudden death in animals overexpressing ace2. electrophysiology revealed severe, progressive conduction and rhythm disturbances with sustained ventricular tachycardia that progressed to fibrillation and death [13] . while anti-arrhythmic actions were demonstrated for ang-(1-7) in low concentra-tions (0.22 nm) by stimulating its own receptor, 100-fold higher concentrations of ang-(1-7) lead to arrhythmias by stimulating the at1 receptor [17, 19] . therefore, the overexpression of ace2 may lead to a high increase in the production of ang-(1-7), turning its cardioprotective actions into effects causing arrhythmias by unspecific at1 stimulation. in future studies, the actions of ang-(1-7) and its concentrationdependency on ace2 expression on heart rhythm have to be proven in in vivo experiments with at1-and mas-deficient animals. our data on tissue and species-specific ace2 expression point to the fact that the ras becomes increasingly complex. since we identified an expression pattern markedly different from ace, we conclude that the expression levels of the involved peptidases like ace, ace2, and nep that generate and/or degrade the bioactive peptides of the ras are predic-tive of either the occurrence of vasoconstriction or dilatation or the dominance of pathophysiological stimuli over beneficial conditions. the acute infarction ramipril efficacy (aire) study investigators, effect of ramipril on mortality and morbidity of survivors of acute myocardial infarction with clinical evidence of heart failure imprinting of the murine mas protooncogene is restricted to its antisense rna cell type-specific expression of the mas proto-oncogene in testis a point mutation in the juxtamembrane stalk of human angiotensin i-converting enzyme invokes the action of a distinct secretase cardiac angiotensin-(1-7) in ischemic cardiomyopathy immunocytochemical localization of angiotensin-(1-7) in the rat forebrain vasopeptidase inhibitors: an emerging class of cardiovascular drugs enhanced renal immunocytochemical expression of ang-(1-7) and ace2 during pregnancy novel aspects of the renal renin-angiotensin system: angiotensin-(1-7), ace2 and blood pressure regulation vasopeptidase inhibitors: a new therapeutic concept in cardiovascular disease? angiotensin-converting enzyme 2 is an essential regulator of heart function a novel angiotensin-converting enzyme-related carboxypeptidase (ace2) converts angiotensin i to angiotensin 1-9 heart block, ventricular tachycardia, and sudden death in ace2 transgenic mice with downregulated connexins distribution of neutral endopeptidase activity along the rat and rabbit nephron novel angiotensin peptides counterregulatory actions of angiotensin-(1-7) angiotensin-(1-7): cardioprotective effect in myocardial ischemia/reperfusion brain renin-angiotensin system blockade by systemically active aminopeptidase a inhibitors: a potential treatment of salt-dependent hypertension effects of angiotensin ii and angiotensin-(1-7) on the release of [3h]norepinephrine from rat atria ace2 gene expression is up-regulated in the human failing heart insights into angiotensin ii receptor function through at2 receptor knockout mice tissue distribution of ace2 protein, the functional receptor for sars coronavirus. a first step in understanding sars pathogenesis quantitative mrna expression profiling of ace 2, a novel homologue of angiotensin converting enzyme susceptibility to sars coronavirus s protein-driven infection correlates with expression of angiotensin converting enzyme 2 and infection can be blocked by soluble receptor novel peptide inhibitors of angiotensin-converting enzyme 2 immunocytochemistry in brain tissue upregulation of angiotensin-converting enzyme 2 after myocardial infarction by blockade of angiotensin ii receptors angiotensin-(1-7) immunoreactivity in the hypothalamus of the (mren-2d)27 transgenic rat burrell lm. differential tissue and enzyme inhibitory effects of the vasopeptidase inhibitor omapatrilat in the rat angiotensin-converting enzyme 2 is a functional receptor for the sars coronavirus expression of the mouse and rat mas proto-oncogene in the brain and peripheral tissues the role of ace2 in cardiovascular physiology vasodilator action of angiotensin-(1-7) on isolated rabbit afferent arterioles angiotensin-(1-7): an update angiotensin-(1-7) is an endogenous ligand for the g protein-coupled receptor mas remodeling of myocardium and arteries by chronic angiotensin converting enzyme inhibition in hypertensive patients a human homolog of angiotensin-converting enzyme. cloning and functional expression as a captopril-insensitive carboxypeptidase exploring the pathogenesis of severe acute respiratory syndrome (sars): the tissue distribution of the coronavirus (sars-cov) and its putative receptor, angiotensin-converting enzyme 2 (ace2) the angiotensin-converting enzyme gene family: genomics and pharmacology hydrolysis of biological peptides by human angiotensin-converting enzyme-related carboxypeptidase at1 receptor blockade increases cardiac bradykinin via neutral endopeptidase after induction of myocardial infarction in rats vasopeptidase inhibitors: will they have a role in clinical practice? increased angiotensin-(1-7)-forming activity in failing human heart ventricles: evidence for upregulation of the angiotensin-converting enzyme homologue ace2 florian gembardt is paid by a grant from the "deutsche forschungsgemeinschaft" (german research foundation)[grk865]. this study was also supported by the "stiftung zur förderung der wissenschaftlichen forschung an der universität bern". we thank helmut würdemann and susanne gygax for their technical assistance. key: cord-304930-gf3cptnt authors: hinz, sebastian; ellmann, daniel; wegner, christian; bömicke, wolfgang; bensel, tobias title: the digital abutment check: an improvement of the fully digital workflow date: 2020-10-24 journal: case rep dent doi: 10.1155/2020/8831862 sha: doc_id: 304930 cord_uid: gf3cptnt by using modern digitalization techniques, an existing denture can be digitized and aid the provision of a new implant-supported denture according to a fully digital workflow. this includes fully navigated implant surgery and results in an immediately provided prosthetic restoration. however, even with the current digital workflow, it is challenging to achieve a definitive prosthetic restoration in a single treatment session. in order to achieve a definitive denture in as few treatment sessions as possible, we have implemented the digital abutment test. this test modified the existing data set and determined the final restoration. in the present case, the preexisting maxillary removable complete denture was converted into a fixed immediate restoration using the fully digital workflow. the workflow is divided into two treatment phases, each with three treatment sessions, where part of the second phase involves an innovative digital abutment check. the illustrated case shows an effective use of current digital possibilities. special attention was also paid to a minimally invasive course of therapy. once the hard and soft tissues of the oral cavity have been digitally recorded, e.g., by intraoral scanners and modern 3d radiograph technology, these data can serve as the basis for further digital process steps [1] . before implant surgery, the final position of the implants can be determined virtually using planning software and 3d radiograph images. the position of the inserted implants is of crucial importance for the final design of the anchored prosthesis and the longterm survival of the dentures [2] [3] [4] . in this context, template-guided implant surgery allows for the accurate placement of dental implants [2, 3] . a precise surgical template can be fabricated by merging the intraoral-scan data with the 3d radiographic data [5] [6] [7] . for the surgeon, the use of a surgical template results in a predictable and safe treatment procedure. patients additionally benefit from a shorter treatment time, fewer postoperative restrictions, and an overall increase in comfort [8] . as a consequence, template-guided implant placement is becoming increasingly popular. [8] [9] [10] [11] . the implants were placed according to the comfour® system (camlog vertriebs gmbh, wimsheim, germany). four implants are used to immediately rehabilitate the edentulous jaw with a fixed interim restoration. the advantages of the system lie in the maximum expansion of the support polygon through a precisely planned implant position, but especially implant angulation; the distal implants are usually inserted at an angle between 15 and 30 degrees [3, 4, [12] [13] [14] . this allows the prosthetic support field to be expanded posteriorly without compromising relevant anatomical structures and without having to perform extensive bone augmentation measures. the template used in the present report provided a precise implementation of the digitally determined implant position [5, 9-11, 15, 16] . the navigated procedure offered further advantages by eliminating the need for intraoperative flap formation, thus reducing surgical trauma and reducing the postoperative need for analgesics [8, 17] . however, the main challenge for the prosthetic treatment team (dentist, dental technician) in the implementation of a fully digital all-on-x workflow is to transfer the final implant position to the definitive restoration. the deviations between the virtually planned and the real implant position must be balanced out even with guided implantation [18] [19] [20] [21] [22] [23] [24] [25] . digital impressions represent a reliable impression method for the fabrication of implant-supported full-arch frameworks [26] . usually, scan-bodies are screwed onto the implants for digital impression making. these can negatively affect the precision of the digital impression [27] [28] [29] . however, transmission errors due to the use of scan-bodies must be taken into account. a transfer without the use of scan-bodies could increase the precision of the prosthetic restoration. in this present case report, we successfully demonstrate the realization of the final prosthodontic restoration while avoiding inaccuracies caused by screwed-in scan-bodies. this was accomplished by the implementation of the digital abutment check without the use of scan-bodies. the 55-year-old patient first came to the department of prosthodontics (faculty of medicine, martin luther university halle-wittenberg) during an outpatient consultation. the patient reported smoking about 10 cigarettes a day but otherwise had an uneventful medical history. the maxilla was edentulous, and the remaining teeth in the mandible were stable from a periodontological and endotontological point of view. the existing prosthetic and conservative restorations were found to be sufficient and restored a continuous dental arch, which extended from the second left to the second right premolar. according to the patient, the last maxillary teeth had been extracted about one year prior to the initial consultation. since then, he has been wearing a conventionally made removable complete denture. the patient stated that the stability of the prosthesis was not sufficient to eat properly. he also complained about the extensive coverage of the palate. in the course of weighing up the different therapy options, the patient decided on an implant-supported, fixed full-arch prosthesis without palatal coverage. the mandible shortened dental arch was to be maintained in agreement with the patient. case reports in dentistry the aim of the decided upon therapy was to achieve stable, palate-free care, involving little surgical effort and with as few treatment sessions as possible. we decided to use a gentle, minimally invasive procedure without any additional augmentations. the final planning included the insertion of four implants in the upper jaw and a fixed, provisional immediate restoration, which should be transferred to a definitive fixed partial denture (fpd) after the healing period of six months. the treatment was divided into two independent phases. the first treatment phase involves diagnostics and therapy planning, as well as surgical intervention and the immediate provision of an interim restoration. the second treatment phase consists of the transfer of the interim fpd to the definitive fpd after the successful healing period. we decided to use the comfour® system (camlog, wimsheim, germany) to maximise patient comfort during the treatment. the advantages of the comfour® system are the possibility of immediate loading with appropriate primary stability of the implants (>35 ncm) and the targeted avoidance of augmentation by angulation of the posterior implants. 4.1. pretreatment. as the first treatment step, the mandible and the maxillomandibular relationship were digitally recorded intraorally (trios 3 intraoral scanner, 3shape a/s, copenhagen, denmark). the correct fit of the maxillary removable complete denture was checked in advance using low viscosity polyvinyl siloxane (gc fit checker® advanced, gc europe n.v., leuven, belgium). the correct maxillomandibular relationship was checked clinically based on the resting position of the mandible. if the measured parameters are inadequate, dentures would have to be adjusted in advance. alternatively, if the patient does not wear any removable dentures or the maxillomandibular relationship has to be changed, the maxillomandibular relationship can be adjusted with digital measurement systems (jmanalyser +, zebris medical gmbh, isny, germany), due to the fact that these systems offer a digital interface for computer-aided design/computer-aided manufacturing (cad/cam). in the present case, the existing maxillary removable complete denture was scanned in the dental laboratory (rüberling & klar dental laboratory, halle (saale), germany) with a laboratory scanner (e4 lab scanner, 3shape a/s, copenhagen, denmark) ( figure 2) . it was then used as a template for the radiographic and the surgical template and the provisional fpd. the standard triangulation/-tesselation language (stl) data records of the mandible and the maxillomandibular relationship record were matched with the data of the existing complete denture (exocad den-talcad, r+k cad/cam technologie gmbh & co.kg, berlin, germany). the soft tissue situation of the edentulous maxilla was picked up using the base area of the complete denture. this procedure resulted in the manufacturing of the radiographic template. the base of the radiographic template was milled from clear polymethylmethacrylate using a silicone occlusion key (shera-duett-soft, shera werkstoff-technologie gmbh & co.kg, lemförde, germany), the surgical template was placed in the patient and fixed in its definite position with anchor pins (guided anchor pin, nobel biocare ag). for a flapless surgery, the mucous membrane was punched through the drill sleeves and removed. afterwards, the implant bearings were reprocessed using 6-13 mm drill bits. for the correct transmission of the planned threedimensional implant position, the implants (guide cam-log®sl promote plus, camlog vertriebs gmbh) were inserted using the torque wrench up to the marking of the rotation indicator on the drill sleeves. the bone quality corresponded to d2 and the implants performed primary stability (>35 ncm). immediate loading was therefore possible ( figure 6 ). abutments compensating for the implant angulation were connected to the implants (bar abutments, camlog vertriebs gmbh). a flexible handle (comfour®, cam-log vertriebs gmbh) was used to screw in the posterior implants (figure 7 ). 4.6. immediate restoration. titanium adhesive bases (titanium adhesive base for bar abutment, passive fit, camlog, wimsheim, germany) were screwed onto the bar abutments. this resulted in an intraoral and tension-free bonding of the provisional fpd. the static and dynamic occlusion was checked and adjusted. the provisional fpd was then drained and cleaned using alcohol. afterwards, the provisional fpd case reports in dentistry was bonded to the titanium adhesive bases (titanium adhesive base for bar abutment, passive fit, camlog) using autopolymerizing prosthesis repair resin (qu resin, bredent gmbh & co.kg, senden, germany). the basal surface of the interim fpd was elaborated and polished, and then, the interim fpd was tightened to the implants at 15 ncm and the occlusion finally checked. the screw channels were closed with foam pellets and a gypsum-based sealing material (cavit™, 3m deutschland gmbh, seefeld, germany), and a postoperative orthopantomogram was then performed (figure 8 ). (figure 9) 5.1. abutment scan. after a six-month implant healing period, the interim fpd had to be replaced by a definitive screw-retained fpd. for this purpose, the occlusion of the existing interim situation and the maxillomandibular relationship were reevaluated. a digital maxillomandibular relation record was made with the interim restoration in place using an intraoral scan-ner (trios 3 intraoral scanner, 3shape a/s). then, the interim fpd was unscrewed in order to scan the bar abutments screwed onto the implants and the adjacent soft tissues. after the scan was completed, the provisional fpd was screwed back on. check. the stl scan data were sent to the dental laboratory for further processing. in the dental laboratory, the existing planning data record is matched with the new maxillomandibular relation record scan and the abutment and soft tissue scan. the incisive papilla, palatine raphe, and palatine rugae served as points of reference for matching the scans. as a result, changes in the jaw relation and soft tissue, as well as minimal positional deviations of the abutments, can be transferred to the definitive fpd ( figure 10) . the cobalt-chromium alloy (cocrmo) fpd framework (organic cocr, organical dental implant, r+k cad/cam technologie gmbh & co.kg, berlin, germany) was designed in accordance with the generated data set (exocad dentalcad, r+k cad/cam technologie gmbh & co.kg) and subsequently milled (organical® 5x dental milling try-in. the interim fpd was unscrewed in order to try it in the definitive fpd framework and to check the passivity of fit using the sheffield test [30] . in the present case, the fpd scaffold fitted without the need for any adjustment ( figure 11 ). the provisional fpd was then screwed back on, and the definitive fpd scaffold was sent to the dental laboratory for final veneering. inclusion of the fpd. the cocrmo fpd framework was veneered individually in the laboratory using composite resin material (sr chromasit, ivoclar vivadent, schaan, liechtenstein). in the final treatment session, the provisional fpd was removed and the definitive and veneered fpd was screwed on with 15 ncm. the fit of the fpd was optimal; the occlusion was checked and optimized with minimal grinding measures. finally, the screw channels were covered with foam pellets and composite resin (crb-bonding, shofu inc., kyoto, japan; tetric evoflow, ivoclar vivadent, schaan, liechtenstein) ( figure 12 ). the final orthopantomogram was performed (figure 13 ). the present case report demonstrates the effective use of the available modern digital manufacturing processes in dentistry. the treatment procedure integrated consequent digital backward planning, fully navigated implantation, and completely digital dental prosthesis production. the procedure described here is in contrast to most of the other all-on-x concepts, which do not involve purely digital processes [6, 7, [12] [13] [14] . as conventional impressions could be avoided completely in this workflow, the number of individual treatment sessions (session for maxillomandibular relationship record and try-in) and individual session time could be significantly shortened. for example, the entire surgical procedure up to the installation of the provisional fpd could be carried out by an experienced practitioner in about 75 minutes. the relatively short duration of treatment in combination with a minimally invasive procedure lowers the risk of postoperative complaints such as swelling and pain [8, 17] . the key innovation of this case report is the digital abutment check, which is carried out directly using an intraoral scanner without screwed-in scan-bodies. this is possible because the exact geometry of the bar abutments is stored in the cad software databases (organical® dental implant, r+k cad/cam technologie gmbh & co.kg). the direct scan of the bar abutments without the use of scan-bodies again offers advantages in terms of digital impression precision. possible errors due to incorrect positioning of the scan-body on the implants can thus be excluded [27] [28] [29] . ultimately, this in turn influences the exact fit of the final fpd. in the present case report, an indication-oriented application of both 3d printing methods and cam milling methods is also demonstrated. nowadays, surgical templates can be printed with a clinically acceptable fit [31, 32] . if anchor pins have to be used, the 3d printing process is ideal when compared to milling because even with the most 11 case reports in dentistry modern 5-axis milling machines, the tool angle is limited. with 3d printing, the drilling channels for the anchor pins, which are often at an angle of 90°to the actual machining axis, can be more easily realized. the printing material, like the milling material, offers the possibility of sterilization before insertion in the patient during the surgery. the ability to sterilize any used dental laboratory materials in order to avoid the chain of infection during the surgical treatment is essential and not just since the beginning of the covid-19 pandemic situation [33] . the construction of the interim fpd is an additional advantage of the performed digital workflow. the interim fpd was deliberately manufactured using pmma. in contrast to more stable materials like zirconium dioxide, pmma offers potential material-specific benefits. these benefits result in the ability to check and adapt the case reports in dentistry maxillomandibular relationship during the provisional restoration phase. this means that the occlusion of the provisional pmma-fpd could be either easily reduced by grinding or increased by adding self-curing resin material. the higher abrasiveness of the material offers some protection against overloading the implants during the healing process. finally, the definitive fpd may be veneered with ceramic instead of composite resin. in contrast, it is also possible to produce a fully anatomical milled fpd, which can be inserted as the definitive dental restoration. this procedure could avoid the previous scaffold try-in. in this case report, one of the objectives of the treatment procedure was that the denture should be easily repairable. therefore, the veneering material chosen for the definitive fpd was composite resin. however, compared to ceramic veneering material, composite resin enables easier occlusal adaptation to the opposing jaw. in contrast to a conventional treatment process, not only are sessions for the maxillomandibular relationship and possibly the scaffold try-in avoided, but the process described here also creates an accurate adjustment of the definitive restoration. the treatment concept shown in this present case report combines a safe and time-saving digital workflow with demanding, predictable therapy results. in addition, the surgical intervention was not a major burden for the patient. the enormous gain in quality of life exceeds the manageable treatment effort for the patient and is clearly in focus. the patient's wish to switch from a removable complete denture to a fixed, palate-free prosthetic restoration could be fulfilled after three sessions following the end of the first treatment phase. in addition, both the original tooth position and aesthetics could be transferred to the provisional and definitive fpd, producing a harmonious appearance that was familiar to the patient. the data used to support the findings of this study may be released upon application to the department of prosthodontics, martin-luther-university halle-wittenberg, which can be contacted at dr. christian wegner, department of prosthodontics, university hospital halle, magdeburger straße 16, 06112 halle (saale), germany. relationship between the ct value and cortical bone thickness at implant recipient sites and primary implant stability with comparison of different implant types the accuracy of single-tooth implants placed using fully digitalguided surgery and freehand implant surgery accuracy of flapless immediate implant placement in anterior maxilla using computer-assisted versus freehand surgery: a cadaver study the accuracy of computer-guided implant surgery with tooth-supported, digitally designed drill guides based on cbct and intraoral scanning. a prospective cohort study current state of the art of computer-guided implant surgery the all-on-4 concept for full-arch rehabilitation of the edentulous maxillae: a longitudinal study with 5-13 years of follow-up the use of computer-guided flapless implant surgery and four implants placed in immediate function to support a fixed denture: preliminary results after a mean follow-up period of thirteen months guided implant surgery in the edentulous maxilla: a systematic review computer-guided surgery using human allogenic bone ring with simultaneous implant placement: a case report accuracy of computer-guided template-based implant surgery clinical applications and effectiveness of guided implant surgery: a critical review based on randomized controlled trials shortterm report of an ongoing prospective cohort study evaluating the outcome of full-arch implant-supported fixed hybrid polyetheretherketone-acrylic resin prostheses and the all-onfour concept the nobelguide®all-on-4®treatment concept for rehabilitation of edentulous jaws: a retrospective report on the 7-years clinical and 5-years radiographic outcomes the nobelguide® all-on-4® treatment concept 13 dentistry for rehabilitation of edentulous jaws: a prospective report on medium-and long-term outcomes accuracy of computer-guided flapless implant surgery in fully edentulous arches and in edentulous arches with fresh extraction sockets accuracy of virtually planned and conventionally placed implants in edentulous cadaver maxillae and mandibles: a preliminary report static computer-aided implant surgery (s-cais) analysing patientreported outcome measures (proms), economics and surgical complications: a systematic review guidance means accuracy: a randomized clinical trial on freehand versus guided dental implantation accuracy of dental implant placement via dynamic navigation or the freehand method: a split-mouth randomized controlled clinical trial accuracy of computer-aided dynamic navigation compared to computer-aided static navigation for dental implant placement: an in vitro study the influence of guided sleeve height, drilling distance, and drilling key length on the accuracy of static computer-assisted implant surgery influence of surgical guide support and implant site location on accuracy of static computer-assisted implant surgery accuracy of newly developed sleeve-designed templates for insertion of dental implants: a prospective multicenters clinical trial accuracy of computer-assisted template-based implant placement using two different surgical templates designed with or without metallic sleeves: a randomized controlled trial technical accuracy of printed surgical templates for guided implant surgery with the codiagnostixtmsoftware precision and accuracy of a digital impression scanner in full-arch implant rehabilitation comparison of postoperative intraoral scan versus cone beam computerised tomography to measure accuracy of guided implant placement-a prospective clinical study methods used to assess the 3d accuracy of dental implant positions in computer-guided implant placement: a review evaluation of impression accuracy for a four-implant mandibular model-a digital approach improving the fit of implant-supported superstructures using the spark erosion technique comparison of the accuracy of implants placed with cad-cam surgical templates manufactured with various 3d printers: an in vitro study the impact of the fabrication method on the three-dimensional accuracy of an implant surgery template preventing sars-cov-2 transmission in rehabilitation pools and therapeutic water environments the authors declare that they have no conflict of interest. the study was performed as part of the employment of the authors of the department of prosthodontics, faculty of medicine, martin-luther-university halle-wittenberg, halle (saale), germany. key: cord-029402-5gun91ep authors: celi, giuseppe; guarascio, dario; simonazzi, annamaria title: a fragile and divided european union meets covid-19: further disintegration or ‘hamiltonian moment’? date: 2020-07-17 journal: j doi: 10.1007/s40812-020-00165-8 sha: doc_id: 29402 cord_uid: 5gun91ep despite being symmetric in its very nature, the covid-19 shock is affecting european economies in a very asymmetric way, threatening to deepen the divide between core and peripheral countries even more. it is not covid-19 itself, however, but the contradictions within the eu’s growth model and institutional architecture that would be to blame for such an outcome. the dramatic impact of the economic crisis brought on by the pandemic and the threat that it poses to eurozone survival seem to have forced a reluctant germany into action: a minor step, but an important signal. this note analyses the crossroads currently facing europe—the risk of disintegration vis-a-vis the opportunity for a ‘hamiltonian moment’—discussing possible future scenarios in the light of past developments. like viruses, crises too can rapidly change their dna: the financial crisis of 2008 changed from international to regional, from financial to real, eventually turning into an existential threat to the whole european integration project. in the institutional context of the eurozone (ez), the financial crisis soon developed into a sovereign debt crisis, dragging the banks along with it. in the austerity environment that followed, the southern periphery (sp) never completely recovered the losses in output, employment, and fiscal sustainability. thus, the "symmetric" coronavirus shock hit countries that were in highly asymmetric conditions. in fact, not all the countries of the union have the resources needed to intervene in support of their economy, prompting concern that countries with the deepest pockets might be getting an unfair advantage in the eu's single market. far from triggering mutual protection, the covid-19 crisis seems to be paving the way for the same mistakes that followed the 2008 financial crisis. the centrifugal forces threatening disintegration of the european monetary union (emu) seem to have been defused, albeit only in part and only in extremis, at least for the time being. however, the survival of the union depends not only on responding to the severe financial problems caused by the epidemic, but also means addressing the long-term, structural problems that led to the increasing divergences among her members. as chancellor merkel herself acknowledged, "it is in nobody's interest for germany alone to be strong after the crisis". 1 convergence is essential to put the union on a more solid basis so as to guarantee its long-term sustainability. what policies and what reforms should be implemented to pursue this objective? and are they economically and politically feasible? trying to answer these questions, we shall briefly review the institutional and structural causes of the increasing divergence between core and sp, shedding light on three momentous events: the creation of the monetary union, the 2008 financial crisis and the covid-19 shock. the first decade following the introduction of the emu saw continuity in the process of europeanisation embarked upon as from the formation of the common market, based on financial liberalization and market globalization. as argued in celi et al. (2018 celi et al. ( ,2019 , europeanisation meant eu-wide application of a policy of deregulation of goods, labour and capital markets that affected the timing, shape and direction of the european integration process, halting the process of convergence between the core and the sp of the eu. the more developed core (centred on germany) increased its productive and technological capacity; the sp, caught between product competition within the eu and cost competition from emerging economies in the international markets, saw a decline in its manufacturing capacity. 2 with the fall of the soviet union and the entry of the former socialist countries of central and eastern europe in the eu, the eastern periphery (ep) became a key gear of germany's manufacturing matrix (stehrer and stollinger 2015) . a huge flow of direct investments, primarily in the automotive sector, transformed the economies 1 merkel: germany must help other eu states get back on their feet, euractiv.com with reuters 13 mag 2020 https ://www.eurac tiv.com/secti on/econo my-jobs/news/merke l-germa ny-must-help-other -eustate s-get-back-on-their -feet/. 2 these diverging trends are likely to increase as a result of the slow, small and asymmetric response that europe is giving to the ongoing pandemic-driven economic crisis, as confirmed by the macroeconomic evidence provided in this forum by heimberger et al. of the visegrad pact (poland, hungry, slovakia, and check republic) into an essential source of intermediate goods (medium and medium-high quality) for the german industry. a well-qualified, extremely cheap workforce, generous subsidies and tax breaks, as well as geographical proximity and historical links, are among the determining factors of the increasingly tight links between the core and its ep. the impressive growth in manufacturing capacity in the east led to a restructuring in the hierarchical organization of the supply chains across europe: the weaker suppliers in the south were displaced by their cheaper competitors in the east, while the highly specialised suppliers of components in the industrial regions of the south maintained, and even increased, their close links with the german producers. 3 the crowding-out of the less dynamic firms in the sp did not take the form of efficiencyenhancing market selection but rather a generalized reduction of production capacity, contributing to fuel a well-documented (see, among the others, guarascio and simonazzi 2016; dosi et al. 2019 ) process of 'poor tertiarisation' of the sp. on the other hand, the ep's industrial miracle was created by foreign, mostly german, direct investment, with the automotive sector taking the lion's share. so far, we have seen no comparable development of other productive sectors, nor has the automotive sector created spill-over effects in the rest of the economy (krzywdzinski 2019). on the contrary, the surge in the production of components for the automotive sector has partly displaced other productions, leading to an increasing 'mono-specialization' of these economies. despite a growing shortage of skilled labour, wages have remained modest. threats of production shifting further east, to romania, turkey, or to north africa, (pavlinek et al. 2017) 4 are reflected in the adoption of a wage containment policy at home, driving young people with high educational qualifications to emigrate, and weakening the countries' skills base. with domestic demand subdued, the high growth rates recorded by these countries are entirely led by the growth in exports of local production by foreign multinationals (i.e., the so-called "integrated peripheral markets"). while their intensive specialisation in the automotive industry makes them totally dependent on the health of the german automotive industry, the foreign control of production decisions, innovation processes and markets makes it extremely difficult to undertake an independent, less unbalanced development path (celi et al. 2018) . to conclude, the two peripheries-the southern one, made up of the mediterranean economies, and the eastern one, with the prominent role of the visegrad countries-suffer from different fragilities, which descend from their common, albeit diverse, economic and financial dependence on the core. however, the core itself is dependent for its growth on the pattern of specialisation within the eu: the southern markets providing an outlet for its increasing surplus of manufactures, the eastern countries supplying cheap inputs for its industries. this combination of structural divergence and economic interdependence lies behind the fragility of the union as well as of the improbability of its disintegration given the high costs it would entail for core and peripheries alike. in the first period of the emu (2000) (2001) (2002) (2003) (2004) (2005) (2006) (2007) (2008) , the core-sp structural divergence was partly hidden by massive financial flows to the periphery. the 2008 financial crisis, and the ensuing international liquidity crunch, prompted a "sudden stop" of capital flows and a collapse in demand and imports. at that point, the structural and institutional flaws of the emu became evident: the reaction to the crisis aggravated the divergence. with the blame for the crisis put squarely on borrowers, austerity policies were advocated (or imposed) to ensure debtor countries' public and private solvency. with austerity killing demand, growth and imports in the sp, germany, which had built most of its huge trade surplus between 2003 and 2008 by exporting to the periphery, had to find new outlets for its goods. special international conditionsnamely, china's huge growth, which gobbled up german capital goods and highquality durable consumer products (particularly cars), and the vigorous american recovery-supported germany's ability to redirect its trade flows, expand its market shares outside the emu, and make a speedy return to its pre-crisis production levels. the united kingdom, the united states, but above all china, became the most important markets for german exports. the rapid recovery of the german economy pulled the ep along with it: the visegrad countries recorded unparalleled growth in europe. with the abrupt change in the international scenario in 2016, germany's (and the entire emu's) mercantilist strategy was up against the ropes. the brexit referendum, trump's election, and the u-turn in chinese economic policy inaugurated a phase of retreat in international trade. trade with the uk began to suffer due to the increasing uncertainty in future trade relations. when the united states took action to reduce the external deficit, china and germany, the countries with the largest trade surpluses vis-à-vis the united states, were caught in the crosshairs. trade tensions between the us and china put further pressure on international trade. the export-led growth model that had so far supported germany's leadership began to creak. the change in world trade took its toll on german (and eu) growth rates. from the second quarter of 2017, the slowdown in german exports hit industrial production and the gdp, widening the growth gap with china and the usa and dragging the whole emu along with it ( fig. 1) . as the escalation of trade disputes affected relations between the united states and germany 5 (and by extension the eu), the negative effects on europe's (exportled) growth intensified. in the last quarter of 2019, just a few months before the outbreak of covid-19 in the eu, germany's growth rate zeroed. income growth estimates for the rest of europe were consequently reduced. the pandemic arrived in europe from the south: italy was the first country to suffer the contagion. its abrupt, dramatic effects exposed the fragility of the periphery and the crippling effects of austerity policies. since 2010, across the board cuts in social spending had hit the entire range, from health to education, from social assistance to social investment. 6 figures 2, 3 and 4 show the evolution of the share of public expenditure on education and health (divided between general expenditure and hospitals) relative to gdp in the emu, germany and the sp between 2008 and 2018. many hospitals had been closed, the number of beds reduced, medical and nursing staff cut back (for a detailed analysis of the impact that austerity policies had on the italian health care system, see prante et al. 2020 ). it is not surprising that the death toll was higher where intensive care facilities were scarcer. on the eve of the covid crisis, public health accounted for 6.5 percent of the social product in italy and spain, and almost 10% in germany, where per capita healthcare spending did not suffer cuts due to austerity (though it was not completely spared self-imposed restrictions). the covid-19 exposed another aspect of the 'divisive' union (celi et al. 2020) : different capacities to respond to the pandemic crisis. economic ideology shares with austerity the responsibility for the scant endowment of medical equipment and health staff. efficiency, understood as cost reduction, has been taken as the guiding principle. the obsession with competitiveness and reliance solely on the export-led growth model accounts for the almost exclusive emphasis on "tradable" sectors, to the detriment of "non-tradable" sectors (housing, health, education, welfare services in general), considered of lesser importance for international competition. this means that, in the era of austerity, these items have been the first to be sacrificed, in debtor and creditor countries alike. chazan (2020) reports that for years, politicians and health economists in germany have complained that the country has too many hospitals, with the bertelsmann foundation recommending halving the number of hospital, from 1400 to fewer than 600 (chazan 2020 ). only such a radical consolidation-the bertelsmann study arguedwould "improve patient care and mitigate the shortage of doctors and nursing staff". the pandemic succeeded in transforming this "oversupply" into an asset. the same logic of pursuing the lowest cost guided the international location of production, which displaced domestic production and weakened production capacity in the sp. from a regional (european) point of view, this process resulted in a reorganisation of production and trade relations between core, ep and sp. on a global scale, core and peripheries entered into very long and complex gvcs that proved extremely vulnerable in the face of the interruptions prompted by the pandemic. personal protective equipment, respirators, medicines: the emergency has made it clear what it means to lose the capacity to produce domestically, both in quantity and quality, what is urgently needed, bringing the problem of self-sufficiency back to the attention of economists and policymakers. there is no such thing as a symmetric shock. in addition to the grim toll of victims and the incredible pressure on the health systems of all countries, the lockdown of activities to reduce contagion meant a tremendous plunge in production and incomes and enormous pressure on public finances all over the world. however, the lockdown is expected to affect economies differently. the central and eastern european countries have been less affected by covid than the western european countries: not trusting the resilience of their fragile health systems, they have had to rely on rigid social distancing (walker and smith 2020) . even within this group of countries there are differences: thanks to their more robust health systems, the czech republic and slovenia were less constrained by rigid social distancing and able to start economic recovery earlier. moreover, due to their strong productive links with austria-a country relatively less affected by the pandemic which came out of the lockdown earlier-and their favourable positioning in the development of digital economy (wiiw 2020) , their economic outlook is rather better. conversely, it will be tougher for the economies, like those of the sp, which are more dependent on services-tourism and hospitality in particular (fig. 5) -and for cee countries and southern regions that rely to a greater extent on production of intermediate products for final producers, since the latter can better defend themselves from fall in demand by cutting down orders to their suppliers (the so-called "whip effect"). policies have also differed widely across countries and regions. while all the central banks of the developed world promptly intervened to provide almost unlimited . although the stability pact has been temporarily suspended, 7 there are obvious differences in how much member states can spend, depending on their fiscal space. member states are making use of the new flexibility granted by the ec on state aid rules, strictly enforced beforehand to ensure fair competition within the internal market (rios 2020) . germany, which accounts for about a quarter of the eu's gdp, accounts for more than half (52%) of the emergency coronavirus state aid approved by the ec, prompting concerns that countries with the deepest pockets might be getting an unfair advantage by such a sudden (and temporary) abandonment of one of the common market's key pillar (france and italy each account for 17% of the total). an eu official, speaking on condition of anonymity, observed that "if you look at the scale of what germany in particular, but also some others, are doing-any notion of level playing field or single market integrity has gone out of the window." 8 these concerns underpin the ailing south's demand for a joint eu financial plan. in the absence of a prompt and massive common effort, the sp will pay the highest price to the health crisis. indeed, the different firepower will entail a still greater asymmetry in the economic and power relations between the various member states. the ecb, alone among the eurozone institutions, is doing as much as it can to avoid breakdown of the emu. to address the covid-19 crisis, it launched a new asset purchasing programme: the eurosystem's balance sheet shot up from 4692 billion euros on 28 february to 5395 billion by 1st may 2020. despite this massive monetary injection (700 billion in two months) the spread on italian bonds, which had fallen in mid-march following the ecb's announcements, again rose very rapidly, fluctuating in response to political developments. indeed, as tooze and schularick (2020) point out, if, in the 2008 crisis, the liquidity injected into the system by the ecb was enough to prevent deflagration of the banking system, 9 the current crisis would require a coordinated fiscal policy of enormous proportions. despite some recent moves (inaugurated by a merkel-macron agreement), this still does not seem to be looming on the horizon. the newly released 'next generation' (ng) plan, based on the 2021-2027 budget, celebrated by some as a "hamiltonian moment", has yet to qualify as forerunner of an eu-wide up-to-the-challenge fiscal capacity. 10 first of all, it is meant to be temporary and, moreover, it is too little, too late. the plan should mobilize 750 billion euros, 500 in the form of grants and 250 in loans. 8 quote reported by the website euractiv.com. 9 the eurosystem balance sheet (the network of european central banks, guided by the ecb) rose from 1150 billion euros at the beginning of 2007 to 4675 billion euros by the end of 2018; that is, from barely 10% to almost 40% of the euro zone gdp (12 000 billion euros). 10 the ng plan money will be spent over the 2021-2024 period. with an even subdivision over the period, the package amounts to an annual 0.56% of the eu's 2019 gdp, over four years. 7 several parties, including most recently the president of the ecb, christine lagarde, are urging the ec to review the pact before its temporary suspension expires on december 31, 2020. apart from the fact that these are gross figures-once the member states' contributions to the eu budget are subtracted, the net amount received by the neediest countries is much smaller-their disbursement will not start before 2021, will be distributed over a 4-year period, with amounts that grow over time, and, as stated in the ec's "proposal for a regulation" the financial contribution will "be paid in instalments once the member state has satisfactorily implemented the relevant milestones and targets identified in relation to the implementation of the recovery and resilience plan" (ec 2020, art. 17.4.a). as darvas (2020) emphasizes, the incorporation of the ng plan into the eu's next multiannual budget would take advantage of a well-established framework, 'already subject to various checks and balances'. on the other hand, ng resources risk to be trapped in a 'slow-moving machine'. in order to be financed, ng-related projects need to be designed, approved and implemented as part of a process that can take several years. as a result, the timing of disbursements is just the opposite of what would be required to respond to the urgency imposed by the current situation and, even more so, by the expected collapse of incomes that the european economies are going to face. 11 however, the commission expects that barely 24.9% of the total new firepower for grants would be spent in 2020-2022, when the recovery needs will be greatest (darvas 2020) . far from being a tool to counter the immediate effects of the crisis, the ng plan is more similar to the juncker plan, and shares all its weaknesses. 12 it is highly unlikely that countries like italy, severely hit by the pandemic and in persistent financial distress, will be able to afford to refrain from asking for other funds (namely, esm, sure and others for a total amount of about 59 billion euros) which could be paid out immediately, subject to the usual conditionality. the merkel-macron agreement has been hailed as the first step towards a more supportive union. behind the good intentions, there are the concrete interests of both france and germany for the survival of the emu: they look with growing concern at the rise of euroscepticism in the sp. the french economy has been hit hard by the pandemic, and was already in difficulty before. gdp forecasts for 2020 vary widely, but all agree in estimating a fall in the french gdp of much the same proportions as in the case of italy. on the other hand, germany was, together with the netherlands, the main beneficiary of the creation of the euro, and italy and france were the main losers (gasparotti and kullas 2019) . 13 as chancellor merkel told the german lawmakers, "it is essential for germany, as an export nation, that its eu partners also do well". 14 indeed, the history of the eu has taught that excessive german surpluses are deleterious for the south of the eurozone. greater government action, retreat from hyper-globalism, and lower growth rates predate the pandemic. the covid-19 crisis has given yet more voice to calls for protectionist and "beggar thy neighbours" types of policies. it has led countries to prioritize resilience and autonomy in production over cost savings and efficiency through global outsourcing. the same powerful german production platform, so disproportionately export-oriented and dependent on imports of intermediate goods, finds itself vulnerable to a type of shock (the covid-19 pandemic) that disrupts gvcs and threatens to change the existing economic order through permanent disruption of the patterns of demand and production. although transition from an industrial platform designed for export to one for the internal market (a sort of transition from a war to a peace economy) is a formidable challenge, this transformation would benefit germany itself, considering the winds of trade war and the growing uncertainty about the future developments of the global value chains. the european countries are at a crossroad between either letting the union dissolve or radically reforming it. today's darkened geopolitical environment requires europe to act as a whole. however, the emu will remain fragile as long as it chooses to continue to delegate control over its policies to market surveillance. a true "hamiltonian moment", which involves adopting a common fiscal policy in support of the common monetary policy is a matter of urgency. we still have a long way to go. divisions between member countries marked by opposition between debtors and "frugal" creditors, as well intra-country political struggles and conflicting interests, have-even in the face of this dramatic crisisled to the paralysis of the european institutions, with the one exception of the ecb. faced with what she sees as a serious threat to the eu's survival, the german chancellor (and the commission's president ursula von der leyen) have been driven to action. however, as we argued in sect. 3, little can be expected from the ng plan for immediate support. the ability of the sp to emerge from the crisis will increasingly depend on its ability to take advantage of the greater flexibility of eu rules for an efficient use of industrial policy, helping companies and the whole economy to respond to the challenge posed by social and technological innovation, the restructuring of production and the reorganization and shortening of gvcs. the pandemic will have significant repercussions on the international organization of production and gvcs (on this point, see also the contributions to this forum by strange and coveri et al.) . indeed, the countries initially most affected by covid (china, korea, italy) are among the most important suppliers of intermediate goods at the international level. studies on the propagation of economic shocks triggered by natural disasters (such as the earthquake that hit japan in 2011) along the value chains (boehm et al. 2019 ; inoue and todo 2019) found significant supplier substitution effects. anecdotal evidence signals numerous cases of supplier substitution in some countries as a result of the coronavirus (baldwin and tomiura 2020). the extent of these effects depends on the degree of complexity of the production chains, which affects the degree of input substitutability. propagation effects also depend on the presence of "hub" companies interconnected with a large number of supplier and customer firms (inoue and todo 2019) . future developments are uncertain, depending on the relative strength of two opposite effects. on the one hand, greater coordination afforded by digitalisation of production networks could favour substitution effects (especially in cases where value chains are less regionalised and the search for new suppliers is more difficult) (zhenwei quiang et al. 2020 ). on the other hand, processes of reshoring and shortening of value chains could occur, especially where production chains are less complex or automation is more advanced. the second possibility could represent an opportunity to reverse the processes of deindustrialization that have impoverished, above all, the productive fabric of the peripheral countries. a third perspective, probably utopian, could contemplate coordination of coalitions of producers across eu member states. in a situation of strong productive complementarities between countries, the fortunes of the producers (workers and firms) in one country are bound to those in the other. this would call for a coordinated industrial policy at the european level aiming at ensuring a balanced development of the economies of its members through their integration in the european production networks. in emergency situations where production activities are reduced or temporarily suspended (as in the case of coronavirus shock), bilateral agreements (mediated by governments) between producers in different countries should aim at stabilizing employment levels and pre-existing supply contracts between firms through "mutualisation" of the required financial effort. after all, having surprisingly spoken out in favor of the eurobonds, the ceo of volkswagen herbert diess could-at one remove-be also supportive of such a project! material. if material is not included in the article's creative commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. to view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/. thinking ahead about the trade impact of covid-19 input linkages and the transmission of shocks: firm-level evidence from the 2011 tōhoku earthquake crisis in the european monetary union. a core-periphery perspective unravelling the roots of the emu crisis. structural divides, uneven recoveries and possible ways out un'unione divisiva. una prospettiva centro-periferia della crisi europea germany's oversupply of hospital beds aids pandemic fight, the financial times next generation eu: 75% of grants will have to wait until 2023 neodualism in the italian business firms: training, organizational capabilities, and productivity distributions proposal for a regulation of the european parliament and of the council establishing a recovery and resilience facility germany gains most from relaxed eu state aid rules re-prima -tranc he-4-milia rdi-780f3 570-a447-11ea-b19d-c1248 28d4b 5b_previ ew.shtml ?reaso n=unaut henti cated &cat=2&cid=17219 14576 &pids=po&credi ts=1&origi n=https %3a%2f%2fwww .corri ere. it%2fint ernat ional %2fpre mium%2f20_giugn o_01%2frec overy -plan-tutti -ostac oli-fondi -europ eiralle ntato re-prima -tranc he-4-milia rdi 20 years of the euro: winners and losers. an empirical study, cep study a polarized country in a polarized europe: an industrial policy for italy's renaissance firm-level propagation of shocks through supply-chain networks globalisation, decarbonisation and technological change: challenges for the german and cee automotive supplier industry foreign direct investment and the development of the automotive industry in eastern and southern europe decades of tight fiscal policy have left the health care system in italy ill-prepared to fight the covid-19 outbreak eu countries use looser state aid rules to uphold troubled firms the central european manufacturin core: what is driving regional production sharing? (no. 2014/15-02) the shock of coronavirus could split europe-unless nations share the burden. the guardian why has eastern europe suffered less from coronavirus than the west? the vienna institute for international economic studies foreign direct investment and global value chains in the wake of covid-19: lead firms of gcv acknowledgements open access funding provided by università di foggia within the crui-care agreement. key: cord-168710-a5pst4gf authors: jalilian, abdollah; mateu, jorge title: a hierarchical spatio-temporal model to analyze relative risk variations of covid-19: a focus on spain, italy and germany date: 2020-09-28 journal: nan doi: nan sha: doc_id: 168710 cord_uid: a5pst4gf the novel coronavirus disease (covid-19) has spread rapidly across the world in a short period of time and with a heterogeneous pattern. understanding the underlying temporal and spatial dynamics in the spread of covid-19 can result in informed and timely public health policies. in this paper, we use a spatio-temporal stochastic model to explain the temporal and spatial variations in the daily number of new confirmed cases in spain, italy and germany from late february to mid september 2020. using a hierarchical bayesian framework, we found that the temporal trend of the epidemic in the three countries rapidly reached their peaks and slowly started to decline at the beginning of april and then increased and reached their second maximum in august. however decline and increase of the temporal trend seems to be sharper in spain and smoother in germany. the spatial heterogeneity of the relative risk of covid-19 in spain is also more pronounced than italy and germany. started from wuhan, the capital of hubei province, china in december 2019, the outbreak of 2019 novel coronavirus disease has spread rapidly across more than 200 countries, areas or territories in a short period of time with so far over 4.4 million confirmed cases and 296 thousand confirmed deaths (world health organization, 2020) . the spread of covid-19 across and within countries has not followed a homogeneous pattern (giuliani et al., 2020) . the causes of this heterogeneity are not yet clearly identified, but different countries have different levels of national capacity based on their abilities in prevention, detection, response strategies, enabling function, and operational readiness (kandel et al., 2020) . besides, different countries have implemented different levels of rigorous quarantine and control measures to prevent and contain the epidemic, which affect the population movement and hence the spread pattern of covid-19. given the highly contagious nature of covid-19, the spatial pattern of the spread of the disease changes rapidly over time. thus, understanding the spatio-temporal dynamics of the spread of covid-19 in different countries is undoubtedly critical. the spatial or geographical distribution of relative location of incidence (new cases) of covid-19 in a country is important in the analyses of the disease risk across the country. in disease mapping studies, the spatial domain of interest is partitioned into a number of contiguous smaller areas, usually defined by administrative divisions such as provinces, counties, municipalities, towns or census tracts, and the aim of the study is to estimate the relative risk of each area at different times (lee, 2011; lawson, 2018) . spatio-temporal models are then required to explain and predict the evolution of incidence and risk of the disease in both space and time simultaneously (anderson and ryan, 2017) . estimation of area-specific risks over time provides information on the disease burden in specific areas and identifies areas with elevated risk levels (hot spots). in addition, identifying the changes in the spatial patterns of the disease risk over time may result in detecting either regional or global trends, and contributes to make informed and timely public health resource allocation (wakefield, 2007) . to account for the underlying temporal and spatial autocorrelation structure in the spread of covid-19, available data on the daily number of new cases and deaths in different countries/regions have already been analyzed in a considerable number of studies. for example, kang et al. (2020) used moran's i spatial statistic with various definitions of neighbors and observed a significant spatial association of covid-19 in daily number of new cases in provinces of mainland china. gayawan et al. (2020) used a zero-inflated poisson model for the daily number of new covid-19 cases in the african continent and found that the pandemic varies geographically across africa with notable high incidence in neighboring countries. briz-redón and serrano-aroca (2020) conducted a spatio-temporal analysis for exploring the effect of daily temperature on the accumulated number of covid-19 cases in the provinces of spain. they found no evidence suggesting a relationship between the temperature and the prevalence of covid-19 in spain. gross et al. (2020) studied the spatio-temporal spread of covid-19 in china and compare it to other global regions and concluded that human mobility/migration from hubei and the spread of covid-19 are highly related. danon et al. (2020) combined 2011 census data to capture population sizes and population movement in england and wales with parameter estimates from the outbreak in china and found that the covid-19 outbreak is going to peak around 4 months after the start of person-to-person transmission. using linear regression, multilayer perceptron and vector autoregression, sujath et al. (2020) modeled and forecasted the spread of covid-19 cases in india. as pointed out in alamo et al. (2020) , there are many national and international organizations that provide open data on the number of confirmed cases and deaths. however, these data often suffer from incompleteness and inaccuracy, which are considerable limitations for any analyses and modeling conducted on the available data on covid-19 (langousis and carsteanu, 2020) . we highlight that we are yet in the center of the pandemic crisis and due to the public health problem, and also to the severe economical situation, we do not have access to all sources of data. thus reseachers know only a portion of all the elements related to covid-19. in addition, data on many relevant variables such as population movement and interaction and the impact of quarantine and social distancing policies are not either available or accurately measured. combined with the unknown nature of the new covid-19 virus, any analysis such as the present study only provides an approximate and imprecise description of the underlying spatio-temporal dynamic of the pandemic. nevertheless, having a vague idea is better than having no idea, and the results should be interpreted with caution. currently, a wealth of studies have appeared in the very recent literature. many of them follow the compartmental models in epidemiology, partition the population into subpopulations (compartments) of susceptible (s), exposed (e), infectious (i) and recovered (r), and fit several variations of the classical deterministic sir and seir epidemiological models (peng et al., 2020; roda et al., 2020; bastos and cajueiro, 2020) . we believe that considering stochastic components is important, if not essential, to explain the complexity and heterogeneity of the spread of covid-19 over time and space. for this reason, in the present work we propose a spatio-temporal stochastic modeling approach that is able to account for the spatial, temporal and interactions effects, together with possible deterministic covariates. we acknowledge that the proposed model in its current form requires development and refinements as more information becomes available, but at the stage of the pandemic we are now, it can provide a reasonable modeling framework for the spatio-temporal spread of covid-19. this is illustrated by modeling the daily number of new confirmed cases in spain, italy and germany from late february to mid august 2020. the r code for implementing the proposed model can be made available upon request. we also provide a shiny web application (chang et al., 2020 ) based on the model discussed in this paper at https://ajalilian.shinyapps.io/shinyapp/. the structure of the paper is the following. the open data resources used in this study are introduced in section 2. a model for the daily number of regional cases is considered in section 3. as described in section 4, this model explains the spatio-temporal variations in the relative risk of each country in terms of a number of temporal, spatial and spatio-temporal random effects. the results of fitting the considered model to the number of daily confirmed cases in spain, italy and germany are given in section 5. the paper concludes in section 6 with a few last remarks. governmental and non-governmental organizations across the world are collecting and reporting regional, national and global data on the daily number of confirmed cases, deaths and recovered patients and provide open data resources. incompleteness, inconsistency, inaccuracy and ambiguity of these open data are among limitations of any analysis, modeling and forecasting based on the data (alamo et al., 2020) . particularly, the number of cases mainly consist of cases confirmed by a laboratory test and do not include infected asymptomatic cases and infected symptomatic cases without a positive laboratory test. in this study, we focus on the daily number of confirmed cases in spain, italy and germany and used the following open data resources. italy: data on the daily accumulated number of confirmed cases in the 20 regions of italy are reported by the civil protection department (dipartimento della protezione civile), a national organization in italy that deals with the prediction, prevention and management of emergency events. these data are available at the github repository https://github.com/ pcm-dpc/covid-19 and are being constantly updated every day at 18:00. germany: the robert koch institute, a federal government agency and research institute responsible for disease control and prevention, collects data and publishes official daily situation reports on covid-19 in germany. data on the daily accumulated number of confirmed cases in the 16 federal states of germany extracted from the situation reports of the robert koch institute are available at the github repository https: //github.com/jgehrcke/covid-19-germany-gae and are being updated on a daily basis. table 1 summarizes the number of regions, study period and country-wide daily incidence rate of the data for each country. data on distribution population of the considered countries are extracted from the gridded population of the world, version 4 (gpwv4), which provides estimates of the number of persons per pixel (1 degree resolution) for the year 2020 (center international earth science information network (ciesin) columbia university, 2018). these data are consistent with national censuses and population registers. 3 modeling daily regional counts suppose that a country, the spatial domain of interest, is partitioned into regions a 1 , . . . , a m , defined by administrative divisions such as states, provinces, counties, etc (see table 1 ). let y it denote the number of new covid-19 cases in region the expected number of new cases is given by e it = p i it , where p i is the population of region a i and it is the incidence rate of covid-19 in region a i at time t. under the null model of spatial and temporal homogeneity of the incidence rate it = 0 and provides an estimate for e it , where is an estimate of the country-wide homogeneous daily incidence rate (waller et al., 1997) . the estimated daily incidence rate per million population (10 6 0 ) so far is around 68, 46 and 29 for spain, italy and germany, respectively (see table 1 ). 3.2 distribution of daily regional counts consul and jain (1973) introduced a generalization of the poisson distribution, which is a suitable model to most unimodal or reverse j-shaped counting distributions. given nonnegative random rates λ it , i = 1, . . . , m, t = 1, . . . , t , we assume that y it 's are independent random variables following the generalized poisson distribution with and the parameterization (zamani and ismail, 2012 ) thus ϕ is the dispersion parameter and the case ϕ = 0 represents the ordinary poisson distribution (no dispersion) with here, parameter α controls the shape (power) of the relation between the conditional variance of y it |λ it and its conditional mean. for example, the relation between (zamani and ismail, 2012) . the underlying random rates λ it , i = 1, . . . , m, t = 1, . . . , t , account for the extra variability (overdispersion), which may represent unmeasured confounders and model misspecification (wakefield, 2007) . variations of the random rate λ it relative to the expected number of cases e it provide useful information about the spatio-temporal risk of covid-19 in the whole spatial domain of interest during the study period. in disease mapping literature, the nonnegative random quantities are called the area-specific relative risks at time t (lawson, 2018, section 5.1.4). obviously eθ it = 1 and which means that the temporal and spatial correlation structure of the underlying random rates λ it determine the spatio-temporal correlations between θ it 's. temporal correlation ar(2) ζ i spatial correlation due to distance between regions gmrf ξ i spatial correlation due to neighborhood relation between regions bym by ignoring these correlations, the standardized incidence ratio θ it = y it / e it provides a naive estimate for the relative risks (lee, 2011) . however, in a model-based approach the variations of the relative risks are often related to regional and/or temporal observed covariates and the correlation between θ it 's are explained in terms of regional and/or temporal random effects using, for example, a log linear model (wakefield, 2007; lee, 2011; lawson, 2018) . in the present study, we consider the log linear model where µ is the intercept and d i is the population density of region a i , i.e. the population of a i , p i , divided by the area of a i . the population density is standardized to have mean 0 and variance 1 and β is its regression coefficient. moreover, η it is a zero mean random effect which represents spatio-temporal variations in relative risks due to temporal and spatial trend and correlation. among many different possibilities, we assume that η it takes the additive form where δ i represents the temporal trend, ε t accounts for temporal correlation and ζ i and ξ i explain spatial correlation due to spatial distance and neighborhood relations among regions a 1 , . . . , a m , respectively (see table 2 ). the latent (stochastic) temporal trend δ t is expected to be a smooth function of t. since the second order random walk (rw2) model is appropriate for representing smooth curves (fahrmeir and kneib, 2008) , δ = (δ 1 , . . . , δ t ) is assumed to follow a rw2 model, i.e., where 2 , . . . , t −1 are independent and identically distributed (i.i.d.) zero mean gaussian random variables with variance 1/τ δ . here the precision parameter τ δ > 0 acts as a smoothing parameter enforcing small or allowing for large variations in δ t (fahrmeir and kneib, 2008) . to account for temporal correlation, we assume that ε t follows a stationary autoregressive model of order 2, ar(2); i.e., ε t = ψ 1 (1 − ψ 2 )ε t−1 + ψ 2 ε t−2 + t , t = 2, . . . , t, where −1 < ψ 1 < 1 and −1 < ψ 2 < 1 are the first and second partial autocorrelations of ε t and 2 , . . . , t are i.i.d. zero mean gaussian random variables with variance 1/τ ε . on the other hand, to account for spatial correlation, we assume that ζ = (ζ 1 , . . . , ζ m ) follows a gaussian markov random field (gmrf). more specifically, we assume that ζ is a zero mean gaussian random vector with the structured covariance matrix where i m is the m × m identity matrix, 0 ≤ ω < 1 and e max is the largest eigenvalue of the m × m symmetric positive definite matrix c = [c ii ]. the entry c ii of matrix c represents to what extend the regions a i and a i are interconnected. for example, c ii can be related to a data on commuting or population movement between regions a i and a i . in absence of most recent and reliable movement data between the regions of spain, italy and germany, we set c ii to be the euclidean distance between the centroids of a i and a i . in addition to interconnectivity and correlations due to spatial distance, the neighbourhood structure of regions a 1 , . . . , a m may induce spatial correlation among relative risks of regions because neighbouring regions often tend to have similar relative risks. to include spatial correlation due to neighborhood structure of regions in the model, we assume that ξ = (ξ 1 , . . . , ξ m ) follows a scaled version of the besag-york-mollié (bym) model (besag et al., 1991) ; i.e., ξ is a zero mean gaussian random vector with (riebler et al., 2016) here q − denotes the generalized inverse of the m × m spatial precision matrix q = [q ii ] with entries where n i is the number of neighbors of region a i and i ∼ i means that regions a i and a i share a common border. the parameter τ ξ > 0 represents the marginal precision and 0 ≤ φ ≤ 1 indicates the proportion of the marginal variance explained by the neighborhood structure of regions (riebler et al., 2016) . in a bayesian framework, it is necessary to specify prior distributions for all unknown parameters of the considered model. the gaussian prior with mean zero and variance 10 6 is considered as a non-informative prior for the dispersion parameter of generalized poisson distribution, log ϕ, and for the parameters of the log linear model for the relative risks µ, β, log τ δ , log τ ε , log τ ζ , log τ ξ , log ω 1−ω , 1−ψ1 and log 1+ψ2 1−ψ2 . the prior distribution for the α parameter of the generalized poisson distribution is considered to be a gaussian distribution with mean 1.5 and variance 10 6 . table 3 summarizes the model parameters and their necessary transformation for imposing the non-informative gaussian priors. since all random effects of the model are gaussian, the integrated nested laplace approximation (inla) method (rue et al., 2009) can be used for deterministic fast approximation of posterior probability distributions of the model parameters and latent random effects (martins et al., 2013; lindgren et al., 2015) . the r-inla package, an r interface to the inla program and available at www.r-inla.org, is used for the implementation of the bayesian computations in the present work. the r code can be made available upon request. the initial values for all parameters in the inla numerical computations are set to be the mean of their corresponding prior distribution. the initial value of α is chosen to be one (see table 3 ). for count data y it and in a bayesian framework, a probabilistic forecast is a posterior predictive distribution on z + . it is expected to generate values that are consistent with the observations (calibration) and concentrated around their means (sharpness) as much as possible (czado et al., 2009) . following a leave-one-out cross-validation approach, let be the event of observing all count values except the one for region a i at time t. dawid (1984) proposed the cross-validated probability integral transform (pit) for calibration checks. thus, pit it is simply the value that the predictive distribution function of y it attains at the observation point y it . the conditional predictive ordinate (cpo) is another bayesian model diagnostic. small values of cpo it (y it ) indicate possible outliers, high-leverage and influential observations (pettit, 1990) . for count data, czado et al. (2009) suggested a nonrandomized yet uniform version of the pit with which is equivalent to the mean pit can then be comparing with the standard uniform distribution for calibration. for example, a histogram with heights table 4 presents the bayesian estimates (posterior means) for every parameter of the considered model fitted to the daily number of new covid-19 cases in spain, italy and germany. the corresponding 95% credible intervals of the model parameters are also reported in parentheses. comparing the estimated parameters among different countries, it can be seen that the dispersion parameter ϕ of the generalized poisson distribution for italy is higher than spain and germany, but its shape parameter α is around 1.5 for the three countries, which implies that the variance of the daily counts in each region is approximately a quadratic function of their mean. the coefficient of the population density is not significantly different from zero for spain and italy, but is positive for germany which indicates that regions with higher population density have larger relative risks. the precision parameters of the temporal random effects imply that the temporal trend δ t has at least 35 times larger contribution (smaller precision) than ε t which represents temporal correlation. the opposite signs of ψ 1 and ψ 2 indicate rough oscillations in ε t . the spatial random effect ζ i has larger contribution (smaller precision) than ξ i in the total variations of the relative risks only in spain, while for italy and germany it is the opposite. this could be a result of large euclidean distance between spain continental european territory from two archipelagos territories, which is affecting the considered covariance structure of ζ i . in summary, the higher contribution (lower precision) in the total variations of the relative risks for spain, italy and germany is due to the temporal trend, spatial correlation and finally temporal correlation, respectively. this may hint that spatial correlations have a greater impact on the relative risks of covid-19 than temporal correlations. the bayesian estimates and 95% credible intervals for the temporal trend δ t , t = 1, . . . , t , are shown in figure 1 . these plots can be interpreted as a smoothed temporal trend of the relative risk in the whole country. in fact, figure 1 suggests that the covid-19 epidemic in all three countries rapidly reached their peaks and slowly started to decline at the beginning of april and then increased and reached its maximum in august. in addition, the second wave of the epidemic seems to be stronger in spain and germany shows a more smoother trend during the study period. figure 2 shows the the posterior means of the spatial random effects ζ i and ξ i , i = 1, . . . , m, on the corresponding map of each country. the plot illustrates spatial heterogeneity of the relative risk of covid-19 across regions in each country, particularly in spain. regions with positive (negative) ζ i + ξ i values are expected to have elevated (lower) relative risks than the the baseline country-wide risk during the study period. in order to see how the estimated relative risks under the fitted model are in agreement with the observed data, figure 3 shows the spatially accumulated daily number of cases m i=1 y it , t = 1, . . . , t , and their expected values under the fitted model, namely the posterior mean and 95% credible interval of m i=1 e it θ it , t = 1, . . . , t . except some discrepancies for spain and italy, the observed values are inside the 95% credible intervals and close to the expected values under the fitted model. figure 3 in addition shows 4-days ahead forecasts of the total daily number of new cases at the end of study period of each country. finally, histograms of the normalized pit values described in section 4.4 are obtained using j = 20 from the fitted models and plotted in figure 4 . the normalized pit values for the fitted models to data do not show a clear visible pattern and the histograms seems to be close to the standard uniform distribution. the above results and more details on observed and predicated values from the fitted model are also provided in an interactive shiny web application at https://ajalilian.shinyapps.io/shinyapp/. there are some limitations in the analyses and modeling of data on the number of new cases of covid-19, including data incompleteness and inaccuracy, unavailability or inaccuracy of relevant variables such as population movement and interaction, as well as the unknown nature of the new covid-19 virus. nevertheless, understanding the underlying spatial and temporal dynamics of the spread of covid-19 can result in detecting regional or global trends and to further make informed and timely public health policies such as resource allocation. in this study, we used a spatio-temporal model to explain the spatial and temporal variations of the relative risk of the disease in spain, italy and germany. despite data limitations and the complexity and uncertainty in the spread of covid-19, the model was able to grasp the temporal and spatial trends in the data. however, the posterior predictive checks using the normalized probability integral transform (pit) showed that there is room for the model improvements. obliviously, there are many relevant information and covariates that can be considered in our modeling framework and improve the model's predictive capabilities. one good possibility would be considering most recent and accurate human mobility amongst regions. we would expect our model would benefit from this information, which right now can not be accessed. moreover, the considered spatio-temporal model in this paper is one instance among many possibilities. for example, one possibility is to include a random effect term in the model that represents variations due to joint spatio-temporal correlations; e.g., a separable sptaio-temporal covariance structure. however, the considered model was 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authors declare that they have no conflict of interest. key: cord-294815-mhqe3xjz authors: kuì�chenhoff, h.; guenther, f.; hoì�hle, m.; bender, a. title: analysis of the early covid-19 epidemic curve in germany by regression models with change points date: 2020-10-30 journal: nan doi: 10.1101/2020.10.29.20222265 sha: doc_id: 294815 cord_uid: mhqe3xjz we analyze the covid-19 epidemic curve from march to end of april 2020 in germany. we use statistical models to estimate the number of cases with disease onset on a given day and use back-projection techniques to obtain the number of new infections per day. the respective time series are analyzed by a poisson trend regression model with change points. the change points are estimated directly from the data without further assumptions. we carry out the analysis for the whole of germany and the federal state of bavaria, where we have more detailed data. both analyses show a major change between march 9th and 13th for the time series of infections: from a strong increase to a stagnation or a slight decrease. another change was found between march 24th and march 31st, where the decline intensified. these two major changes can be related to different governmental measures. on march, 11th, chancellor merkel appealed for social distancing in a press conference with the robert koch institute (rki) and a ban on major events with more than 1000 visitors (march 10th) was issued. the other change point at the end of march could be related to the shutdown in germany. our results differ from those by other authors as we take into account the reporting delay, which turned out to be time dependent and therefore changes the structure of the epidemic curve compared to the curve of newly reported cases the first phase of the covid-19 pandemic in germany was managed relatively successful in comparison to other countries in europe. therefore, it is worth taking a closer look at the course of the pandemic in germany, which has already led to controversial discussions. this particularly concerns the important question about the effectiveness of various control measures. there are several publications using data from different countries on the effects of control measures, see, e.g., [1] , [2] and [3] . as [4] point out, many of such studies are undermined by unreliable data on incidence. many papers use data provided from the johns hopkins university (jhu) [5] . these data are based on cumulative registered cases in different countries, which induces several problems, particularly the fact that not all cases are reported and that there is delay between the day of infection and the reporting day. furthermore, the systems of reporting vary between countries, which makes comparisons between countries difficult. therefore we focus on the analysis of the epidemic curve in bavaria and germany. the availability of case based data for bavaria and detailed data for disease onset for germany is essential for our analysis. in a recent paper on germany by [6] , the authors use a complex bayesian modeling approach based on the daily registrations in the jhu data. an important claim by [6] is that the lock-down-like measures on march 23rd were necessary to stop exponential growth, however, this result contradicts for example results by the german rki [7] . furthermore, these approaches were critically questioned by [8] and [9] , where the latter emphasized the importance of taking into account the delay by reporting and incubation time, when analyzing the possible effect of non pharmaceutical interventions. we follow this line of argument and use a statistical model to estimate daily numbers of infected and of persons with disease onset on a certain day. for bavaria, we use detailed case-based data, while a modeling approach is utilized for german data. we analyze the respective epidemic curves using a segmented regression model with change points. the paper is organized as follows. in section 2, we present the data and the the strategy of estimating the relevant daily counts. then the segmented regression model, which is the basis for further analyses, is presented. in section 3, we present the results followed by a discussion in section 4. the latter is not always known: partly because it could not be determined and partly because the case did not (yet) have any symptoms at the time of entry into the data base. a procedure for imputation of missing values regarding the disease onset has been developed by [10] , using a flexible generalized additive model for location, scale and shape (gamlss; [11] ), assuming a weibulldistribution for time t d > 0 between disease onset and reporting date. we estimate the delay time distribution from data with disease onset and impute missing disease onsets based on this model. for the german data, no individual case data were available, so instead we used estimated disease onset data provided by the robert koch institute (rki), see [12] and [7] . the method used by the rki is similar to our approach applied to bavarian data [10] . to interpret the course of the epidemic and possible effects of interventions, case based data on time of infection is essential. however, as such data is generally not available, one simple approach is to shift the curve to the past by the average incubation period. the average incubation period for covid-19 is about five days [13] . a more sophisticated approach is to use the incubation period distribution as part of an inverse convolution, also known as backpropagation, in order to estimate the number of infections per day from the time series of disease onsets [14, 15] . we assume a log-normal distribution for the incubation time with a median of 5.1. days and a 95% percentile at 11.5 days [13] . these are the same values as used by [6] . for our calculation, we use the back-projection procedure implemented in the r package surveillance [16] . to analyze the temporal course of the infection we use the following poisson regression model with over-dispersion and change points (see [17] , [18] ): where e(y t ) is the expected number of new reported cases at time t, k is the number of change points, and x + = max(x, 0) is the positive part of x. the change points are used to partition the epidemic curve y t into k + 1 phases. these are characterized by different growth parameters. in the phase before the first change point cp 1 the growth is characterized by the parameter β 1 , in the 2nd phase between cp 1 and cp 2 by β 2 = β 1 + γ 1 . the next change is then at time cp 2 . in the 3rd phase between cp 2 and cp 3 the growth parameter is given by β 3 = β 1 + γ 1 + γ 2 . this applies accordingly until the last phase after cp k . the quantities exp(β j ), j = 1, . . . , k + 1 can be interpreted as daily growth factors. since model (1) is a generalized linear model given the change points, the parameters of the model (including the change points) can be estimated by minimizing the quasi likelihood function for the poisson model. due to the estimation of the change points the numerical optimization problem is not straight forward. for the estimation of the model we use the r-package segmented, see [19] . the starting values are estimated by discrete optimization using all possible integer suitable combinations of change points. the number of change points k is varied step-wise up to a maximum of k = 4. it is examined whether the increase of the number of break points leads to a relevant improvement of the model fitting (over-dispersion parameter). models with more than 4 change points since they are hardly interpretable and the danger of overfitting is high. we apply the segmented regression model to time series of the estimated daily numbers of infections for bavaria and germany. since the back propagation algorithm yields an estimate for the expected values of the number of daily infections and does so by inducing a smoothing effect, as a sensitivity analysis for the location of the breakpoints, we also apply the model to the time series of the daily number of disease onsets. when comparing the results, it should be taken into account that the onset of the disease is on average 5 days after infection. in figure 1 , the three different time series of daily cases (reported, disease onset and estimated infection date) are presented. the delay between the three time series for bavaria and germany is evident. furthermore, the curves do not just differ by a constant delay, but there is some change in structure of the curves. the curve relating to the date of infection is clearly smoothed due to the back projection procedure (cf. section 2.2) and has a clear maximum both for bavaria and germany. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 30, 2020. ; for the bavarian data on disease onset, the model with k = 4 change points gives the best result with an estimate of the over-dispersion parameter of 3.8, i.e., the variance of y t is 3.8 times higher than the value of var(y t ) = e(y t ) otherwise expected under the assumption of the poisson regression model. the over-dispersion for a model with k = 3 change points is substantially higher (4.5), which suggests that the model with four change points should be preferred. table 1 , left panel. the model delivers five phases starting with a steep increase, which is slowed down in the second phase. in the third phase starting at 15th-17th of april, the increase is stopped and there is decrease in number of disease onsets in the fourth phase, which is accelerated in the fifth phase. the poisson model for the infection date gives a substantially better fit than the disease onset model. the model with four change points has an underdispersion by the the factor 0.39 compared to 0.79 for the model with three change points. therefore, we use the model with three change points to avoid overfitting. the result can be seen in figure 2 (right panel) and in table 1 (right panel). the phases are similar to those for the disease onset, but the change from increasing curve (phase 1 and 2) to a decreasing phase (phase 3) is direct without a plateau in between. taking the mean incubation period of five days into account, we combine the results for the two models for bavaria, which implies four phases of the epidemic: 1st phase there is a substantial increase in new infections in both models. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 30, 2020. ; https://doi.org/10.1101/2020.10.29.20222265 doi: medrxiv preprint the results for the german data are presented in figure 3 and in table 2 . for the disease onset model, the overdispersion is substantially lower for the model with four change points than with three change points. however, the overdipersion of the model with four change points is rather high (20.1) and the confidence intervals for the change points are rather big, especially for the first part of the time series where two change points are estimated. while the distinction in the first three phases is unclear, there is a clear turning point between march 14th and march 18th. the fifth phase with a further slowdown starts at the end of april. as can be seen from figure 3 there are further estimated change points in both models, which have wide confidence intervals and do not fit well together in the models. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 30, 2020. ; https://doi.org/10.1101/2020. 10.29.20222265 doi: medrxiv preprint the present analysis is a retrospective, exploratory analysis of the german and bavarian covid-19 reporting data during mar-apr 2020. the analysis does not include cases that have not been recorded. if the proportion of undetected cases changes over time, this can distort the curve and thus the determination of the change points. therefore, additional data on daily deaths and hospital admissions and the number of tests performed should be considered. furthermore, it is possible to estimate the proportion of undetected cases with the help of representative studies such as the one currently conducted in munich, see [20] . our analysis is based to a considerable extent on imputed data, see [10] , which is a results of missing data w.r.t. the disease onset. since changes in behavior do not occur abruptly, the assumption of change points is also problematic in itself. therefore, the interpretation of change points should always be done in conjunction with a direct observation of the epidemic curve. our analysis is based on the onset of the disease (more precisely: the onset of symptoms) and a back projection to the date of infections, and therefore, despite its limitations, is better suited to describe the course of the epidemic than the more common analysis of daily or cumulative reported case numbers. in the analysis of the bavarian and the german data in different settings, the main result is the change point, where the exponential growth was stopped and is clearly visible between march 9th and 13th. the timing of this change point coincides to the implementation of the first control measures: the partial ban of mass events with more than 1000 people. furthermore, in a press conference on march 11th chancellor merkel and the president of the rki appealed to self-enforced social distancing (https://www.bundesgesund heitsministerium.de/en/coronavirus/chronologie-coronavirus.html. furthermore, the extended media coverage from bergamo, italy, as well as the voluntary transition to home-office work could be related to this essential change in the course of the pandemic. in bavaria and in germany, the change point at the end of march of infection date is apparent. this change point is associated with different measures taken in march (closing of schools and stores on march 16th and the shutdown including contact ban on march 21st). since there were many measures administered simultaneously, it is not possible to attribute individual measures to the development of the epidemic curve. the claim by [6] , that the shutdown on march 21st was necessary to stop the growth of the epidemic is not supported by our analysis. there is a change 10 . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 30, 2020. point in the epidemic curve after that date, but the major change from an exponential growth to a decrease was before the shutdown. the difference in results can be explained by the different data bases used for the respective analyses. while [6] use data based on daily registered cases, in our analysis, data on disease onset are included. as can be seen from figure 1 and from the results of our data analysis, the delay distribution of the time between disease onset and reporting day changed over time. using this information is a crucial difference between our analysis and that of [6] . in a recent technical addendum [21] the authors re-fit their model on more appropriate data. these analysis -in our opinion -clearly show that the effective reproduction number decreased earlier than in their initial analysis, however, they attribute the decrease to a sir model peculiarity, where a linear decrease in the contact rate can lead to the incidence curve dropping despite r(t) > 1. the above discussions illustrate how complex the interpretation of even simple sir models is and the question is, if such sir modeling is not too simple to really allow for questions to be answered model based (no age structure, no time varying reporting delay, no incubation delay). in contrast, our approach is more data driven with a minimum of modeling assumptions and without the need to include strong prior information about the change points. directly using a segmented curve with exponential growth (decline) is in line with common models of infectious diseases in its early stages, where the limitation of the spread by immune persons plays no role. the problem of using complex models with many parameters for the evaluation of governmental measures has also been highlighted by [22] . our approach is similar to that of [9] . however, using change point analysis for variables derived from daily new infections appears problematic, since assumptions modeling the reproduction number r(t) or the cumulative numbers are questionable. more specifically, the use of the time-varying reproduction number r(t), a standard measure to describe the course of an epidemic is challenging, as different definitions have been proposed in the literature that also imply different interpretations (see [23, 24] ). however, the analysis of r(t) as a relative measure can be useful, when one wants to analyze data from different countries with non comparable reporting systems, see [3] . we prefer the direct use of a poisson regression model with a more plausible assumptions about the error terms instead of using ols for logarithmic case numbers. furthermore, we apply a direct maximum likelihood estimation of the change points of the segmented regression model. for the interpretation of the model based on disease onsets, we also use a simple difference of five days to take the incubation time into account. our results are similar to that of [9] . however, the claim that there is no evidence for the effect of governmental measures is not supported by our analysis. our result is in line with that of [25] , where a stop of exponential growth in great britain has been before the shutdown. furthermore, the effect of governmental measures as whole is clearly documented in the literature, see, e.g., [1] and [2] .our result on a possible effect of the ban of mass events is also in line with the results of [3] . . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 30, 2020. ; the temporal connection between the change points in our analysis and various control measures should be interpreted as an association, rather than a direct causal relationship. in the end many other explanations exists and from a simple time series analysis it is not possible to say to what extent the population already had changed their behavior voluntarily, as for example observed in mobility data [26] , and in what way the measures contributed to this. more speculative alternative explanations would include the possibility of a seasonal effect on coronavirus activity (e.g. related to temperature) or changes in test capacity or the case detection ratio. however, given the re-emergence of the epidemic in the fall of 2020 at high test capacity and at relatively high temperatures shows that contact behavior is the major explanatory factor for virus activity. nevertheless, any analysis of observational time series data including only a limited amount of explanatory factors has to be interpreted with care and with respect to the many uncertainties which remain regarding covid-19 [27] . despite the limitations of the approach, we argue that it is advantageous and important to directly interpret the epidemic curve and the absolute number of cases, rather than indirect measures like the r(t). furthermore, the reproduction rate does not contain information about how many people are currently affected, or whether the infected persons belong to risk groups. the course of the time-varying reproduction number calculated by us for bavaria fits well with the change point analysis [10] . a value of r(t) >1 corresponds to a rate of increase >1, noting that the time delays in the interpretation of r(t) must be kept in mind. it should be noted, that the presented analysis is retrospective. control measures have to be decided based on a completely different level of information than what the retrospectively established epidemic curve suggests. the simple observation of the course of the reported case numbers by reporting date is also problematic because this course is strongly influenced by the reporting behavior and the methods and capacities of the test laboratories. typically, substantially fewer cases are reported at weekends than during the week. therefore, the estimation [10] is an important step to estimate the better interpretable curve of new cases, but is limited by assumptions and limitations itself, that need to be considered when interpreting the results. since the impact of the measures also depends on how they are implemented by the population (compliance), the results cannot be directly transferred to the future. nevertheless, it remains a remarkable result that the clear turning point of the early covid-19 infection data in germany is associated with non drastic measures (no shutdown) and strong appeals by politicians. all data used for the analyses and all code to reproduce the models, figures and tables in the manuscript are openly and freely available from https://gi thub.com/adibender/covid19-changepoint-analysis-germany-bavaria. all 12 . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted october 30, 2020. ; analyses were performed using the r programming language [28] . figures were created using r package ggplot2 [29] . estimating the effects of non-pharmaceutical interventions on covid-19 in europe physical distancing interventions and incidence of coronavirus disease 2019: natural experiment in 149 countries the temporal association of introducing and lifting non-pharmaceutical interventions with the time-varying reproduction number (r) of sars-cov-2: a modelling study across 131 countries. the lancet infectious diseases lockdown-type measures look effective against covid-19 but evidence is undermined by unreliable data on incidence an interactive web-based dashboard to track covid-19 in real time. the lancet infectious diseases inferring change points in the spread of covid-19 reveals the effectiveness of interventions the limits of estimating covid-19 intervention effects using bayesian models a phenomenological approach to assessing the effectiveness of covid-19 related nonpharmaceutical interventions in germany nowcasting the covid-19 pandemic in bavaria. medrxiv flexible regression and smoothing: using gamlss in r. the r series schätzung der aktuellen entwicklung der sars-cov-2-epidemie in deutschland -nowcasting the incubation period of coronavirus disease 2019 (covid-19) from publicly reported confirmed cases: estimation and application a method of non-parametric backprojection and its application to aids data associations of age and sex on clinical outcome and incubation period of shiga toxin-producing escherichia coli o104:h4 infections monitoring count time series in r: aberration detection in public health surveillance estimating regression models with unknown breakpoints modelling covid-19 outbreak: segmented regression to assess lockdown effectiveness segmented: an r package to fit regression models with broken-line relationships. r news protocol of a population-based prospective covid-19 cohort study munich model-based and model-free characterization of epidemic outbreaks -technical notes on dehning the limits of estimating covid-19 intervention effects using bayesian models a new framework and software to estimate time-varying reproduction numbers during epidemics association of public health interventions with the epidemiology of the covid-19 outbreak in wuhan, china did covid-19 infections decline before uk lockdown ? estimating the impact of mobility patterns on covid-19 infection rates in 11 european countries covid-19's known unknowns r: a language and environment for statistical computing elegant graphics for data analysis we would like to thank katharina katz and manfred wildner from the bavarian state office for health and food safety (lgl) for providing the data and for useful discussions. we also thank nadja sauter for help with visualizations. key: cord-033219-uwzgbpeo authors: naumann, elias; möhring, katja; reifenscheid, maximiliane; wenz, alexander; rettig, tobias; lehrer, roni; krieger, ulrich; juhl, sebastian; friedel, sabine; fikel, marina; cornesse, carina; blom, annelies g. title: covid‐19 policies in germany and their social, political, and psychological consequences date: 2020-09-28 journal: nan doi: 10.1002/epa2.1091 sha: doc_id: 33219 cord_uid: uwzgbpeo many policy analyses on covid‐19 have been focusing on what kind of policies are implemented to contain the spread of covid‐19. what seems equally important to explore are the social and political consequences of the confinement policies. does the public support strict confinement policies? what are the social, political, and psychological consequences of the confinement policies? the question of how legitimate a policy is among the public is at the core of democratic theory. its relevance also stems from the expected consequences of public support on behavior: the more someone supports a policy, the more someone is likely to follow the policy even if the policy is not strictly enforced. in this paper, we will focus on germany, briefly summarize the main policies during the first 6 weeks of confinement and then explore political attitudes, risk perceptions, and the social consequences of the lockdown. many policy analyses of the covid-19 pandemic have focused on what kind of policies are implemented to contain the spread of the disease and on how effective these policies are in reducing the number of new infections and deaths. what seems equally important to explore are the political, social, and psychological consequences of the containment policies. in this paper, we focus on germany and provide an overview of the main policies that were implemented in an attempt to halt the spread of covid-19 during the first 8 weeks of confinement. we complement this with results of a daily survey, the german internet panel (gip), which allows us to capture the immediate political, social, and psychological consequences of the confinement. first, does the public support strict confinement policies, and how does this support change over time? the question of how legitimate a policy is among the public and how public opinion and policies are linked is a prominent and widely researched topic in political and social sciences. theoretical and empirical research support the claim that it is, in fact, an interrelationship: public opinion affects policy-making (brooks & manza, 2006; burstein, 2003; page & shapiro, 1983) and policies affect public opinion (ebbinghaus & naumann, 2017; mettler & soss, 2004; pierson, 1993) . these policy feedback effects then, in turn, alter attitudes (kumlin & stadelmann-steffen, 2014) . as lockdown policies have been so quickly introduced and as the public most likely did not have any attitude regarding these policies before the onset of the covid-19 pandemic, this seems to be one of the few examples where policies were clearly enacted before the emergence of public opinion. hence, we focus rather on how the lockdown policies might have affected public attitudes. skocpol (1992:58) refers to policy feedback as the ways "policies, once enacted, restructure subsequent political processes," and pierson (1993) distinguishes two main types of feedback effects. first, resource and incentive effects link policies to the self-interest of people since they determine how resources are distributed, provide incentives, and thus shape the costs and benefits of actors. hence, we would expect that the more threatened people feel by the pandemic, the higher they perceive the risk of being infected to be, and the lower their support is. moreover, the more apparent the economic costs of the lockdown become over time, the lower the support should be. second, interpretative effects provide a mechanism to link policies and attitudes via values since they serve as sources of information and meaning. for example, policies "frame the meaning and origins of societal problems by identifying target groups for government action and defining solutions" (mettler & soss, 2004:62) . let us take the labor market and possible reasons for unemployment as an example. when the government promotes job-training programs, the focus is on a lack of skills, and when wage subsidies are introduced, the focus is on the structural limitations of the labor market and potential consequences of globalization, whereas strict regulations of the access to unemployment benefits shifts the focus to individual behavior and self-discipline (gusmano, schlesinger, & thomas, 2002) . so, policies can alter frames and the way people think about an issue (chong & druckman, 2007) and we expect that policies themselves shape the framing and perception of the pandemic and should have an effect on reform preferences but also on risk perceptions. second, we explore the social consequences of the lockdown and particularly focus on the labor market. the closure of non-essential businesses but also macro-economic consequences of the global covid-19 crisis had an immediate effect on the labor market and led to lay-offs and short-time work (see for example fuchs-schündeln, kuhn, & tertilt, 2020) . moreover, many employers extended possibilities for remote work and flexible work arrangements so that employees had the opportunity to work and to stay at home. at the same time, employees in essential areas of the economy who are not able to work remotely face an increased risk of being infected. do these negative consequences affect everyone equally? we would rather expect the opposite. germany's labor market is characterized by a pronounced "insider-outsider" divide and has a considerable amount of low wage and fixed-term employment, while the core workforce in standard employment is well protected by labor regulations (emmenegger, häusermann, palier, seeleib-kaiser, 2012) . hence, immediate lay-offs, for example, are not possible for those in regular employment. furthermore, labor market measures to buffer the negative crisis consequences for employees and companies are mostly targeted at the core workforce. as for the possibilities to work remotely, most jobs in which this is a viable option are in well-paid occupations that require a high level of education (dingel & neiman, 2020) . in summary, we expect that existing social inequalities will rather be increased by the confinement policies. third, we examine the psychological consequences of the lockdown. we explore the extent to which people feel threatened by covid-19. feelings of threat play an important role in shaping attitudes and behavior. if threat perceptions are too low, people might not support confinement policies or might not follow them if they are not strictly enforced. too strong threat perceptions might impair people in their daily lives if, for example, they do not leave their home any more. moreover, there is a growing political economy literature that argues that subjective (mis-)perceptions of societal trends are very important in explaining political attitudes and behavior. for example, alesina, miano, and stantcheva (2018) show that natives' usually overestimate the share of migrants and underestimate their labor market integration. these misperceptions are then one important factor in understanding anti-migrant attitudes. similarly, we would expect that people rather overestimate their own infection risk (overestimation of small probabilities) but over time they might adapt their perceptions to reality (see breznau, 2020) . in what follows, we will first provide a brief overview of how the covid-19 pandemic unfolded in germany and how the government reacted to it. this provides the background against which we will then present our results and will show how public attitudes and perceptions changed during this period. in figure 1 , we provide a summary of the first half of 2020 and show daily case numbers and the cumulative numbers of deaths in germany. moreover, the government response index shows the reaction of the german government to the pandemic aggregating containment and closure policies, economic policies, and health system policies (hale, webster, phillips, & kira, 2020) . the initial period of the covid-19 pandemic in germany resembles very much the experience of many other european countries. the government knew about covid-19 in china and its potential threat also for europe already in late december 2019. yet, the first confirmed case in germany was found on january 27, 2020. the government response to this was the introduction of contact tracing systems, the mandated isolation of the few infected people, and a first information campaign mainly recommending good hand hygiene and reassuring the population that the isolation of the infected worked well in keeping the virus at bay. the situation did not change until the end of february when the number of confirmed infections started to increase, in particular in some local hotspots. moreover, the italian experience with the pandemic led to doubts that it would be possible to contain the virus in germany by the initial measures that had been taken. "the situation in italy also changes our assessment of the situation: corona has arrived in europe as a pandemic" german health minister jens spahn remarked on february 24th. yet, the government was still reticent to introduce strict lockdown measures. it was recommended to cancel big public events of more than 1,000 participants, and it was also recommended to close schools and childcare if confirmed infections were established. at the same time, large public events like the carnival in cologne took place as planned with several thousand attendees. this changed very quickly in mid-march, when the number of daily cases increased within 2 weeks from less than 100 to 4,000 (see figure 1 ) and as also the first covid-19-related deaths were recorded. on march 12, schools and childcare facilities were closed and the government issued recommendations regarding social distancing. on march 17th, the borders were closed, and on march 18th, chancellor angela merkel announced the general lockdown with stay-at-home orders. "this is serious," she remarked in her speech to the nation "please, take it seriously, too." these measures went into effect on march 21st and were then further extended twice until the beginning of may. at the same time, the government reassured the population that they would do everything necessary to buffer the negative consequences of the lockdown. the debt brake was suspended, and the government announced an extra federal budget of 150 billion euros. short-time work ("kurzarbeit") was introduced which allows firms to temporarily reduce hours worked while providing employees with income support from the state for the hours not worked. on april 22nd, the subsidy was increased to up to 80% of the regular salary. in mid-april, some states started to make the wearing of face coverings obligatory in public transportation and shops. by april 27th, face masks were obligatory in public transportation and shops in all german states. germany reached its peak of the first wave in terms of daily infections in early april when the 5-day moving average of new infections per day reached almost 6,000. yet, the lockdown and stayat-home orders which had gone into effect on march 21st seem to have been very effective since case numbers decreased quickly in the second half of april, and also, the increase in the number of deaths slowed down in the beginning of may when it has reached about 8,000 deaths. the government (and the public) started to discuss re-opening plans at the end of march, and the first restrictions were lifted in may. as we are mainly interested in the public reactions to the lockdown, we restrict the following analysis to the time between march 20 (i.e. from when survey data is available) and may 14 when the first re-openings occurred (marked in gray in figure 1 ). in summary, having a high performing medical system but little past experience with pandemics, germany tended to show a later, slower, and weaker policy response compared to some other countries (capano, howlett, jarvis, ramesh, & goyal, 2020) . to capture public reactions of the german population, we use data from the german internet panel (gip). the gip is based on a random probability sample of the general population in germany aged 16 to 75. the study started in 2012 and was supplemented with additional participants in 2014 and 2018. the panel participants were recruited offline using strict statistical procedures (blom, gathmann, & krieger, 2015) . every other month, panel participants are invited to take part in a voluntary online survey. for the mannheim corona study (mcs), the gip launched a special survey on march 20th. the sample was divided into eight random subsamples. the subsamples 1-7 were assigned to a specific day of the week, while the eighth subsample serves as control group and is not surveyed. within one week, the questionnaire remains exactly the same for all participants. between 411 and 643 (on average 489) respondents take part in the study every day, allowing for the analysis of daily but also weekly changes in attitudes and behavior. in our analysis, we use a response propensity weight, which projects the characteristics of the msc participants to the general gip study using data on employment status and occupational sector. moreover, a raking weight was used to extrapolate the characteristics of msc participants to those of the general population of germany based on age, gender, marital status, level of education, household size, and federal state. we use two survey questions as indicators for the "public support for" and "evaluation of" the lockdown policies. respondents are asked whether they think that the societal benefits of the current policies outweigh their economic costs. answer categories ranged from 1, the societal benefits are greater than the economic costs to 7, and the economic costs are greater than the societal benefits. we also provided respondents with a list of lockdown policies, and respondents should choose all the policy measures they think are appropriate to deal with the covid-19 pandemic (see appendix for the exact wording of questions). to examine the economic consequences of the lockdown, we explore how the employment situation changes over time. we distinguish four different employment status (employed, short-time work, furloughed with and without pay, and unemployed) and also whether the employed work on-site or remotely. finally, we explore the psychological reactions of the public focusing on how threatened people feel by the covid-19 pandemic, how they rate their individual infection risk and their ability to control an infection, and the perceived likelihood of severe illness if infected (see appendix for the exact wording of questions and response scale). daily data on policies are available from january 1, 2020, and the survey data are available on a daily basis starting on march 20, 2020. as we are primarily interested in the lockdown policies and their effect on the public, we restrict our analysis to the period between march 20, 2020, to may 14, 2020. in mid-may, germany began to gradually lift some of the lockdown measures and started to re-open the country. how did the public react to the lockdown measures? we first look at political reactions and distinguish between performance evaluations and support for specific policies. figure 2 shows how the public evaluates the consequences of the lockdown policies. we reversed the scale in the questionnaire so that higher values on the 7-point scale mean that the population thinks that the societal benefits are greater than the economic costs. we see that at the beginning of our period of observation, at the peak of the first wave and briefly after strict lockdown measures had been introduced, that the public evaluates the policies quite positively and in general supports the evaluation that the societal benefits of the lockdown outweigh its economic costs. this evaluation remains stable at around 4.6 during the first two weeks but then begins to steadily decline already in early april and continues to drop weekon-week until the beginning of may. at the end of our period of observation, the evaluation dropped below 4 on the 7-point scale as around 50% of the population in germany felt that the lockdown had more negative than positive consequences. in figure 3 , we move from the general performance evaluation to support for specific lockdown measures. the graph shows which share of the population supported each of six different policies. we see that most of the policies receive tremendous support in the first weeks of the lockdown. more than 90% of the population supported closing public facilities (like schools and universities), closing borders, and prohibiting public gatherings with more than 100 participants. a lockdown and strict stay-at-home order also received majority support. the public was more critical toward closing public transportation and also toward tracking mobile phones of infected people without their consent, although notably about a third did support such a policy. over time, with declining case numbers and higher awareness for the economic costs of the lockdown measures, support steadily declined for all policies. we observe the steepest decline in support for closing public facilities which fell from 95% support in week 1 to around 40% support at the beginning of may. the population in germany became equally critical toward a stay-at-home order and slightly less than 10% of the population supported a stay-at-home order in may. other measures lost support, including banning international travel (−25 percentage points) and prohibiting gatherings of more than 100 participants (−5 percentage points). briefly before the first re-opening started, a majority still supported these two measures. also, only very few people (around 5%) did not support any of the lockdown measures. overall, during the lockdown, the public in germany became most critical about those policies which had the strongest | 7 negative impact on their daily lives, such as the measures regarding the closures of public facilities and stay-at-home orders, whereas banning international travel or prohibiting larger public events were still supported by a majority. although our empirical data only provide evidence on one very strict version of a tracking and tracing policy, the results suggest that the public sees a benefit in these kinds of measures as support did not decline very much over time. in addition to the political consequences, the lockdown also had negative effects on the economy and the labor market in particular. here, we focus on the workforce and explore who is affected most by the negative consequences of the lockdown. does the covid-19 crisis increase existing social inequalities? our results suggest that it does. figure 5 shows the employment situation depending on the level of school education, and we distinguish between low (without or with basic school-leaving qualifications-hauptschulabschluss), middle (intermediate school-leaving qualification-mittlere reife), and high (with higher education entrance qualification (fach-hochschulreife) education) levels. we restrict our analysis to those respondents who were employed before the lockdown (i.e., in january 2020). hence, our results show which groups were able to keep their jobs, who switched to remote work, but who lost their job, were furloughed or were sent on short-time work. overall, our results show that the lower the level of education, the higher the proportion of people who changed to short-time work, to furlough without pay, or who were laid off (figure 4 ). job loss for someone with a low or middle education is twice as likely as for someone with a high level of education. among those who kept their jobs and were able to work about the same hours as in january 2020, employees with a high level of school education are more often working remotely (more than 40 percent in march and april) than employees with a lower level of education. the majority of those with a low or medium school education work on-site (between 62 -64 percent in march). in summary, high education reduces the risk of job loss and at the same time provides the privilege to work remotely. the negative consequences of the covid-19 lockdown hence increase existing social inequalities along two dimensions. the lower educated lost their jobs, were suspended without pay, or experienced a partial income loss by short-time work to a much higher degree than higher educated workers. what's more, if they were able to keep their jobs, they tended have to work on-site, facing higher risks of infection. these social inequalities are linked to political attitudes and policy evaluations. additional analyses (not shown here) confirm that the lower educated are much more critical of the lockdown policies and rather tend to say that the economic costs are higher than the societal benefits. to better understand public reactions to the lockdown in germany, we argue that it is crucial to look more specifically at public perceptions. in figure 5 , we show how threatened the public felt by the covid-19 pandemic and how the population rated its own infection risk (both on the left y-scale). moreover, we explore whether people thought that they were at risk of a severe illness if infected and whether they felt in control of their own infection risk. in the first two weeks, shortly after the lockdown had been introduced but before the peak of the first wave of infections, threat perceptions were highest and the population rated the degree they felt personally threatened above 5 on the 11-point scale ranging from 0 (indicating no perceived threat at all) to 10 (indicating an extreme perceived threat to me). also, the population thinks that almost 15 out of 100 people will get infected in the next 7 days. this is a very major overestimation of the actual infection risk. both the threat perception and the individual infection risk then steadily decreased over time. in contrast, the subjective risk assessment of having a severe illness in case of infection and also the feeling of having control over an infection remains more stable over time. in summary, the steady decrease of feelings of threat and perceived risk might be one explanation for why the lockdown slowly lost public support over time. additional analyses show that such a correlation also exists at the individual level, as the more someone felt threatened, the higher degree of support they indicated for lockdown policies and the more positive was their overall evaluation of the benefits of the lockdown. in this paper, we have summarized the political response to the covid-19 pandemic in germany and focused on the period between the occurrence of the first case in january to the end of the lockdown in mid-may 2020. our analysis shows that germany followed a containment strategy for the first 2 months until mid-march, focusing on isolation of the infected and on contact tracing but refraining from stricter policy measures which would affect the daily life of those not infected. this changed very quickly during the first two weeks of march when the daily new cases increased from below 100 to around 1,000. in response, germany very quickly moved from a containment strategy to a strategy focused on delaying the spread of the virus and within 3 weeks moved from prohibiting large events with more than 1,000 participants to a lockdown with a national stay-at-home order. our analysis of survey data starting at the peak of the first wave briefly after the lockdown was introduced shows very high approval rates of these policy measures which might explain their success in effectively delaying the spread and reducing new infections to below 1,000 per day by mid-may. also, germany managed to keep the number of deaths at a very low level throughout the crisis (see contributions by malandrino (2020) on italy and by colfer (2020) , covering the uk, in this issue). yet, our analysis also shows that the widespread support for the containment and delay policy measures steadily decreased over time as did feelings of threat and subjective risk perceptions. moreover, the negative economic consequences of becoming unemployed or of moving to short-time work did not affect everyone equally but did track existing social inequalities. while economic and social policies provided support to buffer these negative consequences in the short run, it is unclear whether the policies will also be able to adequately address medium-and long-term consequences of the lockdown. hence, the conclusions and policy implications drawn from our analysis are clearly limited to these short-term effects and are clearly hampered by the fact that we are trying to explore an ongoing phenomenon. the external validity of our findings for other countries and institutional settings is of course also hampered by the specificities of the german case. germany has a strong economy and labor market, a comparably well-functioning welfare state, and a stable government that has been in office for several years. this might explain both the success but also the high approval of the lockdown policies in the country (breznau, 2020) . in summary, our analysis clearly shows that the lockdown policies feed back into the political process by altering political attitudes and public risk perceptions (pierson, 1993; skocpol, 1992) . this raises some doubts that the acceptance of policies and the willingness of citizens to comply with lockdown measures during a potential second wave would be as widespread and as strong as they were during the first wave of the pandemic. information campaigns, a societal discussion reflecting on the experiences of the lockdown, but also social policies that address some of the social inequalities the pandemic has exposed (see for example lynch, 2020) might help to prepare the population for subsequent waves and for subsequent pandemics. how to cite this article: naumann e, möhring k, reifenscheid m, et al. covid-19 policies in germany and their social, political, and psychological consequences. eur policy anal. 2020;00:1-12. https://doi.org/10.1002/epa2.1091 question text (english translation) what do you think about the consequences of the current confinement policies in germany: are the economic costs greater than the societal benefits, or are the societal benefits greater than the economic costs? 1-the societal benefits are greater than the economic costs. … 7-the economic costs are greater than the societal benefits. policy support which of the following policy measures do you think are appropriate for dealing with the current situation? please tick all that apply. -closing public facilities (e.g., universities, schools, and nursery schools) -closing boarders -prohibit events and public gatherings with more than 100 participants -general stay-at-home order -closing of public transportation -tracking of mobile phones of infected persons for contact tracing (without consent) -i do not support any of these measures. to what degree do you feel personally threatened by the coronavirus pandemic? no threat at all to me … 10 extreme threat to me we would like to know how likely you think it is that you or someone like you will be infected with covid in the next 7 days. please think of 100 persons who are very similar to you, that is, they have a similar age, a similar health, live in your neighborhood, have a similar occupation and a similar lifestyle. what do you think, how many of these 100 persons will be infected with covid in the next 7 days? immigration and redistribution (no. w24733) setting up an online panel representative of the general population: the german internet panel the welfare state and risk perceptions: the novel coronavirus pandemic and public concern in 70 countries social policy responsiveness in developed democracies the impact of public opinion on public policy: a review and an agenda mobilizing policy (in)capacity to fight covid-19: understanding variations in state responses framing theory herd-immunity across intangible borders: public policy responses to covid-19 in ireland and the uk. european policy analysis. forthcoming how many jobs can be done at home? welfare state reforms seen from below: comparing public attitudes and organized interests in britain and germany the age of dualization: the changing face of inequality in deindustrializing societies the short-run macro implications of school and child-care closures policy feedback and public opinion: the role of employer responsibility in social policy oxford covid-19 government response tracker health equity, social policy, and promoting recovery from covid-19 conflict in decision-making and variation in public administration outcomes in italy during the covid-19 crisis the consequences of public policy for democratic citizenship: bridging policy studies and mass politics effects of public opinion on policy when effect becomes cause protecting soldiers and mothers https://orcid.org/0000-0003-1415-0678 roni lehrer https://orcid.org/0000-0002-9202-9278 key: cord-253720-s6hwui6n authors: andraz, jorge m.; rodrigues, paulo m.m. title: monitoring tourism flows and destination management: empirical evidence for portugal date: 2016-03-26 journal: tour manag doi: 10.1016/j.tourman.2016.03.019 sha: doc_id: 253720 cord_uid: s6hwui6n we propose the use of a tool recently introduced by gayer (2010), known as the “economic climate tracer”, to analyze and monitor the cyclical evolution of tourism source markets to portugal. considering the period 1987–2015, we evaluate how tourism to portugal has been affected by economic cycles. this tool is useful as it clearly illustrates the evolutionary patterns of different markets, and allows us to identify close relationships with economic fluctuations. we found that german tourism plays a leading role, since its movements are followed with delays by tourism flows from other countries, and exhibits higher resilience to shocks. also, domestic and spanish tourism have both displayed less irregular behaviors than tourism from other source markets. on the contrary, tourism from the netherlands and the uk, have displayed irregular patterns, which demonstrates the urgency to diversify tourism source markets to reduce the country's vulnerability to external shocks and economic cycles. business cycles are recurrent phenomena in all economies and are transversal to all economic sectors. tourism is not an exception, as this sector is particularly vulnerable to economic fluctuations. this vulnerability reinforces the relevance of developing tools that allow for a clear understanding of the sector's cyclical stance in order to inform the authorities and to manage the adoption of measures to diversify and, simultaneously, to reduce the country's dependency on a reduced number of tourism source markets. this issue is of particular importance for portugal as tourism plays a central role on the country's economic performance. according to the world travel and tourism council [wttc] (2013), the total contribution of tourism to gdp in 2012 was usd 26.4 billion, corresponding to 15.9% of gdp, and it is expected to grow by 1.6% per annum to usd 31.0 billion, corresponding to 6.3% of gdp, by 2023. the total contribution to employment was 860,500 jobs in 2012, or 18.5% of total employment and it is expected to grow 1.0% per annum to 954,000 jobs, or 20.7% of total employment, by 2023. about a quarter of foreign investment is motivated by tourism trade. these figures provide an overall picture of the importance of tourism for portugal. both the increasing number of tourists and the sector's strategic importance have led portuguese economic and political agents to pay special attention to this sector by taking active measures towards its sustainability. it is therefore not surprising that private and public organizations are increasingly interested in obtaining a deeper understanding of the tourism cycles of the main origin markets and monitoring their evolution. over the last decades business cycle regimes have been implicitly taken into account in the analysis of tourism with different objectives (see, inter alia, andraz, gouveia and rodrigues, 2009; collins & tisdell, 2004; crouch, 1996; witt & witt, 1995; lim & mcaleer, 2002; lim, 1997; and ramos & rodrigues, 2013) . most of these studies have focused on the tourism demand side and little attention has been devoted to the effects of different regimes on the tourism supply side. research on tourism cycles was, to the best of our knowledge, first considered by gouveia and rodrigues (2005) . this article provides a dating approach of the tourism demand cycle based on the method described in harding and pagan (2003) . using concordance and recursive concordance indices, gouveia and rodrigues (2005) establish a strong degree of cycle synchronization between tourism and economic cycles and identify delay effects between them. in a recent study guizzardi and mazzocchi (2010) , using a structural time series approach, also conclude that tourism demand is driven by delay effects of the overall business cycle. therefore, a better understanding of the cyclical stance of tourism to portugal and how each market has reacted to the major turning points, accounting for their heterogeneous behavior to regime changes, is of great relevance to tourism agents when looking for source markets. this paper aims to provide such valuable information regarding domestic tourism and tourism coming from the main international source markets to portugalegermany, the netherlands, spain and the united kingdom (hereafter uk). methodologically speaking, in this paper we consider the "economic climate tracer" proposed by gayer (2010) and apply it to the series of the monthly number of overnight stays of tourists in portugal. the approach consists on the graphical representation of the standardized level of a smoothed indicator, in this case based on the hodrick and prescott (1997) filter in order to eliminate shortterm fluctuations, on its month-on-month changes. the resulting diagrams can be divided into four quadrants, allowing for the association of the temporal evolution of the smoothed variables to the different phases of the tourism cycle. the rest of the paper is organized as follows. in section 2 we present the data and a rigorous description of the methodology used in the analysis. in section 3 we discuss the main results in terms of each market position with respect to the tourism cycle and briefly describe the major events that have likely been at the origin of the major turning points. in section 4 we report the main conclusions and lessons for tourism destination management as well as the limitations of our approach. the data used in this paper correspond to monthly overnight stays in hotels, apartment hotels, tourist apartments, tourist villages, motels, bed and breakfasts, inns, guest houses and camping parks of domestic tourists and international tourists coming from the uk, the netherlands, germany and spain. these series are used as a proxy for tourism activity (hereafter tourism). the option for using the number of overnight stays as a proxy for tourism was dictated by the lack of consistent information on other variables, such as, e.g. tourists' expenditures. however, this variable has been widely used in literature focused on the evaluation of tourism (see, for example, aguayo, 2011; dritsakis, 2004; and archer & fletcher, 1996) . this proxy for tourism has also been used in recent works (see e.g. paci & marrocu, 2014; and cort es-jim enez, 2008) , as it reflects the length of stay and therefore provides information about the occupation rate of tourism facilities. in this way, it can be more informative than other variables, such as the number of arrivals, which do not provide information on such dimensions, or tourism expenditures, for which decisions on the adoption of price deflators can be an issue. this study uses data covering a long period, from january 1987 to september 2015, during which several economic downturns have occurred. this period provides a rigorous picture about the reactions of tourism from different source markets to portugal and, thereby, allows us to identify general trends. the data were collected from the annual issues of tourism statistics (ine, 2008 (ine, , 2009 (ine, , 2010 (ine, , 2011 , published by statistics portugal (the national institute of statistics in portugal). summary statistics of these variables are provided in table 1 and they reflect the relevance of the source markets considered. overall, the five source markets considered represent around 75.0% of the total number of overnight stays in the country. the first position belongs to domestic tourism with an average of 30.9% over the period under analysis, and is followed by the uk with an average of 19.7% and germany with an average of 12.5%. the last positions are shared by the spanish and the dutch markets, which together represent an average close to 12.0% of the total number of overnight stays in the country. by considering three sub-periods, we identify interesting trends, which are quite informative on the reactions of the different tourism segments. we notice steadily decreasing patterns in tourism coming from germany, the uk and the netherlands, and increasing trends in the number of overnight stays of domestic and spanish tourists. the methodology used to analyze the cyclical evolution of tourism in portugal is inspired in the economic climate tracer developed by gayer (2010) . the approach consists of the graphical representation of the standardized level of a smoothed indicator computed using the hodrick and prescott (1997) filter (in order to eliminate short-term fluctuations) on its month-on-month changes. the standardized levels of tourism on the y-axis are plotted against their month-on-month changes on the x-axis. this approach provides an attractive visual tool for the inspection of tourism series through circular movements across the four quadrants of the graphs, corresponding to the four growth cycle phases. these phases can be characterized in a counter-clockwise rotation as follows: above average and increasing (upper-right quadrant, corresponding to "expansion"), above average but decreasing after having reached the peak (upper-left quadrant, corresponding to "downswing"), below average and decreasing (lower-left quadrant, corresponding to "recession") and below average but increasing after having passed the trough (lower-right quadrant, corresponding to "upswing"). the peaks occur in the upper center of the graph, in the transition from "expansion" to "downswing", while the troughs are located in the lower center, in the transition from "recession" to "upswing". therefore, the resulting diagrams can be divided into four quadrants allowing, in this way, for the association of the temporal evolution of the smoothed variables to the different phases of the tourism cycle: the first quadrant corresponds to the expansion phase and is observed when the standardized series are above their means and increasing; the second quadrant indicates that the cycle entered in downswing, i.e., when the standardized series are above their means but decreasing; the third quadrant indicates recession since it corresponds to the case where the standardized series are below their means and decreasing; and finally, the fourth quadrant indicates that the cycle entered into an upswing as the standardized series are below their mean but increasing. this classification follows the conventional notion of the business cycle and offers a simple and clear method to characterize the development of economic indicators throughout the cycle and may also be used as a monitoring tool for destination management when applied to the number of overnight stays. the tourism industry is not immune to shocks caused by economic fluctuations or financial instability (see neumayer, 2004) . on the contrary, it is very sensitive to these shocks as they impact negatively on tourists' confidence and income. the uncertainty about the economic evolution in each country is regarded with caution and imposes serious limitations to tourism flows. however, the reaction of economies to shocks can be quite diverse given the structural and political differences they exhibit and consequently the impact on destinations can differ depending on the composition of the tourism source markets "portfolio". to understand the evolution of tourism it is important to review the world events that occurred over the last decades and which clearly marked the tourism world cycle. fig. 1 displays the cycle of visitor exports 1 . the early 1990's were characterized by successive fluctuations of tourism worldwide. this instability translated into a deep recession in the early 2000's. after a recovery period until 2007, tourism suffered again a downturn, but from 2010 onwards there was an oscillating recovery. the evolution of the tourism cycle ( fig. 1 ) mirrors the chronology of the economic crisis of the national bureau of economic research (www.nber.org/cycles.html). the recessive periods in tourism observed in fig. 1 were motivated, or at least were partially explained by a series of unusually deep and sequential negative events that hit the world economy in the 1990s and the 2000s. among them there is the european monetary system (ems) currency crisis in 1992 and 1993, which were precipitated by the german reunification in 1990, followed by the subsequent raise of german interest rates, which seriously affected large european economies like the uk and france. the 1990s were also the stage for crises that started in specific regions of the world but soon spread across the globe, such as the asian crisis in 1997, the russian crisis in 1998 and the brazilian crisis in 1999 which, in turn, spread out to argentina. in general, these crises were caused by short-term commercial bank debt and/or securities market investment and were followed by huge capital outflows and severe currency speculation. in the case of the asian crisis, banks, non-banks and corporations over-borrowed and foreign banks and private investors over-lent. all these episodes originated significant down and upswings of the global economy impacting countries differently, and this evidence is not surprising given, on the one hand, the economic and financial globalization and the dimension of the us economy and, on the other hand, the specific structural and cyclical conditions that prevailed in each country. in what concerns the tourism cycles, we can report three major crisis periods from fig. 1 , 2004) and also the severe acute respiratory syndrome (sars) outbreak in november, 2002. the recent financial crisis that broke in the us in 2007 has spread to all economies generating serious effects on employment and domestic demand. therefore, the impacts on the tourism industry were unavoidable. all these events have lead tourists to reduce their travels or change destinations and, therefore, they deeply marked tourism demand. the impacts of crisis on destinations are more or less pronounced depending on the impact of events on the source markets responsible for the main tourism flows. it is unquestionable that all countries were impacted by the worldwide events responsible for the up-and downswings in world tourism. that is, in all countries there are downswings in tourism flows over the periods 1990e1995, 2000e2005 and recently since 2007. these movements are possibly more pronounced in some countries than in others, which clearly suggests that countries have reacted differently to external shocks. if this is the case, this information is obviously of valuable importance to tourism agents in portugal since it can be a guide to identify which source markets are less sensitive to external shocks and to endeavor efforts to maintain and/or increase tourism flows from those countries, and which markets are more prone to those shocks in order to look for market diversification. the tracer that is used in this paper can therefore be a useful tool for the analysis of the degree of resilience of the source markets to crises. fig. 2 illustrates the evolution of the domestic tourism cycle in portugal. we observe that domestic tourism remained in the expansion quadrant over the 2000s, reaching the peak by the beginning of 2010. since then, and after a short decline as a result of the economic and financial crisis that culminated with political and economic austerity measures, we notice a recovery reflected in the steady location of the demand in the first quadrant, exhibiting increasing growth movements. this evolutionary behavior of domestic tourism to portugal reflects, although with different magnitudes, the negative effects of the different crises that impacted the world tourism cycle. however, the negative effects of the recent financial crisis on domestic tourism were not very pronounced when compared to foreign tourism. domestic tourism in portugal is obviously not independent of the structural economic context the country has experienced. since 2002 portugal has been going through a problem of economic stagnation with an annual economic growth of less than 2.0% (lower than the eu average). it recorded a zero growth in 2008, followed by a 2.9% contraction in 2009 (european commission, 2014). due to the economic downturn and the fiscal stimulus packages in response to the crisis, the fiscal balance deteriorated to a record deficit of 9.9% and 10.2% of gdp in 2009 and 2010, respectively (oecd, 2014). since 2009 portugal has faced an economic recession together with a continuous growth of public debt, austerity policies, nationalization of banks, and difficulties in deficit control. the low growth rates and the successive deficits implied an increase of the public debt from 50.7% in 2000 to 108.2% in 2011 (european commission, 2014). as a result, the moody's investors service and other rating agencies cut portugal's sovereign bond rating in the summer of 2010, which led to an increased pressure on the portuguese government bonds. this brief description highlights the devastating effects of the global crisis on the portuguese public finances and economy. from the late 2009, fears about the ability of the country to fulfill its sovereign debt liabilities dictated the raise of risk premiums to a point where the access to capital markets was no longer an option and a debt default soon became imminent. this context dictated the urgency in negotiating a bailout in the form of a memorandum of understanding with the consortium composed by the european commission, the european central bank and the international monetary fund (known as "troika") and severe austerity measures that have led to a substantial increase of unemployment and significant wage reductions. this crisis has been by far the most devastating to the portuguese economy, and it has originated inevitable effects on domestic tourism, leading to a significant reduction of the demand for foreign destinations by portuguese tourists and consequently to an increase in domestic tourism, as reflected by the positive evolution in recent years; see fig. 2 . fig. 3 illustrates the evolution of the international demand cycle dynamics of the four main source markets to portugal from january 1987 to september 2015. as before, all series were smoothed through the hodrick-prescott filter to eliminate short-term fluctuations. the smoothed series are then plotted against their month-on-month variation. the graphs in fig. 3 report the dynamics of tourism flows from the international source markets considered, which drive tourism from the lower quadrants to the upper quadrants. two main distinctive aspects emerge from the graphs, which cannot be dissociated from the economic and political context experienced by markets over the sample period. the first is related to the distinctive movements reported by tourism flows in their trajectory across quadrants. starting from the upswing quadrant (fourth quadrant), in the early 1987 tourism flows to portugal enacted positive growth trends with level increases over the 1990s. these movements toward the expansionary quadrant (first quadrant) were shared by tourism flows from all sources, although with episodes of short cycles that constitute the main distinctive feature among source markets. these short cycles were observed in tourism from all sources, with the exception of tourism coming from germany, which exhibited positive and increasing growth rates (fig. 3a) . these short cycles translated into rather irregular paths in the case of tourism from the netherlands and spain in their movement towards the expansion phase ( fig. 3b and c, respectively) . in fact, their paths were characterized by the occurrence of successive and persistent mini-cycles with recessive movements towards the recession (third quadrant) and upswing (fourth quadrant) quadrants, reporting reductions in growth and levels, until they finally reached the expansionary quadrant by mid of 2000. tourism from the netherlands continued to report large volatility over the 2000s. over the first half of 2000 it moved to the downswing quadrant and then to the expansion quadrant, reaching the peak by the end of 2013. we also notice a strengthening of this ascending movement up to 2015. tourism from spain moved to the expansion quadrant in 2005, reached its peak in 2010, and after a short passage through the downswing quadrant, it registered an inversion towards the expansion quadrant. the behavior of tourism from germany and the uk (fig. 3a and d, respectively) also followed similar, but smoother, patterns. in fact, tourism from germany entered the expansion phase by the middle of the 1990s and reached the peak by the end of 1999. tourism from the uk entered the expansion phase in the second half of the 1990s and after a short cycle, reached a peak in 2006. these countries followed a similar path over the 2000s moving together to the recession quadrant by the end of 2007. tourism from these countries to portugal enacted a steadily recovery trajectory by 2010 until 2015. the second aspect that emerges from the data is the leading role of tourism flows from germany, motivated by a smooth evolutionary path and continuous high growth rates over the 1990s. this growth engine explains the fact that german tourism flow path is one-step ahead of the other source markets. tourism from germany moved to the expansion quadrant and reached the peak in the 90s, long before tourism flows from other markets. we also notice that the recession period tourism flows experienced over the first half of 2000s was felt by german tourism earlier and with shorter duration. therefore, it seems that tourism from germany is more resilient to crises and that its trajectories are followed by tourism from other source markets. to better understand the cyclical dynamics just described, as well as the apparent leading role of the german tourism flows to portugal, it is useful to briefly characterize the economic context of each source market. the ascending path of tourism from germany over the 90s (fig. 3a) coincides chronologically with the huge economic growth observed in the aftermath of the country's reunification (gr€ omling, 2008). between 1990 and 1992, the german average real gdp growth was 4.5%, which exceeded its long-term average. however, in the following period, germany enacted an adjustment process towards its long-term potential growth with lower growth rates. over the second half of the 1990s, the average gdp growth rate was almost 1 and 2 percentage points lower than that of the emu/eu countries and the united states, respectively, while the annual average increase in employment in germany fell short of that of the us. this context coincides with an inversion path of tourism flows to portugal, which dictated the end of the expansionary path and the occurrence of the peak by the end of the decade. at the beginning of the 2000s, the german economy practically stagnated. the lowest gdp growth figures were observed in 2002 (þ1.4%), in 2003 (þ1.0%) and in 2005 (þ1.4%), together with high unemployment rates. these problems, together with the country's aging population led to the implementation of a set of reforms, which have become known as agenda 2010. the contraction of the german nominal gdp in the second and third quarters of 2008 drew a scenario of technical recession following the path observed at the global and european scales. the german government's response to this downturn path translated into the approval of a package of economic stimulus measures to prevent the unemployment rates to rise. over this period, we observe a downturn of tourism flows to portugal and the first signs of economic recovery started to emerge in 2010 and are reflected in fig. 3a through persistent movements towards the boom quadrant. we notice that the german tourism cycle is similar to those of the uk and the netherlands. they all exhibit a contraction at the beginning of the 2000s which came to an end ten years later, around 2010. the british economy registered a period of more than 10 years of continuous economic growth, from the mid-1990s to 2005. the downturn that followed imposed huge oscillations in british tourism to portugal, which attained the peak just before the recent financial crisis (fig. 3d) . tourism from the netherlands and spain were also particularly affected between 1990 and 1995 (see fig. 3b and c, respectively). in both cases, there were significant reductions in levels and growth rates and both end in the upswing quadrant in the second half of the 1990s. the dutch tourism moved to the boom quadrant and reached the peak around 2000. this movement is coincident with the strong performance of the dutch economy in the second half of the 1990s, which is referred to as the "dutch miracle". real gdp growth reached 3.7% on average (clearly above the european union average of 2.7%). the unemployment rate dropped from 6.6% in 1996 to 2.5% in 2001. this positive conjuncture is reflected in a positive evolution of tourism to portugal. this economic boom appears to have been mainly motivated by an overheating of the economy, but the slowdown that followed seems to have been the result of the global downturn and the turmoil in financial markets, and consequently tourism suffered a reduction in levels and growth. in fact, we observe that tourism flows moved to the downswing quadrant around 2001 recording continuous reductions in levels up to 2005. however, as a result of the efforts on public finances' consolidation, the country reached a government surplus of 0.6% by the end of 2006. this economic performance also tourism from spain exhibits a similar pattern. after having stepped backwards in the periods 1990e1995 and 2005e2010 it entered the boom quadrant in the second half of the 2000s. however, the recent financial crisis has imposed a slowdown by 2007. we observe a reduction in levels and growth rates and the peak was reached in 2010 after which tourism moved to the downswing quadrant. however, the spanish tourism flows rapidly returned to the expansion quadrant, having registered increasing growth rates in the last years. our results show that tourism source markets to portugal react differently to economic adverse shocks depending on internal economic and political particularities and that tourism from germany seems to have a leading reaction to economic fluctuations. in this paper we illustrate the usefulness of the approach introduced by gayer (2010), known as the "economic climate tracer" to analyze and monitor the cyclical evolution of tourism demand, through an application to portugal. we analyze the tourism flows of domestic tourists and tourists coming from the main international source markets -germany, the netherlands, spain and the uk -which together represent on average 75.0% of the total number of overnight stays in the country. it is shown, through the analysis of the economic evolution in the tourism source economies from 1987 to 2015 that the climate tracer is a useful tool to illustrate the evolutionary patterns of the different markets and therefore an important source of information to support economic and policy agents in decision making. this analysis highlights three relevant issues. first, we concluded that tourism flows from germany, the netherlands and the uk exhibit decreasing trends over the period under analysis, whereas domestic tourism and spanish tourism report increasing trends. second, tourism from all source markets, including the domestic market, reported levels below the average with increasing growth rates by the end of the 1980s, and all are currently reporting growth rates and levels above their averages. third, in-between, tourism flows from different source markets to portugal depicted different behavior paths which are not independent of the economic and financial environments in each country. domestic tourism and tourism from spain exhibited the less irregular patterns in their evolutionary path between 1987 and 2015. despite the two recessive episodes in 1995 and 2007, which are certainly a result of economic recessions, they followed rather smooth and similar trajectories. possibly, the crises episodes over the 1900s and 2000s have impacted on the decisions of traveling, leading tourists to choose closer destinations. this could possibly explain the less irregular patterns of the portuguese and spanish tourism. tourism from the netherlands, the uk and germany reported larger oscillations, revealing thereby higher sensitivity to economic cycles. we also noticed that tourism from germany has played a leading role since its movements seem to have been followed by other source markets. in general, this paper provides evidence that there is a narrow relation between economic context and tourism flows to portugal. recession periods dictate tourism contractions, while economic expansions are reflected in persistent increases of tourism flows. it also provides evidence that markets react differently to economic and political, or even terrorist events. the domestic and spanish tourism are segments that may mitigate external adversities, and therefore, the investment in advertising campaigns should be directed to these markets, while promotional actions should be reinforced in order to guarantee the sustainability of other international segments, for which portugal has been a traditional holiday destination. notwithstanding, these results should be interpreted with caution. the source markets here considered are in different maturity stages. the evolution of tourism from different sources is perhaps not independent from their destination life cycle stages. portugal has been a traditional destination for british tourists since the 1960s, while tourism from the netherlands, or even germany or spain is more recent. therefore, linking the evolutionary paths with the corresponding destination life cycle stages of each market may provide additional insights on the cyclical behavior of tourism and is left for future research. research. international journal of forecasting, 11, 447e475. world travel and tourism council. (2013) . travel and tourism economic impact 2013-portugal. jorge m. andraz ph.d in economics and professor of economics and econometrics at the university of algarve, he is a member of the centre for advanced studies in management and economics of the university of evora (cefage-ue). his main research interests are focused on tourism, applied macro econometrics, time series econometrics, economic growth, financial economics and tourism economics. he has published several books about the economic effects of public investment in portugal. he is also the author of several publications in influential international journals. he belongs to the referee board of several international scientific journals. paulo m. m. rodrigues senior economist at the economics and research department of the bank of portugal and professor of econometrics at nova school of business and economics of universidade nova de lisboa (lisbon, portugal). he was a jean monnet fellow at the european university institute in florence, italy and visiting scholar at the institute for advanced studies in vienna, austria, the university of british columbia, vancouver, canada, the university of navarra, spain and the university of the balearic islands, spain. research interests include timeseries econometrics, financial econometrics, empirical finance and macroeconomics, and tourism economics. he has published a number of peer-reviewed articles in several internationally renowned scientific journals. impact of tourism on employment: an econometric model of 50 ceeb regions. regional and sectoral economic studies modelling and forecasting the uk tourism growth cycle in algarve the economic impact of tourism in the seychelles which type of tourism matters to the regional economic growth? the cases of spain and italy cointegration analysis of german and british tourism demand for greece report: the economic climate tracer: a tool to visualize the cyclical stance of the economy using survey data wirtschaftswissenschaftliche beitr€ age from julius-maximilians-universit€ at würzburg, lehrstuhl für volkswirtschaftslehre, insbes tourism demand for italy and the business cycle a comparison of two business cycle dating methods post-war us business cycles. an empirical investigation tourism statistics tourism statistics tourism statistics 2010 tourism statistics review of international tourism demand models a cointegration analysis of annual tourism demand by malasia for australia the impact of political violence on tourism: dynamic crossnational estimation tourism and regional growth in europe the importance of online tourism demand forecasting tourism demand: a review of empirical we are grateful to two anonymous referees and editor professor steve page for useful comments and suggestions. the first author is pleased to acknowledge financial support from fundação para a ciência e a tecnologia (grant uid/eco/04007/2013) and feder/ compete (poci-01-0145-feder-007659). key: cord-303489-ve1fgnyg authors: klabunde, thomas; giegerich, clemens title: how high and long will the covid-19 wave be? a data-driven approach to model and predict the covid-19 epidemic and the required capacity for the german health system date: 2020-04-17 journal: nan doi: 10.1101/2020.04.14.20064790 sha: doc_id: 303489 cord_uid: ve1fgnyg background an objective: in march 2020 the sars-cov-2 outbreak has been declared as global pandemic. most countries have implemented numerous social distancing measures in order to limit its transmission and control the outbreak. this study aims to describe the impact of these control measures on the spread of the disease for italy and germany, forecast the epidemic trend of covid-19 in both countries and estimate the medical capacity requirements in terms of hospital beds and intensive care units (icus) for optimal clinical treatment of severe and critical covid-19 patients, for the germany health system. methods: we used an exponential decline function to model the trajectory of the daily growth rate of infections in italy and germany. a linear regression of the logarithmic growth rate functions of different stages allowed to describe the impact of the social distancing measures leading to a faster decline of the growth rate in both countries. we used the linear model to predict the number of diagnosed and fatal covid-19 cases from april 10th until may 31st. for germany we estimated the required daily number of hospital beds and intensive care units (icu) using clinical observations on the average lengths of a hospital stay for the severe and critical covid-19 patients. results: analyzing the data from germany and italy allowed us to identify changes in the trajectory of the growth rate of infection most likely resulted from the various social distancing measures implemented. in italy a stronger decline in the growth rate was observed around the week of march 17th, whereas for germany the stronger decline occurred approximately a week later (the week of march 23rd). under the assumption that the impact of the measures will last, the total size of the outbreak can be estimated to 155,000 cases in germany (range 140,000-180,000) and to 185,000 cases in italy (range 175,000-200,000). for germany the total number of deaths until may 31st is calculated to 3,850 (range 3,500-4,450). based on the projected number of new covid-19 cases we expect that the hospital capacity requirements for severe and critical cases in germany will decline from the 2nd week of april onwards from 13,500 to ~2500 hospital beds (range 1500-4300) and from 2500 to ~500 icu beds in early may (range 300-800). conclusion: the modeling effort presented here provides a valuable framework to capture the impact of the social distancing measures on the covid-19 epidemic in european countries and to forecast the future trend of daily covid-19 cases. it provides a tool for medical authorities in germany and other countries to help inform the required hospital capacity of the health care system. germany appears to be in the middle of the (first) covid-19 outbreak wave and the german health system is well prepared to handle it with the available capacities. on march 11 th 2020 the world health organization (who) declared the covid-19 outbreak as pandemic. the steep increase of covid-19 cases in china, iran, italy, france, germany and other european countries resulted in to tens of thousands of severe cases requiring hospitalization as well as in thousands of critical cases due to progression to life-threatening respiratory distress that require intensive care unit (icu) admission (fig. 1) . the dramatic rate of cases that progresses has created a significant strain in the national health systems of these countries and has led to a significant shortage of icus equipped with extra-corporeal membrane oxygenation (ecmo) to save the lives of very critical covid-19 cases. since early march several european governments have implemented numerous control measures to reduce the transmission of the disease and decrease the number of new daily cases of covid-19 so that fewer patients need to seek treatment at any given time and avoid overwhelming hospital capacity, commonly referred as "flattening the curve". the strategy to achieve of the flattening of the curve of covid-19 cases in europe has consisted of (1) early detection of new cases and primary contacts followed by self-quarantine or hospitalization, (2) promoting the adherence to hygiene standards like washing hands and (3) . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04.14.20064790 doi: medrxiv preprint parts of the population by "social distancing". in germany these "social distancing" measures have evolved over time from banning gatherings of more than 1000 participants (issued on march 9 th ), university and school closures (issued on march 16 th ), to prohibiting gatherings of more than two people (issued on march 23 rd ). these restrictions have put a significant burden on german society and have reduced the quality of life for most. there has been a mounting interest on how long these measures and restrictions will last and when can they be lifted safely. on the other hand, medical professionals are expecting a surge of covid-19 patients reaching the hospitals soon and wonder when and how hard it will hit them. germany has significantly expanded its hospital capacity by increasing the number of icu beds and ecmo units in order to prepare for the expected wave of covid-19 patients and to prevent overwhelming the health system. a registry has been formed to track all occupied and readily available intensive care beds in germany to ensure that possible regional peaks of critical covid-19 cases can be treated by transferring the influx of patients to nearby health systems with availability [1] . as of april 12 th this registry covers approximately 19,700 icu beds with 11,376 occupied beds and 8325 available beds. this indicates that there is available capacity for any upcoming influx of new critical and severe cases. over the past weeks mathematical modeling of the covid-19 pandemicespecially sir (susceptible, infectious, recovered) modelshas provided important insights to better understand the spread of virus sars-cov-2 and to evaluate how various potential scenarios of control measures could impact the dynamics of the covid-19 out-break [2, 3] . these simulation studies have informed decision making for national governments on how to react to this coming covid-19 epidemic. simulated estimates of the size of the epidemic in germany if no control measures were implemented [4] and have provided a strong rationale for the closures of school and universities in the uk [5] . other simulations have shown that a contact-tracing app that builds a memory of proximity contacts and immediately notifies contacts of positive casesand potentially asks for self-isolationmight significantly reduce the transfection rate especially by pre-symptomatic covid-19 cases thus reducing the spread of the virus [6] . due to the underlying mechanistic model structure of sir-based models that include representations of mobility information of society it is possible to explore multiple control measure scenarios and thus estimate the impact of certain measures at a very early stage of the epidemic. usually, an epidemic follows an exponential growth at an early stage, peaks and then at the inflection point of the total case curve the growth rate declines again. this decline of the growth rate is either achieved by reaching herd immunity or by implementation of measures to hinder the transmission of the virus. as soon as the impact of these measures become apparent in the decline of the daily growth rate, empirical or so-called top-down methods can be applied to model the data (e.g. logistic growth model, gompertz model, exponential growth rate decline model). these top-down modeling methods can then provide . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04.14.20064790 doi: medrxiv preprint insights regarding the stage of the epidemic, allow the prediction of future trends of the outbreak and estimate its final size [7] [8] [9] . since early april 2020 the numbers of daily new covid-19 cases in germany and italy appear to be either constant with similar numbers of new infections each day or declining (see figure 1 ), indicating that the epidemic has moved from the exponential growth phase into a linear growth phase in these countries. with this new data becoming available, we have used an exponential decline of the growth rate model to analyze the trajectory of the daily growth rate [10] . thus, we have captured and quantified the dynamics of the epidemic in these countries and described the impact on the growth rate measures have had taken. using this approach, we have captured a specific date for both countriestwo to three weeks after the start of these measurementswhen the spread of the epidemic significantly slowed down. in a second step we have used the model to forecast the dynamics of the epidemic in italy and germany and to estimate the number of daily and cumulative total covid-19 cases. this allowed us to address the question of how long the epidemic will last in both countries. in a third step we have used these forecasts of diagnosed covid-19 cases to estimate the number of severe and critical cases for each day of april and may to provide an estimate for the daily required capacity of hospital beds, in particular icu beds with ecmo equipment to treat the predicted severe and critical covid-19 cases in germany. we have used an exponential decline of growth rate model to analyze the trajectory of the daily growth rate in germany and italy. we also evaluated two well established growth models, the logistic function and the gompertz function, but decided in favor of the exponential decline model as the model structure allows to easily capture differences in the growth curve that may result from the social distancing measures. the exponential growth rate decline model defines the growth rate as ratio of new cases today versus total cases yesterday as shown in equation (1) and assumes the growth rate is following an exponential decline function given in equation (2) . the parameter  characterizes how fast the growth rate is decreasing. high values of  indicate a slow decline of the growth rate, whereas low values indicate that the growth rate is declining fast and that the ratio of new cases versus total cases will reach zero more rapidly. with the given model a logarithmic plot of the daily growth rate trajectory thus provided a straight line and allowed us to derive  from the slope by linear regression. . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.04.14.20064790 doi: medrxiv preprint assuming the measures have an impact on the decline of the growth rate, we would expect a discontinuity in the logarithmic plot of the data. for each country we obtained two fits with different values for , capturing the dynamics before and after the impact of the implemented control measures became visible. for germany data was obtained from the website of the robert koch institute (rki) [11] . for italy the data was taken from the coronavirus covid-19 global cases published by the center for systems science engineering (csse) at johns hopkins university (jhu) [12] . for germany and italy, we used the reported data up to april 9 th for modeling and parameter estimation. as a second step we used the exponential decline of growth rate model to predict the cumulative diagnosed covid-19 and the daily new cases for germany and italy beyond april 9 th . as described before a linear regression of the logarithmic plot of the growth rate data between march 23 rd and april 9 th for germany and between march 17 th and april 9 th for italy, respectively, allowed us to model the growth rate using equation (2) . here we could identify the values for  and the intercept as well as their standard deviation and confidence intervals. this allowed us to estimate the expected growth rate for each day beyond april 10 th , as well as an upper and lower limit of the growth rate based on the 95% confidence interval of the linear model. for the prediction of the number of total cases for april 10 th onwards by equation (3) we calculated the expected number of total covid-19 cases using the calculated growth rate value and its upper and lower limit. this allowed us to project the uncertainty in the parameter identification from the logistic regression model into a confidence interval for the predicted covid-19 cases. (3) we have used the predicted number of covid-19 cases (including the confidence intervals of these predictions) in the remaining of april and may to estimate the daily required capacity of hospital beds, in particular icu beds with ecmo equipment to treat the predicted severe and critical covid-19 cases in germany. we used assumptions adapted from thomas-rüddel et al. [13] on the fraction of diagnosed covid-19 cases requiring hospitalization and the subset of cases that progress to intensive care along with the average length of each disease state of an covid-19 patient (summarized in figure . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.04.14.20064790 doi: medrxiv preprint 2). after first symptoms appear on day 0 for an average covid-19 patient, we assume ~7 days to reported diagnosis (labeled with d in figure 2 ) [14] . for severe cases we assume ~7 days from first symptoms to hospitalization [15] , for critical cases ~8 days from first symptoms to icu and for fatal cases ~14 days from first symptoms to death (labeled with m in figure 2 ) [16] . thus we expect a time period of ~7 days between reported diagnosis and death. we assume an average duration of hospital stay for severe and critical cases of 12 days [17] , an average duration of a stay in intensive care unit of 6 days for fatal critical cases and of 12 days for critical cases that recover [17] . we assume that ~20 % of covid-19 cases are severe and require hospitalization, ~25% of the severe cases developed into critical cases requiring intensive care and ~50% of the icu patients have a fatal outcome [17] . we have used an exponential decline of the growth rate modelwith the growth rate being defined by daily new cases today versus daily total cases yesterdayto analyze the trajectory of the daily growth rate in germany and italy. figure 3 shows the plot of the daily growth rateusing a logarithmic function for linearizationfrom march 1 st to april 9 th in italy and germany. by fitting the data using linear regression, we obtained two fits of the data that are shown in blue and orange. . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.04.14.20064790 doi: medrxiv preprint with the value for  being identified we predicted the trend for new daily cases and accumulated total cases for germany and italy assuming that the same control measures remain in place until the last day of may. we projected beyond april 10 th using a value for  of 10.3 and 12.4 days for germany and italy, respectively, that has been determined from the regression analysis using data from the day the impact of the measures have become visible until april 9 th . figure 4 shows the observed data in blue for the total and daily new covid-19 cases and the projected cases in the same graph in red. for the projections of the total covid-19 cases an estimate of the total case range (upper and lower bound) is given that results from the uncertainty in the parameter identification from the linear regression. . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.04.14.20064790 doi: medrxiv preprint . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.04.14.20064790 doi: medrxiv preprint based on these projections the total number of cases in germany by end of may can be predicted to be 140,000 to 180,000 with a peak in the cases around april 1 st . for italy the estimated total size of the epidemic is predicted to be 175,000 to 200,000 cases. evidently these projections assume that the decline of the daily number of new cases continues to follow the exponential trend due to successful control measures taken by both countries. how high will be the covid-19 patient wave for the german health system? when will it hit? how many people will die? we have used the prediction of the newly diagnosed covid-19 cases for germany to estimate the daily capacity requirements for hospital beds and icus as well as daily death rates for april and may in germany. mrz. apr. apr. apr. mai. mai. . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.04.14.20064790 doi: medrxiv preprint estimated calculated to 3850 (range 3508 to 4450 using the growth rate confidence interval of 95% for the expected diagnosed patients beyond april 10 th ). next, figure 6 provides an estimate for every day in april or may for the required capacity of hospital beds, in particular icu beds with ecmo equipment, to adequately treat the predicted severe and critical covid-19 cases in germany. we made assumptions on the fraction of mild, severe, critical or fatal covid-19 cases and on the average length of the required hospitalization and/or intensive care for each disease state (see methods and figure 2) . we used the observed number of diagnosed covid-19 cases as input before april 10 th and the number of projected covid-19 cases after april 10 th . for the projections beyond april 10 th a confidence interval is given that results from the uncertainty in the parameter identification from a linear regression. according to the model the number of severe cases requiring hospitalization is expected to peak in the first week of april at ~13,000. the maximum of ~2500 critical cases requiring intensive care with ecmo capability is expected at in the first week of april. this is in good agreement with the reported number of covid-19 cases on icus in germany of 2.405 on april 12 th [1, 11] . based on the expected number of new covid-19 cases we would expect that the capacity needs for severe and critical cases will decline from the 2 nd week of april onwards from ~13,500 to ~2500 (range 1500 to 4300) for hospital beds and from ~2500 to ~500 (range 300 to 800) for icu units, respectively. predicted severe and cricial cases in hospital at given day . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.04.14.20064790 doi: medrxiv preprint in this study we have captured the trajectory of the daily growth rate of covid-19 cases in germany and italy with an exponential decline model. analyzing the data from germany and italy allowed us to identify changes in the trajectory of the growth rate that most likely are the result from the various "social distancing" measures that have been implemented to reduce the transmission of covid-19. for italy a stronger decline in the growth rate has been observed starting around the week of march beyond the analysis of the given data the data-driven modeling approach presented allowed to describe the observed data with a mathematical model and to provide predictions of new and cumulative covid-19 cases for both countries. the predictions suggest that the peak of the epidemic in terms of newly diagnosed cases has passed not only in italy (in late march), but that also in germany (early april). under the assumptions that the impact of the control measures on the transmission of the virus will last for the duration of the simulated time period, the total size of the epidemic can be estimated to be 155,000 cases for germany (range 140,000 to 180,000) and to be 185,000 cases for italy (range 175,000 to 200,000) for italy. evidently these projections assume that the decline of the daily number of new cases will continue to follow the exponential trend due to successful measures taken in both countries. we have used the predicted daily new diagnosed covid-19 cases in germany to estimate the number of daily new severe, critical and fatal covid-19 cases allowing us to estimate the actual requirements for hospital beds and icus at any given day for april and may. based on the projected number of new covid-19 cases we would expect that the capacity needs for severe and critical cases will decline from the 2 nd week of april onwards from ~13,500 to ~2500 hospital beds in early may (range 1500 to 4300) and from ~2500 to ~500 icu beds in early may (range 300 to 800), respectively. the german hospital register tracks all occupied and available intensive care beds in germany [1] . as of april 12 this register covers approximately 19,700 icu beds with 11,376 occupied beds and 8,325 available beds. compared to the expected now decreasing demand for icu beds this indicates that there is sufficient capacity for the new critical and severe covid-19 cases. in other words, we are just in with respect to the requirements for the german hospitals middle of the wave -that has been expected to hit and possibly overwhelm the german health system -has been reached and it can be well covered by the . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.04.14.20064790 doi: medrxiv preprint available capacities. our analysis covers germany as a single entity and does not offer the granularity that may be needed to identify regional short comings of hospital capacities in areas that are more severely effected by the covid-19 epidemic. evidently projections in the future come with certain limitations. first the projection for new covid-19 cases assume a continuation of (similar) control measures of social distancing having the same impact on the growth rate of new cases. they can only provide a trend, can't be applied to project further out into the future and obviously are not able to predict the size of a second wave (or whether there would be one at all). in addition, for the calculations used above to estimate the risk for the overwhelming of the german health care system, several assumptions are based on clinical data from the epidemic in china. evidently due to differences in the age distribution of patients and in the health system between both countries these can only be estimates for the situation in germany. nevertheless, it appears that several of these assumptions translate into projections of death rate and capacity needs for icu beds that are in-line with the observed clinical findings in germany. we estimate the total rate of fatalities per diagnosed covid-19 case to be 2.5% for germany, resulting from the assumption that 20% of the diagnosed cases are severe, 25% of the severe cases get critical and 50% of the critical cases are fatal. on april 12 th for 2.2% of diagnosed covid-19 cases in germany a fatal outcome has been reported [11] . while the epidemic is still ongoing, this formula to calculate the final death rate can be misleading and may lead to a too low number as of today the outcome is unknown for a non-negligible proportion of these diagnosed patients [18] . in other words, current deaths belong to a total case figure of the past, not to the current case figure in which the outcome (recovery or death) of a proportion (the most recent cases) hasn't yet been determined. applying the recommended equation to calculate the case fatality ratio (cfr) by death at day d / cases at day d-x and assuming a time of 7 days between reported diagnosis and death an average death rate for germany of ~2.9 % can be obtained from the data up to april 12 th (total death by april 12 th / total cases by april 5 th ) [10] . assuming 2.5% of diagnosed cases will have a fatal outcome 7 days later we calculated the expected daily deaths in germany (see figure 5 ). the maximum of new deaths per day of ~150 is expected for april 10 th . as shown in figure 5 most of the daily death calculations match well the data. some differences between the predictions and observed data are evident for the daily new fatalities, which have unexpected high values from april 8 to april 10. this difference may be attributed to covid-19 outbreaks in nursing homes leading to unexpectedly high case numbers in this period. it is also noteworthy that with the number of diagnosed covid-19 cases as input, the assumptions on the length of hospital stays for critical patients and the assumed fraction of 5% critical cases of all diagnosed covid-19, we expected the maximum of ~2500 critical cases requiring intensive care with ecmo capability at the first week of april. this is in good agreement with the reported number of covid-19 cases currently in icus in germany of 2405 on april 12 th [1, 11] . . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 14.20064790 doi: medrxiv preprint in conclusion, we are convinced that regardless of numerous included assumptions derived from clinical observations and regardless of the given uncertainty of the model projections beyond april 10 th , the model predictions can help to capture the impact of social distancing measures on the epidemic in european countries, to understand the dynamics of the epidemic with respect to diagnosed and fatal cases and to estimate the required daily capacity for german hospitals. thus, it appears to be a valuable tool for germany or other countries to provide guidance and support decision making in the health care system with respect to how much hospital capacity is required to be well prepared for the (next) wave. forecasting the worldwide spread of covid-19 based on logistic model and seir model quantifying undetected covid-19 cases and effects of containment measures in italy modellierung von beispielszenarien der sars-cov-2-epidemie 2020 in deutschland on behalf of the imperial college covid-19 response team. impact of nonpharmaceutical interventions (npis) to reduce covid19 mortality and healthcare demand quantifying sars-cov-2 transmission suggests epidemic control with digital contact tracing rational evaluation of various epidemic models modeling and forecasting trend of covid-19 estimation of the final size of the second phase of the coronavirus epidemic by the logistic model generalized logistic growth modeling of the covid-19 outbreak in 29 provinces in china and in the rest of the world covid-19) daily situation report of the robert koch institute an interactive web-based dashboard to track covid-19 in real time coronavirus disease 2019" (covid-19): update für anästhesisten und intensivmediziner märz 2020 schätzung der aktuellen entwicklung der sars-cov-2-epidemie in deutschland -nowcasting clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumoniain wuhan, china updated understanding of the outbreak of 2019 novel coronavirus (2019-ncov) in wuhan for the china medical treatment expert group for covid-19 /funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint we are thankful to munkhjargal schöpfel (klinikum koblenz) for sharing her own professional experience with covid-19 patients, for being a sounding board while this work has been performed and for the supportive daily discussions. we gratefully acknowledge susana zaph (sanofi us) for her thorough and mindful revision of the manuscript. . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.04.14.20064790 doi: medrxiv preprint key: cord-278508-h145cxlp authors: streng, andrea; prifert, christiane; weissbrich, benedikt; liese, johannes g. title: continued high incidence of children with severe influenza a(h1n1)pdm09 admitted to paediatric intensive care units in germany during the first three post-pandemic influenza seasons, 2010/11–2012/13 date: 2015-12-18 journal: bmc infect dis doi: 10.1186/s12879-015-1293-1 sha: doc_id: 278508 cord_uid: h145cxlp background: previous influenza surveillance at paediatric intensive care units (picus) in germany indicated increased incidence of picu admissions for the pandemic influenza subtype a(h1n1)pdm09. we investigated incidence and clinical characteristics of influenza in children admitted to picus during the first three post-pandemic influenza seasons, using active screening. methods: we conducted a prospective surveillance study in 24 picus in bavaria (germany) from october 2010 to september 2013. influenza cases among children between 1 month and 16 years of age admitted to these picus with acute respiratory infection were confirmed by pcr analysis of respiratory secretions. results: a total of 24/7/20 influenza-associated picu admissions were recorded in the post-pandemic seasons 1/2/3; incidence estimates per 100,000 children were 1.72/0.76/1.80, respectively. of all 51 patients, 80 % had influenza a, including 65 % with a(h1n1)pdm09. influenza a(h1n1)pdm09 was almost absent in season 2 (incidence 0.11), but dominated picu admissions in seasons 1 (incidence 1.35) and 3 (incidence 1.17). clinical data was available for 47 influenza patients; median age was 4.8 years (iqr 1.6–11.0). the most frequent diagnoses were influenza-associated pneumonia (62 %), bronchitis/bronchiolitis (32 %), secondary bacterial pneumonia (26 %), and ards (21 %). thirty-six patients (77 %) had underlying medical conditions. median duration of picu stay was 3 days (iqr 1–11). forty-seven per cent of patients received mechanical ventilation, and one patient (2 %) extracorporeal membrane oxygenation; 19 % were treated with oseltamivir. five children (11 %) had pulmonary sequelae. five children (11 %) died; all had underlying chronic conditions and were infected with a(h1n1)pdm09. in season 3, patients with a(h1n1)pdm09 were younger than in season 1 (p = 0.020), were diagnosed more often with bronchitis/bronchiolitis (p = 0.004), and were admitted to a picu later after the onset of influenza symptoms (p = 0.041). conclusions: active screening showed a continued high incidence of a(h1n1)pdm09-associated picu admissions in the post-pandemic seasons 1 and 3, and indicated possible underestimation of incidence in previous german studies. the age shift of severe a(h1n1)pdm09 towards younger children may be explained by increasing immunity in the older paediatric population. the high proportion of patients with underlying chronic conditions indicates the importance of consistent implementation of the current influenza vaccination recommendations for risk groups in germany. influenza is one of the most common vaccine-preventable viral diseases, with the highest morbidity reported for children and elderly patients [1, 2] . influenza infections during childhood usually present as mild respiratory upper airway disease, but severe complications and fatalities also occur, especially in children less than 2 years of age and in children with underlying chronic conditions [2] [3] [4] [5] [6] [7] . however, 40-50 % of influenza-associated fatalities occur in previously healthy children [4, 8] . before the influenza a(h1n1)pdm09 pandemic in 2009/ 2010, comparisons of clinical characteristics between patients infected with different influenza types (a vs. b) and between patients infected with different influenza a subtypes showed only small differences when controlling for age [9, 10] . during the pandemic, however, some studies observed increased morbidity and mortality among children compared to previous seasonal influenza [6, [11] [12] [13] , while other studies described the clinical features of a(h1n1)pdm09 as being similar or even milder [14, 15] . acute respiratory distress syndrome (ards) and fatal viral pneumonia was observed more frequently during the pandemic [16] . post-pandemic surveillance was recommended, as circulation of a(h1n1)pdm09 was expected to continue for several years, gradually assuming a seasonal influenza pattern [16] . in germany, influenza sentinel surveillance on outpatients of all ages [17] confirmed that the first postpandemic season 2010/11 was dominated by influenza a(h1n1)pdm09 (62 %), co-circulating with influenza b (37 %) whereas a(h3n2) was rare (<1 %). during the second season 2011/12, a(h1n1)pdm09 was rare (1 %), whereas a(h3n2) was diagnosed in 75 % of cases and co-circulated with influenza b (24 %). in the third season 2012/13, all three types/subtypes co-circulated in similar proportions (34 % a(h1n1)pdm2009, 31 % a(h3n2), and 35 % b). information on the incidence and clinical characteristics of severe paediatric influenza resulting in intensive care treatment and/or fatal outcome is still limited in germany, and post-pandemic data is thus far available only for the season 2010/11 [18] [19] [20] . based on cases recorded by a nation-wide paediatric intensive care unit (picu) reporting system, the pre-pandemic (2005/06-2007/08), pandemic (2009/10) and post-pandemic (2010/ 11) annual incidence of severe influenza cases per 100,000 children below 15 or 17 years of age was estimated as 0.05, 0.8-1.0, and 0.4, respectively [18] [19] [20] . the data so far available indicated a shift towards younger children in a(h1n1)pdm09 cases from the pandemic to the first post-pandemic season [20] . in these studies, it remained unclear whether the higher pandemic and post-pandemic incidence in children was caused by higher influenza activity, heightened physician awareness, more frequent or more sensitive influenza testing, or a more severe course of disease of a(h1n1)pdm09 [18] . furthermore, all these previous studies may have been affected by underreporting, as influenza cases were reported at the discretion of the picu physician without systematic screening for influenza in patients with severe acute respiratory infection. in the study presented here, we used active screening to estimate the incidence of laboratory-confirmed influenzaassociated picu admissions in one of germany's largest federal states during the first three post-pandemic seasons. furthermore, we described the clinical characteristics of influenza picu patients and compared patients with severe a(h1n1)pdm09 disease between the post-pandemic seasons. prospective, active surveillance was conducted in picus of paediatric hospitals in bavaria, germany. on december 31 st , 2010 roughly 2,001,700 children <17 years of age were registered in bavaria [21] , representing 16 % of the german population in this age group [22] . the annual study population was defined as the sub-group of all children in bavaria at least 1 month and <17 years of age. all 30 paediatric hospitals in bavaria equipped for paediatric intensive care treatment of children older than 1 month of age were invited to participate. these picus reported a total of 432 intensive care beds (median 14, iqr [11] [12] [13] [14] [15] [16] , including 207 beds (median 9, iqr 6-12) equipped with ventilation facilities. , all patients who fulfilled the following inclusion criteria were enrolled: i) admission to a participating picu with suspected acute respiratory infection (ari) of the upper or lower respiratory tract, with arirelated symptoms (for example, coryza, cough, or sore throat); ii) age at picu admission due to ari at least 1 month and below 17 years of age; iii) parental written informed consent. enrolled children with pcr-confirmed influenza were classed as influenza-associated ari. the picu physician documented demographic characteristics, underlying chronic medical conditions, influenza vaccination status, diagnostic findings, ari-associated diagnoses and complications, treatment, duration of hospital and picu stay, and outcome in a structured questionnaire. a respiratory sample, usually a flocked nasopharyngeal or pharyngeal swab, was collected on the day of picu admission for pcr-confirmation of influenza. microbiological testing for bacteria or fungi was at the discretion of the picu physician; pathogens detected at usually sterile sites or in tracheal aspirates were classified as bacterial or fungal co-infection. pcr confirmation of influenza was performed either at the local laboratories of the participating picus using influenza-specific pcr, or (in the majority of cases) at the central laboratory at the institute of virology and immunobiology of the university of würzburg using multiplex pcr for respiratory viruses. for the latter, respiratory samples were placed in a viral transport medium (mast diagnostica gmbh, reinfeld, germany). at the central laboratory, they were tested using the commercial multiplex pcr 'ftd® respiratory pathogens 21' (fast track diagnostics, luxembourg) to screen for respiratory viruses (sensitivity and specificity of 99-100 % compared to singleplex pcr assays for all included viruses in clinical samples). pathogens detected by the test kit included influenza a and b viruses, respiratory syncytial virus (rsv), parainfluenza virus (piv) 1-4, coronavirus (cov) nl63, oc43, hku1, and 229e, human metapneumovirus (hmpv), human bocavirus (hbov), adenovirus (adv), rhinovirus (rhv), enterovirus (ev), parechovirus (pv), and additionally mykoplasma pneumoniae. samples positive for influenza a and b virus rna in the multiplex pcr were further analysed to determine the subtype and lineage, respectively. primers and probes specific for influenza a(h1n1)pdm09 were included in the 'ftd respiratory pathogens 21' kit. all samples positive for influenza a virus rna but negative for influenza a virus (h1n1)pdm09 rna were tested by a pcr specific for influenza a virus h3. all data was entered into a microsoft access database and transferred to ibm spss 21.0 for statistical analysis. data was analysed descriptively (percentages, or median with inter-quartile range, iqr). comparisons between groups were assessed for significance (p < 0.05, twosided) using pearson's chi 2 -test or fisher's exact test for categorical data, and the mann-whitney u-test for continuous data. the minimum incidence of influenza-associated picu admissions per 100,000 children <17 years of age was calculated for each season based on the observed number of influenza picu patients with a residential address in bavaria. to correct for non-participating picus, the estimates of the total number of picu influenza cases treated in all eligible picus in bavaria per season were derived taking into account the annual percentage of participating picus. the annual study population was used as denominator. a similar questionnaire and case definition had been used in previous studies on influenza-related picu admission [18, 19] . key variables were extracted from these publications for comparison purposes. data from streng et al. [18] and the present study were pooled for statistical comparison of pre-and post-pandemic seasons. the study was approved by the ethical committee of the medical faculty, university of würzburg, germany. based on the observed cases, the minimum incidence for pcr-confirmed influenza-associated picu admission per 100,000 children <17 years of age in bavaria was calculated as 1.15/0.36/1.03 for seasons 1/2/3, respectively. taking into account that the observed cases were based on data from 67 %/47 %/57 % of all eligible picus, the total number of influenza-associated picu admissions in bavaria was estimated and corrected incidences were calculated as 1.72/0.76/1.80 per 100,000 children <17 years. subtype-specific corrected incidences were 1. 35 (table 2) . after onset of ari symptoms, children were admitted to hospital after a median interval of 3.0 days; 83 % were transferred to the picu on the day of hospital admission or the following day (table 2) . two long-term hospitalized children (4.2 %) required picu treatment due to ari and were diagnosed with suspected nosocomial influenza a(h1n1)pdm09 infection. median length of picu stay was 3.0 days and median length of total hospital stay was 7.5 days (table 2) . underlying chronic medical conditions were reported for a total of 36 influenza picu patients (76.6 %) ( table 3) . chronic neurological diseases were most frequent (34.0 %), followed by chronic lung disease (25.5 %), preterm birth (21.3 %), cardiac malformations (17.0 %), obesity (10.6 %), genetic disorders (8.5 %), and immunocompromising conditions (8.5 %). of 36 influenza picu patients with underlying chronic conditions, four (11.1 %) were too young (<6 months of age) to have been immunized against influenza, and for two patients (5.6 %), data on their influenza vaccination status was unavailable. twenty-nine (80.6 %) patients from this risk group had not been vaccinated against influenza although they would have been eligible. one immunocompromised child (2.8 %) had been vaccinated in october 2012, but was diagnosed with a(h3n2) in january 2013. one or more specific influenza-associated diagnoses/complications were reported for 42 (89.4 %) of the 47 children ( table 4 ). the most frequent diagnosis was influenzaassociated pneumonia (61.7 %), followed by bronchitis/ bronchiolitis (31.9 %), and secondary bacterial pneumonia (25.5 %). ards was reported for 10 (21.3 %) and sepsis for six children (12.8 %); other complications were rare. thirty-nine of the 47 patients (83.0 %) underwent a chest radiograph. in addition to influenza, laboratory-confirmed co-infections were reported for 16 children (34.0 % out of 47 (1)). the majority of the 47 picu patients were treated intravenously with antibiotics (72.3 %), and with antipyretics (70.2 %) ( five children (10.6 %), infected with a(h1n1)pdm09, died at an age of 4 to 11 years; four were male patients ( table 6 ). four of these children suffered both from severe neurological conditions (two children with previous peripartal asphyxia and spastic tetraparesis; one child with cerebral paresis and tetraspasticity; one child with congenital cerebral disorder), and from chronic pulmonary conditions; two of these four children were also born pre-term. influenza-associated pneumonia was diagnosed in all four of these children; three additionally had secondary bacterial pneumonia, and one child also developed sepsis. for the fifth child, obesity was reported as the only risk factor; and sepsis and suspected encephalitis as complications. bacterial co-pathogens were detected in three of these five children and suspected in one child; two viral and two fungal co-infections were also reported. all five children received intratracheal ventilation, antibiotics and catecholamines; two were additionally treated with antiviral medication. death occurred 1, 2, 4, 19, and 26 days after picu admission, with ards reported as cause of death in three children. sequelae were reported for five patients (10.6 %): state after surgery due to pleural effusion/empyema in two children; increased oxygen requirements in two children who had previously already received oxygen therapy at home; damage of the lung after high-pressure ventilation in one child. table 2 ). figure 1 shows the difference in age distribution between both seasons, and the high proportion of children below 2 years of age as opposed to low proportions in all other age groups in season 3. after onset of symptoms, children were admitted to a picu after a significantly shorter period, with a median of 3 days (iqr 1-4) in season 1 compared to 6 days (iqr 2.0-7.5) in season 3 ( table 2 ). in season 1, significantly fewer children were diagnosed with bronchitis/bronchiolitis (table 4 ), and they tended to require cpap treatment less frequently than in season 3 (11.1 % vs. 41.7 %, p = 0.084, table 5 ). in the pre-pandemic period, median duration of picu stay was longer (19 days) , and children were more often diagnosed with encephalitis/encephalopathy (25 %) and co-infections (65 %) than in later periods ( table 7) . the proportion of children with influenza-associated pneumonia was highest (74 %) during the pandemic, whereas secondary bacterial pneumonia (17 %), bronchitis/ bronchiolitis (12 %) and sepsis (6 %) were reported less frequently during the pandemic than in the pre-and post-pandemic seasons. oseltamivir treatment decreased significantly in the post-pandemic period (table 7) . during the first three post-pandemic seasons 2010/11, 2011/12 and 2012/13, active screening of children with acute respiratory infection admitted to 24 paediatric intensive care units in bavaria identified a total of 51 pcr-confirmed influenza cases, resulting in annual incidence estimates of 1.7, 0.7, and 1.8 influenza-associated picu admissions per 100,000 children, respectively. these figures would, by extrapolation, correspond to a total number of 559 children with influenza-associated picu admission in germany within the 3-year post-pandemic period, with an annual average of 186 children. this is almost 28 times as high as the annual average of six to seven influenza-associated picu admissions detected by nation-wide picu surveillance in germany during three pre-pandemic years without active screening [18] . furthermore, the incidence estimates for the subtype a(h1n1)pdm09 derived from our active screening study were higher in the first and third post-pandemic seasons (1.35 and 1.17, respectively) than previous incidence estimates for picu patients in the pandemic (0.8-1.0) and the first post-pandemic (approximately 0.4) season in germany [19, 20] . thus, our results indicate possible underreporting in previous studies, and show a continued high level of a(h1n1)pdm09-associated picu admissions even 3 years after the pandemic. in our study, the proportions of children with bacteriaassociated complications (secondary bacterial pneumonia, sepsis) were similar to the proportions observed during the pre-pandemic period, but appeared higher than those observed during the pandemic 2009/10 [19] . the lower proportions observed during the pandemic might be explained by the time shift of the peak of influenza cases, which was observed as early as november 2009 in germany [19] . thus, the pandemic influenza peak did not coincide with the seasonal peak of streptococcus pneumoniae, the bacterial pathogen most frequently associated with community-acquired influenza [23] . antiviral treatment patterns changed considerably during the post-pandemic period, with a decrease in the proportion of paediatric influenza cases receiving oseltamivir from previously 50 % [18] and 61 % [19] to 19 %. oseltamivir is considered to be most advantageous when administered within the first 48 h of influenza disease. the reduced use in the post-pandemic period may therefore be partly due to the fact that median time between onset of influenza symptoms and picu admission was longer than during the pandemic (3 vs. 2 days [19] ). increasing uncertainty regarding the effectiveness of oseltamivir in the treatment of paediatric influenza may also have played a role [24, 25] . post-pandemic oseltamivir treatment was associated with co-infections and longer picu stay, suggesting that it were mainly children with severe complications or with serious underlying conditions who received this medication. in our study, about two-thirds of influenza cases and all fatalities were a(h1n1)pdm09-associated. during the postpandemic seasons 1/2/3, the proportion of a(h1n1)pdm09 cases among the picu patients was 79 %/14 %/65 % and, thus, considerably higher than the proportion of this subtype reported among outpatients by national influenza surveillance (65 %/1 %/34 %) [17] . this observation suggests that a(h1n1)pdm09 may be associated more often with a severe course of influenza requiring picu treatment than other influenza types/ subtypes. similar observations on the proportion of a(h1n1)pdm09-associated picu admissions have been reported in the united states [9] . comparison of picu patients with a(h1n1)pdm09 between the post-pandemic seasons showed that median age was 1.7 years in the third season and, thus, significantly lower than in the first season. a significant age shift towards younger children, from a median age of 5 to 3 years, had already been observed in a comparison of the pandemic and the first post-pandemic season in germany [20] . the continued shift towards younger patients in the third season is likely to be due to increasing immunity in the older paediatric population, after previous contact with a(h1n1)pdm09. seroprevalence data from germany had already shown evidence for a(h1n1)pdm09 infection in as many as 25 % of children aged 1-4 years and 48 % of 5-17 year-old children for the pandemic season 2009/10 [26] . a similar shift towards younger hospitalized children [27, 28] and towards younger children with severe paediatric a(h1n1)pdm09-associated influenza from the pandemic season to the first post-pandemic season had also been detected in other european countries [28] [29] [30] [31] . in germany, paediatric influenza vaccination for pandemic influenza a(h1n1)pdm09 was recommended and funded for all children as monovalent vaccination from october 2009 to july 2010 [32] . for seasonal influenza, however, paediatric influenza vaccination was and is currently recommended only for specific risk groups with underlying chronic conditions [33] . vaccination uptake was low, even in this target group. pre-pandemic vaccination rates were 5 % for all children and about 15 % for children with chronic underlying conditions in 2007/2008 [34] . for the pandemic and post-pandemic seasons, no data on vaccination rates is available for children, but vaccination rates as low as 14 % (2009/10) and 11 % (2010/11) were reported for adults, with a vaccination rate of only 17 % even for risk group adults [35] . in our study, more than 75 % of influenzaassociated picu patients were children with underlying chronic conditions. analysis of their reported influenza [20] ). data are given in %, by age group and season. season 1: oct10-sep11 (n = 18), season 3: oct12-sep13 (n = 13); season 2: oct11-sep12 (n = 1) is not shown vaccination status showed that among these were a high proportion of vaccine-eligible but unvaccinated children. patients with chronic conditions too young to be vaccinated and other paediatric risk groups, such as otherwise healthy children below 2 years of age, are not covered by the current german recommendation. all these groups could profit considerably from universal influenza vaccination for children, either directly or by herd protection. in contrast to the situation in germany, in the united states universal influenza vaccination for all children older than 6 months of age has been established, and vaccination coverage reached a level of approximately 41 % in 2013 [36] . compared to 348 influenza-associated paediatric deaths observed in the united states during the pandemic 2009/10, only 79 were observed in the strong a(h1n1)pdm09 season 2013/14 [37] . this might partly be explained by increasing immunity in children after previous a(h1n1)pdm09 infection, but may in part also be a result of the influenza vaccination program [37] . in england, a universal childhood vaccination programme with a new live attenuated influenza vaccine (laiv) with intra-nasal application was started in the 2013/14 influenza season [38] . first results showed an overall uptake of 53 % in primary school aged children, indicating a good acceptance of laiv, and suggesting direct and indirect impacts on disease incidence, including reduction of paediatric influenza-associated hospitalisations. to our knowledge, our study is the first in europe to investigate paediatric influenza in picu patients during the first three post-pandemic seasons after the 2009/10 pandemic. the strengths of our study include the multicentre design covering the majority of picus in bavaria, the active screening for influenza in patients admitted to picus, and pcr-confirmation of all influenza cases. a limitation is that the corrected incidence estimates were based on the assumption that participating and nonparticipating picus treated a similar number of severe paediatric influenza patients. although picus of both groups were of similar size, some of the non-participating picus, where paediatricians indicated lack of time as reason for non-participation, may have treated a higher number of patients, or patients with higher acuity. further limitations include potential over-and underreporting in participating picus. on the one hand, due to different hospitalization rules some children may have been admitted to picus mainly for the purpose of monitoring their course of influenza disease more closely, thus resulting in an overestimate of severe cases. on the other hand, some parents of children with severe influenza may have refused study participation, or children with a fulminant course of influenza disease may have died before they were admitted to a picu [4] . thus, the high incidence estimates derived in this study may still underestimate the true burden of severe influenza. [19] b key data from this study were pooled with data from streng et al. 2011 [18] and compared using fisher's exact test or mann-whitney u-test, respectively the incidence estimates of influenza a(h1n1)pdm09associated picu admissions, derived from active screening of picu patients with acute respiratory infections, reached similarly high levels in the first and third postpandemic seasons. both incidence estimates were higher than those previously reported by nation-wide picu surveillance for the pandemic and the first post-pandemic season, suggesting possible underreporting in previous studies without active screening. comparison of the first and third post-pandemic seasons indicated an age shift of severe a(h1n1)pdm09 towards younger children, which might be explained by increasing immunity in the older paediatric population. the large proportion of children with underlying chronic conditions indicates the need for a more consistent implementation of the current recommendations for influenza vaccination of specific risk groups in germany. these children could also profit from herd protection, if universal influenza vaccination was successfully introduced in germany. authors' contributions as designed the study, coordinated data collection, performed the analysis, interpreted the data, and drafted the manuscript. bw and cp performed multiplex pcr and subtyping on laboratory specimens, interpreted virological data, and revised the manuscript. jgl supervised the study, supported data interpretation, and revised the manuscript. the clinical data were collected by the bavarian picu study group on influenza and other viral ari, from oct 2010 to september 2013. all authors read and approved the final manuscript. group on influenza and other viral ari participants and their affiliations while participating during the study period städtisches klinikum münchen gmbh, klinikum harlaching städtisches klinikum münchen gmbh, klinikum schwabing christoph schmidtlein 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2009/10 pandemic season in england burden and characteristics of influenza a and b in danish intensive care units during the 2009/10 and 2010/11 influenza seasons first influenza season after the 2009 pandemic influenza: characteristics of intensive care unit admissions in adults and children in vall d'hebron hospital änderung der empfehlung zur impfung gegen influenza analyse regionaler unterschiede der influenza-impfraten in der impfsaison influenza a(h1n1)pdm09 antibodies after pandemic and trivalent seasonal influenza vaccination as well as natural infection in update: influenza activity -united states influenza activity -united states, 2013-14 season and composition of the 2014-15 influenza vaccines uptake and impact of a new live attenuated influenza vaccine programme in england: early results of a pilot in primary school-age children, 2013/14 influenza season the authors thank all participating hospitals, and picu and university staff involved in data collection and virological testing. karin seeger we thank for helpful comments on the manuscript. the study was supported by an unrestricted grant from glaxosmithkline gmbh & co. kg, munich, germany. apart from financial support, the company was not involved in any part of the study. the publication was funded by the german research foundation (dfg) and the university of wuerzburg in the funding programme open access publishing. • we accept pre-submission inquiries • our selector tool helps you to find the most relevant journal submit your next manuscript to biomed central and we will help you at every step: key: cord-333413-8buawes0 authors: liebing, j.; völker, i.; curland, n.; wohlsein, p.; baumgärtner, w.; braune, s.; runge, m.; moss, a.; rautenschlein, s.; jung, a.; ryll, m.; raue, k.; strube, c.; schulz, j.; heffels-redmann, u.; fischer, l.; gethöffer, f.; voigt, u.; lierz, m.; siebert, u. title: health status of free-ranging ring-necked pheasant chicks (phasianus colchicus) in north-western germany date: 2020-06-16 journal: plos one doi: 10.1371/journal.pone.0234044 sha: doc_id: 333413 cord_uid: 8buawes0 being a typical ground-breeding bird of the agricultural landscape in germany, the pheasant has experienced a strong and persistent population decline with a hitherto unexplained cause. contributing factors to the ongoing negative trend, such as the effects of pesticides, diseases, predation, increase in traffic and reduced fallow periods, are currently being controversially discussed. in the present study, 62 free-ranging pheasant chicks were caught within a two-year period in three federal states of germany; lower saxony, north rhine-westphalia and schleswig-holstein. the pheasant chicks were divided into three age groups to detect differences in their development and physical constitution. in addition, pathomorphological, parasitological, virological, bacteriological and toxicological investigations were performed. the younger chicks were emaciated, while the older chicks were of moderate to good nutritional status. however, the latter age group was limited to a maximum of three chicks per hen, while the youngest age class comprised up to ten chicks. the majority of chicks suffered from dermatitis of the periocular and caudal region of the head (57–94%) of unknown origin. in addition, intestinal enteritis (100%), pneumonia (26%), hepatitis (24%), perineuritis (6%), tracheitis (24%), muscle degeneration (1%) and myositis (1%) were found. in 78% of the cases, various mycoplasma spp. were isolated. mycoplasma gallisepticum (mg) was not detected using an mg-specific pcr. parasitic infections included philopteridae (55%), coccidia (48%), heterakis/ascaridia spp. (8%) and syngamus trachea (13%). a total of 8% of the chicks were avian metapneumovirus (ampv) positive using rt-pcr, 16% positive for infectious bronchitis virus (ibv) using rt-pcr, and 2% positive for haemorrhagic enteritis virus (hev) using pcr. all samples tested for avian encephalomyelitis virus (aev), infectious bursal disease virus (ibdv) or infectious laryngotracheitis virus (iltv) were negative. the pool samples of the ten chicks were negative for all acid, alkaline-free and derivative substances, while two out of three samples tested were positive for the herbicide glyphosate. pheasant chick deaths may often have been triggered by poor nutritional status, probably in association with inflammatory changes in various tissues and organs as well as bacterial and parasitic pathogens. theses impacts may have played a major role in the decline in pheasant populations. a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 the original distribution area of the ring-necked pheasant (phasianus colchicus) ranged from the black sea over the dry areas of central asia to the east of asia to south korea and siberia [1] . the romans introduced the pheasant to europe around 500 ad, from where it spread through regular release throughout central and western europe [2] . according to current published data, the pheasant mainly prefers structurally semi-open land, using trees and hedges as cover, and also occupies adjacent sparse forests and reedy areas [3] . most pheasants seek shelter under trees to be protected from natural predators. however, some subspecies spend the night on the ground or among dense reeds. their resting places during the day are usually well-hidden hedges, where sand-baths are taken in carved hollows [1] . adult pheasants mainly feed on plants, consuming different parts of the plant such as seeds, berries, tubers, root shoots and leaves, as well as green sprouts. however, on occasions, their diet is supplemented by animal protein, preferably in the form of insects [1] . for chicks, smaller ground-level insects are especially important during the first weeks of life. they feed on a variety of species of insects such as spur cicadas (delphacidae), bugs (heteroptera), sawfly wasps (tenthredinidae) and butterfly caterpillars (lepidoptera larvae) [1, 4, 5] . this diversity is particularly important for a healthy growth [6, 7] . for example, a diet based only on aphids can lead to delayed plumage development due to inadequate amino acid supply [8] . in germany, the pheasant is a typical soil-breeding bird of the agricultural landscape. the main part of the german population is found in southwest lower saxony, north rhine-westphalia and schleswig-holstein. the population level reached its plateau between 1960 and 1970 in lower saxony. during this period, the hunting bag statistics (state registered numbers of hunting animals, in this case pheasants), i.e. the absolute number of pheasants killed, amounted to approximately 300,000 pheasants in germany [9] . in the severe winter of 1970 and the following wet spring of 1971, the population of pheasants and many other wild living animals declined [9, 10] . the hunting bag was reduced to an average of about 80,000 pheasants and declined further. not only was the pheasant population subjected to this decline, but also that of many other farmland birds [11, 12, 13] . around 2007/2008, the population showed another severe decline of unknown cause. in germany, the renewable energy sources act (erneuerbare-energie-gesetz: renewable energy sources act describes the implementation of ecological energy generation in germany) amendment of 2004 with an advancement in biogas, triggered the doubling of corn cultivation. consequently, huge areas of fallow land disappeared in lower saxony [14] . the contributory factors to the ongoing decline in the pheasant population, such as the effects of pesticides, infectious agents, predation, increasing traffic and human populations as well as reduced fallow periods, are currently the subject of controversial discussion among different stakeholders [15, 16, 17, 18] . some authors see a correlation between the changes in agriculture and the decline in the populations of many farmland birds [19, 20] . in the third week of life, 70% of the chicks' diet consists of insects. gradually, the insect percentage is reduced. from the sixth week of life, the diet is similar to that of adult birds. previous studies [21, 22] associated the decline in the number of many farmland birds with the use of insecticides. if chicks are unable to find a sufficient number of insects during the first weeks of life, they have to search a larger range of their habitat, which can lead to malnutrition and weakening. thus, harmless ubiquitous pathogens may have negative effects on chicks [23, 24, 25, 26, 27, 28] . investigations carried out led to the assumption that there is no specific epidemic infectious agent currently circulating in the adult pheasant population [29] . many hunters report that especially the number of chicks has declined, with more older birds making up the hunting bag. however, the authors found serological evidence of certain viruses (infectious bronchitis virus (ibv), avian encephalomyelitis virus (aev) and infectious bursal disease virus (ibdv)) which typically cause chick mortality. these pathogens infected adult and young pheasants, but the pathogenicity in chick and subadult populations is considerably more serious than in adult birds [29, 30] . in addition, other factors may weaken the population and pathogens become more important. based on these findings, our study focused on pheasant chicks up to eleven weeks of age. previous studies on pheasants indicated that the most sensitive age class for infectious diseases was pheasant chicks, possibly due to a higher susceptibility [30, 31] . the aim of our research was to assess the health state of free-living pheasant chicks in order to check the animals for lesions indicative of infections or toxic substances. the findings should contribute to understanding the causes for the decline in the pheasant population in north-western germany. in 2014 and 2015, the institute for terrestrial and aquatic wildlife research (itaw), university of veterinary medicine hannover, foundation, hannover and the wildlife research institute, state office for nature, environment and consumer protection of north rhine-westphalia caught free-living ring-necked pheasant chicks from lower saxony (cuxhaven, grafschaft bentheim, emsland, osnabrück, vechta), north rhine-westphalia (coesfeld, warendorf) and schleswig-holstein (dithmarschen) to assess the health state by means of pathological, microbiological, virological, parasitological and toxicological investigations. the caught chicks were grouped into three age classes (ac) based on the feather markings of the hand-wings. age class one (ac1) included chicks up to three weeks of age, ac2, chicks from four to six weeks of age and ac3, chicks older than six weeks and up to 11 weeks. an animal experiment permit was obtained from the responsible veterinary office of the lower saxony state office for consumer protection and food safety (laves) (permit number: 33.14-42502-04-14/1486). the study areas comprised 11 hunting regions with 15 traps in lower saxony (hemmoor, meppen, neuenkirchen, osten, strücklingen, vechta, wilsum,)11 regions with 10 traps in north rhine-westphalia (ahlen, dülmen, lippstadt, welte) and 4 districts with 4 traps in schleswig-holstein (warwerort) (fig 1) . the catching period lasted from may until august. in 2014, the investigated chicks were three to 11 weeks old. in 2015, the age of the chicks varied from one-day-old to eleven-week-old chicks. at the age of 11 weeks, the young pheasants were considered as sexually mature. after the catch, the mother hen was released and at maximum, half of the chicks in the trap were taken for analysis (mostly onethree chicks at random). in 2014, the traps had a size of 2.3 m 2 and were covered with iron bars with a mesh-size of 1 cm 2 . in 2015, the traps were slightly adapted based on experience from 2014, using a cover made of loose polyethylene netting with a mesh-size of 1 cm 2 . a piece of string was used as a trigger so that both trap doors closed when the chicks moved forward. corn was used to attract the hen and her chicks. afterwards, the chicks were transported alive to the university of veterinary medicine hannover for examination. the time span from catch to examination took on average about five hours. in 2014, the chicks were stunned by a head blow and killed by exsanguination. in 2015, the chicks were euthanised with an intravenous injection of pentobarbital-sodium (boehringer-ingelheim, ag & co. kg, ingelheim, germany). the nutritional condition score was evaluated macroscopically by the thickness of the pectoral muscles and the body fat percentages as good, moderate, poor or cachectic. as described by curland et al. [29] , animals in a good body condition revealed a vast amount of fatty tissue within the thoracic and abdominal regions, whereas animals with a moderate body condition demonstrated reduced amounts of body fat tissue. animals in a poor body condition possessed only low amounts of fat reserves, these frequently associated with pectoral muscle atrophy. in contrast, cachectic animals lacked fat reserves and exhibited serous atrophy of the coronal myocardial fatty tissue. the necropsy was carried out in accordance with the standard protocol [31] . representative samples of the following tissues and organs were collected, fixed in 10% neutral-buffered formalin and routinely embedded in paraffin wax: the skin of the head and abdomen, skeletal muscle (musculus pectoralis, musculus quadriceps), ischiadic nerve, brachial plexus, nose with infraorbital sinus, eye with lacrimal gland, bone with bone marrow, trachea, thymus, thyroidal gland, lung, heart, liver, pancreas, spleen, kidney, crop, proventriculus, gizzard, intestine, adrenal gland, gonads, bursa of fabricius and brain. paraffin sections of 3-5 μm were stained with haematoxylin and eosin (he) for histological examination. in selected cases, periodic acid schiff (pas) reaction, ziehl-neelsen stain, brown-brenn stain and turnbull's blue stain were performed [32] . for parasitological examinations, samples of the small intestine were collected from all 62 chicks at necropsy. at the same time, skin and plumage of the chicks were macroscopically examined for ectoparasites. for coproscopical examination, the combined sedimentation-flotation method was performed: the faecal sample was filled into a tea strainer (mesh size 1 mm) and rinsed in a beaker with a jet of water. the filtrate containing helminth eggs and protozoan oocysts was allowed to sediment for 30 min. afterwards, the supernatant was decanted and the sediment transferred to a 15-ml centrifuge tube filled with saturated zinc sulphate solution (znso 4 , specific gravity 1.30) and centrifuged at 450 x g for 5 min. the liquid surface was transferred onto a slide with a wire eyelet and examined microscopically. if at least one egg or oocyst was detected, the sample was classified as positive. a semiquantitative classification was applied using the following key: one-two eggs or oocysts were categorised as mild, six-ten eggs or oocysts as moderate, 11-20 eggs or oocysts as severe; if more than 20 eggs or oocysts were detected, the shedding intensity was classified as by mass [29] . the fresh samples, consisting of brain, trachea and caecal tonsils, as well as the bursa of fabricius were placed in rnalater1 (sigma-aldrich chemie gmbh, münchen, germany). samples were analysed by rt-pcr for avian metapneumovirus (ampv), infectious bronchitis virus (ibv), avian encephalomyelitis virus (aev) and by pcr for infectious bursal disease (ibdv) and infectious laryngotracheitis as described in [33, 34] . serum was taken from all birds to check for antibodies against avian influenza virus (aiv) subtypes h5, h7 and h9. eight additional liver samples from chicks with hepatitis were analysed for the presence of haemorrhagic enteritis virus (hev) by pcr [29] . for microbiological investigations for mycoplasma, 13 tracheal swabs, six tracheal tissue samples and three periorbital skin tissue samples were taken [29] . the samples were directly transferred to mycoplasma cultivation medium (sp4). detection of mycoplasma by pcr. for dna extraction, swabs were soaked and rubbed in 350 μl phosphate buffered saline (pbs). using the dneasy 1 blood & tissue kit (qiagen gmbh, hilden, germany) in accordance with the manufacturer's instructions, 100 μl of the liquid was taken for dna extraction. for dna extraction of tissue samples and the single colony subcultures, the fluid medium from culturing (2 ml) was centrifuged at 4000 x g for 45 minutes. the remaining pellet was incubated with 180 μl lysis buffer (atl buffer, qiagen, gmbh) and 20 μl proteinase k (qiagen gmbh) for two hours at 56˚c. all samples and single colony subcultures were screened via mycoplasma-genus-specific pcr (target: 16s rrna gene sequence) for dna of mycoplasma spp. as described by [35] and modified [36] . from all single colony subcultures, an additional pcr (target: 16s-23s rrna sequence (intergenetic transcribed spacer region)) was performed [37] . furthermore, all samples were examined via mycoplasma gallisepticum-specific pcr [38] . the pcr products were sequenced by a commercial dna sequencing service (lgc genomics gmbh, berlin, germany). the sequences of the pcr products were aligned with the 16s rrna gene and 16s-23s rrna isr sequences of mycoplasma spp. in the ncbi database using blast (ncbi, bethesda, md, usa) algorithm [39] . mycoplasma culture. the samples were cultured using sp4 liquid and agar media produced in house as described previously [34] . each sample was immersed in the sp4 broth and afterwards removed and stored for further investigations. the broth was diluted (ten-fold dilution up to 10 −2 ) and an aliquot of 50 μl each was transferred onto agar media. both, liquid and solid media were incubated at 37˚c with 5% co 2 in a humidified environment for up to ten days. broth was examined for colour change and agar plates for colony growth daily. in case of colour change, or after five days, an additional "subculture" on agar media was performed. in case of mycoplasma growth, several single colony subcultures were performed at least twice in order to ensure pure species cultures. each third single colony subculture was stored at -80˚c until further investigation by molecular biological methods [36, 40] . liver samples of nine pheasants were screened for herbicide glyphosate and other pollutants (for details see s1 table) . of these nine samples, one sample was taken from a ten-chick ratchet in ac1, while the remaining eight samples were single-samples from ac3 with liver or kidney inflammation. the samples were stored directly after autopsy at -80˚c. toxicological samples (n = 10), 7 g liver pool samples, were used to detect substances by means of the gas chromatography-mass spectrometry ( during the two-year-period, a total of 62 chicks were caught: 29 birds in lower saxony, 27 in north rhine-westfalia and six in schleswig-holstein. fourteen chicks were allocated to ac1, 16 to ac2 and 32 to ac3. of the investigated animals, 34 were female, 17 male and for 11 chicks, macroscopic gender estimation was unknown; histological samples were not taken. the nutritional status in ac1 was predominantly poor (n = 12; 85.7%) or cachectic (n = 2, 14.3%). in ac2, approximately nine (56.3%) of the chicks were well fed and seven (43.8%) were moderately fed. the majority of birds in ac3 were well fed (n = 25, 78.1%), some were moderately fed (n = 6, 18.8%) and one chick (3.1%) was in a poor body condition (table 1) . to an excessive amount, mild to severe cutaneous abrasions with feather loss, lacerations and/ or subcutaneous haemorrhages of the head were noticed in one out of two chicks (50%) in ac1, nine out of 16 chicks (56%) in ac2 and 11 out of 20 chicks (55%) in ac3 trapped with the tt1. one out of 12 animals (8%) in ac1 and nine out of 12 individuals (75%) in ac3 that had been trapped with tt2 were more mildly affected by those lesions. histological examination of the skin from the head revealed various types of inflammatory alterations which occurred solely or concurrently in one individual (table 2 ). in all age classes and independent of trap type, mainly perivascular predominantly lympho-histiocytic dermatitis admixed with occasional heterophils and plasma cells of varying degrees was present (fig 2) . this type of inflammation was in some cases accompanied by follicular aggregations of lymphocytes sometimes with secondary follicle formation (ac3, tt2). in addition, ulcerative (fig 3) , occasionally necrotising, suppurative and pustular inflammatory changes were found more often in chicks trapped with tt1 than with tt2, these in many cases being associated with dermal and/or subcutaneous haemorrhages of varying degrees. only a few animals showed no cutaneous alteration in this localisation. the abdominal skin of the chicks was rarely affected by perivascular dermatitis; single individuals were mainly affected by lymphohistiocytic or pustular dermatitis. crops, glandular stomachs and gizzards were variably filled (table 3 ). however, it should be noted that the chicks had spent up to five hours in the traps. the mentioned parts of the digestive tract contained grains, green food, and, inside the gizzard, grit stones. in one chick (7%) in ac1, in seven chicks (44%) in ac2 and in ten chicks (31%) in ac3, the quality of the intestinal content was associated with hyperaemic intestinal mucosa and perianal attachment of faeces suggestive of catarrhal enteritis. histologically, one animal (3%) in ac3 showed focally severe ulcerative stomatitis at the gums and one chick in ac3 focally moderate lympho-histiocytic ingluvitis. in single chicks in ac3, nematodes without reactive inflammatory changes were found in the crop. furthermore, single individuals showed erosive and heterophilic inflammation of the gizzard, occasionally associated with intralesional nematodes which were not differentiated here. the intestinal mucosa in all animals showed a mild to moderate infiltration with eosinophils, lymphocytes and a few plasma cells. in eight out of 16 chicks (50%) in ac2 and in four out of 32 chicks (13%) in ac3, reproduction stages of protozoal organisms, most likely coccidia sp., were found histologically within the epithelium (fig 4) . predominantly mild focal lymphohistiocytic hepatitis was observed in one out of 14 chicks (7%) in ac1, in four out of 16 chicks (25%) in ac2, and in ten out of 32 chicks (31%) in ac3. single individuals in ac3 showed multifocal granulomatous hepatitis with severe acute coagulation necrosis (fig 5) . in eight out of 14 chicks (57%) in ac1, a mild to severe diffuse fatty change in hepatocytes was present. nematodes with the morphology consistent with syngamus trachea were found in the trachea of none of the 14 chicks in ac 1, in five out of 16 chicks (31%) in ac2 and in ten out of 32 (31%) chicks in ac3. histologically, tracheal parasitism in most animals was associated with multifocal lympho-histiocytic, occasionally granulomatous or ulcerative tracheitis of variable extent. in single animals, subepithelial lymphoid follicles were found. in the lung, focal or multifocal interstitial, mild to moderate lymphohistiocytic pneumonia was observed in one out of 14 chicks (7%) in ac1, in three out of 16 chicks (19%) in ac2, and in six out of 32 chicks (19%) in ac3. focal or multifocal, mild to moderate granulomatous, occasionally necrotising pneumonia was present in three individuals (19%) in ac2 and in two individuals (6%) in ac3. one animal in ac3 suffered from severe suppurative to necrotising pneumonia. there was no evidence of viral, bacterial, fungal or parasitic agents in these lungs, even in the histological special stains. hyperplasia of bronchus-associated lymphoid tissue was noticed in two chicks (13%) in ac2 and in three chicks (9%) in ac3. numerous lungs showed acute haemorrhages. the kidneys displayed focally mild interstitial infiltrations consisting mainly of lymphocytes and macrophages in two chicks (13%) in ac2 and five chicks (16%) in ac3. independent of the age class, a mostly moderate diffuse infiltration with plasma cells was observed in almost all examined lacrimal glands. miscellaneous findings included focally mild lymphocytic myocarditis in one chick (3%) in ac3 (fig 6) , focally moderate lymphohistiocytic perineuritis (n. ischiadicus) in one chick in both ac2 (19%) and ac3 (3%), severe subacute hyaline degeneration of skeletal muscles with histiocytic infiltration in one chick (3%) in ac3, focal chronic suppurative myositis in another chick (3%) in ac3, and single protozoal cysts, most likely sarcosporidia sp., in the skeletal musculature of two individuals (6%) in ac3 without inflammatory changes. in many brains, perivascular and parenchymatous haemorrhages were observed without reactive changes. of all 62 chicks tested, 8% of the chicks were positive for avian metapneumovirus (ampv) using rt-pcr, 16% positive for infectious bronchitis virus (ibv) using rt-pcr, and 2% for haemorrhagic enteritis virus (hev) using pcr. none of the 37 chicks tested for hev were positive using pcr. tracheae of 33 chicks and caecal tonsils of ten birds were tested by the coronavirus-rt-pcr and were negative for the respective virus. all samples tested for avian encephalomyelitis virus (aev), infectious bursal disease virus (ibdv), or infectious laryngotracheitis virus (iltv) were negative. the pool samples of the ten chicks were completely negative for all acid, alkaline-free and derivative substances as listed in s1 table which summarises the substances tested and the detection limits. two out of three samples tested for the herbicide glyphosate were positive (0.044 mg/kg, 0.095 mg/kg). since the 1970s, a population decrease in ring-necked pheasants has been observed. especially in 2007/2008, the population decline intensified [41] . the present investigation revealed that the randomly trapped pheasant chicks displayed inflammatory lesions in different organs. in association with environmental stressors and a depleted nutritional status, these health changes may increase pheasant chick mortality, thus contributing to the population decrease. the dermatitis detected was often of a non-purulent character, mostly perivascularly accentuated with different cellular compositions of gradual variable infiltrations by lymphocytes, plasma cells and macrophages. especially on the head, this alteration additionally displayed pustular and lymphocytic inflammation. it was possibly itch-or parasite-induced. avian pox was excluded due to lack of pathognomonic and histological changes [42] . these alterations occurred in chicks as young as one or two days of age. six out of 12 chicks (50%) in ac1 already showed these alterations, with different types and degrees of inflammation. m. gallisepticum (mg) is an important etiological differential diagnosis, especially inducing periocular dermal swelling with lymphocytic inflammation [43] . however, this pathogen was ruled out by the investigations. nevertheless, various mycoplasma spp. were isolated in 15 out of 21 (71.4%) of the investigated chicks. however, the role of these mycoplasma spp. as a potential cause of periorbital skin alterations in pheasants is still unclear, but should be considered in following investigations in pheasants. as some birds were rt-pcr positive for ibv or ampv, it has to be elucidated further whether these viruses may have contributed to these lesions, as they are known to be respiratory disease associated. the inflammations might be itch induced following insect or tick bites. furthermore, the head injuries with lacerations and haemorrhages resulted from catching caused by the chicks jumping against the iron bars of the traps. these injuries did not appear anymore after exchanging these bars for loose nylon mesh. a total of 65% of the 26 pneumonia cases were of an eosinophilic character and were most likely caused by syngamus trachea in ten cases. all cases of granulomatous inflammation were free of acid-fast bacteria as shown by the ziehl-neelsen stain. therefore, the cause of this granulomatous inflammation remains unknown. other possible agents able to induce pneumonia, bronchopneumonia, tracheitis and bronchitis were not detected. a prevalent eosinophilia tracheitis (94%) occurred in almost all cases in connection with detected parasites at different stages including coccidia, heterakis/ascaridia spp. and syngamus trachea. the degrees of inflammation were mainly mild up to moderate so that the clinical relevance is rather subordinate. the proventriculitis can have many origins. a histologically similar disease, that of gizzard erosion in broilers is often caused by an interaction between vitamin deficiency, fungal infections and stress situations after consuming mycotoxins. with periodic acid schiff reaction (pas) and brown-brenn stain, fungi, gram-positive and gram-negative bacteria were excluded [44] . as ampv, ibdv, coronavirus and siadenovirus were excluded by pcr, a viral cause is relatively unlikely. marek's disease is doubtful as well due to the lack of other typical organ changes [45] . it is possible that the birds may have been exposed to mycotoxins or pesticides that caused proventriculitis. based on localisation, size and shape of the eggs found in the proventriculus, a nematode-infection with dyspharynx nasuta probably resulted [46] . the inflammation of the livers showed lymphocytic and lymphohistiocytic characters. the causes for these inflammatory changes are manifold and may include infectious as well as noninfectious agents. in three cases, the inflammation was granulomatous and necrotising. using ziehl-neelsen stain, acid-resistant bacteria were excluded. differential diagnoses for granulomatous and necrotising hepatitis include toxic, ischemic or infectious causes [47, 48] . in the presented investigations, only a limited number of samples could be investigated for pesticides. therefore, it is difficult to directly link pathological findings to any of the investigated chemicals. further investigations are needed to elucidate the role played by pesticides in the declining pheasant populations as their habitat is regularly exposed to different chemicals used in agriculture. the main findings in the study were the poor nutritional status in the younger age groups and the increasing occurrence of various inflammation when the birds were ageing. as no direct cause for the inflammation was found and the inflammation affected various organs, it might be more a sign of various pathogens affecting the chicks. this seems to be more a sign of a weakened immune system, unable to defeat facultative pathogenic organisms. this is in line with the poor nutrition status, which triggers the development of diseases. no suspected virus infection was detected though. virus infections cannot be ruled out completely as a cause as viruses obviously circulate in the adult pheasant population and infected chicks die quickly. therefore, such cases were not among the sampled animals as the study focused on live chicks which still followed the hen. due to predation, decomposition and vegetation in the field, diseased pheasants are difficult to retrieve for health examinations and therefore were not included here. concerning parasites, low coccidian infections can be regarded as desirable to build up a protective immunity against reinfections. however, intestinal changes of the chicks show that coccidia sometimes considerably damage the intestinal mucosa due to severe infections, which may lead to a reduction in nutrient uptake. furthermore, a severe syngamus sp. infection can occlude the tracheal lumen, resulting in suffocation of the chicks, or their general condition deteriorates to such an extent that they become easy prey for predators. all these findings point to an effective complexity that either chicks die of starvation or their immune system becomes weakened. it seems that when the effects of maternal antibodies slowly diminish and the chicks have to mobilise their own immune system, the chicks become weakened as their immune system is not sufficiently developed. also, it is known from poultry that the development of the immune system is influenced by nourishment and that malnutrition can negatively influence the immune system [31, 49, 50] . this hypothesis has not been confirmed yet in pheasants. not only pheasants, but also many other farmland birds have to cope with the intensive agricultural landscape. this change in habitat and the use of pesticides make it increasingly difficult to find insects that are vital for the chicks during their first weeks of life. a whole concatenation of circumstances could be explained by this connection; namely, the rather poor nutritional status, a possibly weakened immune system and the increased susceptibility to diseases. additionally, it is possible that the chicks are easier prey for predators due to various inflammations or poor physical condition, too. also, the weather can have a greater influence. supporting information s1 table. toxicological investigation of substances and limits of detection. highlighted in bold are the substances found in the pheasant samples. (docx) s1 data. (pdf) data curation: j. liebing. formal analysis handbuch der vö gel mitteleuropas edition parasitoses of pheasants (phasianus colchicus) in confined system the pheasant: ecology, management and conservation phasianus colchicus) seine naturgeschichte, aufzucht und hege effect of protein levels in the diet on the growth of pheasants early nutrition causes persistent effects on pheasant morphology importance of insect prey quality for grey partridge chicks perdix perdix: a self-selection experiment analyse der rückgangsursachen der fasanenbesätze in niedersachsen. (unpublished) jägerstiftung natur+mensch. institute for terrestrial and aquatic wildlife research retrospektive zum rückgang des fasans agricultural intensification and the collapse of europe's farmland bird populations the second silent spring? farming and birds in europe: the common agricultural policy and its implications for bird conservation eeg stellt kulturlandschaft auf den kopf effects of cropping practices on declining farmland birds during the breeding season responses of plants and invertebrate trophic groups to contrasting herbicide regimes in the farm scale evaluations of genetically modified herbicide-tolerant crops weeds in fields with contrasting conventional and genetically modified herbicide-tolerant crops. i. effects on abundance and diversity influence of autumn applied herbicides on summer and autumn food available to birds in winter wheat fields in southern england the swiss agri-environment scheme promotes farmland birds: but only moderately birds as useful indicators of high nature value farmlands: using species distribution models as a tool for monitoring the health of agro-ecosystems declines in insectivorous birds are associated with high neonicotinoid concentrations host mortality, predation and the evolution of parasite virulence parasites and the dynamics of wild mammal populations differential body condition and vulnerability to predation in snowshoe hares prevalence, intensity and aggregation of intestinal parasites in mountain hares and their potential impact on population dynamics. international host manipulation by parasites in the world of dead-end predators: adaptation to enhance transmission? interactions between sources of mortality and the evolution of parasite virulence investigation into diseases in free-ranging ring-necked pheasants (phasianus colchicus) in northwestern germany during population decline with special reference to infectious pathogens effects of early feeding and dietary interventions on development of lymphoid organs and immune competence in neonatal chickens: a review romeis mikroskopische technik kompendium der geflü gelkrankheiten modified live infectious bursal disease virus (ibdv) vaccine delays infection of neonatal broiler chickens with variant ibdv compared to turkey herpesvirus (hvt)-ibdv vectored vaccine experimental haematobiochemical alterations in broiler chickens fed with t-2 toxin and co-infected with ibv prevalence of mycoplasmas in eggs from birds of prey using culture and a genus-specific mycoplasma polymerase chain reaction genus-and species-specific identification of mycoplasmas by 16s rrna amplification high inter-species and low intra-species variation in 16s-23s rdna spacer sequences of pathogenic avian mycoplasmas offers potential use as a diagnostic tool das vorkommen von mykoplasmen bei storchnestlingen in brandenburg und sachsen-anhalt basic local alignment search tool recovery of mycoplasmas from birds wild und jagd-landesjagdbericht 2010/2011. ni ministerium für ernä hrung, landwirtschaft, verbraucherschutz und landesentwicklung a retrospective studie of skin lesions in wild turkeys (meleagris gallopavo) in the eastern usa, 1975-2013 mycoplasma gallisepticum in pheasants and the efficacy of tylvalosin to treat the disease hard af segerstad c. mycotic proventriculitis in gray partridges (perdix perdix) on two game bird farms causes of gizzard erosion and proventriculitis in broilers first report of five nematode species in phasianus colchicus linnaeus (aves, galliformes, phasianidae) in brazil / primeiro registro de cinco espécies de nematóides em phasianus colchicus linnaeus (aves, galliformes, phasianidae) no brasil necrotizing hepatitis in a domestic pigeon (columba livia) hepato nephropathology associated with inclusion body hepatitis complicated with citrinin mycotoxicosis in a broiler farm early nutrition programming (in ovo and posthatch feeding) as a strategy to modulate gut health of poultry nutrition-mechansims of immunosuppression we wish to thank the hunting associations of lower saxony, north rhine-westphalia and schleswig-holstein for supporting the study. furthermore, special thanks go to the laboratory personnel for their excellent technical assistance in the laboratory investigations. key: cord-279557-hk77e3pp authors: drosten, christian; seilmaier, michael; corman, victor m; hartmann, wulf; scheible, gregor; sack, stefan; guggemos, wolfgang; kallies, rene; muth, doreen; junglen, sandra; müller, marcel a; haas, walter; guberina, hana; röhnisch, tim; schmid-wendtner, monika; aldabbagh, souhaib; dittmer, ulf; gold, hermann; graf, petra; bonin, frank; rambaut, andrew; wendtner, clemens-martin title: clinical features and virological analysis of a case of middle east respiratory syndrome coronavirus infection date: 2013-06-17 journal: lancet infect dis doi: 10.1016/s1473-3099(13)70154-3 sha: doc_id: 279557 cord_uid: hk77e3pp background: the middle east respiratory syndrome coronavirus (mers-cov) is an emerging virus involved in cases and case clusters of severe acute respiratory infection in the arabian peninsula, tunisia, morocco, france, italy, germany, and the uk. we provide a full description of a fatal case of mers-cov infection and associated phylogenetic analyses. methods: we report data for a patient who was admitted to the klinikum schwabing (munich, germany) for severe acute respiratory infection. we did diagnostic rt-pcr and indirect immunofluorescence. from time of diagnosis, respiratory, faecal, and urine samples were obtained for virus quantification. we constructed a maximum likelihood tree of the five available complete mers-cov genomes. findings: a 73-year-old man from abu dhabi, united arab emirates, was transferred to klinikum schwabing on march 19, 2013, on day 11 of illness. he had been diagnosed with multiple myeloma in 2008, and had received several lines of treatment. the patient died on day 18, due to septic shock. mers-cov was detected in two samples of bronchoalveolar fluid. viral loads were highest in samples from the lower respiratory tract (up to 1·2 × 10(6) copies per ml). maximum virus concentration in urine samples was 2691 rna copies per ml on day 13; the virus was not present in the urine after renal failure on day 14. stool samples obtained on days 12 and 16 contained the virus, with up to 1031 rna copies per g (close to the lowest detection limit of the assay). one of two oronasal swabs obtained on day 16 were positive, but yielded little viral rna (5370 copies per ml). no virus was detected in blood. the full virus genome was combined with four other available full genome sequences in a maximum likelihood phylogeny, correlating branch lengths with dates of isolation. the time of the common ancestor was halfway through 2011. addition of novel genome data from an unlinked case treated 6 months previously in essen, germany, showed a clustering of viruses derived from qatar and the united arab emirates. interpretation: we have provided the first complete viral load profile in a case of mers-cov infection. mers-cov might have shedding patterns that are different from those of severe acute respiratory syndrome and so might need alternative diagnostic approaches. funding: european union; german centre for infection research; german research council; and german ministry for education and research. in june, 2012, a coronavirus belonging to a group of viruses that had previously only been detected in bats was cultured from respiratory secretions of a patient who had died from severe acute respiratory infection. 1 the same agent was retrospectively detected in clinical samples from a hospital outbreak of severe acute respiratory infection that occurred in jordan in april, 2012, marking the fi rst known occurrence of the virus in people. 2 the agent has been named middle east respiratory syndrome coronavirus (mers-cov). 3 as of june 10, 2013, 55 laboratory-confi rmed cases had been reported in jordan, saudi arabia, the uk, france, italy, germany, and tunisia. 3 31 individuals with laboratory-confi rmed infection had died. few virological data have become available for mers-cov cases, and there is no information about the viral genome sequence, which could identify important epidemiological characteristics. [4] [5] [6] here, we provide a full description of a fatal case of mers-cov infection imported to munich, germany, from abu dhabi, including a chronological profi le of virus concentrations in diverse body compartments. we fully sequenced the mers-cov genome, and therefore could do a chronologically calibrated phylogenetic analysis with all available mers-cov genome sequences. these data were complemented by novel sequence data from an unlinked case treated in germany in 2012. 7, 8 we report data for a patient who was admitted to the klinikum schwabing (munich, germany) in march, 2013. investigation was done as part of a public health intervention according to the german infection protection act. written consent for scientifi c assessment was obtained from the patient's spouse as part of the patient treatment contract. we did diagnostic rt-pcr and indirect immunofl uorescence, following who recom mendations. 7, 9 for serum neutralisation tests, we grew vero b4 cells to subconfl uence in 24-well plates. pre-incubation reactions contained 25 plaque-forming units of mers-cov (emc strain) in 100 μl of medium, mixed one-to-one with serum samples from the patient prediluted in medium. the starting dilution was a tenth. after 1 h incubation at 37°c, each well was infected for 1 h at 37°c with the total 200 μl pre-incubation reaction. supernatants were removed and overlaid with avicell resin as described by herzog and colleagues. 10 assays were terminated and stained after 3 days. we defi ned neutralisation titres as the serum dilution reducing the number of plaques in four parallel wells in summary by greater than 90%. antibodies were tested by immunofl uorescence assay. 7 all clinical materials stored in the ward and laboratories were gathered and submitted for virological diagnostic tests. from the time of laboratory diagnosis, respiratory, faecal, and urine samples were obtained. we designed two diff erent sets of primers generating overlapping amplicons (available on request). the fi rst set consisted of 70 amplicons, 386-800 bp in length, with all primers containing two strong watson-crick bps at their 3 ends, so as to bind the template with high affi nity. the second set consisted of 68 amplicons, 415-761 bp in length, with primers that had no more than two strong bps in their fi ve 3 terminal nucleotides and no strong pairings in the two 3 positions. this method of primer design can decrease sensitivity, but it prevents mispriming within the product, which can improve the success of amplifi cation. after rt-pcr, we sequenced all fragments on a roche 454 junior instrument (roche, penzberg, germany) and assembled in geneious (version 6.1.2). virus quantifi cation was done with standard calibration curves that were based on quantifi ed in-vitro transcribed rna for the upe target gene. 9 we constructed a maximum likelihood tree of the fi ve available complete mers-cov genomes with phyml 11 and the gtr+gamma model of molecular evolution; we assessed phylogenetic support with 1000 bootstrap replicates. we inferred a timescale by linear regression of genetic divergence from the root against time of collection of the samples. the root was placed such that the correlation coeffi cient was maximised. a phylogenetic tree based on all available mers-cov sequences was calculated with phyml 11 on a concatenated 4012 bp dataset with the hky substitution model. reduction of the dataset was determined by the small number of sequence fragments that could be retrieved from a stored clinical sample containing a small amount of the virus, derived from a patient treated in essen, germany. the sponsors of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report. the corresponding authors had full access to all the data in the study and fi nal responsibility to submit for publication. on march 8 (day 0), the patient-a 73-year-old man from abu dhabi, united arab emirates-abruptly developed fl u-like symptoms, with fever and non-productive cough. he was admitted to mafraq hospital (abu dhabi) on day 2 (fi gure 1), and was diagnosed with pneumonia. he was intubated on day 9 because of progressive hypoxia and acute respiratory distress syndrome (fraction of inspired oxygen 60%; positive end-expiratory pressure 10 cm h 2 o). the patient had received intensive antimicrobial treatment with meropenem, levofl oxacin, vancomycin, caspofungin, aciclovir, and oseltamivir during his stay in an intensive care unit in abu dhabi, without major improvement in his pulmonary function. the patient was transferred to klinikum schwabing (munich, germany) on march 19, 2013 (fi gure 1). the patient had been diagnosed with multiple myeloma in 2008, and had received several lines of treatment in the previous few years, such as high-dose chemotherapy with autologous stem-cell transplantation in 2009. at relapse of his multiple myeloma in november, 2012, he was given lenalidomide plus dexamethasone. relatives reported that the patient owned camels, and had taken care of a diseased animal shortly before onset of symptoms. no animal samples, or further details about potential sources or exposures could be retrieved. during his stay in munich, we recorded thrombocytopenia (table 1) . thrombocytopenia was also reported in the fi rst described case of mers-cov infection, 1 in two of four patients from a family cluster in saudi arabia, 12 and in the two cases reported from france. 5 the patient developed renal insuffi ciency on day 14, and required dialysis. despite continuous invasive ventilation and antibiotic treatment, the patient's health status deteriorated. death occurred on day 18 and was due to septic shock, with signs of haemolysis and acute coagulation disorder (fi gure 1, table 1). after hospital admission in munich, infection with mers-cov was suspected on the basis of treatment-refractory acute respiratory distress syndrome, combined with the geographical origin of the patient. bronchoalveolar fl uid was obtained on march 20 and 22 (days 12 and 14). mers-cov was detected in both samples by rt-pcr. we also detected herpes simplex virus type 1 dna 13 (6·4 × 10⁴ to 1·9 × 10⁷ copies per ml) and rhinovirus rna 14 (3·7 × 10⁵ to 2·1 × 10⁹ copies per ml) by (rt-)pcr in both samples. mers-cov rna concentrations in respiratory samples ranged from 933 to 1·2 × 10⁶ genome copies per ml. virus concentrations seemed to be higher in samples taken earlier in the course than in those obtained later (fi gure 2). concentrations were more variable in tracheobronchial samples than in bronchoalveolar lavage samples (fi gure 2), which was ascribed to variation in volumes of saline solution applied during removal of tracheobronchial samples. notably, suction catheters without opening at point of care and stored for as long as 5 days at 8°c in a refrigerator in the intensive care unit tested consistently positive but yielded up to roughly 3·5log 10 lower rna concentrations than did those in fresh tracheobronchial aspirates taken on the same days (fi gure 2). immunofl uorescence assays yielded endpoint titres on day 16 of infection (table 2 ). an igm-specifi c immunofl uorescence assay confi rmed recent infection in the same serum sample (table 2) . plaque-reduction neutralisation test confi rmed mers-cov specifi city of detected antibody titres (table 2) . these titres were somewhat lower than those recorded for serum samples from an unlinked non-fatal case of mers-cov treated in germany in 2012. 8 serum samples from this patient had been taken later than they were for our patient (table 2) . we tested two urine samples on day 12, one on day 13, and one on day 16. one of the two samples on day 12, and the sample from day 13 were positive, meaning that the virus was not present in urine after renal failure (day 14), with a maximum virus concentration of 2691 rna copies per ml on day 13. both stool samples obtained on day 12 and the fi ve on day 16 were positive, with up to 1031 rna copies per g, which is a concentration close to the lowest detection limit of the assay. we recorded a low virus concentration in one of two oronasal aspirate samples taken from the intubated patient on day 16 (5370 copies per ml). one dialysate sample and two serum samples on day 16 , and one serum sample on day 18 were negative. although we obtained several isolates for the herpes simplex virus type 1, repeated attempts to isolate mers-cov were unsuccessful. herpes simplex virus is a frequent bystander infection in intubated patients, and is known to not aff ect the cardiorespiratory prognosis and outcome. 15 we sequenced the full mers-cov genome directly from respiratory samples (genbank accession number kf192507). we subjected all available mers-cov genome sequences to phylogenetic analysis, including a correlation and regression analysis of known dates of virus isolation versus tree branch lengths (fi gure 3). we estimated the rate of evolution as 1·6 × 10 -³ substitutions per site per year. the time of the common ancestor of all fi ve viruses for which genomes are available was halfway through 2011 (fi gure 3). the virus in our patient clustered with a sequence from a virus imported into the uk from qatar. 16 to compare this sequence with that of another virus from the same region, we reanalysed a stored clinical sample from another case of mers-cov infection imported into germany in october, 2012. this sample contained low concentrations of rna, so the genome of the virus had not been successfully sequenced previously. 8 after many attempts to recover rt-pcr fragments from the available bronchoalveolar lavage sample, we could sequence 12 fragments, covering 4012 nucleotides of the mers-cov genome (genbank accession number kc875821). a concatenated alignment of homologous sequence portions of all available mers-cov sequences was subjected to phylogenetic analyses, confi rming a clustering of sequences from qatar and the united arab emirates (fi gure 3). a sequence from a patient with a history of travel to pakistan and saudi arabia branched next to this cluster. during and up to 10 days after the course of treatment, 14 health-care workers who had direct contact with our patient or patient-derived materials reported mild respiratory symptoms. samples were taken from the upper respiratory tract and tested by two diff erent rt-pcr assays for mers-cov. none yielded positive results. by contrast, one patient who had had direct contact with the patient with mers-cov was infected with hcov-nl63, a common human coronavirus, and four patients were infected with rhinoviruses. these rhinoviruses were not all mutually related, and none was related to the rhinovirus detected in the patient with mers-cov (appendix). follow-up of all contact patients, including investigation for subclinical infections, is in progress. we have outlined the chronological follow-up of a patient with mers-cov, in which we used quantitative virological diagnostic tests (panel). viral loads were highest in the lower-respiratory tract. the viral sequence from this patient clustered with sequences from nearby qatar. laboratory data are crucial for diagnostic recommendations, to make projections about prognosis, and to estimate infection risks. without quantitative laboratory data from well documented cases of mers-cov infection, most considerations had been made on the basis of an assumed analogy to severe acute respiratory syndrome (sars). 12, [18] [19] [20] however, elementary traits of the virus, such as its receptor usage and sensitivity to type i and type iii interferon, diff er substantially from that of the sars coronavirus, suggesting that diff erences in disease patterns (eg, in organ tropism or in virus shedding) might exist. [21] [22] [23] [24] [25] we focused on these aspects with quantitative virus testing in all relevant body compartments, including viral loads in non-respiratory samples. 5, 12 however, our patient-like most other cases anecdotally reported so far-had an underlying disease that could aff ect virus shedding patterns. only analysis of a large number of patients can yield general fi gures about qualitative virus data. faecal shedding was of particular interest, because patients with sars regularly showed high virus concentrations and prolonged virus excretion in stools that led to the use of stool samples, even for routine sars diagnostic tests. 18, 20, 26 diarrhoea was reported in two descriptions of mers-cov clusters, and it was speculated that faecal virus shedding might have occurred. 5, 12 however, no laboratory data for virus in stool samples were provided. our patient had low faecal virus concentrations that were close to the lowest detection limit on days 12 and 16 of illness. in the only other description so far, one stool sample from a patient with mers-cov had a negative result. 16 stool samples from many patients, including those with early stages of disease, should be tested to assess whether faecal sources could have a role in transmission, or whether mers-cov diff ers from sars in this aspect. another important fi nding was that we recorded low concentrations of virus in urine samples. this fi nding is surprising, because early kidney failure during the course of mers-cov infection has been reported, and kidney cells in laboratory models are highly permissive for mers-cov replication. 5, 12, 23 the fact that the virus was present in urine but not in the blood suggests autonomous virus replication in the kidneys, potentially without active secretion of virus into the urine. however, renal failure due to specifi c viral infection or immunopathogenesis is not necessarily indicated, because the patient had received several doses of potentially nephrotoxic antimicrobial agents in a setting of underlying multiple myeloma. post-mortem examinations are urgently needed to clarify whether kidney failure in mers-cov infection is a primary and preventable result of viral infection, or a secondary complication of severe systemic disease. 27, 28 quantitative virus data are needed to orient diagnostics and hospital infection control measures. the recorded viral load profi le, with highest rna concentrations in bronchoalveolar lavage and tracheobronchial aspirates, confi rms suggestions made in another report about the preferential use of lower-respiratory-tract samples for virus diagnostic tests. 5 notably, the reported overall stability of detectable virus rna in closed suction catheters indicates a straightforward and non-contagious way to collect diagnostic samples even from non-intubated patients. oronasal swabs should not be preferentially submitted for testing, especially in patients presenting late in their disease course with substantial lower respiratory involvement. 5 our data for stool, urine, and blood samples suggest a fairly low infection risk during non-respiratory care procedures. the absence of detectable virus in blood matches reports made in an earlier case of mers-cov infection. 16 however, guery and colleagues 5 reported low semi-quantitative virus measurements in the blood of one of their patients. moreover, initial experimental studies suggested that mers-cov infected vascular endothelial cells. 25 however, quantitative data suggest a low risk from general laboratory procedures involving blood. by contrast, the low virus concentrations and failure to isolate infectious virus from respiratory secretions should not be taken as a general indication of airway-associated infection risks. virological monitoring of the patient started only late in the disease course, at a time when the infectiousness of the virus could already have been reduced (as suggested by the occurrence of neutralising antibodies). the fact that we could not isolate mers-cov could have been due to the concomitant presence of herpes simplex virus type 1, which overgrew some of the diagnostic cell cultures. we searched pubmed for reports published in english at any time before june 7, 2013. we used the search term "mers-cov or hcov-emc". we identifi ed 29 reports linked to middle east respiratory syndrome coronavirus (mers-cov), starting with zaki and colleagues' initial report, 1 in which a previously unknown coronavirus isolated from the sputum of a 60-year-old man is described. when we used the search term "mers-cov", we identifi ed four reports, 2,5,12,17 none of which provided quantitative viral load profi les of infected patients. our report provides the fi rst complete viral load profi le in a case of mers-cov infection. the distribution of viral loads in the respiratory tract suggests lower-respiratory-tract samples should be taken preferentially. low concentrations of the virus in stool, urine, and blood samples suggests little virus excretion-at least in our patient-from body compartments other than the respiratory tract. furthermore, coronaviruses that infect people are generally diffi cult to isolate, particularly in late phases of disease. only two successful isolations of mers-cov have been reported worldwide so far. 1, 5 these isolations were done on day 4 of disease, 5 and day 7 of disease. 1 our samples were taken on days 12 and 14, and the sample from day 12 was stored for 3 days before cell culture. isolation success cannot provide any information about infectiousness of the patient. even a highly concentrated rhinovirus does not seem to have been transmitted from the patient, suggesting that eff ective protective measures were in place during treatment of the intubated patient in the intensive care unit. the sequence data from this and another patient treated in germany enable an extended analysis of phylogeny, hinting at a geographical structure of the mers-cov tree. specifi cally, viral sequences from the eastern part of the arabian peninsula cluster together and stem from one common ancestor whose date of existence is projected to be after that of viruses from jeddah and jordan. date estimates will probably be refi ned when more sequences become available. moreover, whether the reported geographical structure represents repeated transfer from a geographically structured viral reservoir population and limiting chains of person-to-person transmission or multiple sustained lineages of human infections is unclear. with only fi ve complete genome sequences available as yet, genetic data are urgently needed to establish the spatial and temporal distribution of cases, estimate the number of independent human chains of transmission, and thus better assess the threat that mers-cov poses to world health. four sequences from a continuing hospital outbreak in al-hasa, saudi arabia, have now been deposited in genbank. preliminary phylogenetic analyses confi rm the clustering of viruses from the eastern part of the arabian peninsula (qatar: strains england2 and essen; abu dhabi: strain munich; al-hasa: genbank accession numbers kf186564-kf186567). cd designed the virological studies, phylogenetic analysis, and virological data analysis. ms, whar, gs, ss, wg, hgu, tr, ms-w, fb, and c-mw contributed to clinical data generation and analysis. ms, vmc, rk, dm, sj, and ar contributed to fi gures. vmc, rk, dm, sj, mam, sa, and ud generated and analysed virological data. ar did phylogenetic analysis. cd, whaa, hgo, and c-mw interpreted data. cd, ms, vmc, fb, ar, and c-mw wrote the report. whaa advised the public health intervention. hgo and pg coordinated the public health intervention. we declare that we have no confl icts of interest. isolation of a novel coronavirus from a man with pneumonia in saudi arabia middle east respiratory syndrome coronavirus (mers-cov); announcement of the coronavirus study group middle east respiratory syndrome 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respiratory herpes simplex virus type 1 infection/colonisation in the critically ill: marker or mediator? severe respiratory illness caused by a novel coronavirus genetic characterization of betacoronavirus lineage c viruses in bats revealed marked sequence divergence in the spike protein of pipistrellus bat coronavirus hku5 in japanese pipistrelle: implications on the origin of the novel middle east respiratory syndrome coronavirus the severe acute respiratory syndrome the aetiology, origins, and diagnosis of severe acute respiratory syndrome identifi cation of a novel coronavirus in patients with severe acute respiratory syndrome effi cient replication of the novel human betacoronavirus emc on primary human epithelium highlights its zoonotic potential dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-emc human coronavirus emc does not require the sars-coronavirus receptor and maintains broad replicative capability in mammalian cell lines human cell tropism and innate immune system interactions of human respiratory coronavirus emc compared to those of severe acute respiratory syndrome coronavirus tropism of and innate immune responses to the novel human betacoronavirus lineage c virus in human ex vivo respiratory organ cultures severe acute respiratory syndrome multiple organ infection and the pathogenesis of sars acute renal impairment in coronavirus-associated severe acute respiratory syndrome this work was supported by a european research project on emerging diseases detection and response (emperie; contract no 223498). cd has received infrastructural support from the german centre for infection research, which included full funding of the position of vc. virological analyses were partly support by the german ministry for key: cord-255465-sc1yzzsn authors: krasteva, gabriela; pfeil, uwe; drab, marek; kummer, wolfgang; könig, peter title: caveolin-1 and -2 in airway epithelium: expression and in situ association as detected by fret-clsm date: 2006-08-11 journal: respir res doi: 10.1186/1465-9921-7-108 sha: doc_id: 255465 cord_uid: sc1yzzsn background: caveolae are involved in diverse cellular functions such as signal transduction, cholesterol homeostasis, endoand transcytosis, and also may serve as entry sites for microorganisms. hence, their occurrence in epithelium of the airways might be expected but, nonetheless, has not yet been examined. methods: western blotting, real-time quantitative pcr analysis of abraded tracheal epithelium and laser-assisted microdissection combined with subsequent mrna analysis were used to examine the expression of cav-1 and cav-2, two major caveolar coat proteins, in rat tracheal epithelium. fluorescence immunohistochemistry was performed to locate caveolae and cav-1 and -2 in the airway epithelium of rats, mice and humans. electron-microscopic analysis was used for the identification of caveolae. clsm-fret analysis determined the interaction of cav-1α and cav-2 in situ. results: western blotting and laser-assisted microdissection identified protein and transcripts, respectively, of cav-1 and cav-2 in airway epithelium. real-time quantitative rt-pcr analysis of abraded tracheal epithelium revealed a higher expression of cav-2 than of cav-1. immunoreactivities for cav-1 and for cav-2 were co-localized in the cell membrane of the basal cells and basolaterally in the ciliated epithelial cells of large airways of rat and human. however, no labeling for cav-1 or cav-2 was observed in the epithelial cells of small bronchi. using conventional double-labeling indirect immunofluorescence combined with clsm-fret analysis, we detected an association of cav-1α and -2 in epithelial cells. the presence of caveolae was confirmed by electron microscopy. in contrast to human and rat, cav-1-immunoreactivity and caveolae were confined to basal cells in mice. epithelial caveolae were absent in cav-1-deficient mice, implicating a requirement of this caveolar protein in epithelial caveolae formation. conclusion: these results show that caveolae and caveolins are integral membrane components in basal and ciliated epithelial cells, indicating a crucial role in these cell types. in addition to their physiological role, they may be involved in airway infection. caveolae are omega-shaped invaginations of the plasma membrane measuring 50 to 100 nm in diameter. they are found in numerous cell types such as type i pneumocytes, endothelial cells, adipocytes, fibroblasts, smooth muscle cells, cardiac and striated muscle cells [1] . caveolar formation is dependent on the expression of caveolins. three caveolins (cav) are known. cav-1 and cav-2 are widely expressed, whereas cav-3 is thought to be restricted to muscle cells [2] . cav-1 is expressed in two isoforms, cav-1α and cav-1β, exhibiting a cell type-specific distribution (endothelial vs. alveolar type-1 cells) in the alveolar region [3] . caveolae are involved in diverse cellular functions such as organizing signal transduction mechanisms, endocytosis and intracellular transport [2] . several pathogenic microorganisms selectively use caveolae to enter cells [4] . after accumulation in the caveolae, they are delivered to the endoplasmatic reticulum bypassing the classical endosome-lysosome trafficking and thereby preventing inactivation [5, 6] . it has been shown that the infectivity of ctype human adenovirus can be greatly reduced by the expression of a dominant negative cav-1 mutant in plasmocytic cells [7] , indicating that caveolae are involved in this process. in addition, it was recently shown for chlamydia pneumoniae that it co-localizes intracellularly with cav-1 and cav-2 after infection, and a role of these proteins for the developmental cycle of chlamydiae is discussed [8] . also, the human coronavirus 229e that is known to induce respiratory tract infections enters cells via a caveolae dependent mechanism [9, 10] . although the airway epithelium serves as entry site for microbes, fulfils functions that are associated with caveolae such as endo-and transcytosis, and harbors receptors that are associated with caveolae [1] , the expression of caveolins, their interaction, and the presence of caveolae in tracheal and bronchial epithelial cells have not yet been determined. interestingly, the presence of "vesicles that sometimes are connected with the membrane" has earlier been described at the electron-microscopic level in mouse basal cells [11] . moreover cav-1 and cav-2 were detected in cell lines derived from bronchial epithelium [12] , pointing to the presence of caveolae in the airway epithelium. both cav-1 and cav-2 exhibit a similar expression, but seem to have different functions. cav-1 is sufficient to drive caveolar formation [13] . in general, it is thought that cav-2 alone is not sufficient for caveolae formation, and the absence of caveolae in cav-1-deficient mice is associated with marked reduction in cav-2 levels [14] . in contrast, although caveolae are still present in cav-2 deficient mice, these mice show the marked pathological alveolar phenotype of cav-1 deficient mice [15] . this indicates that cav-2, although not able to form caveolae on its own, has profound influences on caveolar function. since a selective association of cav-2 but not cav-1 was described with chlamydia species other than chlamydia pneumoniae it is likely that both proteins can have divergent functions during infectious processes making it necessary to examine the presence and localization of both proteins. in view of these facts, it is pivotal to gain insight in the cellular expression of caveolae and caveolins in bronchial and tracheal epithelium. we therefore examined the expression of cav-1 and cav-2 on the mrna and protein level, determined the distribution of cav-1α, cav-1β, and cav-2 by immunohistochemistry and examined the presence of caveolae by electron microscopy. to address the molecular composition of caveolae, we determined the molecular association of cav-1α and cav-2 in tracheal epithelial cells in tissue sections by double-labeling indirect immunofluorescence combined with confocal laser scanning microscopy (clsm) and fluorescence resonance energy transfer (fret) analysis. this study was performed on 1) wistar rats (150-250 g) of either sex, kept either under standard laboratory conditions or under specified pathogen-free (spf) conditions, and 2) cav-1-deficient mice [14] and the corresponding c57/bl6 wild-type mice that were kept under spf conditions. the animals were held according to the german guidelines for the care and use of laboratory animals. they were killed by inhalation of an overdose of isoflurane (abbott, wiesbaden, germany). total rna from abraded tracheal epithelial cells of adult wistar rats (n = 6) was isolated by using the rneasy method according to the manufacturer'sprotocol (qiagen, hilden, germany). the epithelial cells from the trachea were abraded using cotton swabs that were carefully rolled over the epithelial layer. contaminating dna was degraded using 1 u dnase-i (invitrogen, karlsruhe, germany) per µg of total rna, and reverse transcription was done for 50 min at 42°c using 200 u superscript ii reverse transcriptase (invitrogen) per µg of rna. rt-pcr was performed by adding 1 µl cdna, 0.5 µl of each genespecific intron-spanning primer pair for cav-1 or cav-2 (20 pm; mwg biotech, ebersberg, germany, total rna was isolated from abraded tracheal epithelial cells of rats (n = 6, spf; n = 3, standard conditions) and reverse-transcribed as described above. real-time pcr was performed in an i-cycler (bio-rad, munich, germany) using a quantitec sybr green pcr kit (qiagen). primer sets for cav-1 and -2 amplifying the sequences corresponding to nucleotides 25-147 and 392-497, respectively, were used ( table 1 ). the pcr conditions included initial denaturation in one cycle of 10 min at 95°c followed by 40 cycles of 20 s at 95°c, 20 s at 59°c, and 20 s at 72°c. all analyses were done in triplicate. as a basis for the relative mrna quantification, the mean cycle thresholds (ct) for cav-1 and cav-2 were calculated. the corresponding threshold cycles of the target gene were subtracted from mean β-mg-ct according to: the relative expression (re) of cav-2 compared to that of cav-1 was calculated as follows: the pcr products were analyzed by electrophoresis on a 2% tris-acetate-edta agarose gel. laser-assisted microdissection (using a microbeam system, p.a.l.m. microlaser technologies, bernried, germany) was used to isolate epithelial cells from cryosections of tracheae of rats (spf, n = 6; normal conditions, n = 2). serial cryosections (6 µm) were collected on membrane slides (p.a.l.m. microlaser technologies), previously radiated with uv-light (254 nm) for 30 min. for each cup, the amount equal to 50% of the epithelium of a transverse section of a trachea was collected within 2 h after preparing the sections. rna isolation and purification were performed using rneasy micro kit (qiagen) according to the manufacturer's protocol, but omitting the dna digestion step. ten µl rna were incubated at 70°c for 10 min. rt-mix was added (2 µl 10 × pcr buffer ii, 100 mm tris-hcl, 500 mm kcl, ph 8.3; 4 µl mgcl 2 , 25 mm; 1 µl dntps, 10 mm; 1 µl random hexamers, 50 mm; 0.5 µl rnase inhibitor, 20 u/µl; 1 µl mulv reverse transcriptase, 50 u/µl; 0.5 µl h 2 o; all reagents from applied biosystems). rna was reverse-transcribed for 75 min at 43°c, followed by inactivation of the reverse transcriptase by heating the rna samples for 5 min at 99°c. for subsequent pcr, 4 µl cdna, 2.5 µl 10 × pcr buffer ii, 2 µl mgcl 2 (15 mm), 0.5 µl dntps (10 mm), 0.5 µl of each primer (20 pm; primer sets spanning the region 25-147 for cav-1 and 392-497 for cav-2), 0.2 µl amplitag gold polymerase (5 u/µl, all reagents from applied biosystems) and 14.8 µl h 2 o were applied. cycling conditions were 4 min at 95°c, 50 cycles with 20 s at 95°c, 20 s at 59°c, 20 s at 73°c, and a final extension at 73°c for 7 min. to control for smearing of rna during the cutting procedure, areas of dried o.c.t. compound (sakura, zoeterwoude, the netherlands) similar in number and size to the samples of picked epithelial cells and directly adjacent to the luminal side of the tracheal epithelium were applied. control reactions for each primer pair included the absence of template. the pcr products were separated by electrophoresis on a 2% tris-acetate-edta agarose gel. sequencing of the pcr products was done by mwg biotech. antibodies and their sources were as follows: anti-caveolin-1α (anti-cav-1α; immunohistochemistry (ihc) 1:400, western blotting (wb) 1:500), polyclonal from rabbit (sc-894; santa cruz biotechnology, heidelberg, germany); anti-caveolin-1αβ (anti-cav-1αβ; ihc 1:200; wb 1:500), monoclonal from mouse (clone 2297; transduction laboratories, heidelberg, germany); anti-caveolin-2 (anticav-2; ihc 1:200), monoclonal from mouse (clone 65; transduction laboratories); anti-endothelial nitric oxide synthase (anti-enos; ihc 1:100), monoclonal from mouse (clone 3; transduction laboratories); anti-surfactant protein d (anti-sp-d; ihc 1:100), monoclonal from mouse (clone vi f11, dianova, hamburg, germany), anti-villin, polyclonal from rabbit (ihc 1:2,000, [16] ). secondary antibodies used in this study for immunohistochemistry were: fitc-conjugated donkey antimouse-lg, f(ab') 2 fragments (1:200; dianova), cy3-conjugated donkey anti-rabbit-ig (1:2,000; chemicon, temecula, ca, usa), cy5-conjugated donkey anti-rabbit-ig, f(ab') 2 fragments (1:50; dianova), and cy3-conjugated donkey anti-mouse-ig (1:1,000; dianova). secondary antibodies used in this study for western blotting were: horseradish peroxidase-conjugated goat anti-rabbit-igg or horseradish peroxidase-conjugated goat anti-mouse-igg (both 1:10,000; pierce, rockford, usa). for conventional electron microscopy, tracheae of wistar rats (normal conditions, n = 2), cav-1 deficient mice (spf, n = 2), and c57/bl6 mice (spf, n = 3) were prepared as follows: the vascular system was flushed via the ascending aorta with a rinsing solution containing heparin (2 ml/l; 10,000 u; ratiopharm, ulm, germany), polyvinylpyrrolidone (25 g/l, mw 40.000; roth, karlsruhe, germany) and procaine hydrochloride ( unfixed tissue of wistar rats, cav-1-deficient mice (spf, n = 2), wild-type mice (spf, n = 2), and 10% neutral formalin-fixed and paraffin-embedded human bronchi (n = 4) were used for immunohistochemical analysis. lungs from rats and mice were inflated via the trachea with o.c.t. compound diluted with an equal amount of 0.1 m phosphate buffer (ph 7.4), orientated on a piece of filter paper, and shock-frozen in melting isopentane. cryosections (10 µm) were cut, fixed (either with acetone at -20°c and air dried for 10 min or with 4% pfa for 20 min and washed) and incubated for1 h in 5% normal goat serum containing 5% bsa in 0.005 m phosphate-buffered saline (pbs). primary antibodies were diluted in 0.005 m phosphate buffer containing 0.01 % nan 3 and 4.48 g/l nacl and applied overnight at room temperature. these antibodies were appliedeither singly or in combination for doublelabeling immunofluorescence. primary antibody combinations were as follows: mouse anti-cav-1αβ/rabbit anticav-1α; mouse anti-cav-2/rabbit anti-cav-1α; mouse anti-enos/rabbit anti-cav-1α; mouse anti-sp-d/rabbit anticav-1α; mouse anti-cav-2/rabbit anti-villin. after a washing step, cy3-conjugated donkey anti-rabbit-ig was applied for 1 h and after a second washing step the slides were incubated with fitc-conjugated f(ab') 2 donkey antimouse-ig. sections wererinsed, postfixed for 10 min in 4% pfa, rinsed again and coverslipped with carbonatebuffered glycerol (ph 8.6). sections from human bronchi (6 µm) were deparaffinated and incubated with anti-cav-1α and anti-cav-2 antibody as described above. slides were evaluated with an epifluorescence microscope (zeiss, jena, germany) using appropriate filter sets and with a confocal laser scanning microscope (leica-tcs sp2 aobs;leica, mannheim, germany). specificity of the anti-cav-1α antibody was validated by incubation of cryosections from cav-1 deficient mice. the specificity of the anti-cav-1αβ and anti-cav-2 antibodies was previously shown by other groups in experiments with cav-2 deficient mice [17] . here, we characterized these antibodies by western blotting. additional controls included omission of the primary antibodies. for western blot analysis, abraded tracheal epithelial cells of wistar rats (n = 5), hearts and lungs from wistar rats, lungs from cav-1-deficient mice and from wild-type mice (each n = 2) were homogenized by a mixer mill (mm 300, qiagen) with lysis buffer containing 10 mm tris (ph 7.5), 50 mm nacl, 1% triton x-100, 60 mm octylglucoside (sigma-aldrich chemie gmbh, munich, germany), and one complete mini protease inhibitor cocktail tablet (roche diagnostics gmbh, mannheim, germany) per 10 ml buffer. after incubation of the protein solutions at 4°c for 1 h, they were centrifugedfor 5 min at 14,000 rpm. equal amounts of proteins for each tissue were applied as judged by staining of gels with simply bluetm safe stain (invitrogen, carlsbad, usa) stained gels. ten µl appropriately diluted protein solution and 2 µl of 5 × sample buffer (320 mm tris-hcl, ph 6.8, 5% sds, 50% glycerol, 0.25 mg/ml bromphenol blue and 1% β-2-mercaptoethanol) were boiled for 5 min at 95°c. the samples were subjected to 15% sds-page under reducing conditions and subsequently transferred to a nitrocellulose membrane (bio-rad) by semidry blotting. the nitrocellulose membranes were stained with ponceau s to confirm the protein transfer from the gels to the membrane. after subsequent washing in 25 mm tris-buffered saline with 0.05% tween-20 (ttbs), the unspecific binding sites were saturated by incubation with 10% non-fat dry milk in ttbs for1 h at room temperature. the membrane was incubated overnight at 4°c with anti-cav-1α, -1αβ and -2, primary antibodies, diluted in 5% non-fat dry milk in ttbs. the secondary antibodies were diluted in 2.5% non-fat dry milk in ttbs and incubated for 1 h at room temperature. super signal west pico chemiluminescence substrate (pierce) was used for visualization. controls were done by omitting the primary antibody, and the specificity of the anti-cav-1α and anti-cav-2 antibodies was verified in lung homogenates from cav-1-deficient mice. fret is a nonradiative energy transfer between two fluorophores (a donor and an acceptor) that can be detected only if the two fluorophores are less than 10 nm apart. we used fret combined with clsm and double-labeling indirect immunofluorescence as a technique for measuring close spatial association of proteins in tissue sections [18] . cav-1 and cav-2 were labeled using conventional indirect double-labeling immunofluorescence technique (anti-cav-1α from rabbit labeled with cy5-conjugated secondary reagent, anti-cav-2 antibody labeled with cy3conjugated secondary reagent). both primary antibodies were applied simultaneously. after a washing step, cy3conjugated donkey anti-mouse-ig was applied for 1 h and after a second washing step the slides were incubated with cy5-conjugated f(ab') 2 donkey anti-rabbit-ig. for control of the species-specificity of the secondary reagents, only the anti-cav-1 antibody and both secondary antibodies were applied. fret was quantified by the acceptor photobleaching method using a clsm (tcs-sp2 aobs, leica). in this method, fret is detected by measuring the intensity of fluorescence of the donor before and after bleaching of the acceptor. the clsm settings were as follows: detection of cy3: 52% laser power at 543 nm, detection at 555-620 nm; cy5: 20% laser power at 633 nm, detection at 639-738 nm. a region of interest was photobleached 10 times at 100% activity using the 633 nm laser and maximal zoom to destroy the acceptor fluorophore (cy5) and the change in cy3 signal (∆if) was determined in the photobleached area where ∆if = d da -d db , d da is the fluorescence intensity of the donor after photobleaching of the acceptor, and d db is the fluorescence intensity of the donor before photobleaching of the acceptor. differences among experimental group and control group in the fret-experiments were analysed with the kruskal-wallis test followed by mann-whitney test using spss software, version 11.5.1 (spss gmbh software, munich, germany), with p ≤ 0.05 being considered as significant and p ≤ 0.01 as highly significant. rt-pcr analysis of total mrna isolated from rat lungs and abraded tracheal epithelial cells revealed expression of cav-1 and cav-2. pcr products were of the expected size and the sequence was verified by sequencing. no bands were observed in control reactions that included absence of dna template or the reverse transcriptase ( figure 1a) . we quantified the relative expression of cav-1 and cav-2 in tracheal epithelial cells in rats held under standard conditions or spf conditions. in both groups, cav-2 expression was higher than that of cav-1. cav-2 expression levels were 22.2 times higher than that of cav-1 under standard conditions and 25.8 times higher in animals housed under spf conditions ( figure 1b) . in accordance to the results obtained in abraded epithelial cells, mrna for cav-1 was detected in 17/18 samples of microdissected tracheal epithelial cells collected from 5 rats (spf). cav-2 mrna was present in all microdissected samples (n = 15, 4 spf rats). the identity of the pcr products was validated by sequencing. no mrna for cav-1 and cav-2 was detected in areas next to positive tissue that contained o.c.t. compound only, but no cells. this result indicates that the mrna signal detected in the epithelium for cav-1 and cav-2 was not caused by contamination originating from caveolin-containing adjacent cells ( figure 1a ). using the anti-cav-1α antibody, we detected a single band of approximately 22 kd in rat abraded tracheal epithelial cells (figure 2a) . a band of 22 kd and a band of 18 kd, corresponding to cav-1β, were detected in abraded tracheal epithelial cells using an anti-cav-1αβ antibody (figure 2b) . bands of the same molecular weight were detected in lung and heart homogenates. using an antibody to cav-2, we detected a band of 15 kd (γ-isoform) that was close to the detection limit, an 18 kd band (αisoform), and a 21 kd band (β-isoform) ( figure 2c ). in lung homogenates of wild-type mice, cav-1α-immunoreactive bands of 22 kd, 37 kd, and 48 kd were detected, which were absent in lung homogenates from cav-1 deficient mice ( figure 2d ). using an antibody to cav-2 for western blot analysis of lung homogenates from wild-type mice we detected 18 kd and 21 kd bands. no cav-2 bands were detected in lung homogenates from cav-1deficient mice ( figure 2e ). in rat, cav-1-immunoreactivity was detected in epithelial cells of the large airways ( figure 3a ). in contrast to large cartilaginous airways, no cav-1-immunolabeling was detected in the epithelium of the small non-cartilaginous airways of the rat ( figure 3d ). in addition, cav-1-immunoreactivity was observed in tracheal and bronchial smooth muscle cells, in vascular endothelial cells and in unidentified cells in the lamina propria, probably fibroblasts. in the alveolar region, we observed cav-1-immunoreactivity in endothelial cells and in type i alveolar epithelial cells. differences in the labeling patterns obtained with the anti-cav-1α and the anti-cav-1αβ antibody were noted. the labeling with the anti-cav-1α antibody was stronger in the endothelium, whereas labeling of the anti-cav-1αβ antibody was stronger in the epithelium (cf. figures 3a, b) . also, the number of the epithelial cells that were immunoreactive for cav-1αβ was higher than that of the cells immunoreactive for cav-1α ( figures 4a-c) . cav-2-immunoreactivity was found in the same cell types as cav-1-immunoreactivity. interestingly, not all of the cells that showed cav-2-immunofluorescence were cav-1α-immunoreactive ( figures 4d-f) . the cav-2-immunolabeling of the epithelium was stronger than that of smooth muscle cells ( figure 3c ). as for cav-1, no labeling for cav-2 was observed in the epithelial cells of the small bronchi ( figure 3f ). throughout the rat trachea and large bronchi, we found cav-1α-and cav-1αβ-immunoreactivity 1) in the ciliated cells, identified by their typical morphology and by immunolabeling with a monoclonal antibodyto enos [19] (figure 5a ), and 2) in the basal cells, identified by their typical morphology. unlike ciliated cells, brush cells immunoreactive for villin were not labeled for cav-2 (figure 5b ). most of the secretory cells that were labeled with anti-sp-d [20] were not cav-1-immunoreactive ( figure 5c ). in human bronchi, the ciliated and the basal cells were immunoreactive for cav-1α ( figures 5d-f) . the anti-cav-2 antibody gave no signal in paraffin-embedded human tissue. punctate cav-1α labeling was localized at the basolateral membrane and in the apical area of the ciliated cells underneath the luminal plasma membrane. in the mouse respiratory epithelium, cav-1α-immunoreactivity was confined to basal cells ( figure 6d ). the specificity of the cav-1-immunostaining was confirmed by the absence of cav-1α-immunolabeling in cav-1-deficient mice ( figure 6g ). in agreement with the immunohistochemical results, we observed caveolae at the basolateral cell membrane of the ciliated cells and at the cell membrane of the basal cells in rat trachea (figures 6a-c) . caveolae were more frequent in basal cells. in agreement with the immunohistochemical findings in the mouse trachea, caveolae were only found in the basal cells ( figures 6d-f) . basal cells were devoid of caveolae in tracheae of cav-1-deficient mice ( figures 6g-i) . conventional indirect double-labeling immunofluorescence with subsequent fret-clsm analysis was conducted to determine whether cav-1 and cav-2 are in close apposition in airway epithelial cells in situ, thereby indicating an association of both proteins and formation of hetero-oligomers. distinct increase of fluorescence (∆if) was observed in the bleached area with a median value of 2.72 (n = 16 regions of interest of tracheae obtained from 4 rats; figure 7) . a false-positive fret signal that can be caused by cross-reactivity of secondary antibodies was excluded by applying both secondary antibodies to sections incubated with anti-cav-1 α antibody only (median ∆if = 0.287). since the caveolins are membrane proteins, we measured ∆if in the region of the basolateral plasma membrane. ∆if measured in this region was higher (∆if = 4.795) than that in the whole bleached area. the ∆if measured in the controls in the same region was low (∆if = 0.55). the difference between ∆if observed in the experimental group as compared to the corresponding controls was highly significant (p < 0.001, mann-whitney test; figure 7f ). no increase in the donor fluorescence (∆if) could be detected in the airway epithelial cells that were immunoreactive for cav-2, but not for cav-1α (data not shown). the present study demonstrates for the first time the expression of cav-1 and -2 in epithelial cells of the trachea and large bronchi. electron microscopy demonstrated that, indeed, ciliated and basal cells possess caveolae. it has been shown that muscarinic receptors as well as βadrenergic receptors may translocate to caveolae upon agonist binding [21, 22] . these receptors are involved in the regulation of ciliary function [23, 24] . in addition, several proteins involved in ca 2+ -dependent signaling processes, including the ca 2+ -pump and ca 2+ -atpase, are localized to caveolae as shown in renal and intestinal epithelial cells [25] . therefore, caveolae are likely to be involved in the fine-tuned regulation of epithelial cytosolic ca 2+ -concentration and in regulation of ciliary function. several pathogenic microorganisms selectively use caveolae to enter cells [4] . since the caveolae are localized at the basolateral surface of the ciliated cells, it is conceivable that they may be involved in the process of endocytosis of infectious agents after epithelial damage. indeed, adenoviruses require damage of the integrity of the epithelia or of the tight junctions to get access to the basolateral membrane of the ciliated cells to be infectious [26] . basal cells are much more susceptible to infection with adenoviruses [7, 27] . accordingly, we observed more caveolae in basal cells than in ciliated epithelial cells. it has been shown for the adenovirus2 that it can enter the cell via its receptor car that is also localized basolaterally in ciliated cells and in basal cells. since adenovirus2-car is endocytosed via clathrin-coated pits, caveolae, at first sight, seem not to be western blotting important in this process. nevertheless, another receptor for adenovirus2 is major histocompatibility complex (mhc) class 1. this also is localized in the basolateral membrane of ciliated cells and in basal cells. mhc class 1 is also the receptor for simian virus 40 that is endocytosed via caveolae. this indicates a role for caveolae in the infection of airway epithelium by these adenoviruses. furthermore, the infectivity of c-type human adenovirus can be greatly reduced by the expression of a dominant negative cav-1 mutant in plasmocytic cells indicating that caveolae can serve as an alternative entry site for these viruses [28] . in addition, it was recently shown for chlamydia pneumoniae that it co-localizes with cav-1 and cav-2 in the cytosol in hela cells after cellular entrance [8] , indicating a role for caveolins in infectious processes after microbial entry. since the loss of cav-1 was accompanied with loss of caveolae in tracheal epithelial cells in cav-1-deficient mice, cav-1 is required for the formation of caveolae in these cells. in addition, the stabilization and the transport of cav-2 to the plasma membrane are dependent on the expression of cav-1 [29, 30] . our results from fret experiments also prove that cav-1α and cav-2 are closely associated in ciliated and in basal cells, indicating that both proteins are involved in the formation of caveolae. interestingly, we found considerably higher expression of cav-2 mrna than cav-1 mrna, indicating that cav-2 could immunohistochemistry, rat have roles independent from cav-1 once it has reached the plasma membrane. indeed, it has been shown for cav-2 that it associates with chlamydial inclusions independently of cav-1 [8] . we observed differences in the labeling intensities for cav-1α and cav-1αβ among cell types. cav-1α-immunoreactivity was stronger in endothelial cells compared to epithelial cells. in contrast, cav-1αβ-labeling was stronger in the epithelium than in the endothelium of the large airways. in line with this observation, western blots showed a strong protein expression of cav-1β in abraded tracheal epithelium but not in lung and heart homogenates. cav-1β is less efficient in the formation of caveolae [31] , which could be an explanation for the lower number of caveolae found in epithelial cells compared to endothelium where the α-isoform is predominantly expressed [3] . the β-isoform of cav-1 is derived from an alternative translational starting site that creates a protein truncated by 32 amino acids [32] and lacks the phosphorylation site tyr 14. this site has been shown to be phosphorylated upon stimulation of cultured cells by epithelial growth factor (egf), leading to neoformation of caveolae [33] . since egf is considered as a key factor for repair of the bronchial epithelium [34] , caveolae containing the α-isoform might be involved in this process. it is tempting to speculate that certain caveolae may exist that contain predominantly the β-isoform. such caveolae might be involved in other signaling cascades. if both isoforms are present in caveolae, cav-1β could be a negative regulator for signaling cascades relying on the phosphorylation of cav-1α. we found caveolin-1 and -2 only in the large airways of mice and rats, limiting caveolar function to larger airways in these species. it has to be kept in mind, however, that many human intrapulmonary bronchi are considerably double-labeling immunofluorescence, clsm, large airways, rat figure 4 double-labeling immunofluorescence, clsm, large airways, rat. (a-c) cav-1α-(a) and cav-1αβ-immunoreactivity (b) were colocalized in the basal cells (doubled arrowheads) and basolaterally in a subset of columnar epithelial cells (arrows). some cells exhibited cav-1αβ-but not cav-1α-immunoreactivity (arrowheads). (d-f) cav-1α (d) and cav-2 (e) were localized at the basolateral membrane. co-localisation of cav-1α and cav-2 (f, arrowheads). we observed cells that were only cav-2-immunoreactive (f, arrows). epithelium = e larger than the rat trachea. since we have found cav-1 also in human intrapulmonary bronchi, caveolins are likely to be present throughout a substantial part of the human bronchial tree. in summary, we conclude that ciliated and basal cells of the trachea and large bronchi possess caveolae resulting from an association between cav-1α and cav-2. since caveolae are implied in a variety of different functions in other cell types, they are likely to be important also for these functions in the airway epithelium. cav-immunoreactive epithelial cell types the author(s) declare that they have no competing interests. pk and gk conceived and designed the study. gk performed the immunohistochemical analysis, the western blot experiments and the laser-assisted microdissection with subsequent rt-pcr analysis. gk and pk performed detection of close association of cav-1 and cav-2 in epithelial cells by double-labeling indirect immunofluorescence and fret in tissue sections of the rat trachea and large bronchi the fret analysis. up and gk carried out the quantitative rt-pcr. wk, gk, and pk analyzed the electron microscopic specimens. md generated and genotyped the cav-1 deficient mice. pk and gk performed the statistical analysis. the manuscript was drafted by gk, wk, and pk. caveolae: from cell biology to animal physiology role of caveolae and caveolins in health and disease cell type-specific occurrence of caveolin-1alpha and -1beta in the lung caused by expression of distinct mrnas caveolae in the uptake and targeting of infectious agents and secreted toxins caveolar endocytosis of simian virus 40 is followed by brefeldin a-sensitive transport to the endoplasmic reticulum, where the virus disassembles caveolar endocytosis of simian virus 40 reveals a new two-step vesicular-transport pathway to the er lack of high affinity fiber receptor activity explains the resistance of ciliated airway epithelia to adenovirus infection caveolin-2 associates with intracellular chlamydial inclusions independently of caveolin-1 development of a transgenic mouse model susceptible to human coronavirus 229e human coronavirus 229e binds to cd13 in rafts and enters the cell through caveolae untersuchungen am trachealepithel verschiedener säuger towards an in vitro model of cystic fibrosis small airway epithelium: characterisation of the human bronchial epithelial cell line cfbe41o de novo formation of caveolae in lymphocytes by expression of vip21-caveolin loss of caveolae, vascular dysfunction, and pulmonary defects in caveolin-1 gene-disrupted mice caveolin-1 null mice are viable but show evidence of hyperproliferative and vascular abnormalities evidence for the association of villin with core filaments and rootlets of intestinal epithelial microvilli caveolin-2-deficient mice show evidence of severe pulmonary dysfunction without disruption of caveolae fret-clsm and double-labeling indirect immunofluorescence to detect close association of proteins in tissue sections distribution of the novel enos-interacting protein nosip in the liver, pancreas, and gastrointestinal tract of the rat increased surfactant protein d in rat airway goblet and clara cells during ovalbumin-induced allergic airway inflammation redistribution of muscarinic acetylcholine receptors on human fibroblasts induced by regulatory ligands internalization of beta-adrenergic receptor in a431 cells involves non-coated vesicles atp regulation of ciliary beat frequency in rat tracheal and distal airway epithelium effects of beta-agonists on airway epithelial cells calcium pump of the plasma membrane is localized in caveolae basolateral localization of fiber receptors limits adenovirus infection from the apical surface of airway epithelia efficient adenovirusmediated gene transfer to basal but not columnar cells of cartilaginous airway epithelia efficient species c hadv infectivity in plasmocytic cell lines using a clathrin-independent lipid raft/caveola endocytic route expression of caveolin-1 is required for the transport of caveolin-2 to the plasma membrane. retention of caveolin-2 at the level of the golgi complex caveolin-2 localizes to the golgi complex but redistributes to plasma membrane, caveolae, and rafts when co-expressed with caveolin-1 isoforms of caveolin-1 and caveolar structure caveolin isoforms differ in their n-terminal protein sequence and subcellular distribution. identification and epitope mapping of an isoform-specific monoclonal antibody probe epithelial growth factor-induced phosphorylation of caveolin 1 at tyrosine 14 stimulates caveolae formation in epithelial cells epithelial damage and response we thank k. michael for expert technical help with the figures and g. kripp from the electron microscopy unit of the institut für anatomie und zellbiologie for the embedding and cutting of the electron microscopic specimens. the laser-assisted microdissection for subsequent rt-pcr analysis was done in cooperation with the z-project of the sfb 534. this study was supported by the deutsche forschungsgemeinschaft (sfb 547, c1; gk 534, both to wk) and by a young scientist grant from the faculty of medicine of the justus-liebig-universität giessen to pk. we also thank prof. dr. robert leroy snipes for linguistic correction of the manuscript. key: cord-226245-p0cyzjwf authors: schneble, marc; nicola, giacomo de; kauermann, goran; berger, ursula title: nowcasting fatal covid-19 infections on a regional level in germany date: 2020-05-15 journal: nan doi: nan sha: doc_id: 226245 cord_uid: p0cyzjwf we analyse the temporal and regional structure in mortality rates related to covid-19 infections. we relate the fatality date of each deceased patient to the corresponding day of registration of the infection, leading to a nowcasting model which allows us to estimate the number of present-day infections that will, at a later date, prove to be fatal. the numbers are broken down to the district level in germany. given that death counts generally provide more reliable information on the spread of the disease compared to infection counts, which inevitably depend on testing strategy and capacity, the proposed model and the presented results allow to obtain reliable insight into the current state of the pandemic in germany. in march 2020, covid-19 became a global pandemic. from wuhan, china, the virus spread across the whole world, and with its diffusion, more and more data became available to scientists for analytical purposes. in daily reports, the who provides the number of registered infections as well as the daily death toll globally (https://www.who.int/). it is inevitable for the number of registered infections to depend on the testing strategy in each country (see e.g. cohen and kupferschmidt, 2020) . this has a direct influence on the number of undetected infections (see e.g. li et al., 2020) , and first empirical analyses aim to quantify how detected and undetected infections are related (see e.g. niehus et al., 2020) . though similar issues with respect to data quality hold for the reported number of fatalities (see e.g. baud et al., 2020) , the number of deaths can overall be considered a more reliable source of information than the number of registered infections. the results of the "heinsberg study" in germany point in the same direction (streeck et al., 2020) . a thorough analysis of death counts can in turn generate insights on changes in infections as proposed in flaxman et al. (2020) (see also ferguson et al., 2020) . in this paper we pursue the idea of directly modelling registered death counts instead of registered infections. we analyse data from germany and break down the analyses to a regional level. such regional view is apparently immensely important, considering the local nature of some of the outbreaks for example in italy (see e.g. , france (see e.g. massonnaud et al., 2020) or spain. the analysis of fatalities has, however, an inevitable time delay, and requires to take the course of the disease into account. a first approach on modelling and analysing the time from illness and onset of symptoms to reporting and further to death is given in jung et al. (2020) (see also linton et al., 2020) . understanding the delay between onset and registration of an infection and, for severe cases, the time between registered infection and death can be of vital importance. knowledge on those time spans allows us to obtain estimates for the number of infections that are expected to be fatal based on the number of infections registered on the present day. the statistical technique to obtain such estimates is called nowcasting (see e.g. höhle and an der heiden, 2014) and traces back to lawless (1994) . nowcasting in covid-19 data analyses is not novel and is for instance used in günther et al. (2020) for nowcasting daily infection counts, that is to adjust daily reported new infections to include infections which occurred the same day but were not yet reported. we extend this approach to model the delay between the registration date of an infection and its fatal outcome. we therefore analyse the number of fatal cases of covid-19 infections in germany using district-level data. the data are provided by the robert-koch-institute (www.rki.de) and give the cumulative number of deaths in different gender and age groups for each of the 412 administrative districts in germany together with the date of registration of the infection. the data are available in dynamic form through daily downloads of the updated cumulated numbers of deaths. we employ flexible statistical models with smooth components (see e.g. wood, 2017) assuming a district specific poisson process. the spatial structure in the death rate is incorporated in two ways. first, we assume a spatial correlation of the number of deaths by including a long-range smooth spatial death intensity. this allows to show that regions of germany are affected to different extents. on top of this long-range effect we include two types of unstructured region specific effects. an overall region specific effect reflects the situation of a district as a whole, while a short-term effect mirrors region specific variation of fatalities over time and captures local outbreaks as happened in e.g. heinsberg (north-rhine-westphalia) or tirschenreuth (bavaria). in addition we include dynamic effects to capture the global changes in the number of fatal infections for germany over calendar time. this enables us to investigate the impact of certain interventions, such as social distancing, school closure, complete lockdowns and lockdown releases, on the dynamic of the infection and hence on the number of deaths. modelling infectious diseases is a well developed field in statistics and we refer to held et al. (2017) for a general overview of the different models. we also refer to the powerful r package surveillance . since our focus is on analysing the district specific dynamics of fatal infections we here make use of poisson-based models implemented in the mgcv package in r, which allows to decompose the spatial component in more depth. the paper is organized as follows. in section 2 we describe the data. section 3 highlights the results of our analysis. the remaining sections provide the technical material, starting with section 4 where we motivate the statistical model, which is extended by our nowcasting model in section 5. extended results as well as model validation are given in section 6, while section 7 concludes the paper. we make use of the covid-19 dataset provided by the robert-koch-institute for the 412 districts in germany (which also include the twelve districts of berlin separately). the data are updated on a daily basis and can be downloaded from the robert-koch-institute's website. we have daily downloads of the data for the time interval from march 27, 2020 until today. the subsequent analysis was conducted on may 14, 2020, and was performed considering only deadly infections with registration dates from march 26, 2020 until may 13, 2020 (the day before the day of analysis). the data contain the newly notified laboratory-confirmed covid-19 infections and the cumulated number of deaths related to covid-19 for each district of germany, classified by gender and age group. each data entry has a time stamp which corresponds to the registration date of a confirmed covid-19 infection. this means that the time stamp for a fatal outcome always refers to the registration date and not to the death date. due to daily downloads of the data we can derive the time point of death (or to be more specific, the time point when the death of a case is included in the database). we obtain the latter by observing a status change from infected to deceased when comparing the data from two consecutive days. the robert-koch-institute collects the data from the district-based health authorities (gesundheitsämter). due to different population sizes in the districts and certainly also because of different local situations, some health authorities report the daily numbers to the robert-koch-institute with a delay. this happens in particular over the weekend, a fact that we need to take into account in our model. we refrain from providing general descriptive statistics of the data here, since these numbers can easily be found on the rki webpage, which also gives a link to a dashboard to visualize the data (see also https://corona.stat.uni-muenchen.de/maps/) before we discuss our modelling approach in detail, we want to describe our major findings. first, table 1 shows that age and gender both play a major role when estimating the daily death toll. as is generally known, elderly people exhibit a much higher death rate which is for the age group 80+ around 100 times higher than for people in the age group 35-59. a remarkable difference is also observed between genders, where the expected death rate of females is around 40% (≈ 1 − exp(−0.503)) lower than the death rate for males. furthermore, we see that significantly less deaths are attributed to infections registered on sundays compared to weekdays, due to the existing reporting delay during weekends. our model includes a global smooth time trend representing changes in the death rate since march 26th. this is visualized in figure 1 . the plotted death rate is scaled to give the expected number of deaths per 100.000 people in an average district for the reference group, i.e. males in the age group 35 -59. overall, we see a peak in the death rate on april 3rd and a downwards slope till end of april. however, our nowcast reveals that the rate remains constant since beginning of may. note that this recent development cannot be seen by simply displaying the raw death counts of these days. the nowcasting step inevitably carries statistical uncertainty, which is taken into account in figure 1 by including best and worst case scenarios. the latter are based on bootstrapped confidence intervals, where details are provided in section 6.3 later in the paper. our aim is to investigate spatial variation and regional dynamics. to do so, we combine a global geographic trend for germany with unstructured region-specific effects, where the latter uncover local behaviour. in figure 2 we combine these different components and map the fitted nowcasted death counts related to covid-19 for the different districts of germany, cumulating over the last seven days before the day of analysis (here may 14, 2020). while in most districts of germany the death rate is relatively low, some hotspots can be identified. among those, traunstein and rosenheim (in the south-east part of bavaria) are the most evident, but greiz and sonneberg (east and south part of thuringia) stand out as well, to mention a few. a deeper investigation of the spatial structure is provided in section 6, where we show the global geographic trend and provide maps that allow to detect new hotspot areas, after correcting for the overall spatial distribution of the infection. on the day of analysis, we do not observe the total counts of deaths for recently registered infections, since not all patients with an ongoing fatal infections have died yet. we therefore nowcast those numbers, i.e. we predict the prospective deaths which can be attributed to all registration dates up to today. this is done on a national level, and the resulting nowcast of fatal infections for germany is shown in figure 3 . for example, on may 14, 2020 there are 25 deaths reported where the infection was registered on may 5th (red line on may 5th). we expect this number to increase to about 50 when all deaths due to covid-19 for this registration date will have been reported (blue line on may 5th). naturally, the closer a date is to the present, the larger the uncertainty in the nowcast. this is shown by the shaded bands. details on how the statistical uncertainty has been quantified are provided in section 5 below. the fit of this model has been incorporated into the district model discussed before, but the nowcast results are interesting in their own right. the curve confirms that the number of fatal infections is decreasing since the beginning of april. note that the curve also mirrors the "weekend effect" in registration, as less infections are reported on sundays. further analyses and a detailed description of the model are given in the following sections. let y t,r,g denote the number of daily deaths due to covid-19 in district/region r and age and gender group g with time point (date of registration) t = 0, . . . , t . here t = t corresponds to the day of analysis, which is may 14, 2020 and t = 0 corresponds to march 26, 2020. note that time point t refers to the time point of registration, i.e. the date at which the infection was confirmed. even though the time point of infection obviously precedes that of death, registration can also occur after death, e.g. when a post mortem test is conducted, or when test results arrive after the patient has passed away. we set the day of death to be equal to the day of registered infections in this case. the majority of fatalities with registered infection at time point t have not yet been observed at time t, as these deaths will occur later. we therefore need a model for nowcasting, which is discussed in the next section. for now we assume all y t,r,g to be known. we model y t,r,g as (quasi-)poisson distributed according to where we specify λ t,r,g through λ t,r,g = exp{(β 0 + age g β age + gender g β gender + weekday t β weekday the linear predictor is composed as follows: • β 0 is the intercept. • β age and β gender are the age and gender related regression coefficients. • β weekday are the weekday-related regression coefficients. • m 1 (t) is an overall smooth time trend, with no prior structure imposed on it. • m 2 (s r ) is a smooth spatial effect, where s r is the geographical centroid of district/region r. • u r0 and u r1 are district/region-specific random effects which are i.i.d. and follow a normal prior probability model. while u r0 specifies an overall level of in the death rate for district r over the entire observation time, u r1 reveals region specific dynamics by allowing the regional effects to differ for the last 14 days. • pop r,g is the gender and age group-specific population size in district/region r and serves as an offset in our model. we here emphasize that we fit two spatial effects of different types: we model a smooth spatial effect, i.e. m 2 (s r ), which takes the correlation between the death rates of neighbouring districts/regions into account and gives a global overview of the spatial distribution of fatal infections. in addition to that we also have unstructured district/region-specific effects u r = (u r0 , u r1 ) , which capture local behaviour related to single districts only. the district specific effects u r are considered as random with a prior structure for r = 1, . . . , 412. the prior variance matrix σ u is estimated from the data. the predicted values u r (i.e. the posterior mode) exhibit districts that show unexpectedly high or low death tolls when adjusted for the global spatial structure and for age-and gender-specific population size. model (1) belongs to the model class of generalized additive mixed model, see e.g. wood (2017) . the smooth functions are estimated by penalized splines, where the quadratic penalty can be comprehended as a normal prior (see e.g. wand, 2003) . the same type of prior structure holds for the region-specific random effects u r . in other words, smooth estimation and random effect estimation can be accommodated in one fitting routine, which is implemented in the r package mgcv. this package has been used to fit the model, so that no extra software implementation was necessary. this demonstrates the practicability of the method. the above model cannot be fitted directly to the available data, since we need to take the course of the disease into account. for a given registration date t, the number of deaths of patients registered as positive on that day, y t,r,g , may not yet be known, since not all patients with a fatal outcome of the disease have died yet. this requires the implementation of nowcasting. we do this on a national level, and cumulate the numbers over district/region r and gender and age groups g. this allows to drop the corresponding subscripts in the following and we simply notate the cumulated number of deaths with registered infections at day t with y t . let n t,d denote the number of deaths reported on day t + d for infections registered on day t. assuming that the true date of death is at t+d, or at least close to it, we ignore any time delays between time of death and its notification to the health authorities. we call d the duration between the registration date as a covid-19 patient and the reported day of death, where d = 1, . . . , d max . here, d max is a fixed reasonable maximum duration, which we set to 30 days (see e.g. wilson et al., 2020) . the minimum delay is one day. in nowcasting we are interested in the cumulated number of deaths for infections registered on day t, which we define as the total number of deaths with a registered infection at t is apparently unknown at time point t and becomes available only after d max days. in other words, only after d max days we know exactly how many deaths occurred due to an infection which was registered on day t. we define the partial cumulated sum of deaths as on day t = t , when the nowcasting is performed, we are faced with the following data constellation, where na stands for not (yet) available: we may consider the time span between registered infection and (reported) death as a discrete duration time taking values d = 1, . . . , d max . let d be the random duration time, which by construction is a multinomial random variable. in principle, for each death we can consider the pairs (d i , t i ) as i.i.d. and we aim to find a suitable regression model for d i given t i , including potential additional covariates x t,d . we make use of the sequential multinomial model (see agresti, 2010) and define π(d; t, x t,d ) = p (d = d|d ≤ d; t, x t,d ) let f t (d) denote the corresponding cumulated distribution function of d which relates to probabilities π() through f t (d) = p t (d ≤ d) = p(d ≤ d|d ≤ d + 1) · p (d ≤ d + 1) = (1 − π(d + 1; ·)) · (1 − π(d + 2; ·)) · . . . · (1 − π(d max ; ·)) for d = 1, . . . , d max − 1 and f t (d max ) = 1. the available data on cumulated death counts allow us to estimate the conditional probabilities π(d; ) for d = 2, . . . , d max . in fact, the sequential multinomial model allows to look at binary data such that where • s 1 (t) is an overall smooth time trend over calendar days, • s 2 (d) is a smooth duration effects, capturing the course of the disease, • x t,d are covariates which may be time and duration specific. assuming that d, the duration between a registered fatal infection and its reported death, is independent of the number of fatal covid-19 infections, we obtain the relationship note further that if we model y t with a quasi-poisson model as presented in the previous chapter, we have no available observation y t for time points t > t − d max . instead, we have observed c t,t −t , which relates to the mean of y t through (7). including therefore log f t (t − t) as additional offset in model (2), allows to fit the model as before, but with nowcasted deaths included. that means, instead of λ t,r,g as in (2), the expected death rates are now parametrized by λ t,r,g = λ t,r,g exp(log f t (t −t)), where the latter multiplicative term is included as additional offset in the model. we fit the nowcasting model (5) with parametrization (6). we include a weekday effect for the registration date of the infection with reference category "monday". the estimates of the fixed linear effects are shown in table 2 . the fitted smooth effects are shown in figure 4 , where the top panel shows the effect over calendar time, which is very weak and confirms that the course of the disease hardly varies over time. this shows that the german health care system remained stable over the considered period, and hence survival did not depend on the date on which the infection was notified. the bottom panel of figure 4 shows the course of the disease as a smooth effect over the time between registration of the infection and death. we see that the probabilities π(d; ·) decrease in d, where this effect is the strongest in the first days after registration. thus, most of the covid-19 patients with fatal infections are expected to die not long after their registration date. the effect of d becomes easier to interpret by visualizing the resulting distribution function f t (d). this is shown in figure 5 for two dates t, i.e.. april 14th and may 13th. the plot also shows how the course of the disease hardly varies over calendar time: in fact, the small differences between the two distribution functions is dominated by the weekday effect, since the red curve is related to a tuesday while the blue one is from a wednesday. in figure 3 above we have shown the nowcasting results along with uncertainty intervals shaded in grey. these were constructed using a bootstrap approach as follows. given the fitted model, we simulate n = 10 000 times from the asymptotic joint normal distribution (7), where c t −t is the observed partial cumulated sum of deaths at time point t − t. the pointwise lower and upper bounds of the 95% prediction intervals for the nowcast for y t are then given by the 2.5 and the 97.5 quantiles of the set { y (i) t , i = 1, . . . , n}, respectively. in section 3 we presented the fitted death rate, which is the convolution of a smooth spatial effect as well as region specific effects. it is of general interest to disentangle these two spatial components. this is provided by the model. we visualize the fitted global geographic trend figure 7: long term region specific level (left hand side) and short term dynamics (right hand side) of the covid-19 infections m 2 (·) for germany in figure 6 . the plot confirms that up to may 2020 the northern parts of the country are less affected by the disease in comparison to the southern states. the two plots in figure 7 map the region specific effects, i.e. the predicted long term level of a district u r0 (left hand side) and the predicted short term dynamics u r1 (right hand side). both plots uncover quite some region-specific variability. in particular, the short term dynamics captured in the right hand side plot (u r1 ) pinpoint districts with unexpectedly high nowcasted death rates in the last two weeks, after correcting for the global geographic trend and the long term effect of the district. some of the noticeable districts have already been highlighted in section 3 above, but we can detect further districts, which are less pronounced in figure 1 . for instance, steinfurt (in the north-west of north rhine-westphalia), olpe (southern north rhine-westphalia) or gotha (center of thringen) presently show a high rate of fatal infections. a large number of the registered deaths related to covid-19 stem from people in the age group 80+. locally increased numbers are often caused by an outbreak in a retirement home. such outbreaks apparently have a different effect on the spread of the disease, and the risk of an epidemic infection caused by outbreaks in this age group is limited. thus, the death rate of people in the age group 80+ could vary differently across districts when compared to regional peaks in the death rate of the rest of the population. in order to respect this, we decompose the district-specific effects u r in (2) into u 80− r = (u 80− r0 , u 80− r1 ) for the age group 80-and u 80+ r = (u 80+ r0 , u 80+ r1 ) for the age group 80+, where the age group 80-consists of the aggregated age groups 15-34, 35-59 and 60-79. we put the same prior assumption on the random effects as we did in (3), but now the variance matrix that needs to be estimated from the data has dimension 4 by 4. the fitted age group-specific random effects are shown in figure 8 , where the u 80− r are shown in the top panel and the u 80+ r in the bottom panel. most evidently, the variation of the random effects is much higher in the age group 80+ when compared to the younger age groups, as more districts occur which are coloured dark blue or dark red, respectively. when comparing the district-specific short term dynamics of the last 14 days (u r1 ) in figure 8 to those in figure 7 , we recognize that in most of the districts which recently experienced very high death intensities (with respect to the whole period of analysis), these stem from the age group 80+. as mentioned before, this can often be explained by outbreaks in retirement homes. when fitting the mortality model (1) we included the fitted nowcast model as offset parameter. this apparently neglects the estimation variability in the nowcasting model, which we explored via bootstrap as explained in section 5.3 and visualized in figure 3 . in order to also incorporate this uncertainty in the fit of the mortality model, we refitted the model using (a) the upper end and (b) the lower end of the prediction intervals shown in figure 3 . it appears that there is little (and hardly any visible) effect on the spatial components, which is therefore not shown here. but the time trend shown in figure 1 does change, which is visualized by including the two fitted functions corresponding to the 2.5% and 97.5% quantile of the offset function. we can see that the estimated uncertainty of the nowcast model mostly affects the last ten days, with a strong potential increase in the death rate mirroring a possible worst case scenario. in figure 9 we show a normal qq-plot of the pearson residuals in the nowcasting model. apart from some observations in the lower tail, the pearson residuals are distributed very closely to a standard normal distribution when considering the estimate φ = 1.766 of the dispersion parameter in the quasi-poisson model (7). overall, the model seems to fit to the available data quite well. the paper presents a model to monitor the dynamic behaviour of covid-19 infections based on death counts. it is important to highlight that the proposed model makes no use of new infection numbers, but only of observed deaths related to covid-19. this in turn means that the results are less dependent on testing strategies. the nowcasting approach enables us to estimate the number of deaths following a registered infection today, even if the fatal outcome has not occurred yet. moreover, the district level modelling uncovers hotspots, which are salient exclusively through increased death rates. a differential analysis of the number of current fatal infections on a regional level allows to draw conclusions on the current dynamics of the disease assuming a constant case fatality rate, i.e. a stable proportion of death compared to the true number of infections when adjusting for age and gender. a natural next step would now be to consider the nowcasted deaths in relation to the number of newly registered infections, which is, in contrast, highly dependent on both testing strategy and capacity. we consider this as future research, and the proposed model allows us to explore data in this direction. this might ultimately help us in shedding light on the relationship between registered and undetected infections as well as on the effectiveness of different testing strategies. there are several limitations to this study which we want to address as well. first and utmost, even though death counts are, with respect to cases counts, less dependent on testing strategies, they are not completely independent from them. this applies in particular to the handling of post-mortem tests. we therefore do not claim that our analysis of death counts is completely unaffected by testing strategies. secondly, a fundamental assumption in the model is the independence between the course of the disease and the number of infections. overall, if the local health systems have sufficient capacity and triage can be avoided, this assumption seems plausible, but it is difficult or even impossible to prove the assumption formally. finally, the nowcasting itself is not carried out on a regional level, though the model focuses on regional aspects of the pandemic. while it would be desirable to fit the nowcast model regionally, the limited amount of data simply prevents us from extending the model in this direction. analysis of ordinal categorical data real estimates of mortality following covid-19 infection countries test tactics in 'war' 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of publicly available case data covid-19: forecasting short term hospital needs in france. medrxiv spatio-temporal analysis of epidemic phenomena using the r package surveillance quantifying bias of covid-19 prevalence and severity estimates in wuhan, china that depend on reported cases in international travelers infection fatality rate of sars-cov-2 infection in a german community with a super-spreading event smoothing and mixed models case-fatality risk estimates for covid-19 calculated by using a lag time for fatality generalized additive models: an introduction with r we want to thank maximilian weigert and andreas bender for introducing us to the art of producing geographic maps with r. moreover, we would like to thank all members of the corona data analysis group (codag) at lmu munich for fruitful discussions. key: cord-256635-zz58w3ro authors: beermann, sandra; allerberger, franz; wirtz, angela; burger, reinhard; hamouda, osamah title: public health microbiology in germany: 20 years of national reference centers and consultant laboratories date: 2015-08-21 journal: int j med microbiol doi: 10.1016/j.ijmm.2015.08.007 sha: doc_id: 256635 cord_uid: zz58w3ro in 1995, in agreement with the german federal ministry of health, the robert koch institute established a public health microbiology system consisting of national reference centers (nrcs) and consultant laboratories (cls). the goal was to improve the efficiency of infection protection by advising the authorities on possible measures and to supplement infectious disease surveillance by monitoring selected pathogens that have high public health relevance. currently, there are 19 nrcs and 40 cls, each appointed for three years. in 2009, an additional system of national networks of nrcs and cls was set up in order to enhance effectiveness and cooperation within the national reference laboratory system. the aim of these networks was to advance exchange in diagnostic methods and prevention concepts among reference laboratories and to develop geographic coverage of services. in the last two decades, the german public health laboratory reference system coped with all major infectious disease challenges. the european union and the european centre for disease prevention and control (ecdc) are considering implementing a european public health microbiology reference laboratory system. the german reference laboratory system should be well prepared to participate actively in this upcoming endeavor. public health microbiology laboratories play a central role in detecting infectious disease, monitoring outbreak response and providing scientific evidence to prevent and control disease. they have important roles and responsibilities associated with accurate diagnosis, resistance testing and prevention of the spread of infectious disease. for example, outbreak investigations often depend on confirming cases by methods that are not commonly available in a routine laboratory setting. the scientific community, policy makers and pharmaceutical companies rely on advice and information from reference laboratories in order to adjust vaccine and antibiotic production (witze et al., 2014) . according to the european centre for disease prevention and control (ecdc), the five key activities of public health microbiology reference laboratories are reference diagnostics; reference material resources; scientific advice; collaboration and research; and monitoring, alerting and responding (european centre for disease prevention and control, 2010) . in the various european countries, microbiology reference laboratories are defined, organized, maintained and operated differently. we present an overview of germany's public health reference laboratory system. germany is a highly industrialized country with 82 million inhabitants, and is made up of 16 federal states ("länder"). the principal responsibility for public health lies with the 16 states, or with their ministries of health, and with the almost 400 local public health departments. since the 1980s, the federal government ("bundesregierung"), federal assembly ("bundestag") and federal council ("bundesrat") have increasingly taken responsibility for healthcare reform and legislation. specific health issues, such as infectious diseases that threaten public safety and life cycle management of pharmaceuticals, are within the jurisdiction of the federal government. for example, the german protection against http://dx.doi.org/10.1016/j.ijmm.2015.08.007 1438-4221/© 2015 elsevier gmbh. all rights reserved. infection act ("infektionsschutzgesetz," ifsg) as a federal law regulates the prevention and management of infectious diseases in humans. federated states are responsible for all primary aspects of public health, but there are also responsible for the implementation of federal laws, including federal social and labour laws. the robert koch institute (rki) is a federal institute within the portfolio of the federal ministry of health (bundesministerium für gesundheit, bmg). as such the rki is the central federal reference institution in the public health sector responsible for disease monitoring, control and prevention and conducting applied and response-oriented research in the field of disease control and prevention at the federal level. the research activities of the rki are partly directly related to the activity fields of a ministry. although robert koch and his contemporaries built a strong tradition for infectious disease epidemiology in germany in the late 19th and early 20th centuries, this tradition had all but disappeared in the 1930s and 1940s (allerberger, 2013) . in former west germany, the work of the rki as part of the then federal health office (bundesgesundheitsamt, bga) mainly focused on basic science research. the aids epidemic demanded a national public health response which resulted in the creation of the national aids centre in 1988. in 1994, when the bga was dissolved and the rki was assigned additional spheres of competence a combined aids center and infectious disease epidemiology division was created at the rki. in 1995, representatives of the rki, the federal ministry of health and the federal ministry for education and research developed the concept of a network of collaborators whose goal was to intensify epidemiological research and improve infectious disease surveillance (fock et al., 1995) . as part of this concept, the rki implemented a weekly epidemiological bulletin, formed the committee for infectious disease epidemiology, trained epidemiologists for surveillance and outbreak investigation and set up a system of national reference laboratories: national reference centers (nrcs) and consultant laboratories (cls) (petersen et al., 2000) . they were responsible for laboratory surveillance of important pathogens and syndromes. these laboratories are considered national centers of excellence in the field of laboratory science for a particular pathogen or group of pathogens. nrcs establish and use reference methods, and can validate and verify test results from other laboratories (confirmatory testing). nrcs also produce and distribute reference materials for external quality control and assurance. owing to the high level of expertise, resources and infrastructure, nrcs and cls are involved in training and in providing expert advice to national health authorities and other laboratories. moreover, these laboratory scientists work closely together with their epidemiologist counterparts at the rki as well as those at the federal, state and local levels. the nrcs focus on outbreak detection and response and advice the rki in the preparation of case definitions according to the protection against infection act (ifsg). furthermore, the reference laboratories conduct or are involved in laboratory surveillance systems which provide additional information complementing statutory notifications. nrcs and cls are also involved in developing rki guidelines for physicians ("ratgeber für ärzte") as well as investigating outbreaks and conducting epidemiological studies. the following are the basic tasks of nrcs and cls, which include detailed requirements referring to specific pathogens or syndromes as listed in the respective calls for tenders: general catalogue of nrc tasks (1) developing or improving diagnostic procedures; coordinating standardization and distribution of generally accepted test procedures; initiating investigations for quality assurance. (2) diagnosing and subtyping pathogens beyond routine measures, including molecular biological studies to elucidate the epidemiological context. (3) maintaining a strain collection and distributing reference strains or diagnoses of specific reference strains, with the exception of commercially available isolates, such as from the american type culture collection (atcc) and the german collection of microorganisms and cell cultures (dsmz). (4) organizing and coordinating the upkeep of a network of diagnostic facilities. (5) providing a consulting service for public health services laboratories, practicing physicians, hospitals and research institutes; implementing continuing education and handling public relations. (6) collaborating with reference laboratories of other countries as well as collaborating centers of the who, including participating in international ring trials. (7) evaluating and interpreting data in coordination with the rki with the aim of best describing the epidemiological situation relevant for germany; initiating and participating in surveillance projects. (8) monitoring incoming data with the goal of timely detection of outbreaks or outbreak hazards as well as immediate communication with the rki; support of public health services and the rki with complementary studies during outbreak investigations. (9) epidemiological analysis and evaluating the development of resistance and virulence. (10) reporting routinely to and consulting with the rki on relevant issues; participating in developing rki recommendations for diagnostics, therapies and prevention as well as for applied epidemiology of infectious diseases in general. general catalogue of cl tasks 1. consulting (especially with the public health services as well as laboratories, practicing physicians, hospitals and research institutes). 2. working within the framework of quality assurance (participating in studies and inter-laboratory tests, e.g., in cooperation with instand (german eqas), who, eu, and professional associations and participating in further education). 3. improving or developing diagnostic procedures. 4. participating in epidemiological evaluations of the current situation by the rki. 5. carrying out studies within the network of diagnostic facilities. 6. consulting with the rki in developing scientific materials concerned with pathogens or symptoms (e.g., case definitions, rki guidelines for physicians). the number of nrcs increased from 12 in 1995 to 15 in 2009. presently, 19 nrcs have been appointed (table 1) . five laboratories are situated at the rki; the others are located at various universities and research facilities in germany. since 1996, 46 cls have decreased to 40 designated cls, mainly devoted to providing scientific advice (table 2) . currently a total of 59 nrcs and cls located at universities, federal or state institutes and private laboratories are supported for this function by the rki. the high relevance of nrc and cl work for the surveillance of infectious diseases is evident by the wide range of national and international publications. for example, the nrc for mycobacteria and the rki performed analyses of routine laboratory diagnosis data of pediatric tuberculosis in the european union/european economic area (sanchini et al., 2014) . the nrc for helicobacter pylori and the rki examined h. pylori resistance to antibiotics in europe and its relationship to antibiotic consumption (megraud et al., 2013) . another example is the work of the streptococci nrc, which studied the epidemiology of streptococcus pneumoniae serogroup 6 isolates from invasive pneumococcal disease in children and adults in germany (van der linden et al., 2013) . nrcs and cls are also involved in outbreak investigations and epidemiological studies. for instance, the cl for coronaviruses performed contact investigation for an imported case of middle east respiratory syndrome (reuss et al., 2014) , and the influenza nrc was involved in detecting local influenza outbreaks (schweiger and buda, 2013) . the rki and the nrc for surveillance of nosocomial infections examined the question, "how many outbreaks of nosocomial infections occur in german neonatal intensive care units annually?" (schwab et al., 2014) . additionally, the cl for legionella was involved in examining a legionnaires' disease outbreak associated with a cruise liner in august 2003 (beyrer et al., 2007) . dengue virus infections in a traveler returning from croatia to germany were analyzed by the nrc for tropical infection agents (schmidt-chanasit et al., 2010) . the nrc and the rki for meningococcal diseases and h. influenzae examined a cluster of invasive meningococcal disease in young men who have sex with men in berlin (marcus et al., 2013) . nrcs and cls are also involved in evaluating implemented vaccination recommendations and analyzing the effectiveness of the vaccines (kalies et al., 2009; ruckinger et al., 2009 ). for which pathogen a reference laboratory is to be established is decided based on the public health relevance of the pathogen as appraised by the rki and on the needs expressed by the national public health services ("öffentlicher gesundheitsdienst," ögd) . in addition, medical professional societies, the federal ministry of health and other third parties can approach the rki with perceived needs for additional reference laboratories. in the next step, the advisory board for public health microbiology (formerly called the committee for infectious disease epidemiology) assesses the proposal and provides the rki with a recommendation on whether to set up a new laboratory. in addition to the epidemiological relevance, and a declared need from national public health services, the availability of financial resources is another essential criterion. the decision to establish or continue an nrc or a cl is made by the rki, which considers recommendations given by the advisory board for public health microbiology, and must be confirmed by the federal ministry of health. appointments are restricted to three-year periods. the advisory board consists of up to 14 experts, appointed by the rki for periods of three years. the members of this advisory forum are renowned experts in the fields of microbiology, virology, hygiene, epidemiology and public health. occasionally, other national and international professional societies and experts are consulted to achieve a solid appraisal of the candidate laboratories. from 2009 to 2012, numerous important modifications were made to improve the transparency of the tendering and selection processes for the nrcs and the cls. a strict prioritization process, based upon necessity and not upon offer, was implemented. the evaluation process became more rigorous. essential evaluation criteria are public health needs and public health relevance, successful network activities, attestable quality assurance, publications as well as a positive appraisal of the advancement of diagnostic procedures. at the end of each appointment period, an evaluation of the laboratories is performed by the rki in cooperation with the advisory board for public health microbiology, which again consults national and international professional societies and experts. based on the evaluation results, the president of the rki, in cooperation with the federal ministry of health, appoints and reappoints the nrcs and cls. the 2013 evaluation of the cls resulted in the reappointment of 40 cls and the shutdown of nine cls. reasons for closing were, for example, the retirement of the laboratory head (appointments are based on the combination of personal and institutional expertise), decreased public health relevance of the pathogen or an overlapping of the functional areas of responsibility with other cls or nrcs. in the 2013 evaluation of the nrcs, all 19 nrcs were reappointed. in 2007, the 16 nrcs were supported with d1540,000 in total. in 2008, the available funding increased to d2173,000. the nrcs received between d57,000 and d241,000 per year. the decision on the level of funding of individual nrcs is made by the rki, based on criteria such as high consultation effort, high sample appearance and extraordinary public health relevance of the pathogen. in contrast to the nrcs, which have always been financially supported, the cls initially performed their work (mainly consultation) without any financial support. from april to december 2009, the cls received basic funding of d5000 per year (total amount in 2009: d2173,000). in 2010, the available funding increased to d2612,000. the increase in funding was used to upgrade the cls' basic funding to around d10,000 per year. beyond that, the funds had to cover new national networks. in 2014, the 19 nrcs received between d60,000 and d253,000 per year. thirty-three of the cls get d10,200, and seven cls with a high number of samples and extraordinary public health relevance of the pathogen received d16,000 per year. the network projects were funded with approximately d380,000 in 2014. the nrcs have a more comprehensive work package than the cls and therefore the nrc receive a higher funding. public funding does not and cannot cover the total costs of the reference laboratories. since 2010, the sphere of action and the workload of the laboratories have increased due to advancement of methods. at the same time costs in general have increased, but the grant total has remained unchanged. currently, funding increases for individual laboratories can occur only through money shifting from one laboratory to another or through giving up funding for existing nrcs or cls. in order to maintain the current quality and scope an increase in funding for nrcs and cls is urgently needed. since 2005, the rki, in close cooperation with the advisory board for public health microbiology, has worked to foster collaboration between and among the nrcs and the cls. this concept was amended in a workshop with representatives of public health microbiology laboratories of other eu member states in 2008. ten nrc networks were launched at a work conference of the standing working group of nrcs and cls ("ständige arbeitsgruppe nrz/kl") in stuttgart in 2009. these networks covered the following topics: respiratory tract infections; enteral infections; infections in patients with immune deficiency or pregnancy; invasive bacterial infections; zoonoses; mycoses; sexual and blood transmitted infections; infections of the nervous system; antimicrobial resistance; and parasitoses, tropical and vector-borne infections. the aim of these networks was to facilitate the exchange of diagnostic methods among the nrcs and cls, to improve collaboration in planning and performing studies and to enlarge the geographic coverage of these services. furthermore, these networks should provide opportunities to work on issues beyond single pathogens. scientific coordination and administration are supervised by the rki. the advisory board for public health microbiology and external experts play a pivotal role in selecting the proposed network projects. essential selection criteria are public health relevance and the scientific quality of the proposal, the prospect of success and the cost efficiency of the planned network project. moreover, it is important that these projects contribute to expanding the network's characteristics. an exclusion criterion is if the project addresses established nrc or cl tasks. in 2010, the network projects were funded with d400,000 per year, allocated to ten projects (duration 1.5 years). as of 2011, network projects ran for three years. in the funding period 2011-2013, the rki supported eight projects. within the scope of the projects, common database infrastructures were set up, such as tissue material and serums. other projects performed cross-sectional studies to ascertain data on the prevalence and incidence of different pathogens. in 2014, the rki evaluated the present composition and structure of the networks. the evaluations revealed that difficulties with ethical approval and with compliance with data protection and juridical aspects were the most commonly experienced hurdles during the study planning process. recruiting participating laboratories was also a challenge for some projects. it became clear that early involvement of epidemiological and statistical experts is necessary to further optimize study design and case number planning for the specific research questions and to raise the prospects of success for the projects. in addition to this evaluation, the rki organized a network meeting in 2014, in which all nrcs and cls were represented. members of the advisory board for public health microbiology and representatives of the federal ministry of health participated. at this meeting, the networks shared their experiences. potential for improvement from the perspective of the members of the nrcs and cls as well as from the rki and the advisory board for public health microbiology was identified and discussed. as a consequence of this meeting, the rki initiated the following changes: (1) regular network meetings with all nrcs and cls to address the stated need for regular face-to-face meetings, the rki will organize network meetings every three years. the meetings will take place one year before the start of the upcoming funding period for network projects, so that the nrcs, the cls and the rki can elaborate on the content and structure of project submissions. (2) basic funding for the networks the rki will provide annual basic funding to allow for separate meetings of the respective networks, to facilitate exchange among network participants regardless of successful project applications. these meetings can be used for more intensive preparation of new project proposals and should strengthen network cohesion. (3) stronger presence of the networks on the internet to satisfy network demand for the presentation of network projects to a larger professional audience, accepted projects will be presented on the rki's internet site. (4) decrease in the number of funded projects in the past, the rki funded up to eight projects; in 2014, the institute decided to decrease the number of projects funded per period in the future. in the current funding period four projects were selected for funding. in the following period only two projects will be financed. that implies higher financial support for single projects, which could be used to employ a study coordinator. (5) two-stage application procedure for network projects the rki installed a two-stage application procedure for network projects. as the first step, the networks formulate short pre-applications. the rki screens these short concepts for network projects with the help of the advisory board for public health microbiology and external experts. in the case of positive assessment, the networks are asked to submit a detailed project proposal for final evaluation. during the last 20 years, the field of public health microbiology has seen many changes. the everyday work of local public health agencies depends on the professional expertise of national reference centers (nrcs) and consultant laboratories (cls). meanwhile, the public often sees the relevance of public health microbiology only within the context of serious health events. during periods of restricted financial resources, the need for public health infrastructures is consistently questioned. the large ehec o104 outbreak in hamburg during 2011 provides an example of the importance of public health laboratory infrastructures (frank et al., 2011) . during the hamburg outbreak caused by fenugreek sprouts, the german public health system successfully investigated and controlled the outbreak, which would not have been possible without support from the nrc for enteral infections and the cl for hemolytic uremic syndrome (hus). this support would not have been possible without these highly specialized laboratory structures. the work of all other nrcs and cls is also highly relevant, since their work and expertise help in the efforts to contain and prevent higher levels of infectious disease. nevertheless, there is also room for improvement in germany. for example, the anticipating of new outbreak situations that might require cooperation with the responsible veterinarian and food authorities or with other national authorities should be the focus of optimization plans. the creation of a prospective network of eu-wide public health microbiology reference laboratories is currently being discussed within the european union, which will have consequences for the public health laboratory systems of each member state. from this perspective, considerable future challenges to the german public health laboratory system can already be foreseen. thus, the structures established during the past 20 years should be adaptable so that the responding public health infrastructures can react adequately to the upcoming challenges. sandra beermann, franz allerberger, angela wirtz, osamah hamouda and reinhard burger have no financial disclosures to declare. structural requirements and conditions for effective microbiological diagnostics in disease outbreaks legionnaires' disease outbreak associated with a cruise liner core functions of microbiology reference laboratories for communicable diseases epidemiology of infection in germany large and ongoing outbreak of haemolytic uraemic syndrome prioritisation of infectious diseases in public health: feedback on the prioritisation methodology invasive haemophilus influenzae infections in germany: impact of non-type b serotypes in the post-vaccine era a cluster of invasive meningococcal disease in young men who have sex with men in berlin helicobacter pylori resistance to antibiotics in europe and its relationship to antibiotic consumption developing national epidemiologic capacity to meet the challenges of emerging infections in germany contact investigation for imported case of middle east respiratory syndrome reduction in the incidence of invasive pneumococcal disease after general vaccination with 7-valent pneumococcal conjugate vaccine in germany laboratory diagnosis of paediatric tuberculosis in the european union/european economic area: analysis of routine laboratory data dengue virus infection in a traveller returning from croatia to germany how many outbreaks of nosocomial infections occur in german neonatal intensive care units annually? detection of local influenza outbreaks and role of virological diagnostics epidemiology of streptococcus pneumoniae serogroup 6 isolates from ipd in children and adults in germany scientific advice: crisis counsellors we thank all nrcs and cls for their excellent work during the last 20 years. key: cord-285162-srkd3wh0 authors: jung, f.; krieger, v.; hufert, f.t.; küpper, j.-h. title: how we should respond to the coronavirus sars-cov-2 outbreak: a german perspective date: 2020-06-05 journal: clinical hemorheology and microcirculation doi: 10.3233/ch-209004 sha: doc_id: 285162 cord_uid: srkd3wh0 background: in the early phase of the covid-19 pandemic germany missed to set up efficient containment measures. consequently, the number of cases increased exponentially until a lockdown was implemented to suppress the spread of sars-cov-2. fortunately, germany has a high capability for coronavirus lab testing and more than 30,000 icu beds. these capabilities and the lockdown turned out to be an advantage to combat the pandemic and to prevent a health-system overload. aim: the aim was to predict the plateau day of sars-cov-2 infections or deaths. results: the effect on the viral spread of the german measures taken and the impact on the peak of new infection cases is shown. by normalizing daily case numbers, the plateau day of the current outbreak in germany could be calculated to be reached at april 12, 2020 (day 103 of 2020). conclusion: normalized case number curves are helpful to predict the time point at which no further new infections will occur if the epidemic situation remains stable. upon reaching the plateau day during a lockdown phase, a residual time-period of about 2-3 weeks can be utilized to prepare a safe unlocking period. as can be learned from asian countries such as south korea and taiwan there must be strict rules to keep the risk of infection low. those include social distancing, face mask wearing in combination with digital contact tracing and serosurveillance studies. following those rules, a safe dance around the infection curve allows to keep the population at a reduced infection rate. in december 2019, a novel coronavirus emerged in the metropolis of wuhan, china, causing a severe lung disease. on december 31, china informed the who of a total of 27 patients with pneumonia, and already on january 7, 2020, chinese scientists succeeded in identifying the infectious agent. the new coronavirus sars-cov-2 is highly related to the well-known bat-borne sars-cov which emerged in february 2003 [1, 2] and to the middle east respiratory syndrome coronavirus (mers-cov) detected in 2015 [3] . the 2003 global sars outbreak spread to more than two dozen countries in north america, south america, europe, and asia before it was contained. more than 8,000 cases with a mortality of 10-50% depending on age occurred globally [4, 5] . on january 11, 2020, china reported the first death from the new disease covid-19. china reacted with severe counter measures including quarantine and complete highly controlled lockdown of the affected areas. in the following week first cases outside of china were reported from thailand and japan which were imported from wuhan and first evidence of human to human transmission was reported. on january 21, the first imported case appeared in the usa and on january 24, sars-cov-2 emerged globally in many other countries including europe where first cases were reported from france [6] [7] [8] . on january 26, china reported 2000 confirmed cases and 56 covid-19 deaths and measures to contain the spread were strengthened. already on january 23, the chinese government ordered the complete lockdown of social and economic life in wuhan city, later followed by nationwide closure of schools and universities. on january 27, the infection was detected in germany for the first time. an employee of the bavarian company webasto was infected by a chinese visitor to the company who later tested positive for sars-cov-2 after her return home to china and was apparently almost symptom-free in germany. on january 30, the who declared the status of health emergency because of covid-19. however, the federal authority for infectious diseases in germany, robert koch institute (rki), still defined the risk for germany as being low and did not recommend to close borders and stop incoming flights to germany. the experts believed that all emerging sars-cov-2 cases were under control and contact persons quarantined. however, from that time point on the outbreak within germany increased rapidly because dozens of sars-cov-2 infected people returned from ski vacation in tyrol and from italy. failure to impose an early ban on entry into the country from the risk areas in austria, italy and china was a serious mistake, particularly when the strategy to combat the outbreak is based on eradication. besides that, in germany the federal structures of the public health service hampered a straight-forward approach to fight the pandemic. despite the fact that there was strong evidence of rapid person-to-person transmission [9] even before classical clinical symptoms of a respiratory disease were present [10] carnival meetings were held in different regions such as in the district of heinsberg and other cities in the west and southwest of germany pouring oil into the fire of the outbreak. as a result, on march 10, over 300 people in the heinsberg district tested positive for sars-cov-2. on march 17, the rki classified the risk situation for germany as moderate to high. until this point, there were already more than 9,000 confirmed sars-cov-2 cases and 26 covid-19-related deaths in germany. the german public learned about the strategy of herd immunity meaning that at least 60% of the population will be infected to create a protective barrier. at this stage, there was no reliable information on covid-19 mortality. the who calculated the case fatality rate to be 3-4 %, with the true infection fatality rate to be much lower (who situation report 46 as of march 6, 2020). assuming an infection fatality rate of 0.5 % for sars-cov-2, herd immunity of the german population would generate about 250,000 deaths -by covid-19 only. in addition, there would have been further deaths due to massive overload of the german health system. on march 18, german chancellor angela merkel for the first time addressed the population directly in a speech on the coronavirus outbreak. she described the situation as follows: "it is serious. take it seriously, too!" since world war ii, there has been no challenge to the country where national solidarity was so important as right now, she said. on march 22, following a consultation with the federal state's prime ministers, the german chancellor tightened up the measures and announced a total of nine rules of conduct for germany to be valid from midnight on monday, march 23. the central point was "to reduce public life as far as it is justifiable". this included limiting contacts to persons other than those living in the same household to the bare minimum, keeping a minimum distance of at least 1.5 m in public, only two persons not living in the same household are allowed to meet, people are still allowed to go to work, to the doctor, to shop, to do outdoor sports alone, but parties in groups or meetings in parks were not allowed any longer. service and catering establishments as well as restaurants were closed. these guidelines were initially valid for two weeks. universities, schools, and kindergartens were already closed on march 16. until the first day of lockdown in germany on march 23 (day 83; day zero: 01/01/2020), about 29,000 people were already tested positive for the virus. until april 12 (day 103), 127,459 cases and 2996 deaths due to covid-19 were identified in germany. figure 1 shows that until march 20 (day 80), the daily cases of new confirmed infections increased with doubling times between 1-5 days, showing a strong exponential rise of positive tests for sars-cov-2 infections in germany. however, it is unlikely that the obvious decline of the curve after day 80 already reflects official counter measures of the german government. there is a delay of at least 10 days between an infection event and the registration of a positive test due to the virus incubation time of at least 5 days, the test time and the time until the positive result is reported to the authorities. cumulative cases reported until march 20 reflect infection events until march 10, i.e. at a time point when the german public was not officially warned about the covid-19 risks. however, it is possible that the number of positive tests at day 80 was still limited by the overall capacity of pcr-based sars-cov-2 detection. one week after the initial lockdown, on march 30 (day 90), the highest number of new cases per day was reported (fig. 1) . thereafter, the number of new daily cases started to decline continuously. doubling times show a flat course over the first 90 days. then they started to increase strongly by about day 100 (april 9, 2020). at this time point, the test capacity was almost doubled in germany. thus, the declining number of new cases of persons with covid-19-like symptoms should not have been affected any longer by the pcr testing capacity. this result should thus reflect the counter measures of the german government, especially the lockdown since march 23, and the substantial discussions of experts and politicians in public media of germany. doubling times were then steadily increasing, reaching 30 days or more since day 106. korea and japan to document the different strategies followed during the covid-19 crisis. it is obvious that in the east-asian countries measurements were taken right at the beginning of the sars-cov-2 pandemic to contain the virus spread. taiwan and south korea used their knowledge from the first sars pandemic in 2003 and the 2015 outbreak of mers-cov. in south korea, where a religious community initiated a fatal infection cluster in the city of daegu, schools were closed soon, infected persons were efficiently tracked with smartphone apps and rigorous testing for sars-cov-2 infections were performed [3, 11] . taiwan used a combination of big data analytics, community protection and rigorous testing to combat the crisis. as being closely located to the mainland of china, taiwan was at high risk for outbreak of covid-19, but the country was able to implement fast and efficient counter measures [12, 13] . by the end of february 2020, the government of japan recommended closing of schools, entry ban of people from coronavirus risk regions and a stop of sports and cultural events. these early reactions and the fact that the japanese are used to wearing face masks during seasonal influenza [14] seemed to help combat the sars-cov-2 outbreak until end of march 2020. after a period of stagnation, cases in japan were reported to increase again as people were reducing their social distancing in public. however, the total number of confirmed cases is still much lower than reported for european countries. common elements of these asian states were the immediate action of governments to implement certain social distancing strategies and the wearing of face masks in public to reduce the number of new cases, which has proven to be effective to prevent transmission from infected individuals [15] . by contrast, the three european states had some delay in their national responses to the sars-cov-2 pandemic. at the starting points of the outbreak during the end of january 2020, there were neither discussions on travel entry bans nor recommendations on social distancing, and wearing of face masks in the public was also not recommended. this led to a longer phase of exponential growth of sars-cov-2 infections and deaths in germany, france and italy and caused cumulative case numbers to grow significantly higher in comparison to the east-asian countries (fig. 2) . the data were obtained from the following sources: taiwan, south-korea: and japan: www.ecdc. europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-world wide; germany: https://www.rki.de/de/content/infaz/n/neuartiges coronavirus/ fallzahlen.html; france: who.sprinklr.com/region/euro/country/fr, italy: github.com/pcm-dpc/covid19) . the data obtained from the above listed sources is put in to a context described herein with. our policy regarding the information format is prioritizing open source and free software. we therefore make all data retrieved and analyzed hereby available at corona.milliways.online. due to the imperative of social distancing and the lockdown decreed in european countries, the increase in case numbers flattened out considerably. figure 2 shows that for germany the lockdown could allow to keep the cumulative number of cases below 150-200 thousand. this clearly would prevent the collapse of the health system in germany. this is best seen in logarithmic representation. the scope of this work is primarily to provide a forecast for the time when theoretically there will be no more growth of confirmed cases. at that time point the growth of values (e.g. corona cases confirmed) is zero -resulting also in zero slope of the curves in fig. 2 . however, it is not possible to read from this cumulative diagram the exact point in time when no more cases should occur, as the slope at the peak is getting flatter. to overcome this problem, one can plot normalised growth rates (corona cases at day n -corona cases at day n-1) / corona cases at day n) against a linear timeline. this normalization keeps each rate of change in the range between 0% and 100%. by plotting these normalized change rates against the standardized day counts, an approximate linear behaviour can be observed. the approximation lines meet the x-axis at the day when no further infections or deaths will occur -provided that no systematic changes in the underlying social epidemic behaviour occur in the following days. we call this day the "plateau day". this type of analysis enables health-policy makers to adjust in time to the point at which both new cases and deaths will end. figure 3 shows that germany, france and italy reached their calculated plateau days, i.e. the days when no further confirmed sars-cov-2 cases should be found, at day 103, 107 and 101, respectively. the respective plateau day of deaths is 7-14 days later for germany and france, but only 3 days for italy. it can be seen from the curves for germany and italy, that there were still new cases detected at the time point of the plateau day, when the approximation line meets the x-axis. of course, the infection events that led to those newly confirmed cases occurred at least 10 days before and could reflect variations in western-oriented societies tending to behave individually rather than collectively. in contrast, south korea has achieved the fastest descent with only very few further cases detected at the expected plateau date. the same course is to be expected from taiwan. this points out that efficient measures along with a high compliance of a population can lead very quickly to success. in the case of japan, it is different. this country always showed low numbers (see day rate), but there was also a moderate rate of testing (less than 10,000 tests per day). using the actions described above, japan fought their way down to zero on day 82, but then popular events such as the cherry blossom festival occurred, and people started to behave more careless. subsequently, more action such as regional or general lockdown, social distancing etc. is required for japan to keep sars-cov-2 infections low. the coefficient of determination (r 2 ) assesses the quality of fit of the chosen linear model and thus its ability to predict an outcome. since the zero line is reached for taiwan and also south korea and hardly any new cases occur, a prediction of the linear correlation is no longer possible. regarding japan, the fluctuations are too large for successful model fitting (only 8% of the fluctuations are due to time). thus, there are strong other factors that must explain the 92% fluctuation in the "normalized rate of change per day". however, the data show that outcome prediction by a simple linear model is possible for italy, france and germany. a forecast can thus be made when no more cases will occur if social behaviour does not change. table 1 shows times of plateau of corona infections (f(0) in table 1 ) and of deaths calculated according to fig. 3 . in addition, the time delay between plateau of infections and deaths is shown. for those countries, table 1 provides the relevant data in relation to the cumulated cases, population sizes and median age. since march 23 (day 83) a strict lockdown was started in germany. public life was shut down almost completely, schools, kindergartens and universities were closed. many service providers such as hairdressers and all restaurants were closed in germany. because of the lockdown, as many people as possible worked from home. in contrast, not retarding the exponential virus spread in germany characterized by short doubling times in the first weeks of march would have resulted in more than 600,000 sars-cov-2 cases by the end of the month (fig. 4) . that clearly would have knocked out the german health system due to the limited capacity of 30,000 icu beds, because about 5% of infected persons need intensive medical care according to rki information. thus mentioning the dramatic covid-19 risks on march 18 by the german chancellor angela merkel was one of the last chances to address the attention of the german population in order to slow down the sars-cov-2 spread preventing the breakdown of the german health care system. at the beginning of the sars-cov-2 outbreak, the strategy of herd immunity was pursued in germany, the uk and in sweden. the aim was simply to order measures that would flatten the curve in order to limit the number of people infected simultaneously to a level acceptable to the health care system. this strategy is also called mitigation. however, as mentioned above, this mitigation strategy would have caused at least 250 thousand deaths in germany assuming 60% of the population to become infected based on a fatality rate of only 0.5%, this is not comparable to the death toll to be paid yearly for seasonal influenza, but rather to an armed conflict. a comparison with seasonal influenza outbreak is not possible, since the population is immune naïve to sars-cov-2 and the mortality is at least 5 to 10 times higher compared to seasonal influenza. and even the influenza viruses have a high potential to cause severe outbreaks of public concern as documented in the 1918, seasonal influenza outbreaks after 1918 have never brought the german health care system to a collapse. the analysis of available clinical data on covid-19 clearly revealed that symptoms and diagnostic tests could not be explained by impaired pulmonary ventilation alone. what is special about this disease is that it is a kind of microcirculatory disorder, which is obviously associated with generalized endothelial dysfunction [16] . this highly thrombotic syndrome leads to thrombosis and embolism. in many organs such as lung, liver, kidney, brain and myocardium, vascular occlusions occur in branch arteries as well as in branch veins, which can have a hereditary effect on local microcirculation and thus on organ function [16] [17] [18] [19] . in contrast to influenza -which is often erroneously used for comparison -there is a considerable difference in clinical significance here, particularly in irreversible vascular damage and residual organic impairments. the alternative strategy to mitigation is called suppression. germany as well as many other countries initiated this suppression phase with the decision to lock down. this is a decision that has probably saved hundreds of thousands of lives in germany and other states. in the long run, however, the lockdown would entail serious economic and social costs. the lockdown can therefore only be temporary. in order to have a vision of a situation afterwards, it is helpful to compare the development of sars-cov-2 infections in germany with that in asian countries. immediately the main difference of the development can be seen in march. the asian countries south korea, japan and taiwan had moderate increases in case numbers, far below the critical values for their respective health care systems. while in europe the epidemic was contained much too late, taiwan shows how successful early measures can be. following the sars experience of 2003, a national health command centre (nhcc) was established with the central epidemic command centre (cecc) as the central coordinating body. the cecc has rapidly produced and implemented a list of at least 124 action items including border control from the air and sea, case identification (using new data and technology), quarantine of suspicious cases, proactive case finding, resource allocation (assessing and managing capacity), reassurance and education of the public while fighting misinformation, negotiation with other countries and regions, formulation of policies toward schools and childcare, and relief to businesses [12] . these measures were so effective that only 6 patients died from a total of 397 confirmed infections in a population of more than 23 million people. in the case of south korea there was almost no increase any longer at this time. in contrast, germany, italy and france recorded very steep increases from march 5 to 21, with increases being exponential over a period of several weeks. as described above, the curves flattened out with calculated plateau days until mid of april 2020 ( fig. 3 and table 1 ). another comparison is interesting: germany and france on the one hand and japan on the other hand had roughly the same numbers of confirmed cases at the beginning of march. until the end of march (day 91), japan, however, has managed to stabilize these at under 5,000 confirmed cases, while germany had almost 71,000 and france almost 52,000 confirmed sars-cov-2 infections. the charts show that the asian countries have so far coped well with the crisis. however, in the case of japan, it is noticeable that the trend curve has been rising more strongly again since the end of march. the situation in countries like italy, france and spain (not shown) was more than worrying by the end of march 2020. germany, with its very efficient health care system and a high number of icu beds, has managed to achieve the lockdown just in time and prevented an overload of the health care system. what was the reason for these different developments in europe and asia: 1) until the turnaround, europe mainly pursued the strategy of mitigation, with the aim of gradually achieving herd immunity. this led to an exponential increase in case numbers over weeks, thousands of deaths, and a supercritical strain on health care systems in several countries. 2) the asian strategy was different to that: there was a very rapid lockdown to contain the infection and then the countries implemented follow-up measures with the aim of suppressing the virus spread. examples are the complete lockdown in china, and a moderate lockdown in japan (e.g. schools closed, restaurants open). in china, the number of cases was stabilized at under 100,000 confirmed cases (not shown) -at 1.4 billion people, and in japan at under 5,000 infected people -at 126 million. consequently, the number of sars-cov-2 infected persons compared to the total population was low. however, the asian strategy is also based on the aim to avoid any exponential increase of sars-cov-2 cases at any time. the combination of strong suppression with controlled release was elegantly described as "hammer and dance" strategy [20] . virus replication is stopped when the basic reproduction number (r-value) of the virus drops below 1. in the exponential course of infection, the average of r is 2-3, i.e. each infected person infects at least 2-3 people. from the epidemiological side, r must be below 1 to stop the outbreak. however, this contrasts with the civil liberties of citizens. thus it is a "dance" around the curve, since a sensible and democratically legitimate balance must be constantly struck between the medically and epidemiologically necessary suppression measures and the civil liberties of citizens. in japan we recently saw an increase of cases after almost stopping the spread. this might be due to a more carefree behaviour of the people or a simple result of increased virus testing. since the asian countries are ahead of the european countries europe should learn from asia how to manage such an outbreak. given the lack of antiviral therapy or vaccine, the following measures should be implemented during the "dance" phase: 1. large scale pcr-testing to identify and quarantine infected patients and contacts. 2. quantifying sars-cov-2 transmission using epidemic control with digital real-time contact tracing. 3. serosurveillance of the population to figure out the people who have passed infection and acquired immunity. 4. maintaining social distancing and hygiene rules 5. prohibit all major events and maintaining travel restrictions across national and international borders. 6. wearing of surgical masks or even self-made face masks is mandatory since they prevent transmission of human coronaviruses and influenza viruses from symptomatic individuals. 7. introduction of body temperature scans as an additional measure for personal protection during everyday activities. 8. protect all health-and elderly care workers with ppe including n95 /ffp3 masks. 9. travel entry ban for persons from covid-19 risk regions or, alternatively, quarantining those persons upon entry. 10. re-implementation of regional lockdowns in case of endemic outbreak of sars-cov-2. for any lockdown, it is helpful to predict the time point at which no further new infections will occur by using normalized case number curves. upon reaching the plateau day, a residual time-period of about 2-3 weeks must be fixed for safe release. depicting normalized curves as seen in fig. 3 also indicates compliance of the population on the governmental recommendations. following those rules, a safe dance around the infection curve is possible to keep the population at a reduced infection rate in order to get the economy back to work and revitalise social and cultural life. if there is a pandemic with a new pathogen of unknown lethality and mutation rate, a hammer and dance suppression strategy should always be preferred over the strategy of herd immunity to dramatically reduce the evolutionary potential for pathogens. in the above-mentioned article from tomas pueyo a list of measures of varying effectiveness and cost is given. the decision-makers in each country must determine which weapon arsenal or, to put it less martial, which dancing shoes are best suited to permanently limit the spread of the virus. genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding on the origin and continuing evolution of sars-cov-2. national science review innovative screening tests for covid-19 in south korea how we should respond to the coronavirus sars-cov-2 outbreak a decade after sars: strategies for controlling emerging coronaviruses summary of probable sars cases with onset of illness from 1 rapidly increasing cumulative incidence of coronavirus disease (covid-19) in the european union/european economic area and the united kingdom first cases of coronavirus disease 2019 (covid-19) in france: surveillance, investigations and control measures potential scenarios for the progression of a covid-19 epidemic in the european union and the european economic area influenza-associated pneumonia as reference to assess seriousness of coronavirus disease (covid-19) transmission of 2019-ncov infection from an asymptomatic contact in germany covid-19 national emergency response center e, case management team kcfdc, prevention. contact transmission of covid-19 in south korea: novel investigation techniques for tracing contacts response to covid-19 in taiwan: big data analytics, new technology, and proactive testing the preventive strategies of community hospital in the battle of fighting pandemic covid-19 in taiwan wearing face masks in public during the influenza season may reflect other positive hygiene practices in japan respiratory virus shedding in exhaled breath and efficacy of face masks endothelial cell infection and endotheliitis in covid-19. the lancet contrast enhanced ultrasonography (ceus) to detect abdominal microcirculatory disorders in severe cases of covid-19 infection: first experience large-vessel stroke as a presenting feature of covid-19 in the young the hammer and the dance key: cord-254148-wc762p6v authors: prell, tino; siebecker, frank; lorrain, michael; eggers, carsten; lorenzl, stefan; klucken, jochen; warnecke, tobias; buhmann, carsten; tönges, lars; ehret, reinhard; wellach, ingmar; wolz, martin title: recommendations for standards of network care for patients with parkinson’s disease in germany date: 2020-05-13 journal: j clin med doi: 10.3390/jcm9051455 sha: doc_id: 254148 cord_uid: wc762p6v although our understanding of parkinson’s disease (pd) has improved and effective treatments are available, caring for people with pd remains a challenge. the large heterogeneity in terms of motor symptoms, nonmotor symptoms, and disease progression makes tailored individual therapy and individual timing of treatment necessary. on the other hand, only limited resources are available for a growing number of patients, and the high quality of treatment cannot be guaranteed across the board. at this point, networks can help to make better use of resources and improve care. the working group pd networks and integrated care, part of the german parkinson society, is entrusted to convene clinicians, therapists, nurses, researchers, and patients to promote the development of pd networks. this article summarizes the work carried out by the working group pd networks and integrated care in the development of standards of network care for patients with pd in germany. of evidence-based treatment guidelines, the selection of motivated practitioners, regular training, commitment to compliance with the guidelines, patient-centered treatment, and transparent outcome quality [9, 12] . the core element of patient care within a network should be the implementation of a standardized treatment pathway. this defines the best possible sequence of treatment steps on the basis of guidelines and medical expertise. if possible, all patients within a network should be treated with specialized neurologists, registered neurologists, and gps working in a collaborative manner. there should be flowing boundaries to allow equal, individual care concepts based on medical necessity. in our opinion, the establishment of such a treatment pathway must be individually oriented in each network to the corresponding network structures, regional characteristics, and resources available in each case, making simple transferability between different networks impossible. nevertheless, core elements will certainly be available in different networks. this review, therefore, provides an overview of evidence-based recommendations for the network care of patients with pd within the framework of a multisectoral, multiprofessional setting. the authors met in cologne in 2019 for a roundtable discussion and to organize the foundation of the working group pd networks and integrated care, part of the deutsche gesellschaft für parkinson und bewegungsstörungen (dpg). the working group has the following aims: synchronization of supply networks in germany, development of minimum standards, development of joint research projects, further development of nursing staff qualifications, and development of qualification standards for therapy groups. the dpg working group pursues the goal of improving patient care in close cooperation with other physicians, therapists, and patient support groups. the roundtable discussion was sponsored by dpg (travel costs). following introductions and stated aims, various points of interest (existing german network structures and aims, communication strategies, standards of network care, etc.) were discussed. no formal votes were taken at the meeting. the discussions identified general points of agreement. to give recommendations for a standard of network care, one has to acknowledge the existing care paths for patients with pd in germany. typically, the initial symptoms are not identified as parkinsonism or pd-specific symptoms by the patients themselves. instead, they usually approach their gp with motor or even more important and frequent nonmotor complaints (e.g., obstipation, pain and depression). occasionally, physiotherapists treating back pain or degenerative joint symptoms realize that these are the first signs of motor symptoms (e.g., rigidity) related to pd and that the patient should be referred for a pd diagnostic workup. patients who live in rural areas are more likely to have their gp identify symptoms as being related to pd (13) . however, the gp model in germany is not as rigid as in other countries, and many citizens not only have a primary care physician but can also consult specialists (e.g., internal medicine, orthopaedists, etc.), depending on their prior health care contacts and requirements throughout their lifetime. parkinsonism refers to a clinical presentation characterized by the presence of bradykinesia plus rest tremor or rigidity [13] . bradykinesia is a generalized slowing of movements and repetitive motion fatigue. it may present as hypomimia ("masked face"), hypophonia, worsening of fine-motor tasks, micrographia, difficulty turning in bed, or reduced arm swing with side difference. additionally, distinct changes of gait and balance, like short steps, shuffling gait, and uncertainty when turning around are common. rigidity is the resistance that can be assessed clinically by passively flexing and extending a patient's limb. typically, the patient complains about stiffness and pain, which often manifests as shoulder or back pain. while kinetic and postural tremors may occur, the rest tremor is the most common type of tremor in early pd. patients with these clinical signs should be referred to a neurologist for further diagnosis, because, in germany, the time between the appearance of the first symptoms and the diagnosis is significantly longer when patients with these symptoms see their gp [5] . patients with symptoms that may be related to pd should be asked about pd-typical nonmotor signs such as sensory symptoms (loss of smell, pain), depressed mood, rapid eye movement-sleep behavior disturbance, periodic limb movement disorder, or constipation, which frequently occur years before motor signs are realized. thus, one recommendation for standard of care in the initial phase of the disease course is physician awareness of the first signs of pd (which could be achieved with better information and secondary prevention standards in the network) and early referral of patients to a movement disorder specialist (which could be achieved by specific disease management programmes). the movement disorder specialist should be a neurologist with many years of experience caring for patients with pd. in germany, there are specific recommendations for patient referral in this context that can guide decisions in the outpatient setting [6] . in 2015, the official international parkinson and movement disorder society (mds) clinical diagnostic criteria for pd were proposed [13] . the benchmark for these criteria is an expert clinical diagnosis. however, the criteria can be easily applied by clinicians with less expertise in pd diagnosis [14] . in the mds criteria, motor symptoms remain the core feature of the disease, defined as bradykinesia plus rest tremor or rigidity (explicit instructions for defining these symptoms are given). after consideration of absolute exclusion criteria (which rule out pd), red flags, and supportive criteria, the diagnosis of clinically established pd or probable pd can be made, or pd can be ruled out. besides anamnesis, clinical assessment with cerebral imaging (cranial mr imaging [mri] is preferred) should be performed to exclude symptomatic causes of pd symptoms. in case of divergent clinical and mri-based diagnoses, the clinical assessment should take precedence. however, a differentiated approach is required for the numerous subsequent apparatus and drug tests. the evidence shows that levodopa and apomorphine tests are not as meaningful as standard levodopa therapy in differentiating between established pd and atypical parkinson's syndrome. a negative test does not rule out a response to longer-lasting levodopa treatment. this suggests that levodopa and apomorphine tests should not be routinely used in differential diagnosis but may be valuable in specific clinical situations [15] . a reduction in olfactory capacity is a sensitive but not specific indicator of pd. therefore, standardized olfactory tests are only recommended in combination with other diagnostic procedures for the diagnosis of pd. striatal dopamine active transporter-single photon emission computed tomography (spect) imaging should be used early in the course of the disease to detect a nigrostriatal deficit in clinically unexplained parkinsonism or tremor syndrome [15] . in contrast, the postsynaptic (i 123-iodobenzamide) spect should not be used for the differential diagnosis of established parkinson's syndrome (syn. idiopathic parkinson syndrome) to differentiate atypical neurodegenerative disease variants. the myocardial 123 mibg-spect can be used to distinguish multiple system atrophy from pd [15] . in addition, functional brain imaging with positron emission tomography is a valuable diagnostic tool for the differential diagnosis of idiopathic parkinson syndrom and atypical parkinsonism [16, 17] . for clinical neurological confirmation of the diagnosis and therapy control, the patient should be examined after 3 months, and thereafter according to clinical need but at least once a year [15]. because even proven experts have to revise the diagnosis of an ips during the course of the disease, the diagnosis should be reviewed at regular intervals. with the rising availability of electronic patient records, another recommendation is that a standard set of information should be generated and stored in the record of each patient with pd after the results of the first diagnostic tests. this information should be available for the patient and his or her health care provider team. referral to a movement disorder specialist is important to improve the accuracy of diagnosis, for case selection and to provide guidance in terms of specialized device-aided therapies, namely, dbs, levodopa/carbidopa intestinal gel (lcig) and apomorphine. consultation from the medical staff of a specialized center may improve motor function and the quality of life in patients in advanced pd stages [18, 19] . patients with the following constellations and symptoms should be referred to a movement disorder specialist even if the disease duration is <4 years [20] [21] [22] : referral to a movement disorder specialist should also be considered for the patient to have access to the most innovative treatment and clinical research options. a substantial number of patients are highly interested in contributing to research, the opportunities for which are typically limited to regional neurologists. recommendations for these patient referrals in the outpatient setting in germany have been proposed [6] . some health care insurance systems reimburse treatment of patients with pd in specialized units. a well established and frequently used multiprofessional inpatient treatment concept in germany is pd multimodal complex treatment (pd-mct). prerequisites for patients taking part in mct are documented physician diagnosis of pd, a constant anti-parkinsonian drug titration, and the application of activating therapies (at least 7.5 h/week). it involves physicians, physiotherapists, occupational therapists, speech therapists, and other specialists for the optimization of pd treatment [3] and usually lasts 7 to 21 days. this therapy programme has been shown to be effective, with a reduction of motor symptoms and nms [23, 24] . richter et al. [3] performed an analysis of 55,141 inpatients with pd who were integrated into this mct from 2010-2016. they found that a large majority of patients with pd need to leave their residence county for an inpatient stay in a specialized pd unit. this limited access to multimodal therapy programmes means that patients sometimes have to travel long distances to receive specialized therapy [3] . there are no generally valid definitions of which patients should be treated within the complex programme and which should not. in view of the heterogeneity, it is difficult to make binding statements about this. a prerequisite should be that the motor or nmss can no longer be satisfactorily treated by outpatient therapy. another prerequisite should be that patients are dealing with limitations in their activities of daily life and have a reduced quality of life. this can be the case, for example, with side effects under oral therapy, motor deterioration, or the high burden of nms. other typical indications for inpatient treatment would be the discontinuation of dbs or the initiation and optimization of therapy with lcig or apomorphine. however, as the disease progresses and progressive limitations in mobility and cognition are observed, the benefits of inpatient treatment must be weighed against the increasing risk of delirium. overall, clinical experience shows a substantial benefit of pd-mct for a large number of patients. the preselection process could ideally be managed by network structures and players. additionally, the positive effect achieved by intense medical and nonmedical intervention should be maintained after release by immediate intensified ambulatory intervention and home-training concepts in order for the patients to benefit from the positive experience. this would be an important incentive for the patient to take part in pd-mct. for patients with pd who need to adapt to complex medication schemes, drug pumps, or dbs devices, a classical outpatient or inpatient setting is not appropriate to sufficiently address clinical problems, while in a neurologist's office or even in a movement center, outpatient clinic time and staff capacities are limited and the results of changes in medication or stimulation of the dbs device can only be monitored in the next (often late) consultation. an in-house stay is associated with an artificial environment that does not reflect the individual's everyday life demands and is less suited for patients with dementia who often cannot cope with an altered environment. furthermore, many patients with pd decline hospitalization for personal reasons such as job issues or having to care for other family members. for these patients, at the border between inpatient and outpatient care and the need for sophisticated treatment strategies, the new comprehensive, individual, and interdisciplinary concept of a pd day clinic has proven to be effective [25] . in the meantime, in germany, several university clinics with a pd focus have established this or a similar pd day clinic concept to close the gap in pd care that have been found to be a transnational issue [26] [27] [28] . the concepts and standards of qualified pd day clinics have been certified recently by the tüv and the german parkinson patient society [29] . in general, a neurologist should be responsible for long-term medical care of patients with pd, and movement disorder specialists should be involved when there is a special issue. however, for various reasons, this is not always possible. neurologists may not be available in rural areas, and even for patients in nursing homes, access to specialized neurological treatment is often limited. this is an important issue, because the number of patients in long-term care facilities will rise sharply in the coming decades [30] . for patients with pd, the interaction between the gps and neurologists is essential. pd networks can make a decisive contribution to ensuring high-quality care of these patient groups. medical treatment is not the only option to control the motor symptoms and nms during the course of the disease. other nonmedical treatment options from other specialists are frequently necessary to improve functional status, performance of daily activities, and quality of life. these specialists include, among others, physiotherapists, occupational therapists, speech therapists, pd nurse specialists, and social workers [31] . specific recommendations for physiotherapists, physicians, and patients with pd were published in the european physiotherapy guidelines for parkinson's disease [32] . health professionals must have sufficient pd-specific knowledge and expertise [33] . physiotherapy has a positive impact on functional activities involving gait, transfers, and balance [32, 34] . the occupational therapist focuses on enabling performance and engagement in meaningful activities [35] . home-based, individualized occupational therapy can improve the self-perceived performance of daily activities in patients with pd [36] . timely referral to physiotherapy, and occupational therapy is recommended because difficulties in daily activities can occur in every disease stage. given the high prevalence of dysphagia and dysarthria during the course of the disease [37] , speech-language therapy, including swallowing techniques, is frequently necessary for patients with pd. a collaborative approach between these disciplines should focus on complementary and different aspects. therapists have to be aware of each other's expertise, and effective and timely communication is essential [35] . pd networks are promising tools to share information about diagnostic results, current treatment goals, and plans. in addition, there are many different nonphysician pd specialists for inpatient and outpatient care, such as pd nurse specialists or parkinson assistants (passs). their different roles and functions are described in another paper in this issue. depending on the location (inpatient or outpatient), the focus of their tasks can be different. these specialists are often familiar with aspects of case management; medication adherence; provision of information, education, psychosocial support, and coping skills; and caregiver support [38] . patients with pd should have 1) regular access to clinical monitoring and adjustment of medication in consultation with the treating physician; 2) regular contact with caregivers, including home visits, as appropriate; and 3) access to reliable sources of information on clinical and social issues affecting patients with pd and their caregivers/families. these functions could be provided by pd nurse specialists or a pass. the positive therapeutical effects of pd nurse specialists are currently evaluated for their health economic impact [39] . in particular, patients with advanced pd may benefit early from palliative care. doctors and nursing staff can provide information about the final phase so that the family can take advantage of adequate care options. palliative care should be aligned with patient priorities and complement other treatments. therefore, advanced care planning might also increase knowledge about end of life issues. generally, it should start early in the course of the disease. it can be started when particular symptoms occur (pain, dyspnoea, dysphagia, and aspiration) or at the very end of life [40, 41] . besides general markers of advanced disease (frequent infections and hospitalizations, malnutrition, etc.), the palliative performance scale can be used to measure the functional status of a patient and to determine the eligibility for enrolment in a palliative care programme [41, 42] . dysphagia with symptomatic aspiration might be taken as a clear indicator when palliative care should begin, because it also involves a discussion about life-prolonging therapies such as tube feeding. figure 1 provides an overview of common players and structures in a local supply network. information on clinical and social issues affecting patients with pd and their caregivers/families. these functions could be provided by pd nurse specialists or a pass. the positive therapeutical effects of pd nurse specialists are currently evaluated for their health economic impact [39] . in particular, patients with advanced pd may benefit early from palliative care. doctors and nursing staff can provide information about the final phase so that the family can take advantage of adequate care options. palliative care should be aligned with patient priorities and complement other treatments. therefore, advanced care planning might also increase knowledge about end of life issues. generally, it should start early in the course of the disease. it can be started when particular symptoms occur (pain, dyspnoea, dysphagia, and aspiration) or at the very end of life [40, 41] . besides general markers of advanced disease (frequent infections and hospitalizations, malnutrition, etc.), the palliative performance scale can be used to measure the functional status of a patient and to determine the eligibility for enrolment in a palliative care programme [41, 42] . dysphagia with symptomatic aspiration might be taken as a clear indicator when palliative care should begin, because it also involves a discussion about life-prolonging therapies such as tube feeding. figure 1 provides an overview of common players and structures in a local supply network. the therapist network (outpatient) directly surrounding the patient and his or her environment is not only linked to the patient, but therapists are also linked to each other. this results in mutual inter-relationships and a flow of information between all professional groups involved (not only between the directly neighbouring ones). a supraregional supply network in the form of clinics and centers is connected to this ''micro-network''. here, exchange and cooperation results. different stationary and semistationary care options are offered and supplemented with, for example, telemedical services (e.g., medical video observation and sensor-based motion analysis). the therapist network (outpatient) directly surrounding the patient and his or her environment is not only linked to the patient, but therapists are also linked to each other. this results in mutual inter-relationships and a flow of information between all professional groups involved (not only between the directly neighbouring ones). a supraregional supply network in the form of clinics and centers is connected to this ''micro-network". here, exchange and cooperation results. different stationary and semistationary care options are offered and supplemented with, for example, telemedical services (e.g., medical video observation and sensor-based motion analysis). self-management means having knowledge, skills, and confidence to manage daily tasks when living with a chronic disorder such as pd. it includes the concepts of self-management tasks (medical, role, and emotional management) and self-management skills (problem solving, decision-making, resource utilization, the formation of a patient-provider partnership, action-planning, and self-tailoring) [43] . patients with pd should be able to monitor progress and problems and to set, communicate, and harmonize their individual therapeutic goals with all members of the health care provider team. in addition, required information for the individual aspects of the disease symptoms, treatments, and side effects/risks should be tailored to the patient requirements and transferred adequately to the patient. health care providers involved in the care of patients with pd can positively influence self-management skills with distinct approaches that mainly focus on education and support. self-management in pd may, therefore, contribute to slower disease progression, reduced complications, and lowered costs [44] . however, self-management support interventions for patients with pd vary in content, structure, and intensity, and little is known about which existing self-management support programmes are most effective. as indicated by a recent overview of self-management support programmes for patients with pd, clinicians should ensure that the key components of education, goal setting, and guided problem solving are included. moreover, adding these skills to the rehabilitation process and including caregivers and peer support systems seems promising [44] . as mentioned above, pd requires close interaction between different care partners in order to provide the best possible care for the patient. rural location, nursing home residence, and the presence of physical or cognitive impairment are common reasons for limited access to specialized pd health care [45] . a pd network can improve access to specialized health care and manage the distribution of resources, tasks, and responsibilities. by doing so, pd networks can help to avoid unnecessary hospitalization and reduce costs [8] . different methods exist to bring pd-specific knowledge and care to the patients in a pd network structure. in this context, telemedicine has shown promising effects for the management of pd. this includes synchronous methods (videoconferencing) and asynchronous methods (e.g., e-mail, smartphone assessments, remote monitoring, and wearable devices) [10, 11, 46] . telemedicine has the potential to allow pd-specific efficient care to be delivered to more patients and more regularly than a traditional model of care [47] . from the patient's view, telemedicine has the advantages of access to specialists, convenience, and time savings [48] . at present, it is applied in several clinical settings due to sanctions imposed for infection prophylaxis in the current sars-cov-2 pandemic, and it is seen to be a suitable tool with which to give advice and treat patients with pd. it also can be used to support outpatient palliative care teams with special neurological knowledge when the patient chooses to die at home [49] . since 2019, the remuneration of video consultation hours has been based on the insured, basic, or consultation flat rate in germany. nevertheless, telemedicine is still limited by patients' limited access to high-speed internet and usability issues (especially in elderly patients) [46] . nevertheless, with the new digital health act (''digitale-versorgung-gesetz" (dvg)), reimbursement for video-based home telemedicine support has begun in germany, and now, home telemedicine needs to be integrated into pd health care workflows. the german health care system is struggling with the issues of separation of care sectors (e.g., outpatient vs. inpatient care) and considerable differences in the provision of care in urban and rural areas. in order to optimize the specialized care of patients with pd in germany, the current care structures must be changed. this can be achieved by establishing pd networks, which act as a link between outpatient and inpatient treatment as well as between patients, caregivers, gps, nonspecialized neurologists, movement disorder specialists, and other therapists. this is a promising way to ensure that a stage-appropriate and patient-specific therapy for pd can be initiated promptly and maintained permanently in accordance with the current guidelines. additionally, new e-health processes might overcome current barriers and limited access to specialized health care and provide both patients and health care professionals with the potential for future seamless care, a strong interaction between health care partners, and involvement of patients and caregivers. interestingly, many patients with pd are using digital media tools and smartphones and thus have access to digital technology [50] . furthermore, the recently released digital health act (dvg) will enable patient-centered technologies as digital health care applications for better support of trans-sectoral pd health care. especially against the background that some studies have found only limited benefits from specialized network structures, it is very important to provide scientific support for the formation of networks in germany. these studies from england or the netherlands that focus on very limited aspects (e.g., pd nurses, physiotherapy) are only transferable to germany to a limited extent [33, 51] . decision makers, planners, and managers need evidence-based policy options and information on the scope of networks [52] . the dpg working group networks and integrated care is therefore an opportunity to provide a framework for various forms of networks, to facilitate the exchange of experience, and to provide scientific support for the various structures and networks with their regional characteristics. the epidemiology of parkinson's disease: risk factors and prevention nonmotor symptoms in parkinson's disease dynamics of parkinson's disease multimodal complex treatment in germany from 2010-2016: patient characteristics, access to 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committee. international parkinson and movement disorder society evidence-based medicine review: update on treatments for the motor symptoms of parkinson's disease physical therapy and occupational therapy in parkinson's disease otip study group. efficacy of occupational therapy for patients with parkinson's disease: a randomized controlled trial dysphagia in parkinson's disease a guideline for parkinson's disease nurse specialists, with recommendations for clinical practice the cost-effectiveness of specialized nursing interventions for people with parkinson's disease: the nice-pd study protocol for a randomized controlled clinical trial specialist palliative care for parkinson's disease palliative care for parkinson's disease using the palliative performance scale to provide meaningful survival estimates self-management education: history, definition, outcomes, and mechanisms self-management support programs for persons with parkinson's disease: an integrative review patientenperspektive auf die versorgungssituation im krankheitsbild morbus parkinson in deutschland-eine querschnittserhebung the promise of telemedicine for chronic neurological disorders: the example of parkinson's disease the promise of telemedicine for movement disorders: an interdisciplinary approach patient views on telemedicine for parkinson disease telemedicine in palliative care: implementation of new technologies to overcome structural challenges in the care of neurological patients the use of digital technology and media in german parkinson's disease patients effects of community based nurses specialising in parkinson's disease on health outcome and costs: randomized controlled trial this article is an open access article distributed under the terms and conditions of the creative commons attribution acknowledgments: travel costs for experts meeting by dpg. tino prell has received bmbf research grant, and honoraria for presentations/lectures abbvie gmbh, ucb pharma gmbh, desitin gmbh, licher mt gmbh, and bayer ag deutschland. frank siebecker reports no conflict of interest. michael lorrain has received honoraria and compensation for consultancy and lecturing from abbvie, afi, bayer, bial, biogen, desitin, merck, nordrheinische akademie, teva, ucb, and zambon. carsten eggers received payments as a consultant for abbvie inc. ce received honoraria as a speaker from abbvie inc., daiichi sankyo inc., bayer vital inc. ce received payments as a consultant for abbvie inc. and philyra inc. stefan lorenzl reports no conflict of interest. jochen klucken reports institutional research grants from bavarian research foundation; emerging field initiative, fau, eit-health, eit-digital, eu (h2020), german research foundation (dfg), and bmbf, and industry-sponsored institutional iits and grants from teva gmbh, licher mt gmbh, astrum it gmbh, and alpha-telemed ag. he is coemployed by the university hospital erlangen, germany, fraunhofer institute for integrated circuits e.v., germany, and the medical valley digital health application center gmbh, bamberg, germany. he works on advisory boards in the field of healthcare technologies and digital health of different associations of medical professionals, industries, and political authorities. he holds shares of portabiles healthcare technologies gmbh, portabiles gmbh, alpha-telemed ag, and received compensation and honoraria from serving on scientific advisory boards for lichermt gmbh, abbvie gmbh, ucb pharma gmbh; he has lectured at ucb pharma gmbh, teva pharma gmbh, licher mt gmbh, desitin gmbh, abbvie gmbh, solvay pharmaceuticals, bial deutschland gmbh; celgene gmbh, lundbeck-foundation. dr. klucken has a patent related to gait assessments pending. tobias warnecke has received honoraria from abbvie (lecture fees, consultant). abbvie acts as coinitiator of the parkinsonnetwork muensterland+ (pnm+) and is cocontractor of the university hospital of muenster. carsten buhmann has received fees as speaker and/or advisor from abbvie, bial, desitin, grünenthal, licher, novartis, tad pharma, ucb, and zambon. lars tönges has received travel funding and/or speaker honoraria from abbvie, bayer, bial, desitin, ge, ucb, and zambon, and consulted for abbvie, bayer, bial, desitin, ucb, and zambon, in the last 3 years. reinhard ehret reports no conflict of interests. ingmar wellach has received honoraria an compensation for consultancy and lecturing from abbvie gmbh, ucb pharma gmbh, desitin gmbh, bial deutschland gmbh, zambon deutschland gmbh, fagron gmbh & co. kg, grünenthal gmbh, and bayer ag deutschland. martin wolz has received honoraria for presentations/lectures from zambon, valeant, desitin, teva, ucb pharma, abbvie, bial, licher, and daiichi sankyo. key: cord-269559-gvvnvcfo authors: kergaßner, andreas; burkhardt, christian; lippold, dorothee; kergaßner, matthias; pflug, lukas; budday, dominik; steinmann, paul; budday, silvia title: memory-based meso-scale modeling of covid-19: county-resolved timelines in germany date: 2020-08-03 journal: comput mech doi: 10.1007/s00466-020-01883-5 sha: doc_id: 269559 cord_uid: gvvnvcfo the covid-19 pandemic has led to an unprecedented world-wide effort to gather data, model, and understand the viral spread. entire societies and economies are desperate to recover and get back to normality. however, to this end accurate models are of essence that capture both the viral spread and the courses of disease in space and time at reasonable resolution. here, we combine a spatially resolved county-level infection model for germany with a memory-based integro-differential approach capable of directly including medical data on the course of disease, which is not possible when using traditional sir-type models. we calibrate our model with data on cumulative detected infections and deaths from the robert-koch institute and demonstrate how the model can be used to obtain countyor even city-level estimates on the number of new infections, hospitality rates and demands on intensive care units. we believe that the present work may help guide decision makers to locally fine-tune their expedient response to potential new outbreaks in the near future. the covid-19 pandemic continues to hold our way of life on this planet in a tight grip. over the whole world, we have now reached more than 10 million infections [1] . while new infections still rise at alarming pace in the united states, brazil, or india, most other asian and european countries that were hit much earlier by the pandemic seem to have succeeded in reducing the number of new daily cases. this success can largely be attributed to fast and locally tailored political measures that introduced severe travel restrictions [2] [3] [4] [5] [6] and curtailed public life. initially, the measures were met by a largely understanding general public. however, the partial necessity of police enforcement and increasing protest against contact restrictions, locally even encouraged by politicians [7] , demonstrate rising anger, fear, or even mental health problems due to the current situation [8, 9] . thus, it is critical to carefully reopen the economy and reestablish public life, while avoiding a relapse and a potential collapse of the health-care system, which may entail much stricter measures again. to reach this goal, however, decisions must be made quickly and often locally at county level, based on reliable data and trustworthy predictions. clearly, accurate models are of essence to capture the disease dynamics at exactly this spatial meso-scale, to predict the number of new infections per day or the number of patients that may require intensive care. here, we focus on the situation in germany, where county-resolved daily and cumulative infection cases are reliably reported by the robert-koch institute (rki, [10] ). we combine two previous modeling advances [11, 12] into a locally resolved, history-type model that captures the spatiotemporal evolution of the pandemic in germany. we use a generalization of typically known sir-type compartment models that allows for a much better representation of the courses of disease [12] . while becoming infected is well represented by a simple ordinary differential equation (ode), the remaining course of disease is captured rather restrictively by these ode-based, sir-type models [13] . based on the integro-differential model introduced by kermack and mckendrick already in 1927 [14] and recently reintroduced by [12, 13] , we model the spatial spread of covid-19 in the following way: for all s < 0, t > 0 and x ∈ ω with ω ⊂ r 2 open denoting the considered spatial region. the normalized initial history datum is given by ) denotes the normalized number of susceptibles. the weight γ i ∈ l 1 ((0, ∞); r ≥0 )) with γ i l 1 ((0,∞)) = 1 describes the evolution of infectiousness, where γ i (τ ) defines the infectiousness of an individual at τ days after the infection event. the interaction term β ∈ l ∞ ((0, ∞) × ω 2 ; r ≥0 ) denotes the interaction between the infectious and the susceptible population. the considered balance law is of nonlocal-history type. nonlocality as well as history in balance laws are receiving increasing attention to model real world phenomena. they provide a more detailed way to model evolution and can be seen as the mesoscopic link between purely macroscopic and fully microscopic models. in the considered application, the microscopic equivalent-agent models [15] [16] [17] -can be interpreted as a measure valued solution to the proposed model. the classically used compartment models (sir, seir) [18] have been widely used to model the viral spread. their recently revealed relationship to hamiltonian mechanics is quite insightful [19] , demonstrating that they constitute a mere simplification of the here considered integrodifferential equations. in terms of the spatial resolutionwhich of course can also be modeled in the compartment models [20, 21] -the classical sir model can be seen as the singular limit of the interaction term, i.e. β(·, * , ) → b(·)δ( * − ) for a given b ∈ l ∞ ((0, ∞); r ≥0 ). the models are generalized with respect to the evolution of infectiousness of infected individuals. the considered model can represent-based on medical data-any course of infectious-ness, in contrast to, e.g., an assumed exponential decay in the widely used sir model. as introduced in [11] , we discretize our spatial domain ω, germany, at county-level (or even city-level), where current containment rules are steadily evaluated and adapted in case local infection numbers rise up again. our county-interaction network is adapted from the global epidemic and mobility (gleam) model [22, 23] , focusing on mid-and shortrange interactions motivated by the severely restricted air travel [24, 25] . taken together, this spatially resolved integrodifferential model allows us to accurately analyze and predict disease dynamics at its various stages and the effect of local measures. to model the spread of the disease in a discretized spatial setting, we consider a finite partition of the domain ω, i.e. where n denotes the number of counties or cities in germany, depending on the spatial resolution. we obtain the following memory type vector-valued initial value probleṁ is the vector-valued normalized initial history datum. we introduce • to denote the transformation of a vector • into a quadratic diagonal matrix, where the entries along the diagonal equal those of the vector. the time-dependent, vector-valued function s ∈ w 1,∞ ((0, ∞); [0, 1] n ) denotes the normalized number of susceptibles. the matrix-valued function b ∈ l ∞ ((0, ∞); r n ×n ≥0 ) denotes the infection rates and interaction between the considered regions ω k with k ∈ {1, . . . , n }. the existence and uniqueness of a solution of the proposed integro-differential equations-continuous as well as discretized in space-is proven e.g. in [12] for all γ i for which there exists > 0 s.t. γ i | (0, ) ≡ 0. this is a rather natural condition, since the incubation time-the period during which the infected are not yet infectious-is positive. based on the history of s, other quantities and subgroups can be determined directly from including medical data on the various courses and infectiousness levels of the disease via corresponding integration weights: we distinguish between the states infectious γ i , symptomatic γ s , tested and quarantined γ q , hospitalized γ h , in intensive care γ icu , recovered γ r and deceased γ d . following the contribution of [ disease progression in our model: (a) light symptoms, recovering without hospitalization, 95% share; (b) hospitalization, recovering without intensive care, 4% share; (c) patients in intensive care and recovering, 0.4% share; (d) patients in intensive care that eventually die, 0.6% share. figure 1 depicts the four different courses of the disease as represented in our model, including their corresponding state transitions and infectiousness levels. note that only the weighted sum γ i = 4 i=1 share i · γ i ,i is necessary for the solution of eq. (1), but the individual contributions allow for detailed descriptions of disease progression from medical data and corresponding post processing. we normalize the integral over γ i such that it represents the probability of infection. we further assume that patients in courses (b) to (d) will be tested positive and are thereby considered in reported infection numbers. the ratio of total versus detected infections is defined as dark ratio ω, thereby representing the factor of unknown cases. since the dark ratio is not necessarily constant in space, this is taken into account by locally scaling the function γ q that represents the detected and quarantined state of course (a) to the appropriate value. since the dark ratio seems to closely correlate with testing capacities [11] , we introduce federal-state-wise dark ratios ω j , assembled in the vector ω, that vary only over states with j ∈ {1, . . . , 16}, due to locally differing behavior patterns and, in particular, political measures to reduce social contacts, the infection rates vary in space and time. based on our previous findings in [11] , we introduce federal-state-wise initial infection rates β j0 with j ∈ {1, . . . , 16}, and two reduction factors β red 1 and β red 2 representing the major restrictions of 1) cancelling large events and 2) contact restrictions. those model parameters are calibrated using data reported by the rki, as described in sect. 2.3. since the shut-down measures were introduced at slightly different times t j1 and t j2 in the different federal states of germany, we model the time-dependent reduction of infection rates via piece-wise constant functionsβ j1 (t) andβ j2 (t) to obtain the overall infection rates in each state (2) to model cross-county interactions, we adapt the gleam short-and mid-range mobility network [22, 23] as introduced in [11] and capture cross-county infections by where β k are time-dependent infection rates, c k are the crosscounty infection weights, n k is the number of inhabitants in the largest city of county k, n max = 3e6 corresponds to the number of inhabitants in germany's largest city berlin, and r kl is the distance between counties k and l. importantly, β k and c k are identical for all counties within one federal state, such that eq. 3 introduces 16 additional model parameters c j with j ∈ {1, . . . , 16} which need to be calibrated based on reported data in the literature (see sect. 2.3). the parameters for the gleam model are taken from [22] and given in table 1 . figure 2b displays the mobility network across germany [11] . note that both the county-internal as well as the cross-county infections contribute to the basic reproduction number in our spatial model. for the distinction of individual counties, we use the municipal directory (gemeindeverzeichnis) from the german federal statistical office (statistisches bundesamt) [27] , which delivers area, shape and population data. we consider city-wise population data, which is accumulated over the entire county or corresponding spatial domain for the respective model. the center of population of each county serves as its spatial coordinates. the detailed description of the courses of disease allows for elaborate post-processing of the solution to evaluate any described quantity. generally, evaluation differs for cumulative and current quantities. the number of cumulative discovered infections q or the number of deceased d are evaluated by double integrals such as current quantities like infectious i(t), those with symptoms, hospitalized or icu patients follow from expressions such as from data the number of positively tested people on day zero is known, but the integro-differential equation model requires initial values for the infected at each spatial node as well as an initial history as a starting point for the integration. initially, we assume exponential growth in all counties described by the ansatz with ν = 0.345 from fitting an exponential function to rki data on cumulative covid-19 cases in all of germany from march 2 to march 6. the initial estimated number of infected ε at time t = 0 in each county can be calculated by combining eq. (4), the number of initially reported cases q 0 , eq. (6) and the time derivativeṡ. from the result and eq. (6), the initial history can be estimated. the high-resolution network model brings with it the challenge for spatially consistent initial conditions. however, most counties did not yet have any known cases on the very first day, limiting the possibility of simply scaling overall initial infections per county by the dark ratio. thus, for the county-based model we selected the distribution of initial infections according to data for march 16 [10] , linearly scaling down the overall number of infections to the number reported on our starting date march 2. to approach our spatially resolved county-model, we followed a cascade optimization strategy. data analysis and preliminary simulations had shown that we require federalstate-dependent dark ratios ω j and infection rates β j0 , j ∈ {1, . . . , 16} [11] . figure 2a illustrates the estimates for the state-wise dark ratios ω j , which we obtain by assuming a germany-wide identical mortality of μ = 6‰ [26] and fitting to the individually reported death tolls, with ω ≈ 6.5. using state-wise identified dark ratios ω j , we first used a coupled system of 16 nodes connecting each federal state to obtain a germany-wide average β and reduction factors β red 1 and β red 2 by fitting the cumulative data for germany via the following objective function the residual r 1 is minimized using a particle swarm optimization (pso) algorithm described in detail in sect. 2.4 with weights w i = 1/(t end − t start )/max(q rki ), w d = 1/max(d rki ) and w s = 0.1/max(q rki ). we then considered state-wise data to fit β j , j ∈ {1, . . . , 16}, while keeping c = 1, leading to the distribution over ger-many depicted in fig. 2c . we fit the cumulative number of confirmed infections reported by the rki [10] for the time period from march 2 until april 25 with the cumulative number of detected infections q as defined in eq. (4), normalized by the maximum cumulative number of reported infections from the rki. this is the time period during which the various shutdown measures were in place without any noticeable relaxation. on top of that, we include the change-rate of infections on our last day april 25 into the residual vector with the weights the weights are state-wise normalized to balance the contribution of heavily and less affected states. the residual r 2 is again minimized using the pso algorithm. finally, we increased the resolution to full county level, amounting to a coupled system of 401 nodes. to re-balance the changed influence of the larger network, we iteratively fitted statewise cross-county weights c j for ∈ {1, . . . , 16} to match the state-wise cumulative infections of the 16 node state-wise model (q sw ) with the accumulated numbers from the 401 node county-based model (q cw ) on the last day of the fit. we used a damped gradient-descent like algorithm to update c j at iteration i + 1 following the rule empirically, we obtained converged cross-county weights within 30 iterations with a limited step size δc max = 0.25 and a damping exponent ζ = 1.5. the final state-wise distribution of optimized cross-county weights c j is displayed in fig. 2d. particle swarms are distributed optimization schemes that treat each realization of the d optimization variables as particles with a position x i and a velocity v i in a d-dimensional bounded search space. particles are initialized with a uniformly random position within the boundaries of the search space and zero initial speed. for the iteration i > 0 the following set of equations describes the behaviour of any particle: the velocity v i+1 is a linear combination of three quantities. the previous velocity v i weighted with the constant factor a results in an inert motion property. the term p i loc − x i represents a force that pulls the particle towards its local attractor p i loc , which is the best position this specific particle has visited so far. multiplication with the constant weight b loc controls the influence of this quantity. in addition to that the randomized diagonal matrix r i loc with values between 0 and 1 enables optimization in varying directions. the global attractor p i glob represents the best position any particle has visited so far and works analogously to the local attractor with the factor b glob . we chose established values for a, b loc and b glob as summarized in table 2 , used a total of 300 particles and followed the 'nearest' strategy when particles cross boundaries of the search space during optimization [29] . to prevent overly fast convergence to a visited attractor without broad coverage of the search space, we employed a so-called ring topology neighborhood, such that the global attractor of a particle corresponds only to the best local attractor of its two neighbors below and above. this way, good positions are slowly propagated through the whole swarm, allowing for enhanced exploration of the search space, which well balances run-time efficiency and identification of the true global optimum. to validate the model, we evaluated the temporal correlation between model predictions and rki data by computing the pearson correlation coefficient r p , the coefficient of determination r 2 = r 2 p and the corresponding p-value to assess statistical significance via the function [r p , p] = figure 3 shows how the optimized spatially resolved memorybased model with 401 network nodes representing each county of germany well reproduces the cumulative confirmed cases in each of its federal states from march 2 until april 25. for cumulative infection data reported by the rki [10] , we find astonishing and statistically significant (all p < 1e − 12) agreement on the temporal evolution. the only state with an r 2 < 0.98 is bremen-a city-state with overall very low infection numbers and a population of less than 700.000. here our quasi-continuum modeling approach and the underlying exponential growth seem to approach their validity limit, and stochastic effects start to prevail. although only the last data point of reported deaths was considered for parameter identification, the model captures the temporal evolution of covid-19 related deaths in each state of germany with remarkable accuracy (all r 2 > 0.91). here, we observe least agreement in the city-state hamburg. in general, the model better captures the evolution in higher-populated states, with overall more infections and death tolls. we note that our fitting procedure only operates on state-based information. to further validate our model, we compare county-wise cumulative infection numbers q as reported by the rki and our model (fig. 4 left and figure 5 shows how the model informs on the temporal evolution of cumulative confirmed cases, with more detailed resolution on the subgroups of symptomatic, infectious, and hospitalized, patients in the icu, as well as the dead. a first kink in the infectious group is clearly visible at the beginning of march due to the cancellation of major events, which then drops significantly when contact restrictions become effective shortly afterwards. figure 6 shows the model predicted spatial distribution at county resolution of infectious, symptomatic, hospitalized, and patients in intensive care, following from the individual disease courses in fig. 1 . we consider a period from early march, where the exponential growth of the disease started in germany, until early june under the assumption that the contact reduction factors stay in place. in early march, most of the infected were at an early stage of the disease, i.e., most of them were infectious but did not have disease specific symptoms yet (on average, the first symptoms appear on the fifth day after the infection event [26] ). this explains the delay in symptomatic infections clearly visible in fig. 5 . in our model, we assume that most of the symptomatic voluntarily quarantine themselves and no longer infect others, implying that the infectiousness decreases when people move to the symptomatic group (cf. fig. 1 ). the infectious state ends at the latest when the symptomatic have been tested positive for the virus and are quarantined. the symptomatic state of covid-19 lasts approximately nine days on average [26] , explaining why the symptomatic group is about double in size compared to the infectious group in fig. 5 . figure 6 also shows the delay in covid-19 cases that need inpatient treatment or even intensive care. as reported in [26] , infected are typically hospitalized for nine days after the infection event at a probability of 4.5%. as this is encoded in the courses of disease, the snapshot on march 2 reports hardly any hospitalized patients. according to [26] , patients finally, we show how our model can be adapted to locally increase resolution to individual city-or community level. fig. 7 spatial distribution of the infectious (i) on april 2 at county level for all of germany (top) and with locally increased resolution to community-level (bottom). the non-densified part of the domain is greyed out for the sake of better visual contrast. zoomed regions show county-and community resolution for counties erlangen, fürth, nürnberg and their rural surroundings. note that the proposed macroscopic model reaches its validity limit for very low daily new infections within one subregion figure 7 shows the germany-wide county-level simulation (top), with a zoom into the metropolitan area of nürnberg, erlangen and fürth and its surrounding counties. increasing the resolution within this domain to community level (bottom) but maintaining county-level for the rest of germany leads to a network of 464 nodes. the zoom-in clearly shows that county infections are dominated by their largest cities, following the three purple areas that represent nürnberg, fürth and erlangen from bottom to top, underpinning our formulation of the cross-county infection terms (cf. eq. (3)). surrounding communities suffer much less infections due to their much smaller populations. gray areas correspond to rural public space not assigned to a specific community [27] . we have presented a memory-based network model to predict the spatio-temporal outbreak dynamics of the covid-19 pandemic in germany. the model considers the effects of political measures, the cancellation of major events and contact restrictions, and the different possible courses of the disease, which is not possible when using traditional sirtype models. it well represents the evolution of confirmed cases and deaths reported by the rki from march 2 until april 25. we have then used the model to predict the further developments until june and have provided estimates for the county-wise required capacity of the local health care system, i.e. the number of patients that require hospitalization and even intensive care. finally, we have demonstrated that the model can be refined to predict the interaction and local outbreak dynamics at community level. by now, medical data on observed disease progression at most stages during a covid-19 infection is abundantly available and continues to improve. our versatile integrodifferential approach directly integrates these data into the model and can easily be extended, corroborating its superiority over standard sir-type models. in general, the model can thus handle an arbitrary number of courses of the disease. similarly, it may expand to consider region-dependent demographics or varying capacities and quality of treatment of the health-care system. while the model can serve as a valuable tool to assess the effects of new super spreader events-which may occur any time-on the distribution of cases in germany, it reaches its validity limit when the number of infections becomes small. to additionally capture this even smaller scale, a coupling to individual agent-based models [15] [16] [17] may be beneficial. covid-19 dashboard by the center for 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beispielszenarien der sars-cov-2-epidemie 2020 in deutschland the particle swarm-explosion, stability, and convergence in a multidimensional complex space particle swarm optimization in highdimensional bounded search spaces publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations acknowledgements open access funding provided by projekt deal. we cordially thank sarah nistler for tedious data collection and the entire covid-19 modeling group at fau for valuable discussions and feedback on this work.open access this article is licensed under a creative commons attribution 4.0 international license, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the creative commons licence, and indicate if changes were made. the images or other third party material in this article are included in the article's creative commons licence, unless indicated otherwise in a credit line to the material. if material is not included in the article's creative commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. to view a copy of this licence, visit http://creativecomm ons.org/licenses/by/4.0/. key: cord-259562-e1htl489 authors: petzold, moritz bruno; bendau, antonia; plag, jens; pyrkosch, lena; mascarell maricic, lea; betzler, felix; rogoll, janina; große, julia; ströhle, andreas title: risk, resilience, psychological distress, and anxiety at the beginning of the covid‐19 pandemic in germany date: 2020-07-07 journal: brain behav doi: 10.1002/brb3.1745 sha: doc_id: 259562 cord_uid: e1htl489 background: the current covid‐19 pandemic comes with multiple psychological stressors due to health‐related, social, economic, and individual consequences and may cause psychological distress. the aim of this study was to screen the population in germany for negative impact on mental health in the current covid‐19 pandemic and to analyze possible risk and protective factors. methods: a total of 6,509 people took part in an online survey in germany from 27 march to 6 april. the questionnaire included demographic information and ascertained psychological distress, anxiety and depressive symptoms, and risk and protective factors. results: in our sample, over 50% expressed suffering from anxiety and psychological distress regarding the covid‐19 pandemic. participants spent several hours per day thinking about covid‐19 (m = 4.45). psychological and social determinants showed stronger associations with anxiety regarding covid‐19 than experiences with the disease. conclusions: the current covid‐19 pandemic does cause psychological distress, anxiety, and depression for large proportions of the general population. strategies such as maintaining a healthy lifestyle and social contacts, acceptance of anxiety and negative emotions, fostering self‐efficacy, and information on where to get medical treatment if needed, seem of help, while substance abuse and suppression of anxiety and negative emotions seem to be associated with more psychological burden. the new virus sars-cov-2 has now rapidly spread to nearly all countries over the world, and the world health organization (who) declared an international pandemic in march 2020 (ghebreyesus, 2020) . the pandemic comes with a large number of potential stressors that might cause psychological distress and mental health burden (inter-agency standing committee, 2020). potential stressors related to the virus might be the fear of an infection with covid-19 and the consequences for oneself or loved ones. the taken measures that aim to slow down the spreading of the virus also come with lots of stressors such as social isolation, economic consequences, and uncertainty about the future (inter-agency standing committee, 2020). therefore, an increase in psychological distress and negative consequences for the mental health of large populations worldwide can be assumed. in a rapid developing situation with a pandemic of a scale that was not known in the last 50 years, substantial research on the psychological consequences of the pandemic is lacking. first studies provide evidence regarding psychological distress in the context of the covid-19 pandemic. an online survey in the general population in china showed that more than half of the participants rated the psychological impact of the events as moderate-to-severe and 16.5% reported depressive and 28.8% anxiety symptoms of moderate-to-severe intensity during the initial stage of the pandemic. these proportions seemed to be relatively stable-a second survey 4 weeks later showed no significant reduction in those symptoms (wang, pan, wan, tan, xu, mcintyre, et al., 2020) . another study from china showed a lower prevalence of symptoms of psychological distress in chinese workforce during the covid-19 outbreak tan, hao, et al., 2020) , and particularly, individuals with preexisting (mental) health issues seem to suffer from psychological strain in the context of the pandemic . studies that focused on the psychological consequences of previous epidemics or pandemics showed that these were associated with substantial psychological distress and mental health problems, for example, during the ebola epidemic 2014 (greenberg, wessely, & wykes, 2015; mohammed et al., 2015) or the sars outbreak in 2003 (maunder et al., 2006) . the first case in germany was detected in january 2020 (bayrisches staatsministerium für gesundheit und pflege, 2020), and case numbers have been rising afterward (see figure 1 ). in parallel, stepwise more rules appeared to inhibit a further exponential growth of the infection numbers, for example, the closure of all educational, cultural and gastronomical institutions, and a reduction in retail and service sectors (bundesgesundheitsministerium, 2020) . since 23 march, throughout germany, more rigorous national rules became effective, including further closures of institutions and restrictions of physical contact and staying outside. to our knowledge, there is no published research on factors of psychological distress in the general population in germany during the current pandemic. hence, the aim of the present study was to assess psychological distress, anxiety, and depression with regard to the covid-19 pandemic and to analyze possible risk and protective factors. this is a cross-sectional observational study using a convenience sample of the general population in germany via online survey, approved by the ethics committee of charité universitätsmedizin berlin (ea1/071/20) and registered on clinicaltrials.gov (nct04331106). to survey the psychological dimension of the covid-19 pandemic, an online self-report questionnaire via sosci survey was used. data collection started 27 march 2020, when in germany, 42,288 cases of infection and 253 deaths attributed to covid-19 were reported (robert koch institut, 2020) . the end of the first wave of data collection was 10 days later: 6 april 2020, when in germany 95,391 cases and 1,434 deaths were reported (robert koch institut, 2020 the charité. completing the entire survey required 10-15 min. the present paper only examines cross-sectional data of the first wave. further longitudinal measurements will be carried out. all participants gave informed consent prior to participation. figure 1 shows the covid-19 situation in germany during recruitment period regarding cases of infection, death, and recovery. except the minimum age of 18 years, residence in germany, and the ability to complete the questionnaire in german, there were no other inclusion or exclusion criteria. the online questionnaire contained demographic information and the experiences with the virus (e.g., being in quarantine, tested or diagnosed for the coronavirus). additionally, the subjective risk of being infected within the next month was rated from 0% to 100% and the daily average amount of hours spent thinking about covid-19 was recorded. to screen for general anxiety and depressive symptoms, the ultra-brief screening scale of the patient health questionnaire-4 (phq-4) (löwe et al., 2010) was used. the intensity of four items describing major anxiety/depressive symptoms was rated on a 4-point scale from 0 ("not at all") to 3 ("nearly every day"). the phq-4 can be examined as a total score or be divided into an anxiety (gad-2) and a depression subscale (phq-2). to assess selected aspects of anxiety regarding covid-19, nine items were included (e.g., the fear of being infected and the fear of social or economic consequences). all statements were rated on a 6-point likert scale, ranging from 1 ("not true at all") to 6 ("totally true"). additionally, a modified version of the validated dsm-5 severity-measure-for-specific-phobia-adult-scale (beesdo-baum et al., 2012) was used to ascertain the extent of anxiety symptoms caused by the pandemic. the scale consists of 10 items, rated on a 5-point likert scale from 0 ("never") to 4 ("all the time"). the questionnaire inquired eight items regarding protective factors in dealing with the pandemic (e.g., self-efficacy in general, social self-efficacy) and five items targeting risk factors (e.g., suppression, substance use). protective and risk factors were adapted from the recommendations on coping with psychological distress in the pandemic of the inter-agency standing committee (iasc) of the united nations (un) (inter-agency standing committee, 2020). items were rated on a 6-point likert scale. all questions were administered in german. the questionnaire consisted of eight pages. we included only participants who completed at least page 4 (n = 6,509). 93.6% of the participants (n = 5,721) completed all pages. average percentage of missing data on item level was 2.1% (range: 0.0-7.1). missing data were handled by casewise deletion. all analyses were carried out using ibm spss statistics version 25. significance level was set to .05 (two-tailed). for the analysis, descriptive statistics, pearson's and spearman's correlations, and t tests for independent samples were used. 70.1% of the participants were female (n = 4,563), 29.0% male (n = 1,887), and 0.9% identified as diverse (n = 59). mean age was 36.2 years (sd = 11.65, range 18-99). 37.6% reported to have children (n = 37.6%). 15.1% had a secondary school degree (n = 985), 32.4% had a higher education entrance qualification (n = 2,109), and 50.0% had a university degree (n = 3,254). 16.7% of the participants reported to work in a medical context (n = 1,084). 10.7% of the participants suffered from a severe physical illness (n = 695). the participants lived in a household with 2.54 persons on average (including themselves). figure 2 shows the experiences of the participants with covid-19. about one third of the participants knew someone diagnosed with covid-19 or already suspected themselves to be infected. about 7% were currently under quarantine, and <5% had been tested for covid-19. about 1% of the sample had been diagnosed with covid-19. average rating of the risk of being infected with covid-19 within the next month was 38.3% (sd = 25.26, range: 0-100). most participants rated the risk with 50% (21.8%, n = 1,422). the lowest 25% of the sample ranked it as 20.0% or lower. median of risk perception was 40.0%. the highest 25% ranked the risk at least as 50%. average rating of the risk of being infected with influenza ("flu") was 18.2% on average, the participants thought about covid-19 for 4.45 hr/ day (sd = 3.80, range from 0 to 24). 25% of the participants thought <2 hr, while 25% thought 6 hr or more per day about covid-19. 10% reported to think more than 10 hr/day about covid-19. women where to get medical treatment showed significant negative correlations ranging from r = −.07 to r = −.24. the overall score of the modified specific-phobia scale was 10.15 (sd = 6.95), with women showing significantly higher scores than men (m = 10.67, sd = 6.94 vs. m = 8.88, sd = 6.78; p > .001). the participants showed an average phq-4 score of 4.15 (sd = 3.19, range 0-12). 25% of the participants showed a score of at least 6, while 10% of them showed a score of at least 9. women showed a significantly higher phq-4 score (indicating more depressive and anxious symptomatology) than men (m = 4.4 vs. m = 3.5). the participants showed an average phq-2 score of 2.11 (sd = 1.70, range 0-6). 25% of the sample showed a score of at least 3 and 10% a score of at least 5. the average gad-2 score was 2.03 (sd = 1.76, range 0-6). 25% of the participants showed a score of at least 3, while 10% showed a score of at least 5. in this study, we wanted to explore how the current covid-19 pandemic is connected to a psychological burden, especially to upcoming anxiety, among the general population in germany. first, we found that the participants spend a tremendous amount second, we found that the risk perception of getting infected with covid-19 in the next 4 weeks was very high. these data show that as expected, the fear of becoming infected with covid-19 is very prevalent in the general population. even in a time where the prevalence of covid-19 infections seems difficult to estimate, the risk rating of being infected within the next 4 weeks seems to be higher than the expected number of infections in 4 weeks. an infection probability of 40% within the next 4 weeks (the median) would mean over 30 million of infected people in germany by beginning of may which seems rather unlikely when the current development is taken into account (robert koch institut, 2020). our (tham, ibrahim, hunt, kapur, & gooding, 2020 ). in the current situation, fears regarding the covid-19 pandemic have to be seen as normal consequences in an exceptional situation rather than as pathologic reactions (petzold, plag, & ströhle, 2020a , 2020b outbreak , where more than half of the participants reported a moderate-to-severe psychological impact of the covid-19 pandemic on themselves, while about 17% of reported moderate-to-severe depressive symptoms and nearly 30% reported moderate-to-severe anxiety symptoms. interestingly, personal experiences with covid-19 were not strongly connected to covid-19 anxiety. this could mean that psychological and social determinants may have a larger influence on anxiety in that early phase of the pandemic than immediate experiences with this virus itself. this is undermined by our finding that self-efficacy (meaning a person's believe in his or her own ability to master situations or show a certain behavior) showed essential significant negative correlations with covid-19 anxiety. low self-efficacy has been shown to be connected with higher anxiety (bandura, 1988; muris, 2002) . our results make the assumption reasonable that self-efficacy could be a protective factor also against pandemic-driven anxiety and future longitudinal studies should test this assumption. the result that working in a medical context is associated with more anxiety regarding the covid-19 pandemic is in line with findings from a recent study from hospitals in singapore and india that showed high proportions of physical and psychological strain in healthcare workers . a further comparison of different professions in the healthcare sector would be interesting-as for example in a study in singapore nonmedical healthcare workers (e.g., pharmacists, technicians) reported more psychological strain than medical personnel tan, hao, et al., 2020) . these results are of a high practical value as they empirically underpin the recommendations on the reduction of psychological distress in the current pandemic that are given by international or in our sample, the average phq-4 score was with a mean of 4.15 higher than the phq-4 score that has been reported by previous research in the general population of 1.76 (löwe et al., 2010) . with all given precautions, this could show that in the current situation there is an increase in depressive and anxiety symptoms in the german general population. due to the nature of the study, this cannot be interpreted as a robust and reliable research result and should be merely seen as an empirical fundament to build hypotheses in this direction. if elevated levels of anxiety and depression turn out reliable and robust in other studies and especially in the longitudinal course, appropriate interventions should be established to reduce psychological strain-for example, cognitive behavioral therapy . in a first longitudinal study from china (wang, pan, wan, tan, xu, mcintyre, et al., 2020) , a statistically significant but not clinically relevant reduction in ptsd symptoms as a result of the covid-19 pandemic was found from end of january to end of february 2020. at the same time, there were no significant changes regarding anxiety, depression, and stress. furthermore, the study identified protective factors such as confidence in doctors and satisfaction with health information, risk perception and outcome expectation (perceived survival likelihood), and personal precautionary measures (wang, pan, wan, tan, xu, mcintyre, et al., 2020) . in our sample, women showed higher scores of covid-19 anxiety, more time of thinking about covid-19 per day, as well as more depressive symptoms than men. this is in line with the results of other studies regarding the psychosocial distress caused by the covid-19 pandemic (qiu et al., 2020; . up to now, it is not possible to draw conclusions if this is something specific to the covid-19 pandemic as higher values of anxiety and depression are reported in women in general (salk, hyde, & abramson, 2017) . our study represents the first study that assesses psychological distress, anxiety, and depression as well as risk and protective factors in the current covid-19 pandemic in germany. we started recruitment quite early so we assessed our participants still in a situation where case numbers were rising exponentially and media coverage was really large. this allows to study the psychological consequences at an early stage of the pandemic and lays a good basis for further longitudinal follow-ups. with a sample size of over 6,000 participants, our sample is large enough to detect even small effects. our sample was fully registered and approved by the local ethics committee. nevertheless, there are some limitations. we recruited our sample as convenience sample mainly through social media. this might have led to a sample bias. people who are familiar with or have easy access to social media might have been more likely to participate in our study, which might have led to a rather young sample. furthermore, people who show higher levels of psychological distress and anxiety might be more likely to take part in a study like ours. this could have led to an overestimation of these factors in our sample. this strategy of recruitment does reduce the generalizability of our results which is shown by several differences between the demographics in our sample and the general population in germany. the sample shows in comparison with the general population a much higher gender imbalance, a lower average age, and a higher percentage of persons working in a medical context (bundesinstitut für bevölkerungsforschung, 2020). our study is a cross-sectional examination and does not allow any causal interferences. our questionnaire was rather short, using simple scales, not all of them were validated. therefore, all of the study results in general should rather be interpreted as first hints, which might be helpful for further studies as well as to empirically underpin existing recommendations on the reduction in psychological distress in the pandemic. our results suggest that in this early phase of the covid-19 pandemic with low percentages of diagnosed cases in our study population, we can already observe its fundamental impact on anxiety and in the pandemic such as a healthy lifestyle, social support, acceptance of negative emotions, and avoidance of suppression and substance abuse is supported by our data. the authors declare that there is no conflict of interest. the peer review history for this article is available at https://publo ns.com/publo n/10.1002/brb3.1745. the data that support the findings of this study are available from the corresponding author upon reasonable request. moritz bruno petzold https://orcid.org/0000-0002-7801-1434 antonia bendau https://orcid.org/0000-0002-3789-6205 self-efficacy conception of anxiety bestätigter coronavirus-fall in bayern -infektionsschutzmaßnahmen laufen psychometric properties of the dimensional anxiety scales for dsm-v in an unselected sample of german treatment seeking patients retrieved from www.bunde 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covid-19-pandemie: psychische belastungen können reduziert werden dealing with psychological distress by healthcare professionals during the covid-19 pandemia a nationwide survey of psychological distress among chinese people in the covid-19 epidemic: implications and policy recommendations covid-19: fallzahlen in deutschland und weltweit gender differences in depression in representative national samples: meta-analyses of diagnoses and symptoms is returning to work during the covid-19 pandemic stressful? a study on immediate mental health status and psychoneuroimmunity prevention measures of chinese workforce examining the mechanisms by which adverse life events affect having a history of self-harm, and the protective effect of social support when worries make you sick: a review of perseverative cognition, the default stress response and somatic health immediate psychological responses and associated factors during the initial stage of the 2019 coronavirus disease (covid-19) epidemic among the general population in china a longitudinal study on the mental health of general population during the covid-19 epidemic in china reflecting on rumination: consequences, causes, mechanisms and treatment of rumination longitudinal associations between rumination and depressive symptoms in a probability sample of adults mental health considerations during covid-19 outbreak key: cord-287548-3wv9xcxh authors: plümper, thomas; neumayer, eric title: the pandemic predominantly hits poor neighbourhoods? sars-cov-2 infections and covid-19 fatalities in german districts date: 2020-08-20 journal: eur j public health doi: 10.1093/eurpub/ckaa168 sha: doc_id: 287548 cord_uid: 3wv9xcxh background: reports from the uk and the usa suggest that covid-19 predominantly affects poorer neighbourhoods. this article paints a more complex picture by distinguishing between a first and second phase of the pandemic. the initial spread of infections and its correlation with socio-economic factors depends on how the virus first entered a country. the second phase of the pandemic begins when individuals start taking precautionary measures and governments implement lockdowns. in this phase the spread of the virus depends on the ability of individuals to socially distance themselves, which is to some extent socially stratified. methods: we analyse the geographical distribution of known cumulative cases and fatalities per capita in an ecological analysis across local districts in germany distinguishing between the first and the second phase of the pandemic. results: in germany, the virus first entered via individuals returning from skiing in the alps and other international travel. in this first phase we find a positive association between the wealth of a district and infection rates and a negative association with indicators of social deprivation. during the second phase and controlling for path dependency, districts with a higher share of university-educated employees record fewer new infections and deaths and richer districts record fewer deaths, districts with a higher unemployment rate record more deaths. conclusion: the social stratification of covid-19 changes substantively across the two phases of the pandemic in germany. only in the second phase and controlling for temporal dependence does covid-19 predominantly hit poorer districts. in germany, the virus happened to be spread initially via individuals returning from ski holidays in the alps and, to a much lesser extent, through business and other travellers from china, italy and other hotspots, which meant that the majority of infected people in the beginning were relatively young and well-off. 9, 11 once the virus had reached germany, the subsequent spread of infections was facilitated by super-spreader social events such as a carnival session in gangelt, a small town in the district of heinsberg, a beer festival in the small city of mitterteich, district of tirschenreuth, and a wine event in bretzfeld, hohenlohekreis. these super-spreader events create local cluster effects if the social event is mainly attended by locals. in fact, even two months after the above events took place, these were still the districts with the highest number of known infections per 100,000 citizens in germany. figure 1 maps cumulative known sars-cov-2 cases, normalized by population, in german districts on 13 april. even at a first glance we see that the rate of infection declines from south to north and from west to east. even within the western part of germany, regions in which a greater share of the population is catholic also have a higher incidence, which may be correlated to spreader events such as carnival that is much more popular in predominantly catholic regions. 12, 13 the north-south divide appears to be stronger than the east-west divide. this may be down in part to the greater ease by which southern germans can reach by car what turned out to be virus hotspots in ski resorts in northern italy and austria. insert figure 1 about here once the existence and dangers of the pandemic have become public knowledge, people and governments implement precautionary measures and the spread of the virus slows down. 14, 15 at the same time, the geographical pattern of infections slowly changes. for a virus to spread, social interaction between an infected and an uninfected person is required. since the number of new infections remains strongly influenced by the number of active infections in a district, the pattern that has evolved during phase 1 will not disappear quickly. thus, hotspots remain hotspots for some time. but not forever. figure do not affect all people in the same way. 16 the ability to reduce social interactions and to 'stay home' is not distributed evenly in a society. 17, 18 the spread of the virus in phase 2 is shaped by the extent to which individuals manage to reduce their social contacts. in general, white collar activities can be moved to a home office, while other workers still need to commute to their workplace and work if their employer does not lock down the workplace. poorer people find social distancing more challenging than richer people, having less access to resources to shield them from the economically damaging effect of the lockdown. regardless of how and where the virus had spread first in the initial phase of the pandemic, in phase 2 the virus is likely to become a poor man's disease. in fact, we find that in the second phase of the pandemic, poorer and more socially deprived districts start to have higher than average covid-19 mortality rates. the transition from phase 1 to phase 2 is a smooth process rather than a hard cut, as this depends on when people start consciously changing their behaviour and some do so earlier than others. still, a definite break comes with the lockdown. the first german states to go into lockdown were bavaria and the saarland. their curfew begun on 21 march; one day later the whole of germany followed. hartl et al. 19 ideally, we would test our first prediction with data on cases from late march or early april, since it takes roughly a week from the implementation to the effectiveness of policy measures on infection rates. unfortunately, the first date at which we were able to capture the full distribution of confirmed infections and deaths across all german districts is 13 april, with data sourced from the website of the robert koch institute. whilst clearly introducing measurement error as overlapping with the second phase of the pandemic, the strong path dependency of any pandemic means that the cumulative number of infections on 13 april will be sufficiently strongly correlated with the cumulative number of infections around 30 march, which would have been the ideal date. since it takes more time for people to die from covid-19, 13 april may represent close to the ideal end period for phase 1 for our analysis of fatalities. to study our second prediction, we take as our second dependent variable new infections and fatalities that happened in the second period between 14 april and 19 may. these cases occurred after people had time to adjust to the by now fully known risks and the lockdown had been imposed. a major relaxation of the lockdown took place on 19 may such that one can take 19 may as the end of phase 2 of the pandemic. we divide cases and fatalities by a district's population size in 10,000 people. consequently, the dependent variables in our regressions represent cumulative cases or fatalities per capita and cumulative new infections or new fatalities per capita. we estimate our regression models with ordinary least squares and robust standard errors. as our measure of wealth of a district we include the average income subject to income tax in thousands of euro. we also control for the share of the workforce that is universityeducated. this variable is a proxy for the share of the population that can work from a home office and is correlated at r = 0.85 with an index of working from home potential calculated by alipour et al. 20 to measure social deprivation we include the unemployment rate. average taxable income is highly negatively correlated with the unemployment rate at r = -0.58, which is why we include average taxable income and the unemployment rate only in separate regressions. as two proxy variables to account for the way in which the virus first entered germany and spread initially we include the latitude location of a district and the share of its population that is catholic. the former accounts for the ease by which residents could drive to the alps for ski tourism, whilst the latter accounts for the greater popularity of carnival as potential super-spreader events in predominantly catholic districts. 12 in addition, we include dummy variables for whether a district is predominantly urban and is geographically in an extremely remote location. the virus spreads more easily in more densely populated urban habitats 21,22 and while extreme remoteness is often seen as a costly locational disadvantage, 23, 24 it partly protects the local population from infections as there will be less exchange with people from the outside. all data for the explanatory variables are sourced from regional databases of the german statistical offices. table 1 reports results for average taxable income as the central socio-economic explanatory variables, table 2 does the same for the unemployment rate. in the first phase, average taxable income is positively associated with cumulative cases measured on 13 april at the district level. model 1 suggests that a district that has an average income of 10,000 euros higher than the mean income of german districts has 6.3 [95% c.i.: 3.0 to 9.6] additional cases per 10,000 people relative to the district mean. this is a substantively important effect given that the average number of known cumulative cases of german districts on april 13 stood at 14.9 with a standard deviation of 12.3. in phase 2 we regress the cumulative number of known infections between 14 april and 19 may on the same set of variables. during this period, the mean of cumulative new infections per 10,000 people is 6.3 [s.d. = 5.7] . in this period the association between cumulative cases and average taxable income of a district becomes negative but is not statistically significant (model 2). our results also suggest that mortality rates are lower in richer and therefore higher in poorer districts in phase 2 (model 4). taxable income thus shows a negative association with cumulative cases in phase 1 but not in phase 2, demonstrating that the pandemic increasingly affects poorer districts too even if, as in germany, the pandemic started in richer districts. likewise, average income has no systematic association with cumulative deaths in phase 1 but becomes negatively associated with deaths in phase 2. the opposite pattern to what we find for taxable income holds for the unemployment rate (table 2) . districts with a higher unemployment rate reported lower cumulative cases in phase 1 (model 5) and higher cumulative deaths in phase 2 (model 8). hence, regardless of the socio-economic indicator we use, we find that in phase 2 the pandemic increasingly affects poorer and more socially deprived districts too in terms of cumulative infections and actually affects them more in terms of cumulative deaths. insert table 2 about here there are thus interesting differences between our analysis of infection rates and mortality rates. in phase 1, the population of poorer and more socially deprived districts is less likely to get infected with sars-cov-2 than the population in richer and less deprived districts but there are no statistically significant mortality differences between these districts. in phase 2 and controlling for path dependency, the population of poorer and more socially deprived districts is at least equally likely to get infected, but the probability to die from covid-19 is statistically significantly higher. in germany at least, covid-19 increasingly becomes a disease of the poor after lockdown -arguably, because the rich find it easier to follow the rules of social distancing, a result that is consistent with harris. 6 we studied the relationship between socio-economic factors and the covid-19 pandemic in germany, distinguishing between two phases and analysing both infections and fatalities. we have shown that the population of poorer districts is not necessarily more likely to get infected with sars-cov-2. in germany during the first phase of the pandemic, poorer districts and districts with a higher unemployment rate had fewer infection rates. due to the inherent limitations of an ecological study, our analysis at the district level cannot conclusively identify the causal mechanisms. yet, it seems likely that the distribution of the virus during the first phase of the pandemic in germany has been largely influenced by ski tourism. districts geographically closer to the alps are relatively wealthy and have little social deprivation by german standards. as a consequence, the pandemic started in germany predominantly as a rich man's disease. in this initial phase, mortality rates in poorer and more socially deprived districts were not higher though poorer and more socially deprived people tend to have more co-morbidities, which increase covid-19 mortality. 25 since lockdown, however, and controlling for the strong path dependency in the spread of the disease, poorer and more socially deprived districts no longer report lower infection rates and deaths become increasingly concentrated in these districts. the gap in infection rates between richer and poorer districts closes and a gap in mortality rates begins to open with poorer districts now having higher than average mortality rates. the same applies if we employ the unemployment rate as a measure of social deprivation. covid-19 is slowly becoming a poor man's disease. an ecological analysis cannot trace the causal mechanism but it is very likely that more people in richer districts as well as in districts with a higher share of university educated employees could work from home and afford to behave in a socially distanced way than people in poorer and more socially deprived districts. 26 this is entirely consistent with studies from other countries showing a higher mortality rate among individuals with lower socio-economic status, with the higher prevalence of co-morbidities in such individuals one of the likely causal mechanisms. 25 the recent emergence of hotspots in slaughterhouses in the districts of gütersloh and oldenburg indicate that the pandemic has reached the very poor: temporary migrant workers from bulgaria and romania. the subtle difference in results between the 'infections model' and the 'deaths model' is particularly interesting. these results lend indirect empirical support to previous findings suggesting that the case fatality rate, that is, the number of deaths per known infected people, is higher in poorer districts. 27 sorci et al. 28 have used a very different research design to ours, regressing the case fatality rate on a battery of explanatory variables including some socioeconomic factors, whereas our estimates have the population fatality rate as the dependent variable. for their sample they find that higher than average per capita income is weakly associated with lower than average fatality rate. our results are consistent with their findings in both phases: in phase 1 poorer and more socially deprived districts combine a low infection rate with an average death rate, in phase 2 poorer and more socially deprived districts combine an average infection rate with a higher than average death rate. we suspect that this finding results from the higher prevalence of comorbidities in relatively poor districts in germany and with variations in the ability to follow social distancing rules. covid-19 magnifies the effect of behavioural differences on health outcomes, but does not in itself discriminate between rich and poor. all viruses spread through social interactions and we should not be surprised that pandemics crystallize the socio-economic determinants of social interactions and the socio-economic constraints on the ability to follow social distancing rules. none declared. no specific funding was received. the replication data and do-file will be made available on dataverse.org upon publication. • initially, whether covid-19 predominantly affects poorer or richer neighbourhoods depends on how the virus first entered a society. • in germany, the virus mainly entered via tourists returning from ski holidays in the alps and accordingly wealthier districts initially recorded higher and more socially deprived districts recorded lower covid-19 infection rates during the first phase of the pandemic in which the virus could spread largely unhampered by social distancing measures. • lockdown policies have enormous public health benefits controlling the pandemic but also exert a strong effect on the social stratification of covid-19 because the ability to socially distance oneself from others now determines the individual risk of an infection and at the district level covid-19 increasingly becomes a disease of poorer and more socially deprived districts. • controlling for the path dependency of infections, wealthier districts now record lower and more socially deprived districts record higher covid-19 mortality rates during the second phase of the pandemic in which lockdown was in place. covid-19 exacerbating inequalities in the us poverty kills people: after coronavirus we can no longer ignore it. the guardian 5 may who is more susceptible to covid-19 infection and mortality in the states? the subways seeded the massive coronavirus epidemic in new york city. nber working paper 27021 revealing the unequal burden of covid-19 by income, race/ethnicity, and household crowding: us county vs. zip code analyses how coronavirus -a 'rich man's disease' -infected the poor a pandemic in times of global tourism: superspreading and exportation of covid-19 cases from a ski area in austria a hundred days into the coronavirus disease (covid-19) pandemic carnival and citizenship. the politics of carnival culture in the prussian rhineland spreading the disease. the role of culture effective containment explains subexponential growth in recent confirmed covid-19 cases in china a simplified model for expected development of the sars-cov-2 (corona) spread in germany and us after social distancing health versus wealth: on the distributional effects of controlling a pandemic nber working paper 27046 the differential impact of covid-19 across demographic groups: evidence from nyc, unp the determinants of the differential exposure to covid-19 in new york city and their evolution over time, unp measuring the impact of the german public shutdown on the spread of covid19. covid economics, vetted and real-time papers germany's capacity to work from home. discussion paper 13152. bonn: institute for labour economics 2020. and infection risk in rural ecuador rural america and coronavirus epidemic: challenges and solutions the costs of remoteness: evidence from german division and reunification multilevel determinants of breast cancer survival: association with geographic remoteness and area-level socioeconomic disadvantage. breast cancer research and treatment opensafely: factors associated with covid-19 death in 17 million patients my home is my castle -the benefits of working from home during a pandemic crisis: evidence from germany estimating the global infection fatality rate of covid-19 note: 95% confidence interval in parentheses. *** p<0.01, ** p<0.05, * p<0 key: cord-276363-m8di6dpt authors: holm, majbrit v.; blank, patricia r.; szucs, thomas d. title: influenza vaccination coverage rates in europe – covering five consecutive seasons (2001–2006) in five countries date: 2008-06-28 journal: influenza other respir viruses doi: 10.1111/j.1750-2659.2008.00036.x sha: doc_id: 276363 cord_uid: m8di6dpt objective to understand potential drivers and barriers to influenza vaccination in the general population. methods 47 982 household surveys were conducted in five european countries between 2001 and 2006. results overall influenza vaccination coverage increased over the years and reached 26·2% in 2005/06. among the elderly ≥65 years, the rate increased significantly to 67·8% (2005/06). the most common reason for being vaccinated over the 5 years was the perception of influenza as a serious illness, which people want to avoid. the main reason for not getting vaccinated among those never previously vaccinated was feeling that they were unlikely to catch influenza. a recommendation by the family physician was the most encouraging factor for vaccination. the severity of influenza and the efficacy of vaccination are well documented in the medical literature. 1,2 eradication of influenza is impossible but continuous immunization of the population can minimize the impact of the disease. 3 in addition to providing substantial health benefits, vaccination may also be associated with significant economic benefits, not only among the elderly but also among healthy working adults and children. despite this knowledge and ongoing efforts by policy-makers, physicians and other healthcare providers, influenza vaccination rates in the five european countries surveyed remain limited, with the additional effect that manufacturing capacity may be too low for producing a sufficient amount of an appropriate monovalent vaccine when a pandemic occurs. 3 the who states that the risk of a new pandemic is at its highest level since the last pandemic in 1968. 4 this situation might influence the immunization coverage rates in the population. published literature evaluating vaccination coverage rates in europe shows that importance placed on influenza vaccination varies greatly between countries. 3 two recent studies covering several european countries have been published. 5, 6 this report is an update of the earlier work by szucs and muller. we now have data available for five consecutive influenza seasons which allows us to go beyond the usual cross-sectional approach to analyzing vaccination rates. the main focus of this paper is on high-risk group coverage. a second objective is to understand the determinants for being or not being vaccinated, and to describe the populations' opinions regarding influenza and vaccination. in this context, we examine whether the threat of avian influenza had an impact on recent changes in vaccination coverage in the different countries. this survey is an ongoing assessment of influenza coverage rates in france, great britain, italy, spain, and germany. during [7] [8] [9] [10] [11] four target groups were specified. 1. individuals aged ‡65 years 2. individuals who suffer from a chronic illness 3. individuals who work in the medical field 4. combined group of individuals aged ‡65 years or who suffer from a chronic illness or who work in the medical field. for example, in germany the group of chronic illness sufferers is defined according to the german standing commission on immunization, as children, adolescents and adults suffering from chronic diseases of respiratory organs, chronic cardiovascular or liver diseases, as well as nephropathies and diabetes, or other metabolic disorders. in our study, people suffering from heart diseases, pulmonary diseases, diabetes, or other chronic illnesses were included in the chronic illness group. the survey questions have been published previously. 6 the questions covered reasons to get vaccinated this winter, reasons for not getting vaccinated against influenza, and options that would encourage persons to get vaccinated against influenza. for the 2005 ⁄ 06 survey, questions on influenza pandemics and avian influenza were added. the survey populations were representative of the adult population from age 14 years (germany, italy, spain); from age 15 (france), or from age 16 (great britain). in spain, persons above age 75 were not covered. sample weights were applied to correct for small deviations from the applicable age and gender quota and the annual datasets were pooled. statistical evaluation used spss ò version 13 for windows. bivariate associations of categorical variables were assessed using the chi-squared test. a chi-squared test for trend was used to assess time trends. in the case of continuous variables, differences of means were tested using oneway anova. for all statistical tests, two-sided p = 0ae05 was used as the level of statistical significance. ninety-five percent confidence intervals (ci) were reported as appropriate. due to the descriptive nature of these data, no correction for multiple testing was made. covariates identified as predictors of influenza vaccination in univariate analysis were considered as candidates for multivariable analysis. logistic regression was used to identify independent correlates of the outcome of interest, i.e. vaccination coverage. the overall sample consisted of 47 982 persons. in table 1 an overview of the sample is given for the year 2005 ⁄ 06 only. in an earlier publication, similar data can be found for the years 2002 ⁄ 03 and 2003 ⁄ 04. 6 spain was expected to show a lower number of people over 65 years of age, as the survey covered only persons £75 years old. the reason for the great deviation in the number of chronic ill persons in germany compared to other countries remains unclear as there is no difference in the way the question was asked in the five countries. the overall vaccination coverage across countries, based on an average of the country samples, decreased from 22ae5% (95% ci: 21ae6-23ae4%) in season 2001 ⁄ 02 to 21ae3% (95% ci: 20ae5-22ae1%) in season 2002 ⁄ 03. thereafter, it increased to 23ae4% (95% ci: 22ae6-24ae2%) in season 2003 ⁄ 04, to 23ae6% (95% ci: 22ae7-27ae1%) in season 2004 ⁄ 05, and to 26ae2% (95% ci: 25ae3-27ae1%) in season 2005 ⁄ 06 ( figure 2 ). the increase between season 2004 ⁄ 05 and season 2005 ⁄ 06 was statistically significant (p < 0ae001). this was mainly due to significant increases in immunization uptake in germany and italy, where the coverage increased to 32ae5% and 24ae1%, respectively, in 2005 ⁄ 06. adjusting the overall vaccination rate in europe (weighting the population sizes) resulted in an average vaccination rate of 26ae8% in season 2005 ⁄ 06. vaccination rates were highly age-dependent. older age was associated with higher vaccination rates. in season 2005 ⁄ 06 the immunization uptake across all countries was holm et al. ª 2008 the authors higher for all age groups compared to the previous seasons ( figure 1 ). across all five seasons, vaccination rates appeared to be associated with gender in great britain, italy, and spain. in great britain a higher vaccination rate was observed in women, whereas in italy and spain, the majority of the vaccinated were men (details not shown). in the year 2005 ⁄ 06, 39ae0% of the respondents expressed the intention to get vaccinated against influenza in the coming winter of 2006 ⁄ 07. over the years, the proportion of those expressing such an intention was on average 36%, about 13% higher than the actual vaccination rate. the gap was highest in germany (between 15% and 20% over the years) and almost non-existent in italy in season 2005 ⁄ 06. the overall vaccination coverage rate in persons aged ‡65 increased over time ( figure 2 ). the increase between season 2004 ⁄ 05 and season 2005 ⁄ 06 was statistically significant (p < 0ae001). coverage in the elderly was highest in great britain (79%) and lowest in germany and italy (63ae4%). it was significantly different from the population under 65 years of age. since season 2003 ⁄ 04, data on health status in terms of chronic illness were collected. persons with a chronic illness showed significantly higher vaccination coverage than those not suffering from a chronic disease (figure 2) . the highest coverage among the chronically ill persons was found in great britain (66ae4%) and the lowest in france (51ae8%). working in the medical field did not seem to be a driving factor for vaccination as the vaccination coverage rate in this sub-population was not significantly different from the rest of the sample (figure 2) , at the unadjusted level. however, adjustment for age and other covariates revealed the presence of an association ( table 2 ). for persons in the combined target group a significant difference in coverage was found compared to the non-target group population. the vaccination rate in this group increased over the years and the increase in season 2005 ⁄ 06 was significantly different from the previous season. the coverage rate in the combined target group was highest in great britain (60%) and lowest in germany (49%). however, this result could be influenced by the observed difference in the proportion of chronically ill respondents in germany (table 1) . table 2 shows unadjusted odds ratios for the target groups for the year 2005 ⁄ 06. odds ratios across all seasons did not greatly differ from the 2005 ⁄ 06 results. adjusted odds ratios were investigated in logistic regression models. the adjustment took into account gender, age over 65 years, work in medical field, and chronic illness. for years where data on chronic illness were not available, data were only adjusted for the remaining covariates. the odds ratios for the combined target group were only adjusted for age. multivariate adjustment showed significantly higher vaccination rates for healthcare workers in great britain (or: 1ae8, 95% ci: 1ae5-2ae2), france (or: 1ae7, 95% ci: 1ae4-2ae1), italy (or: 1ae4, 95% ci: 1ae1-1ae9), and spain (or: 2ae1, 95% ci: 1ae6-3ae6). the impact of chronic illness on the vaccination rate was significantly lower after multivariate adjustment, mainly due to taking into account the effect of age (germany or: 2ae3, 95% ci: 2ae0; 2ae6, italy or: 5ae0, 95% ci: 4ae2; 6ae0, france or: 3ae4, 95% ci: 2ae7; 4ae2 and spain or: 3ae3, 95% ci: 2ae8; 4ae0). all other odds ratios were not substantially changed by multivariate adjustment (details not shown). for those who reported to have been vaccinated in season 2005 ⁄ 06, the most frequently stated reasons were that influenza is a serious illness that people want to avoid and that they have received a recommendation from their family physician or nurse (table 3 ). in france the most commonly stated reason for vaccination was that the vaccine is provided free. over the 5-year period, the ranking of the cause for getting vaccinated did not change substantially. the proportion of respondents whose decision to get vaccinated was influenced by the recent attention given to avian influenza or a possible influenza pandemic varied from 13% in germany to 1ae3% in spain. it was 8ae6% in great britain, 4ae1% in italy, and 2ae0% in france. across all countries, the persons who gave the threat of avian influenza as a reason for vaccination were not found to be statistically different from other vaccinated persons (table 3) . only the proportion of those vaccinated for first time was statistically higher among the group influenced by the attention given to avian influenza (p < 0ae001). for those of the total survey population who had never been vaccinated, the reasons for not being vaccinated varied across countries over the 5 years of observation. overall, the most frequently stated reasons were no expectation of catching influenza, not having considered vaccination, and absence of a family physician's recommendation ( table 3) . the level of knowledge about influenza and the vaccine among the general population was similar across countries. seventy-nine percent of the respondents agreed with the statement that you can catch influenza even if you are vaccinated against it. sixty-eight percent agreed with the statement that if you catch influenza after having had the vaccine, the infection is less severe. fifty-eight percent said that it is important to get the influenza vaccine each year and 52% agreed that the side effects associated with the vaccine (fever, headache...) are acceptable. most of the participants did not agree with the following statements: the vaccine is not useful if you are in good health and if you have the vaccine, you will not catch influenza. a recommendation by the family physician or nurse, and receiving more information regarding the vaccine being efficacious and well tolerated were regarded as the most important factors that might encourage vaccination (table 3) . data on this question were not available for france. the vaccination coverage rate in the total sample is currently 26ae2% (season 2005 ⁄ 06). a statistically significant increment of 2ae5% was observed between season 2004 ⁄ 05 and season 2005 ⁄ 06. this was mainly due to significant increases in immunization uptake in germany and italy. in germany reimbursement of vaccination for all age groups has been implemented in several federal states to encourage vaccination rates. 12 this may explain the high coverage rates in germany. a sub-analysis of the data obtained in great britain showed that wales reached a vaccination rate of 33ae3% in season 2005 ⁄ 06, higher than the german coverage rate (32ae5%). the immunization rates in the defined highrisk target groups were also increased in season 2005 ⁄ 06. in particular, higher age and suffering from chronic illness were important predictors of vaccination. in the elderly ‡65 years, the lowest coverage was observed in germany and italy and the highest in great britain. in great britain or, odds ratio; ci, confidence interval; p-value, pearson chi-squared. *reference category. holm et al. ª 2008 the authors general practitioners are encouraged to recommend vaccination to eligible high-risk patients, which may have contributed to the high vaccination rates in the target groups. 9 in spain, vaccination coverage increased in those aged ‡60 after the age threshold of vaccination recommendations was reduced to age 60 in some communities. as healthcare workers are in contact with patients, it is critical for this group to be vaccinated in order to reduce transmission of the disease. additionally, they play an important role in the communication and motivation of the public to get vaccinated. however, the vaccination rate among healthcare workers remained low compared to the other high-risk groups. a recent published literature review identified low coverage rates in this professional group to be especially a problem in europe, 13 with vaccination rates between 12% and 25%. 5 our observation of coverage rates increasing from 19% to 25% over the years is consistent with earlier findings. considering the entire population, 39% of the 2005 ⁄ 06 respondents expressed the intention to get vaccinated in season 2006 ⁄ 07. the gap between those who intended to get vaccinated and those who actually received vaccination was stable over the years, at 13% on average. there was, however, substantial variation between countries. the persistence of this gap indicates the potential to increase vaccination coverage rates in europe. however, realizing this potential, activating the correct drivers, and dealing with the barriers to vaccination remains a challenge. only italy seems to have been able to diminish the gap. in season 2003 ⁄ 04 the italian vaccination campaign was intensified by the ministry of health due to the increased focus on severe acute respiratory syndrome. 14 a realistic vaccination coverage rate target in europe could be set at the level of vaccination intentions (39%). in the general population, the characteristics of those who gave the attention to avian influenza -a possible influenza pandemic as a reason for vaccination -were not found to be statistically different from the rest of the vacci-nated group. nonsignificant trends hinted at a larger proportion of women and a slightly lower mean age of this relatively small subgroup. the majority of persons influenced by the attention given to avian influenza were those who were vaccinated for the first time. in the general population, a recommendation from the family physician is the most important encouragement for vaccination. this confirms findings from several previous studies. 5, 15, 16 it was also stated that more information on the vaccines regarding tolerability and efficacy would motivate persons to get vaccinated. we did not cover the vaccination rates of schoolchildren in our article. however, high vaccination coverage in children and subsequent positive external effects will be difficult to achieve at least in some countries. this reason makes high vaccination rates in the risk populations even more important. telephone surveys are an appropriate method to investigate influenza vaccination uptake at the population level. telephone interviews have been used on several occasions to study vaccination rates in europe. 6, 17, 18 the main advantage of telephone interviews is a potentially high response rate obtained in an affordable and fast manner. the selection process based on random dialing of telephone numbers has been shown to be of high quality. 19 in france, the questionnaire was a self-administered mail survey. in mailed questionnaires, there is a high risk of respondents omitting questions and of a low return rate. on the other hand, mailed questionnaires are an even more affordable option for large-scale surveys. 19 the limitations of the present data collection are described in greater detail in an earlier publication. 6 an increasing problem is the use of wireless telephones. in the usa people with landlines had a higher odds (1ae27) of being vaccinated than those with only access to wireless telephones. 20 if this is believed to be similar in europe, we might have slightly overestimated the vaccination rate. the different methodological approach used in france may have affected the reliability of the comparison across countries. this is supported by the fact that the french gave different reasons for and against vaccination compared to the other countries. the who considers the current influenza pandemic risk to be at its highest level since the last pandemic. 4 hence, efforts should be made at all national and international levels to increase vaccination coverage according to the who objectives (i.e. 50% vaccination coverage to be reached in the elderly in 2006 and 75% in 2010). 21 among elderly ‡65 years, a vaccination rate of 50% or higher was reached in all the countries studied. so far, only great britain has reached the 2010 target of 75% with an immunization rate of 79% in season 2005 ⁄ 06. the existence of national targets may provide a partial explanation for this success. 22 vaccines for preventing influenza in the elderly individual and community impact of influenza control of influenza. public health policies influenza vaccination in europe: an inventory of strategies to reach target populations and optimise vaccination uptake influenza vaccination coverage rates in five european countries-a population-based cross-sectional analysis of two consecutive influenza seasons rki-ratgeber infektionskrankheiten -merkblä tter fü r ä rztezielgruppen der impfung the influenza immunisation programme [www document protocole de mise en place de la chimio-prophylaxie dans une collectivité de personnes à risque lors d'une é pidè mie de grippe, en pé eriode de circulation du virus grippal influenza coverages in spain and vaccination-related factors in the subgroup aged 50-64 years zahlt meine kasse fü r die grippeschutzimpfung? influenza vaccination of healthcare workers: a literature review of attitudes and beliefs seasons determinants of adult influenza and pneumonia immunization rates cross-sectional study on influenza vaccination influenza vaccination coverage in elderly people influenza vaccination coverage and reasons to refrain among high-risk persons in four european countries health measurement scales. a practical guide to their development and use telephone coverage and health survey estimates: evaluating the need for concern about wireless substitution prevention and control of influenza pandemics and annual epidemics, 56th wha, 10th plenary meeting department of health. summary of flu immunisation policykey points about flu immunisation policy in england this study was made possible by an unrestricted research grant from aventis-pasteur msd, lyon, france. we thank the geig for making the french data available for analysis. furthermore, we would like to thank bertrand verwee, christine pilet from sanofi pasteur, and matthias schwenkglenks from the european center of pharmaceutical medicine, basel, switzerland, for their comments on the study and on the data analyses. key: cord-339735-6964ktxr authors: empl, michael t.; kammeyer, patricia; ulrich, reiner; joseph, jan f.; parr, maria k.; willenberg, ina; schebb, nils h.; baumgärtner, wolfgang; röhrdanz, elke; steffen, christian; steinberg, pablo title: the influence of chronic l-carnitine supplementation on the formation of preneoplastic and atherosclerotic lesions in the colon and aorta of male f344 rats date: 2014-08-28 journal: arch toxicol doi: 10.1007/s00204-014-1341-4 sha: doc_id: 339735 cord_uid: 6964ktxr l-carnitine, a key component of fatty acid oxidation, is nowadays being extensively used as a nutritional supplement with allegedly “fat burning” and performance-enhancing properties, although to date there are no conclusive data supporting these claims. furthermore, there is an inverse relationship between exogenous supplementation and bioavailability, i.e., fairly high oral doses are not fully absorbed and thus a significant amount of carnitine remains in the gut. human and rat enterobacteria can degrade unabsorbed l-carnitine to trimethylamine or trimethylamine-n-oxide, which, under certain conditions, may be transformed to the known carcinogen n-nitrosodimethylamine. recent findings indicate that trimethylamine-n-oxide might also be involved in the development of atherosclerotic lesions. we therefore investigated whether a 1-year administration of different l-carnitine concentrations (0, 1, 2 and 5 g/l) via drinking water leads to an increased incidence of preneoplastic lesions (so-called aberrant crypt foci) in the colon of fischer 344 rats as well as to the appearance of atherosclerotic lesions in the aorta of these animals. no significant difference between the test groups regarding the formation of lesions in the colon and aorta of the rats was observed, suggesting that, under the given experimental conditions, l-carnitine up to a concentration of 5 g/l in the drinking water does not have adverse effects on the gastrointestinal and vascular system of fischer 344 rats. electronic supplementary material: the online version of this article (doi:10.1007/s00204-014-1341-4) contains supplementary material, which is available to authorized users. l-carnitine is a key component of the so-called carnitine shuttle, a multienzyme transport system that is required to transfer activated long-chain fatty acids (acyl-coas) into the mitochondrial matrix, where they are degraded via β-oxidation (violante et al. 2013) . in the course of this process, l-carnitine is conjugated to acyl-coas by carnitine palmitoyltransferase 1 (cpt1) yielding acylcarnitines, which are then transported to the inner mitochondrial compartment by the carnitine acylcarnitine translocase (cact) in exchange for free carnitine (houten and wanders 2010) . thereafter, carnitine palmitoyltransferase 2 (cpt2) retransforms acylcarnitines to acyl-coa esters, which are then degraded to acyl-coa subunits, thus generating substrates for the citric acid cycle and reducing equivalents for the electron transport chain (houten and wanders 2010) . although l-carnitine is present in plants, the main nutritional sources for humans are foodstuffs of animal origin (mitchell 1978) . depending on dietary habits, daily intake from food sources ranges from <0.16 to 2.4 mg/kg body weight (bw), the bioavailability being generally lower in humans that regularly consume a diet high in l-carnitine (e.g., abundant consumption of red meat) and even lower when high amounts of this compound are supplemented exogenously (harper et al. 1988; rebouche 2004; sahajwalla et al. 1995) . the body concentration of l-carnitine is tightly regulated by an equilibrium between endogenous synthesis (from lysine and methionine), renal reabsorption, and dietary l-carnitine supply, the latter especially influencing the renal clearance rate (evans and fornasini 2003; jeukendrup et al. 1998; rebouche 2004 ). therefore, oral or intravenous dosages above a certain basal or physiological "threshold" level lead to an increased l-carnitine elimination and diminished uptake (evans and fornasini 2003; rebouche and seim 1998) . although the mechanisms of the intestinal absorption of l-carnitine have not yet been fully elucidated, they most likely involve carrier-mediated transport as well as passive diffusion, the latter being the more important intake route for non-dietary (i.e., high) carnitine concentrations (evans and fornasini 2003; li et al. 1992) . active renal reabsorption, intestinal uptake and tissue distribution of l-carnitine are mediated by so-called carnitine/organic cation transporters (octn), two of them (octn1 and octn2) having been identified in humans (tamai 2013) . rare mutations in the slc22a5 gene encoding for octn2 lead to systemic carnitine shortage and consequently to the development of a primary carnitine deficiency (pcd), which in most cases manifests itself clinically in form of a hypoketotic hypoglycemic encephalopathy as well as disorders of the heart and skeletal muscle (erguven et al. 2007; lahjouji et al. 2001) . in contrast, the clinically less severe secondary carnitine deficiency (scd) is caused by organ (e.g., kidney or liver) or metabolic disorders (e.g., impaired fatty acid metabolism), carnitine malabsorption, malnutrition as well as pharmacological treatment (erguven et al. 2007; flanagan et al. 2010) . the treatment of these disorders, especially in the case of pcd, consists in the daily supplementation of l-carnitine in doses (100-400 mg/kg bw or 990 mg 2-3 times/day) adapted to the patients' plasma level (bain et al. 2006; longo et al. 2006) . since the early 1980s, l-carnitine is also being extensively advertised and used by athletes, bodybuilders or even obese individuals as a nutritional supplement with allegedly "fat burning" and performance-enhancing properties (jeukendrup et al. 1998 ), although to date there are no conclusive data supporting these claims neither in rats (eder 2000; melton et al. 2005; saldanha aoki et al. 2004 ) nor in humans (barnett et al. 1994; brass 2000; cerretelli and marconi 1990; grunewald and bailey 1993; jeukendrup and randell 2011; jeukendrup et al. 1998; vukovich et al. 1994) . taking into account the inverse relationship between exogenous supplementation and bioavailability, one must conclude that, when fairly high oral doses are given, a significant amount of l-carnitine would remain in the gut. the unabsorbed compound can be partially degraded to trimethylamine (tma) or γ-butyrobetaine by enterobacteria in the gut lumen of rats and, to a greater extent, humans (koeth et al. 2013; rebouche and chenard 1991; rebouche et al. 1984; zhang et al. 1999) . after absorption, tma is oxidized to trimethylamine-n-oxide (tmno) by hepatic flavin monooxygenases (baker and chaykin 1962; bennett et al. 2013; koeth et al. 2013 ): in addition to that, and following l-carnitine supplementation, tmno can be directly produced in the gut by the gastrointestinal microbiota (koeth et al. 2013) . in an acidic environment and in the presence of nitrite ions, i.e., under conditions which prevail in the upper gastrointestinal tract, the known carcinogen n-nitrosodimethylamine (ndma) can be formed from these amine precursors (bain et al. 2005; lijinsky et al. 1972; loh et al. 2011; tricker and preussmann 1991) . additionally, bacterial metabolism can also lead to ndma formation from amines such as tma and dimethylamine (maduagwu and bassir 1979) . consumption of l-carnitine in doses that are not completely absorbed might thus enhance bacterial ndma production in the colon and consequently contribute to colorectal tumor formation, as has been shown by knekt et al. (1999) and loh et al. (2011) for dietary ndma. therefore, we investigated whether a chronic administration of different l-carnitine concentrations via drinking water leads to an increased number of aberrant crypt foci (acf), which are considered preneoplastic lesions associated with colorectal cancer formation (bird 1995) , in the colon of male fischer 344 rats. as a recent study by koeth et al. (2013) showed that tmno resulting from l-carnitine supplementation promotes atherosclerosis in mice, we additionally examined its influence on the occurrence of atherosclerotic lesions in the aorta of the above-mentioned rats. eighty male fischer 344 ducrl rats (f344 rats) were purchased at 5-6 weeks of age (100-120 g bw) from charles river (sulzfeld, germany) and housed in type iv polycarbonate cages (ehret, emmendingen, germany). the cages were placed in airflow cabinets (uni protect; ehret) operated in a positive pressure mode (50 pa) and providing a temperature of 21-23 °c, a relative humidity of 50-60 %, a maximum light intensity of 45 lux, 15-20 air shifts per hour as well as a 12/12 h day and night cycle. the bedding consisted of poplar granules (lignocel ® select; jrs, rosenberg, germany), which were changed once a week, and the diet was a standard pelleted rodent maintenance diet (cat. nr. 1324; see online resource 1 "specifications of the animal feed" for details on feed composition) purchased from altromin (lage, germany). the animals in each cage had access to tunnel housing made of red polycarbonate (bioscape, castrop-rauxel, germany) and certified carcinogen and toxicant-free aspen rods (abedd ® lab&vet service, vienna, austria) as enrichment. experimental design and procedure upon arrival, littermates were randomly assigned to one of four test groups consisting of 20 animals each and housed pairwise in each cage to minimize distress during the whole experimental period of 58 weeks. animals in the control group (group 1) received drinking (tap) water without any supplementation. water for groups 2, 3 and 4 was supplemented with 1, 2 or 5 g l-carnitine/l for 52 weeks, respectively. l-carnitine (carnipure™; lonza, basel, switzerland) with a purity of 99.5-99.9 % was purchased from denk ingredients (munich, germany). because of a sialodacryoadenitis virus (sdav) infection (see results), the l-carnitine treatment was started in week 6 upon arrival after an acclimatization and recovery period of 5 weeks. to avoid microbial contamination, drinking water was autoclaved before carnitine supplementation and changed twice a week. in the course of water changes, water consumption was recorded, while the weight of the animals was assessed once a week. moreover, the stability of l-carnitine in the water was assessed by liquid chromatography/mass spectrometry (lc-ms) for a period of 7 days under experimental conditions (see online resource 1 "assessment of l-carnitine stability" for details). after the 52-week administration period, individual rats were anaesthetized by co 2 (6 l/min flush) and decapitated. blood was immediately collected for further analysis and the gastrointestinal tract entirely removed and processed as previously described (nicken et al. 2012) . briefly, the colon was removed, washed with phosphate buffered saline (pbs) and opened longitudinally. thereafter, the tissues were fixed in formalin (roti ® -histofix 4 %; carl roth, karlsruhe, germany), stained with methylene blue solution (0.1 % w/v in pbs) and acf formation was assessed using a stereomicroscope (szx16; olympus, hamburg, germany). additionally, the kidneys, liver and spleen were removed and weighed. for histopathologic examination, heart, thoracic aorta and liver were fixed in 10 % neutral buffered formalin. organ trimming was performed in accordance with the registry of industrial toxicology animal-data (rita) and north american control animal database (nacad) guidelines for organ sampling and trimming in rats and mice (morawietz et al. 2004; ruehl-fehlert et al. 2003) , followed by embedding in paraffin wax, sectioning at 2 µm thickness, and staining with hematoxylin and eosin (he). micrographs of representative lesions were obtained using an olympus bx51 microscope equipped with a dp72 12.8 megapixel digital color camera and cellsens standard v. 1.7.1 software (olympus corp., tokyo, japan). figures were further processed with adobe ® photoshop ® v. 7.0 (adobe systems, inc., san jose, ca, usa), thereby adjusting contrast and brightness, if necessary. assessment of the ndma concentration in the urine of the experimental animals urine was collected in the next-to-last week of the study by housing 16 animals (4 from each group) individually in metabolic cages (tecniplast, hohenpeißenberg, germany) for 24 h. gathered urine samples (5-10 ml) were stored in 50-ml tubes (greiner bio-one, frickenhausen, germany) protected from light at −80 °c until analysis. sample extraction was performed using supelclean coconut charcoal spe tubes (sigma-aldrich, schnelldorf, germany) based on the u.s. environmental protection agency method 521 for the detection of nitrosamines in drinking water (munch and bassett 2004) . d 6 -ndma (restek, bad homburg, germany) was added to the urine samples as internal standard prior to sample preparation. the nitrosamines were eluted from the spe tubes using methylene chloride (vwr, leuven, belgium) and concentrated under a gentle stream of nitrogen at 35 °c to a volume of approximately 0.5 ml. an aliquot of 5 µl was injected into the gc-ms. as residue-free urine was not available, the method validation was performed by using synthetic human urine (synthetic urine, nussdorf, germany) spiked with ndma (restek). the samples were analyzed on an agilent 7890a gas chromatograph (waldbronn, germany) coupled to an agilent 5975c mass selective detector (msd) applying the following parameters: column: agilent db-wax (polyethylene glycol, 30 m; 0.25 mm i.d.; 0.5 µm film thickness); carrier gas: helium, 1.9 ml/min, constant flow; oven temperature program: 1 min 35 °c, +20 °c/min, 1 min 200 °c, backflush 3 min 200 °c; programmed temperature vaporization on an agilent multimode inlet: inlet temperature program: 0.06 min 37 °c, +600 °c/min, 5 min 240 °c; vent flow 100 ml/min at 0.34 bar; ionization: 70 ev, ei, sim mode (m/z: 80, 74, 42). statistical analysis of the data was performed with prism v. 6.04 (graphpad software, inc., la jolla, ca, usa). the shapiro-wilk normality test was used to assess probability distribution of the datasets. normally distributed sets were subjected to a one-way analysis of variance (anova) followed by tukey's post hoc test, while non-normally distributed data or data with too few independent experiments to perform a shapiro-wilk test (analysis of ndma levels in rat urine) were subjected to a kruskal-wallis test followed by dunn's post hoc comparison. the relationship between the frequencies of pathohistological findings and l-carnitine treatment was analyzed by means of pearson's chi-squared test. statistical significance was considered if p ≤ 0.05. in the first week upon arrival, the animals showed signs of an sdav infection. sdav is a relatively common and rat-specific coronavirus with high morbidity and very lowto-no mortality (gaillard and clifford 2000; jacoby and gaertner 2006) . the infection was relatively silent, the most prominent clinical symptom being sneezing followed by red-colored nasal discharge. in groups 1, 2 and 3, one animal had to be euthanized before the completion of the study. all other animals completed the study in good general condition. no statistically significant differences were observed between the groups regarding the final body weight, all animals weighing ~410 g at the end of the study (table 1 , "final bw"). similarly, the final weight of the various organs sampled from the different animals did not differ across the groups in a significant manner (table 1 , "kidney, liver and spleen weight"). interestingly, the rats in the highest dose group (group 4) drank significantly more water than the animals in groups 1 (control) and 2 (lowest dose; table 1 , "water uptake"). based on average water consumption of 18.3 ml/ rat/day (table 1 , "water uptake") and an average body weight of 260 g/rat (table 1; regarding acf formation and acf multiplicity (crypts/acf), there was no statistically significant difference between the four groups tested (tables 2, 3) histopathological alterations in the aorta were only seen in one animal of the control group, showing mild focal degenerative changes in the media accompanied by a mild infiltration of macrophages and mineralization ( fig. 1a ; table 3 ). histopathological examination of the heart revealed a mild multifocal chronic lymphohistiocytic myocarditis with myocardial degeneration and fibrosis in about 50 % of the rats, but no statistically significant difference between the groups was observed ( fig. 1b; table 3 ). moreover, all animals displayed a variable degree of bile duct hyperplasia (fig. 1c) , and a high number of animals showed a mild-to-moderate multifocal acute to subacute table 1 physiological data of the experimental animals where applicable, values are shown as mean ± standard deviation * weight of one kidney ▲ calculated on the basis of the mean of the weekly water consumption of two animals/cage a kruskal-wallis test followed by dunn's post hoc analysis b one-way anova followed by tukey's post hoc analysis α significantly different (p < 0.01) when compared to group 1 β significantly different (p < 0.001) when compared to group 2 group 1 (0 g/l) group 2 (1 g/l) group 3 (2 g/l) group 4 (5 g/l) number of animals 19 19 19 20 starting body weight (g) a 105.1 ± 7.9 102.4 ± 7.0 101.9 ± 6.9 101.6 ± 6.9 final body weight (g) a 410.5 ± 19.6 408.5 ± 14.6 413.2 ± 14.1 414.5 ± 18.3 kidney weight (g)* ,a 1.27 ± 0.08 1.26 ± 0.07 1.28 ± 0.1 1.30 ± 0.09 liver weight (g) b 11.4 ± 1.0 11.4 ± 0.9 11.6 ± 0.8 11.9 ± 0.9 spleen weight (g) b 0.82 ± 0.1 0.83 ± 0.08 0.84 ± 0.06 0.84 ± 0.08 water uptake (ml/day/animal) ▲,a 18.1 ± 1.6 18.1 ± 2.1 18.3 ± 1.2 18.8 ± 1.8 α,β table 3 pathohistological findings in the aorta, heart and liver of the animals all pathohistological findings analyzed with pearson's chi-squared test a number of animals with the mentioned alteration/total number of animals analyzed, frequency (%) in parentheses group 1 (0 g/l) group 2 (1 g/l) group 3 (2 g/l) group 4 (5 g/l) (100) 20/20 (100) fig. 1 a aorta of a control animal: mild focal degenerative changes in the media accompanied by a mild infiltration of macrophages and mineralization (arrowheads; l lumen). b heart of an animal of group 4: mild multifocal chronic lymphohistiocytic myocarditis with myocardial degeneration and fibrosis. c liver of a control ani-mal: mild bile duct hyperplasia, associated with mild lymphohistiocytic infiltration. d liver of a control animal: focal suppurative and necrotizing hepatitis. he. scale bars a, b, d 100 µm, scale bar c 50 µm suppurative and necrotizing hepatitis (fig. 1d) , without statistically significant differences between the groups (table 3) . except for a hepatocellular carcinoma in one animal of group 1, no tumors were observed within the livers of the remaining animals. no significant differences regarding the ndma content in the urine of the animals was observed between the test groups (fig. 2) . interestingly, animals receiving 2 or 5 g/l l-carnitine (groups 3 and 4) seem to excrete the lowest amount of ndma, median concentrations reaching 281.9 ng/ml and 267.6 ng/ml, respectively (group 1: 314.2 ng/ml; group 2: 348.8 ng/ml). however, it has to be noted that the differences are not statistically significant and that the amount of urinary ndma strongly varies between the animals tested in each group (fig. 2 ). the final mean body weights of the rats recorded during the course of this study correspond to weights measured in untreated f344 rats of the same age (solleveld et al. 1984) . in contrast, the water uptake of the rats in this study was somewhat reduced when compared to the water uptake of laboratory rats in general (hofstetter et al. 2006 ). although rats administered 5 g/l l-carnitine drank significantly more water than animals in groups 1 and 2, this finding can be considered as biologically irrelevant, and it is questionable whether it is actually related to l-carnitine supplementation. f344 rats have extensively been used in longterm (i.e., 2 years-long) carcinogenicity studies (dinse et al. 2010; solleveld et al. 1984) and are characterized by an extremely low spontaneous incidence rate (0.1-0.6 %) of neoplasms of the small and large intestine (haseman et al. 1998) , rendering them particularly useful for the investigation of putative colon carcinogens. however, acfs seem to spontaneously develop in the colon of f344 rats with a fairly high incidence (40-60 %), even in animals killed at an earlier age than those in the present study (furukawa et al. 2002; tanakamaru et al. 2001) . with an overall frequency of 7.7 % and no statistically significant difference in the number of acfs/animal between the testing groups, acf formation in this study is considered to be spontaneous and not related to l-carnitine supplementation. in addition, the data obtained in the course of this study show that the administration of different l-carnitine dosages does not lead to increased amounts of ndma being excreted via the urine when compared to untreated animals, a fact which might furthermore explain the low acf incidence. even though there was no difference between the test groups, it should be noted that a "basal" ndma level (376.2 ± 169.8 ng/ml on average) was nevertheless observable in the urine of the animals in group 1. this might be the result of its endogenous formation or of a contamination of unknown etiology (kraft et al. 1981; tricker and preussmann 1991; vermeer et al. 1998) . regarding the possible influence of the sdav infection on the outcome of the study at hand, it should be mentioned that the repair processes in the affected tissues (respiratory tract, eye, salivary and lacrimal glands) begin 5-7 days post infection and in the case of the salivary and lacrimal glands are completed after about 21 days (jacoby and gaertner 2006; percy et al. 1988 ). since sdav infection occurred at the very beginning of the study and the animals had 3-4 weeks to recover, we do not suspect any major effect of the virus on the outcome of this study, especially since sdav is not known to interfere with colon tumorigenesis or heart-related pathologies (jacoby and gaertner 2006) . the latter statement as well as the fact that immunocompetent animals develop immunity and recover relatively fast with barely any sequelae (jacoby and gaertner 2006) led to the decision, not to kill the entire colony and to continue the experiment. particularly, male rats develop a plethora of pathologic changes with increasing age, the most common being spontaneous tumors, chronic nephropathy and lesions of the cardiovascular system (coleman et al. 1977; king and russell 2006) . the pathologic findings related to the cardiovascular system described in this study clearly fall in this category. focal myocardial degeneration in conjunction with inflammation (lymphohistiocytic infiltrations) followed by myocardial fibrosis have been described in aged f344 rats as well as other rat strains in incidences comparable to the ones reported herein, especially when the animals were fed ad libitum (blankenship and skaggs 2013; coleman et al. 1977; goodman et al. 1979; hall et al. 1992; keenan et al. 1995a, b; maeda et al. 1985) . in this context, the left ventricular papillary muscle, which was the primarily affected fig. 2 ndma concentrations in the urine of the experimental animals collected in the next-to-last week of the study. shown is the median as well as ndma levels of each individual animal/group (mean of three measurements/sample). the dataset was subjected to a kruskal-wallis test followed by dunn's post hoc comparison location in numerous animals (data not shown), is reported to be a preferred site for these lesions (percy and barthold 2008) . additionally, aging rats commonly exhibit hyperplastic bile ducts (king and russell 2006) . according to coleman et al. (1977) , 75 % of approximately 12-month old f344 rats show bile duct hyperplasia, a finding which contrasts the incidence of 100 % reported in this study, although, still in accordance with the same source, similar incidences were reported in significantly older animals (>18 months). in contrast, control f344 rats used in 2-year carcinogenicity studies of the u.s. national institutes of health carcinogenesis testing program only marginally suffered from bile duct hyperplasia, 24.5 % of male and 12.5 % of female f344 rats being affected (goodman et al. 1979) . the frequency of multifocal suppurative and necrotizing liver lesions observed in this study (68.4-90.0 %) was distinctly above the relatively low incidence of spontaneous necrotizing processes previously described in aged male f344 rats (approx. 6,9 %; hall et al. 1992 ). although we were unable to identify characteristic viral, bacterial, mycotic or parasitic structures within the liver lesions employing routine and special histological staining methods (gram stain, periodic acid schiff-reaction, and groccott silver stain; data not shown), we cannot rule out the possibility that the animals were infected with agents such as clostridium piliforme (tyzzer's disease), salmonella spp. or corynebacterium kutscheri (percy and barthold 2008; thoolen et al. 2010) . however, since all test groups were equally affected, this finding is clearly not related to the l-carnitine treatment. additionally, it should be considered that these lesions were mainly of mild, subclinical grade and acute in character and therefore might have developed only in the last days (or the last week) of the study, thus rendering an influence on acf formation or the onset of cardiovascular lesions unlikely. no definitive (sub-)intimal atherosclerotic lesions were observed in the aortas of the animals. the degenerative changes observed in the aorta of one control rat were interpreted as an incidental finding of unknown etiology and are in agreement with the previously reported rare spontaneous lesions described in old f344 rats (king and russell 2006) . since this finding concerns only one animal in the control group, a carnitine-related cause can be excluded. additionally, it should be noted that rats, except for specially bred strains, generally do not develop atherosclerosis (king and russell 2006; moghadasian 2002) . this fact together with differences in the composition of the gut microbiota, the metabolism of l-carnitine as well as the amount (1.3 g/l) of l-carnitine given to the apolipoprotein e-knockout mice might explain the divergent results of the study at hand to that conducted by koeth et al. (2013) regarding the formation of atherosclerotic lesions. in conclusion, this study provides evidence that the daily administration of l-carnitine in concentrations of 70.4, 140.8 and 351.9 mg/kg bw/day for 1 year does not lead to an adverse effect in the colon or cardiovascular system of male f344 rats. trimethylamine: metabolic, pharmacokinetic and safety aspects disposition and metabolite kinetics of oral l-carnitine in humans the biosynthesis of trimethylamine-n-oxide effect of l-carnitine supplementation on muscle and blood carnitine content and lactate accumulation during high-intensity sprint cycling trimethylamine-n-oxide, a metabolite associated with atherosclerosis, exhibits complex genetic and dietary regulation role of aberrant crypt foci in understanding the pathogenesis of colon cancer findings in historical control harlan rcchan™: wist rats from 4-, 13-, 26-week studies supplemental carnitine and exercise guidance for industry-estimating the maximum safe starting dose in initial clinical trials for therapeutics in adult healthy volunteers l-carnitine supplementation in humans. the effects on physical performance pathological changes during aging in barrier-reared fischer 344 male rats comparison of ntp historical control tumor incidence rates in female harlan sprague dawley and fischer 344/n rats l-carnitine supplementation and lipid metabolism of rats fed a hyperlipidaemic diet a case of early diagnosed carnitine deficiency presenting with respiratory symptoms pharmacokinetics of l-carnitine role of carnitine in disease spontaneous development of aberrant crypt foci in f344 rats common diseases. in: krinke gj (ed) the laboratory rat neoplastic and nonneoplastic lesions in aging f344 rats commercially marketed supplements for bodybuilding athletes histopathologic observations in weanling b6c3f1 mice and f344/n rats and their adult parental strains pharmacokinetics of intravenous and oral bolus doses of l-carnitine in healthy subjects spontaneous neoplasm incidences in fischer 344 rats and b6c3f1 mice in two-year carcinogenicity studies: a national toxicology program update the laboratory rat a general introduction to the biochemistry of mitochondrial fatty acid beta-oxidation viral disease fat burners: nutrition supplements that increase fat metabolism fat metabolism during exercise: a review-part iii: effects of nutritional interventions diet, overfeeding, and moderate dietary restriction in control sprague-dawley rats: ii. effects on age-related proliferative and degenerative lesions diet, overfeeding, and moderate dietary restriction in control sprague-dawley rats: i. effects on spontaneous neoplasms metabolic, traumatic, and miscellaneous diseases risk of colorectal and other gastro-intestinal cancers after exposure to nitrate, nitrite and n-nitroso compounds: a follow-up study intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis urinary excretion of dimethylnitrosamine: a quantitative relationship between dose and urinary excretion carnitine transport by organic cation transporters and systemic carnitine deficiency the effect of enteral carnitine administration in humans nitrosation of tertiary amines and some biologic implications n-nitroso compounds and cancer incidence: the european prospective investigation into cancer and nutrition (epic)-norfolk study disorders of carnitine transport and the carnitine cycle microbial nitrosamine formation in palm wine: in vitro n-nitrosation by cell suspensions nutritional influences on aging of fischer 344 rats: ii. pathology l-carnitine supplementation does not promote weight loss in ovariectomized rats despite endurance exercise carnitine metabolism in human subjects. i. normal metabolism experimental atherosclerosis: a historical overview revised guides for organ sampling and trimming in rats and mice-part 3: a joint publication of the rita and nacad groups version 1.0; document # epa/600/r-05/054) determination of nitrosamines in drinking water by solid phase extraction and capillary column gas chromatography with large volume injection and chemical ionization tandem mass spectrometry influence of a fatrich diet, folic acid supplementation and a human-relevant concentration of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine on the induction of preneoplastic lesions in the rat colon rat pathology of laboratory rodents and rabbits depletion of salivary gland epidermal growth factor by sialodacryoadenitis virus infection in the wistar rat dose translation from animal to human studies revisited kinetics, pharmacokinetics, and regulation of l-carnitine and acetyl-l-carnitine metabolism metabolic fate of dietary carnitine in human adults: identification and quantification of urinary and fecal metabolites carnitine metabolism and its regulation in microorganisms and mammals l-carnitine dissimilation in the gastrointestinal tract of the rat revised guides for organ sampling and trimming in rats and mice-part 1: a joint publication of the rita and nacad groups multiple-dose pharmacokinetics and bioequivalence of l-carnitine 330-mg tablet versus 1-g chewable tablet versus enteral solution in healthy adult male volunteers carnitine supplementation fails to maximize fat mass loss induced by endurance training in rats natural history of body weight gain, survival, and neoplasia in the f344 rat pharmacological and pathophysiological roles of carnitine/organic cation transporters (octns: slc22a4, slc22a5 and slc22a21) essential similarities between spontaneous and meiqxpromoted aberrant crypt foci in the f344 rat colon proliferative and nonproliferative lesions of the rat and mouse hepatobiliary system carcinogenic n-nitrosamines in the diet: occurrence, formation, mechanisms and carcinogenic potential volatile n-nitrosamine formation after intake of nitrate at the adi level in combination with an amine-rich diet peroxisomes contribute to the acylcarnitine production when the carnitine shuttle is deficient carnitine supplementation: effect on muscle carnitine and glycogen content during exercise dietary precursors of trimethylamine in man: a pilot study the authors wish to thank (in alphabetical order) judith bigalk and nicole brauer for excellent technical assistance and dr. laura c. bartel, maria d. brauneis, janine döhring, julia hausmann, anne von keutz, dr. petra nicken, bettina seeger and shan wang for valuable help in taking care of the experimental animals. the authors would also like to acknowledge the financial support of the german federal institute for drugs and medical devices (bonn, germany). key: cord-239527-69bxbhjh authors: montag, felix; sagimuldina, alina; schnitzer, monika title: are temporary value-added tax reductions passed on to consumers? evidence from germany's stimulus date: 2020-08-19 journal: nan doi: nan sha: doc_id: 239527 cord_uid: 69bxbhjh this paper provides the first estimates of the pass-through rate of the ongoing temporary value-added tax (vat) reduction, which is part of the german fiscal response to covid-19. using a unique dataset containing the universe of price changes at fuel stations in germany and france in june and july 2020, we employ a difference-in-differences strategy and find that pass-through is fast and substantial but remains incomplete for all fuel types. furthermore, we find a high degree of heterogeneity between the pass-through estimates for different fuel types. our results are consistent with the interpretation that pass-through rates are higher for customer groups who are more likely to exert competitive pressure by shopping for lower prices. our results have important implications for the effectiveness of the stimulus measure and the cost-effective design of unconventional fiscal policy. the drastic economic downturn accompanying the covid-19 pandemic was met by an unprecedented fiscal response of the german government. on 3 june 2020, a stimulus package worth 130 billion euro was announced. to the general surprise of the public, it included a reduction of the standard value-added tax (vat) rate from 19 to 16 percent and of the reduced rate from 7 to 5 percent for the second half of 2020, at an estimated cost of 20 billion euro or 0.6 percent of gdp. the aim of this fiscal policy is to temporarily reduce prices and stimulate consumption through inflation expectations. for this to work, however, it is crucial that firms pass on the vat reduction to consumers. our paper provides the first estimates of the pass-through rate of the temporary vat reduction for a major sector of the economy. we estimate the pass-through rate for diesel and gasoline using a unique dataset containing the universe of price changes at fuel stations in germany and france in june and july 2020 and employing a differencein-differences strategy. we find that pass-through is incomplete for all types of fuels and very heterogeneous across fuel types. this variation of pass-through rates is consistent with the interpretation that customers of different fuel types are differentially likely to shop for lower prices, resulting in differing competitive pressure. whilst fuel stations pass on most of the vat rate reduction to diesel customers who on average drive more than twice as many kilometers per year than drivers of gasoline driven cars, pass-through rates for gasoline are much lower. studying the effect of the temporary vat rate reduction in the context of the fuel market is particularly interesting for two reasons. first, it is a market where granular data is available in real-time, which allows us to evaluate the effect while it is happening. second, it is a market where price adjustments are costless and in fact happen frequently. thus, despite the temporary nature of the vat rate change, price adjustment costs cannot be held accountable for imperfect pass-through. this paper makes two contributions to the literature. first, our results have implications for the effective design of unconventional fiscal policy. feldstein (2002) proposed that stimulating inflation in an environment where monetary policy is ineffective could be done by targeting household expectations directly. this type of policy was later coined unconventional fiscal policy by d' acunto et al. (2018) . a temporary reduction in the vat rate is only likely to affect household expectations, however, if the reduction is passed on to consumers and they therefore expect prices to be lower temporarily. by analyzing the pass-through rate of the temporary vat reduction, we shed light on a necessary condition for this type of unconventional fiscal policy to be effective. furthermore, we show that by targeting competitive markets where consumers are likely to search for lower prices, policymakers can make unconventional fiscal policy more cost-effective. et al. (2020b) predict that the 2020 temporary vat reduction will successfully increase inflation expectations and expenditure. benzarti, carloni, et al. (forthcoming) show that pass-through is often asymmetric and that prices respond twice as much to vat increases as to decreases. furthermore, whilst the 2007 vat increase was permanent, the current vat change only lasts for six months. conclusions from the 2007 permanent vat increase therefore are not necessarily informative about the 2020 temporary vat reduction. second, we are the first to provide estimates of the average pass-through rate of an unanticipated vat rate change in a major sector of the economy using high-frequency, establishment-level price data. our unique dataset allows us to observe all price changes for around 23, 000 fuel stations across germany and france before and after the temporary vat rate reduction. fuel stations in germany are treated after the 1 july, whereas fuel stations in france are unaffected by the german policy change. thus, we can employ a difference-in-differences strategy, using french fuel stations as control group. previous empirical studies on tax pass-through use aggregate price indices, finding mixed results. they include evidence for under-shifting (e.g. benzarti and carloni, 2019) , full passthrough (e.g. benedek et al., 2019) or over-shifting (e.g. besley and rosen, 1999) . notable exceptions using firm-level price data are kosonen (2015) , studying the effect of a vat reduction for hairdressers in finland, and büttner and madzharova (forthcoming) , who estimate the effect of a large number of vat increases and decreases in the european union (eu) using product-level monthly sales data for home appliances in a panel model across a large number of european countries over time. like kosonen (2015) , we focus on the effect of one particular policy change on one particular market. in contrast to kosonen (2015) , using a control market in a different country allows us to avoid potential general equilibrium effects affecting the control group, which might lead to an over-or under-estimation of the pass-through rate, as noted by benedek et al. (2019) . finally, a feature of high-frequency price data in a market with many price adjustments is that it allows us to trace out the evolution of pass-through rates over time. to estimate the average pass-through rate of the vat reduction, we use a differencein-differences strategy, where we compare daily prices of the three main fuel types sold at fuel stations in germany and france before and after the policy change. 1 supply shocks, in particular fluctuations in the price of crude oil, should affect germany and france similarly and are thus eliminated by time fixed effects. we also account for regional differences in demand over time by controlling for changes in mobility, using regional data from the google covid-19 community mobility report. we find that the pass-through rate for diesel is 83 percent, whereas it is 61 percent for e10 and 40 percent for e5. 2 this translates into price decreases of 2 percent for diesel, 1.5 percent for e5 and 1 percent for e10. at the same time, retail margins for diesel only increased by 0.7 percent, whilst retail margins for e5 and e10 increased by between 10 and 12 percent. 3 our results show that pass-through of the vat rate reduction is fast and substantial but remains incomplete. whilst prices decrease for consumers, margins also substantially increase for sellers. furthermore, there is a substantial difference in pass-through rates 1 this dataset has previously been used by montag and winter (2020) to analyze the effect of price transparency. 2 e5 and e10 are the two main types of gasoline sold in germany, which differ in how much bioethanol they contain. 3 our measure of retail margins only subtracts taxes, duties and the price of crude oil at the port of rotterdam from fuel prices. it includes fuel station and refinery margins, as well as different cost types. the percentage change in retail margins due to the vat change is therefore an underestimate of the actual percentage change in retail margins. between fuel types. since stations sell all three types of fuel, unobserved station characteristics cannot explain these differences. instead, differences in competitive pressure due to different propensities of customer groups to shop for lower prices are consistent with the observed effects. whereas fuel stations pass on more than half of the vat rate decrease to frequent drivers and professional drivers, usually driving diesel cars, as well as to price sensitive gasoline customers who buy the cheaper e10, they pass on less than half of the tax rate reduction to customers of e5 suggesting that they are less responsive to price differentials. the remainder of the paper is structured as follows: section 2 describes the industry, section 3 gives an overview of the data and presents descriptive evidence, section 4 discusses the empirical strategy, section 5 presents the estimation results and section 6 concludes. in 2019, total revenues from retail fuel sales were worth 92 billion euro or approximately 3 percent of german gdp. in addition to its standalone value to the economy, this market has large externalities on the rest of the economy. fuel prices are a key determinant of travel costs, commuting costs and, more broadly, the cost of personal transportation. the first important distinction to make within fuels for passenger vehicles is between diesel and gasoline. 4 in germany, diesel has a volume share of 44 percent of fuel for passenger vehicles with combustion engines and gasoline accounts for the remaining 56 percent. 5 substituting between these two types of fuel is very costly, both on the demand and supply side. 6 within gasoline, there is differentiation according to the octane rating and the share of ethanol. standard gasoline (commonly referred to as super) has an octane rating of 95. it has a volume share of 95.4 percent of the gasoline market. 7 some high-perfomance vehicles will require gasoline with an octane rating of 98 (commonly referred to as super plus), which has a 4.6 percent volume share within gasoline. at the same time, there is no added benefit of fueling super plus if the vehicle can process super. since the price of super plus is always considerably higher, there is no demandside substitution from super to super plus either. as fuel stations do not report prices of super plus to the market transparency unit in germany, it is not part of our analysis. within super, there is a final distinction according to the share of ethanol. standard gasoline has a 5 percent share of ethanol and is thus commonly referred to as e5. in 2011, a new type of gasoline was introduced with a 10 percent ethanol share, referred to as e10. the aim of increasing the share of ethanol is to reduce greenhouse gas emissions and decrease the amount of fossil fuel used in transportation. although e5 and e10 are not taxed differently, e10 is usually around 4 eurocent cheaper than e5. this is partly driven by the relative prices of crude oil and ethanol on the world market and partly by a minimum quota of biofuels that need to be sold by fuel stations. after the introduction of e10 in 2011, there was controversy about whether biofuels damage the engine. although biofuels can pose a significant threat to the engine of a vehicle that is not certified to be compatible with e10, around 90 percent of gasoline-run vehicles, including all vehicles produced after 2012, are compatible with e10. 8 according to the german automobile association, e10 is around 1.5 percent less efficient than e5. 9 all fuel stations in germany are required to sell both types of fuel. nevertheless, in 2019 e5 still had a volume share of 85.6 percent within super and e10 only of 14.4 percent. overall, many motorists who could buy less expensive e10 choose not to do so and buy e5 instead. reasons for this could include preferences or a lack of information, which point towards a lower price sensitivity of e5 customers compared to e10 customers. two further observations can be made about the difference between drivers of gaso-line and diesel passenger vehicles. whereas only 32 percent of registered passenger vehicles in germany have a diesel engine, compared to 66 percent that run on gasoline, frequent drivers tend to use diesel cars. 10 on average, gasoline passenger vehicles drive 10, 800 kilometers, whereas diesel passenger vehicles drive 19, 500 kilometers per year. 11 the largest share of the fuel price consists of taxes. a lump-sum energy tax of 0.6545 euro per liter is levied on gasoline (0.4704 euro per liter for diesel). 12 in addition, there is a 19 percent value-added tax which is levied on the net price of diesel and gasoline, including the energy tax. this value-added tax is temporarily reduced to 16 percent between july and december 2020. to be reported by stations to a government agency, which makes this data available to researchers. 16 furthermore, we add data on the daily price of crude oil, the principal input product for diesel and gasoline, at the port of rotterdam. finally, we use data on daily regional mobility patterns from the covid-19 community mobility report provided by google. our analysis starts on 15 june 2020 and currently goes until 31 july 2020. the 15 june is a natural starting point, as it marks the beginning of the european commission's re-open eu plan and is the date on which france and germany lifted many of their travel restrictions and re-opened their borders. 17 as long as the temporary vat rate reduction remains in place, we plan to extend our period of analysis and estimate how the pass-through rates evolve. using the data on price changes, we construct daily weighted average prices. table 1 shows that the price level is generally higher in france than in germany. gross prices in france increase by around 2 eurocent between the pre-and post-vat cut periods. in germany, gross prices remain constant for e5 and e10 and decrease by 1 eurocent for diesel. at the same time, the increase in the net price in germany is between 2 and 3 eurocent, depending on the fuel type, which is larger than in france and thus suggests that the vat reduction was not completely passed on to consumers. 16 see https://www.prix-carburants.gouv.fr/rubrique/opendata/. 17 see https://reopen.europa.eu/en/. notes: "pre-vat cut" and "post-vat cut" refer to fuel stations in germany and france before and after the reduction of the vat rate, respectively. the pre-vat phase goes from 15 june until 31 june 2020. the post-vat phase starts on 1 july 2020. we also calculate retail margins by subtracting taxes, duties and the share of the price of crude oil that goes into the production of diesel and gasoline, respectively. 18 although these retail margins still contain different cost types, such as the cost of refining or transportation costs, the main source of input cost variation, the price of crude oil, is eliminated. the latter, we aim to capture local changes in the propensity to use a car for professional activities. both of these variables are measured as the percentage change of activities compared to the median value for the corresponding day of the week during the five-week period 3 january to 6 february 2020. the data is disaggregated for 96 sub-regions in france and 16 regions in germany. we use the geolocation of each fuel station to match the measures of local mobility to each station. table 1 shows that mobility patterns in france and germany are similar. whereas visits to retail and recreational facilities were around 10 percent lower in the second half of june compared to the baseline beginning of the year, in july, the number of such visits returned close to their pre-pandemic levels. at the same time, in both countries visits to workplaces were around 15 percent lower in the second half of june compared to the baseline and 20 percent lower in july. this is likely because many people go on vacation in july. it also indicates that overall trends in both countries are very similar. we begin by estimating the average effect of the vat reduction on fuel prices and retail margins in germany. to do this, we compare the evolution of prices and retail margins at fuel stations in germany to stations in france, before and after the decline in the value-added tax. for the three main types of fuel, we focus on two main outcomes: daily fuel prices and retail margins. to causally estimate the effect of the temporary reduction in the vat rate on fuel prices and retail margins, we use a difference-in-differences strategy, and compare stations in germany and france, before and after the reduction in the vat rate. specifically, we estimate the following regression: where y it is the logarithm of the price or retail margin of gasoline or diesel at a fuel station i at date t, and v at it is a dummy variable that equals one for stations affected by the vat reduction at date t. these are fuel stations in germany from 1 july 2020 onwards. x it is a vector of controls, which includes regional mobility data for retail and recreational purposes, and mobility to work. µ i and γ t correspond to fuel station and date fixed effects, respectively. to causally identify the effect of the vat reduction on fuel prices and retail margins, two main assumptions must be satisfied. first, there should be no transitory shocks that would differentially affect fuel stations in germany and france before and after the reduction in vat, other than the policy change itself. second, there should be no spillover effects from the vat reduction in germany onto the fuel market in france. station fixed effects control for any time-invariant differences between fuel stations in france and germany, and date fixed effects capture the transitory shocks, such as fluctuations in the price of crude oil, that identically affect french and german stations. the two countries are similar in their geographic location, size, and wealth. since in our analysis we also focus on a relatively narrow window around the reform, this should alleviate concerns on transitory shocks differentially affecting french and german fuel stations. one might still suspect that certain transitory shocks could confound our empirical strategy. we now discuss the most obvious candidates. on the demand side, public and school holidays in france and germany are highly correlated. travel restrictions put in place due to covid-19 were lifted simultaneously in the two countries. starting from 15 june 2020, residents of the schengen area and the united kingdom could freely cross the territories of france and germany again. most holidaymakers within europe typically travel across several countries in the eu, and as france and germany are both popular travel destinations in close geographic proximity, demand shocks likely hit fuel stations in the two countries in a similar way. in addition, we directly account for demand-related shocks by including regional information on the daily mobility to work and to retail and recreational places as control variables into our empirical specification. way. due to their geographic proximity, the fuel stations in france and germany procure most of their crude oil from similar sources. the two countries are also members of the european single market, which implies harmonized border checks, common customs policy, and identical regulatory procedures on the movement of goods within the eu. finally, no major reforms were implemented in france during our analysis period. in general, there are no fuel price-setting regulations in germany and france, and both countries have mandatory disclosure of fuel prices, which reaffirms our choice of france as a suitable control group. this section presents the effects of the temporary vat reduction on fuel prices and retail margins. we estimate these effects for the three main fuel types: e5, e10, and diesel. table 2 shows the results of estimating the regression model presented in equation 1 using the logarithm of price as an outcome variable. the coefficients in columns (1) to (3) correspond to the effect of the temporary vat rate reduction on e5, e10 and diesel prices without mobility controls. columns (4) to (6) show the effects on prices when we control for mobility. the results in columns (1) to (3) show that the reduction in the vat led to a decline in prices of all fuel products, which is statistically significant at the 1 percent level and economically significant. the average price for e5 decreases by 1.05 percent after the vat reduction, whilst average prices for e10 and diesel decrease by 1.55 and 2.12 percent, respectively. including mobility controls does not significantly change the estimates. reassuringly, however, mobility for retail, recreational, and work purposes positively correlates with fuel prices. when controlling for regional differences in mobility, average prices for e5, e10 and diesel are estimated to decline by 1.01, 1.53 and 2.08 percent, respectively. next, we estimate the pass-through rates of the vat change. under full passthrough, we expect prices for each fuel product to decrease by about 2.52 percent. 20 an estimated decline of 2.08 percent in diesel prices is therefore relatively close to full pass-through. around 83 percent of the vat reduction is passed on to consumers who refuel with diesel. for e10, the pass-through rate is 61 percent. finally, we estimate that 40 percent of the vat decline is passed on to consumers of e5. for all fuel products, pass-through of the vat reduction is fast and relatively high, but incomplete. to show the economic importance of the pass-through rate, we illustrate the actual price development, as well as estimated counterfactual prices under full and zero passthrough until 31 july 2020. figure 1 after the vat reduction, the observed price of e5 is at around 1.27 to 1.28 euro per liter, which is closer to the price that we predict under zero pass-through than to that under full pass-through. the observed e5 price is on average 2 eurocent higher than the counterfactual were the retailers to fully pass on the reduction in the vat rate to consumers. figure 2 shows the vat incidence for e10. the interpretation of the lines is equivalent to figure 1 . in the post-vat reduction period the observed e10 price declines to around 1.23 to 1.25 eurocent per liter. in the full pass-through case, we predict e10 prices to be on average 1 eurocent lower, which is a smaller difference compared to e5. figure 3 presents an analogous graph of value-added tax incidence for diesel prices. 20 with a decrease in the vat rate from 19 percent before the reform to 16 percent after the reform, this is 1.16−1.19 1.19 * 100 ≈ −2.52%. notes: columns (1)-(3) present estimates without mobility control variables on e5, e10, and diesel log prices, respectively. columns (4)-(6) present estimates on e5, e10, and diesel log prices from estimation with mobility controls. all columns use data from 15 june to 31 july 2020. standard errors clustered at the fuel station level in parentheses. * p < 0.10, * * p < 0.05, * * * p < 0.01 among the three fuel products, consumers who fuel with diesel experience the highest pass-through. the observed diesel price in germany, captured by the solid red line, is relatively close to the price that we predict under the full pass-through scenario. on average, consumers pocket about 2.3 eurocent per liter of diesel from the vat reduction. as we would expect, the ranking of pass-through rates corresponds to the ranking of customer groups with respect to their likelihood of shopping for lower prices. as described in section 2, consumers buying e5 are those least likely to search for lower prices. most of these consumers can already save in a similar order of magnitude by switching to e10, but choose not to do so. the incentive for fuel stations to pass on the vat rate reduction to these consumers is therefore also the lowest. in contrast, diesel customers are on average much more likely to be frequent drivers and are therefore much more likely to search for lower prices. fuel stations therefore experience more competitive pressure for diesel customers and are hence more inclined to pass on the vat rate reduction to these customers. table 3 presents the results of estimating the regression model presented in equation 1 using the logarithm of retail margins as an outcome variable. the coefficients in columns (1) to (3) correspond to the effect of the vat rate reduction on e5, e10 and diesel margins without controlling for mobility. columns (4) to (6) show the effects on margins when mobility controls are included. the results in columns (1) to (3) show that the reduction in the vat led to an increase in retail margins for all fuel products, which is statistically significant at the 1 percent level and economically significant. the average retail margin for e5 increases by 11.34 percent after the vat reduction, whilst the average retail margin for e10 and diesel increases by 10.59 and 0.46 percent, respectively. including mobility controls does not significantly change the estimates. after controlling for regional differences in mobility, average retail margins for e5, e10 and diesel increase by 11.68, 10.83 and 0.70 percent, respectively. notes: columns (1)-(3) present estimates without mobility control variables on e5, e10, and diesel log retail margins, respectively. columns (4)-(6) present estimates on e5, e10, and diesel log retail margins from estimation with mobility controls. all columns use data from 15 june to 31 july 2020. standard errors clustered at the fuel station level in parentheses. * p < 0.10, * * p < 0.05, * * * p < 0.01 these findings are in line with the estimated pass-through rates. for diesel, where most of the vat reduction is passed through to consumers, there is only a very modest increase in retail margins. instead for gasoline, particularly for e5, less than half of the vat rate reduction is passed on to consumers and thus the temporary decrease in the vat rate led to an increase in retail margins by 10 to 12 percent. note, that for our measure of retail margins we simply subtract taxes and duties, as well as the share of the crude oil price attributable to the production of diesel and gasoline, from the gross price. the retail margins therefore include the refinery margin, as well as the station margin and different cost types, such as the cost of refining or the cost of transportation. since this means that our estimated retail margin is an overestimate of the actual retail margin, the estimated percentage increase in margins due to the vat rate reduction can be taken as a lower bound. thus, the vat rate reduction likely led to an increase in retail margins of much more than 10 percent. figure 4 illustrates the evolution of retail margins for e5, as well as the counterfactual under full and zero pass-through. the solid red line corresponds to the observed evolution of retail margins at german fuel stations between 15 june and 31 july 2020. in addition, we plot margins predicted under zero and full pass-through scenarios with shortand long-dashed lines, respectively. for e5, the observed evolution of retail margins is closer to the zero pass-through case than to full pass-through. figures 5 and 6 present analogous graphs of the evolution of retail margins under full and zero pass-through for e10 and diesel. in contrast to e5, the observed margins of e10 and diesel are closer to the full pass-through scenario than to zero pass-through. in this paper, we show that, so far, pass-through of the temporary vat rate reduction, as part of the german fiscal covid-19 response, is fast and substantial but remains incomplete for all fuel types. furthermore, we find a high degree of heterogeneity between the pass-through estimates for different fuel types. since the same stations are selling the different types of fuels and the supply structure is very similar, this leaves differences in competitive pressure from different customer groups as a candidate explanation for the differences in the pass-through rates. in particular, the more likely customers of a particular fuel type are to shop for lower prices the higher is the pass-through rate for this fuel type. although fuel markets are not the prime target of unconventional fiscal policy, the mechanisms behind whether and to what extent firms pass on taxes to consumers are the same as for other markets. studying how fuel stations pass on the temporary vat reduction is thus a worthwhile exercise and informs us about market-wide pass-through. a key result is that demand characteristics and competitive pressure play a crucial role in how a temporary tax reduction is passed on to consumers. a key takeaway for policymakers is that by targeting competitive markets with high pass-through rates they can increase the cost-effectiveness of unconventional fiscal policy. in ongoing research we investigate these determinants of pass-through rates in more detail. we construct the price panel and compute retail margins at fuel stations in france and germany as follows. for each fuel station in our data set, we observe a fuel price every time it is changed along with a precise time and date stamp of a change. on average, fuel stations in germany change fuel prices 15 times a day, whereas there is typically one price change a day at french fuel stations. based on the distribution of price changes at german fuel stations, we construct hourly fuel prices from 6 am until 10 pm for each day between 15 june -31 july, 2020. for france, since fuel prices do not change frequently over a day we keep a fuel price at 5 pm for our empirical analysis. for german fuel stations, we compute daily weighted average price from the hourly distribution of price changes that we observe. to construct the weights, we use the data on hourly fueling patterns reported in a representative survey among drivers by the german federal ministry of economic affairs. figure 7 shows shares of motorists in germany who fuel at a given time period during a day. we further re-weight the hourly shares to produce weights for the hours between 6 am and 10 pm. to compute retail margins, we adjust fuel prices to taxes and duties in france and germany, and subtract a fuel share of the price of crude oil, which is a major input cost. in germany, taxes and duties consist of the value-added tax, a lump-sum energy tax, and a fee for oil storage. before the vat reduction, the value-added tax was at the rate of 19%, and starting from 1 july 2020 it is temporarily reduced to 16%. a lump-sum energy tax is at 0.6545 euro per liter for e5 and e10 gasoline, and at 0.4704 euro per liter for diesel. a fee for oil storage is at 0.27 euro per liter for e5 and e10, and at 0.30 euro per liter for diesel. 21 in france, the value-added tax rate is at 20%, with the exception of corsica island, 21 see https://www.avd.de/kraftstoff/staatlicher-anteil-an-den-krafstoffkosten/. varieties of vat pass through who really benefits from consumption tax cuts? evidence from a large vat reform in france what goes up may not come down: asymmetric incidence of value added taxes sales taxes and prices: an empirical analysis unit sales and price effects of preannounced consumption tax reforms: micro-level evidence from european vat unconventional fiscal policy managing households' expectations with unconventional policies unconventional fiscal policy to exit the covid-19 crisis a role for discretionary fiscal policy in a low interest rate environment more and cheaper haircuts after vat cut? on the efficiency and incidence of service sector consumption taxes price transparency against market power assuming that among the other products only jet fuel is of value, we split the price of a barrel into the cost of producing gasoline, diesel, and jet fuel to compute a share of the brent price that corresponds to a particular fuel product. around 54% of the brent oil price per barrel corresponds to the production of 19 gallons of gasoline, and around 34% -to the production of 12 gallons of diesel, which we further transform into the input key: cord-344553-uya1j94u authors: bodova, k.; boza, v.; brejova, b.; kollar, r.; mikusova, k.; vinar, t. title: time-adjusted analysis shows weak associations between bcg vaccination policy and covid-19 disease progression date: 2020-05-06 journal: nan doi: 10.1101/2020.05.01.20087809 sha: doc_id: 344553 cord_uid: uya1j94u in this study, we ascertain the associations between bcg vaccination policies and progression of covid-19 through analysis of various time-adjusted indicators either directly extracted from the incidence and death reports, or estimated as parameters of disease progression models. we observe weak correlation between bcg vaccination status and indicators related to disease reproduction characteristics. we did not find any associations with case fatality rates (cfr), but the differences in cfr estimates are at present likely dominated by differences in testing and case reporting between countries. the reports on a possible use of the well-established and widely used bcg vaccine as a protection against covid-19 (de vrieze, 2020) raised a lot of interest and media coverage. currently, four clinical trials have been designed to evaluate the potential of bcg for protection against the sars-cov-2 infection in health-care workers (bonten, 2020; khattab, 2020; curtis, 2020; cirillo and dinardo, 2020) . these studies are driven by the so called non-specific effects of bcg vaccine on viral infections, observed in animal models, as well as in humans, although the molecular basis of this phenomenon is not completely understood (moorlag et al., 2019) . the associations between bcg vaccination policy and covid-19 disease progression have also been a subject to controversy in data analysis, with some studies claiming significant effects on the number of cases and case fatality rates (miller et al., 2020; berg et al., 2020) , while others criticizing weaknesses of those studies and claiming no statistically significant differences (szigeti et al., 2020; hensel et al., 2020; fukui et al., 2020; singh, 2020) . while correcting for many covariate factors (such as population size, population age distribution, etc.), most of these studies, however, failed to correct for the differences in time progression of the epidemics in each country. covid-19 epidemic usually starts from relatively few imported cases and spreads quickly through exponential growth with high reproduction numbers. at unchecked growth rates, a significant percentage of the country population would be infected before the disease would subside. however, this growth rate only continues until effective measures, such as lockouts or social distancing policies, are introduced, changing the dynamics of the epidemics substantially, with infection rates rarely reaching a significant percentage of the whole population in the first wave flaxman et al. (2020) . in this study, we have estimated a variety of indicators characteristic for different stages of covid-19 epidemics, also adjusting for time since the beginning of the epidemics in each country, and found that several key indicators show weak, but statistically significant, associations with bcg vaccination status. figure 1 : comparison of estimated reproduction numbers r100 (left) and r100+10 (right) between countries with and without the universal bcg vaccination policy. to compare the covid-19 disease progression between countries with recent universal bcg vaccination policy and those without, several parameters derived from the case and death reports in each country were selected. the parameters reflect early-stage disease spread characteristics (when they are likely not yet affected by social distancing policies), early-stage case fatality rates (before potential effects from overwhelmed health care system), and progression of the disease after the changes characteristic for social distancing policies take effect. estimates of early stage r are lower in countries with recent bcg vaccination policies. the reproduction number r, the average number of secondary cases of disease caused by a single infected individual, has been estimated using epiestim package (cori et al., 2013) , based on 7-day windows, the first estimate starting on the day when cumulative number of 100 reported cases have been reached (r100), the second estimate starting on 10th day afterwards (r100+10). in many countries, this time period would not reflect the effects of social distancing policies, but would also somewhat avoid the initial period when the case reporting is likely to be unreliable. in both cases, the countries with recent bcg vaccination policies show lower r estimates ( figure 1 ) and these shifts were statistically significant (mann whitney u-test, p = 0.04 for r100 and p = 0.006 for r100+10). we have also examined the number of days between 10 and 100 reported cases (c10), 100 and 1000 reported cases (c100), 10 and 100 reported deaths (d10), and 100 and 1000 reported deaths (d100). these time periods reflect r in various early stages of the epidemic, longer periods meaning slower spread of the disease. note, that c10 numbers are likely unreliable (due to initial problems in establishing testing and reporting policies in each country), and there are only few countries that reached 1000 reported deaths before our data set cutoff. also note that if we assume a constant case fatality rate within a specific time period (typically 6-10 days) and a specific country, and also assume exponential growth in cases within this time period, the numbers d10 and d100 do not actually reflect the death rate, but instead only depend on the underlying value of r. death reports are likely more accurate than case reports, which are much more affected by testing and reporting policies in each country. on average, all of these time periods are slightly longer in countries with recent universal bcg policies, with statistically significant results for d10 (mann-whitney u-test, p = 0.02). no differences in case fatality rates. we have estimated case fatality rates on days when 100 and 1000 cumulative deaths were first reached in each country (cfr100 and cfr1000 respectively), and also used cmmid methodology (nishiura et al., 2009; russel et al., 2020) to correct for estimation of active cases (ccfr100 and ccfr1000) . while some small shifts were observed between countries with and without recent universal bcg vaccination policies (see supplementary material), these shifts are not statistically significant. significant differences in the coefficients of the vazquez model. one of the difficulties in modelling and predicting the extent of the coronavirus spreading in a population is the divergence of the observed data (the number of confirmed active cases in individual countries) from the trends expected from the traditional sir type models. ziff and ziff (2020) have recently observed that deaths in china do not follow the typical epidemiological curve and instead of an exponential growth they follow a combined polynomial growth with exponential decay (pged). polynomial growth has been also confirmed for multiple other countries (merrin, 2020) and even though the initial spread in many countries is approximately exponential, it is followed by a steady polynomial growth and in a longer run by an exponential decay (komarova and wodarz, 2020) . for a possible explanation of the transition from exponential to polynomial growth, it is natural to look into self-imposed or government-imposed social distancing measures. these measures transform the structure of virus transmitting contact networks in a population, possibly to small-world network structures or even fractal networks. in contrast to small-world networks, social networks under standard conditions contain a significant fraction of nodes with high number of connections (that correspond to potential superspreaders). interestingly, polynomial growth of the number of infections in time in well connected scale-free networks emerges naturally as a consequence of infection initially reaching the highly connected nodes and their neighbors, while their isolation or recovery significantly reduces the interconnectivity of the residual network (szabó, 2020) . theoretical study of the infection spread in scale-free networks by vazquez (2006) leads to an explicit formula for the number of infected individuals in time in a form of pged. the formula contains three key parameters: p -the coefficient of the polynomial growth (not necessary an integer), τ -the rate of decay of the exponential tail (1/τ is an analogue to the rate of removal of individuals from the infected class to inactive recovered class in the traditional sir-type models), and a -the constant prefactor (scaling the total population). based on the value of these parameters, it is straightforward to determine nmax, the number of infected at the peak of the epidemic, which is independent of the choice of the reference time for the start of the infection. these parameters were obtained by the best fit on the linear scale to the data in each of the considered countries/regions. interestingly, we have found that the parameters τ and nmax significantly differ between countries split into two groups-with and without recent universal bcg vaccination policies ( figure 2 ). the τ parameter shifts to the higher values, signifying higher recovery rate in the countries with recent universal bcg vaccination policies (mann-whitney u-test p = 0.04). in addition, these countries have generally lower numbers of infected cases at the peak of the epidemic (nmax) corrected for underreporting (mann-whitney u-test p = 0.002). east and west germany. the case of germany is interesting, since the country has been split into east and west germany in 1949 and reunited in 1990. in east germany, the policies regarding bcg vaccination followed eastern bloc practices, with universal vaccination policy in place between 1951 and 1998. in west germany, the vaccination has been introduced in 1961, but in 1975 it was discontinued in favor of vaccinating high risk groups only. [the information has been reconstructed from the notes in bcg atlas, however we were not able to confirm this from other sources.] in the present crisis, the whole germany follows similar practices in case reporting and treatment of the disease. interestingly, east germany exhibits much lower estimates of r than west germany at the corresponding phases of the epidemic (r100 = 2.8, r100+10 = 1.55 in east germany vs. r100 = 3.14, r100+10 = 2.76 in west germany; see also figure 3 ). also, the death rate from covid-19 seems to be significantly lower in east germany, even when correcting for differences in age distribution (table 1 ). while some of the previous studies have observed associations between bcg vaccination policy and spread of covid-19 (miller et al., 2020; berg et al., 2020) , others criticized their work and showed 3 . cc-by 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 6, 2020. (2020). most of these studies have used indicators that were quite straightforward, such as the number of reported cases per million inhabitants on a particular date. here, we have instead chosen a variety of indicators that reflect characteristics of various phases of the epidemics in each country, and moreover, these indicators were implicitly or explicitly adjusted according to the time from the beginning of the epidemic in each country. in fact, we hypothesize that such time adjustment is one of the key factors in such an analysis considering what we know about the spread of covid-19. in our data, we have observed several statistically significant associations, and we conclude that there is an association between bcg vaccination policy and spread of covid-19. however, whether this association is causal or is merely an observed correlation due to some other common factor, is impossible to say. moreover, most observed shifts in various coefficients are rather small and while the universal bcg vaccination policy may have had a positive impact in some of the countries, the observed impact clearly cannot replace effective policies such as lockdowns and social distancing measures which currently constitute the most effective weapon against the epidemic. at best, the existence of universal bcg vaccination policy may have provided a few days time for governments to effectively institute such policies. one of the interesting observations is that we did not find any correlation between bcg vaccination policy and cfr. while this may suggest a hypothesis that bcg vaccination may help to limit spread, but may not be effective against difficult progression of the disease in susceptible individuals, we would 4 . cc-by 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 6, 2020. reproduction numbers r were estimated using seven day windows using smoothed incidence numbers. be careful to draw such conclusions. this is because the estimates of cfr are clearly unreliable at this point of time, with many countries showing cfr estimates well over 10%. likely, huge differences between countries do not reflect real differences in outcomes of the disease, but rather discrepancies in the amount and effectiveness of testing, with many light or asymptomatic cases remaining undetected. in fact, such a conclusion is partly supported by the evidence from east/west germany, where we can assume consistent reporting of cases and outcomes, and where differences in cfr seem to be consistent with historical differences in bcg vaccination policies, even after correcting for differences in the age distribution of the population. obtaining case and death reports. the information on reported cases, deaths, and recoveries related to covid-19 assembled by john hopkins university center for system science and engineering (dong et al., 2020) has been downloaded from humanitarian data exchange (humanitarian data exchange, 2020) on april 14, 2020. the data set covers reports from 266 countries from january 22, 2020 until april 13, 2020. for further analysis, only 41 countries with at least 100 reported cumulative deaths have been retained. we also used the data set for germany maintained by robert koch institute, containing reported cases, deaths, and recoveries split geographically and into age groups; the data set was downloaded through arcgis (robert koch-institut and bundesamt für kartographie und geodäsie, 2020). for our analysis, the data were split geographically into east germany (brandeburg, mecklenburg-vorpommern, sachsen, sachsen-anhalt, thüringen, and berlin) and west germany (schleswig-holstein, hamburg, niedersachsen, bremen, nordrhein-westfalen, hessen, rheinland-pfalz, baden-württemberg, bayern, and saarland). bcg status of individual countries. for countries included in the study, we have assembled information from the bcg world atlas (zwerling et al., 2011) and from the who-unicef estimates of bcg coverage (world health organization, 2020) (see supplementary materials). based on this information, the countries were divided into positive bcg status (the countries with current universal bcg vaccination policy and countries with past universal policies discontinued after 1990 or with recent reports of high vaccination coverage from who) and negative bcg status (the countries without universal bcg 5 . cc-by 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 6, 2020. . vaccination policy and those that discontinued universal bcg policies and did not satisfy the above conditions). estimation and extraction of indicators. the indicators were extracted from the time series data sets using simple scripts, as outlined in the results (see supplementary material for tables). all of the indicators are computed in time that is relative to a particular milestone, i.e. reaching a particular cumulative number of case reports or death reports. in this way, compared indicators are synchronized at a particular stage of the epidemic. since the number of cases and deaths is highly dependent on the stage of the epidemic, using such synchronized indicators is a key in our analysis. case fatality rate indicators cfr100 and cfr1000 were computed on the days when the cumulative number of reported deaths surpassed 100 and 1000 respectively; the cumulative number of deaths was divided by the cumulative number of reported cases 7 days prior to that date. as alternative indicators for case fatality rates, denoted as ccfr100 and ccfr1000, we have used methodology established by the centre for the mathematical modelling of infectious diseases (nishiura et al., 2009; russel et al., 2020) , systematically compensating for confirmation-to-death delay using lognormal distribution with mean delay of 13 days and a standard deviation of 12.7 days (linton et al., 2020) . regardless of the method, the main problem with cfr indicators is inconsistent reporting on the number of cases in different countries, as this depends highly on testing strategy, reporting methodology, as well as testing capacities of individual countries. thus, cfr estimates are likely dominated by these factors. we are not aware of any simple method that could overcome this problem at this point of time. note that indicators d10 (time from 10 death reports to 100 death reports) and d100 (time from 100 death reports to 1000 death reports), even though based on the numbers of reported deaths, are unlikely to reflect cfr, but instead simply serve as more stable estimates reflecting the underlying reproductive number r. this is because if we assume exponential growth phase and a constant cfr over this period of time, the cfr coefficient will cancel out in the computation of the expected number of days to reach 10-fold increase in the number of deaths. indicators r100 and r100+10 were computed using epiestim r package (cori et al., 2013) . this method is based on bayesian inference, modelling new infections as a poisson process with rate governed by the instantaneous reproduction number and the number and total infectiousness of infected individuals at the current time interval. the instantaneous reproduction number has a gamma-distributed prior and during the inference is assumed to be constant within each seven-day sliding window to yield an estimate at the end of the window. the infectiousness is approximated by the distribution of the serial interval, which is defined as the time between the onset of symptoms of a case and the onset of symptoms of secondary cases infected by the primary case. following previous work (churches, 2020) , we have set the distribution of serial intervals as a discrete gamma distribution with mean of 5 days and standard deviation of 3.4 days. here, we concentrated on monitoring early stages of the epidemic in each country, when such simple exponential growth model is relatively accurate representation of the spread of the disease. moreover, the estimated values are used mostly in the non-parametric mann-whitney test, which only considers their relative ordering, not exact values. to avoid initial uncertainty in the reproductive number estimates due to small numbers of case reports, and to adjust for the differences in the start date of epidemics in each country, the seven-day interval for the first estimate (r100) starts on the day when 100 cases have been reported and the second estimate (r100+10) is taken 10 days later. the case incidence numbers have been smoothed over a window of 7 days in order to account for differences in testing procedures on different days of the week (i.e. no or little testing over the weekend in many countries). such smoothing will not affect the parameters of exponential growth models. it has been verified that confidence intervals at chosen points of time are not unproportionally large. application of vazquez model. the number of infected individuals in the vazquez model (vazquez, 2006; ziff and ziff, 2020) has the form where a, p, and τ are parameters and t = 1 (units are days) corresponds to the first day of an infection. in practice, the available data does not report the number of infected individuals in the population due to 6 . cc-by 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may 6, 2020. . limited testing availability and potential testing errors. therefore we use the total number of active cases (confirmed -recovered -deaths) as a proxy for the total number of infected individuals. in countries with sufficient testing, we assume that the identified active cases represent a constant fraction of the total active cases and the formula for n(t) differs only in the constant factor a. we used a nonlinear least squares method to infer the parameters in the above relationship from the data. however, instead of directly fitting the parameters a, p, and τ , we used an equivalent formulation n(t) = nmax · t tmax p · e p(1−t/tmax) , with parameters nmax (the maximal number of active cases during the infection), p (the power of the polynomial growth term), and tmax = p * τ (the time when the peak is reached). for consistency, we have truncated the data to reduce the impact of testing irregularities during the initial onset of epidemic. therefore we start the data from the day when a certain number of active cases n a was reached. the threshold n a was chosen in proportion to the population in the country to reduce effects of randomness in reporting and to account for the spreading potential. italy served as the reference with a threshold of 200 cases (threshold chosen was always at least 10). mandated bacillus calmette-guérin (bcg) vaccination predicts flattened curves for the spread of covid-19 reducing health care workers absenteeism in covid-19 pandemic through bcg vaccine (bcg-corona) covid-19 epidemiology with r. r views, an r community blog edited by rstudio bcg vaccine for health care workers as defense against covid 19 (badas) a new framework and software to estimate time-varying reproduction numbers during epidemics bcg vaccination to protect healthcare workers against covid-19 (brace) can a century-old tb vaccine steel the immune system against the new coronavirus? science an interactive web-based dashboard to track covid-19 in real time report 13: estimating the number of infections and the impact of non-pharmaceutical interventions on covid-19 in 11 european countries does tb vaccination reduce covid-19 infection?: no evidence from a regression discontinuity analysis exercising caution in correlating covid-19 incidence and mortality rates with bcg vaccination policies due to variable rates of sars cov-2 testing johns hopkins university novel coronavirus (covid-19) cases data application of bcg vaccine for immune-prophylaxis among egyptian healthcare workers during the pandemic of covid-19 patterns of the covid19 epidemic spread around the world: exponential vs power laws incubation period and other epidemiological characteristics of 2019 novel coronavirus infections with right truncation: a statistical analysis of publicly available case data differences in power-law growth over time and indicators of covid-19 pandemic progression worldwide correlation between universal bcg vaccination policy and reduced morbidity and mortality for covid-19: an epidemiological study non-specific effects of bcg vaccine on viral infections early epidemiological assessment of the virulence of emerging infectious diseases: a case study of an influenza pandemic csv mit den aktuellen covid-19 infektionen pro tag (zeitreihe) using a delay-adjusted case fatality ratio to estimate under-reporting. available at the centre for mathematical modelling of infectious diseases repository bcg vaccines may not reduce covid-19 mortality rates propagation and mitigation of epidemics in a scale-free network bcg protects against covid-19? a word of caution polynomial growth in branching processes with diverging reproductive number who-unicef estimates of bcg coverage fractal kinetics of covid-19 pandemic the bcg world atlas: a database of global bcg vaccination policies and practices key: cord-288721-3bv3aak6 authors: schneider, annika; kurz, sandra; manske, katrin; janas, marianne; heikenwälder, mathias; misgeld, thomas; aichler, michaela; weissmann, sebastian felix; zischka, hans; knolle, percy; wohlleber, dirk title: single organelle analysis to characterize mitochondrial function and crosstalk during viral infection date: 2019-06-11 journal: sci rep doi: 10.1038/s41598-019-44922-9 sha: doc_id: 288721 cord_uid: 3bv3aak6 mitochondria are key for cellular metabolism and signalling processes during viral infection. we report a methodology to analyse mitochondrial properties at the single-organelle level during viral infection using a recombinant adenovirus coding for a mitochondrial tracer protein for tagging and detection by multispectral flow cytometry. resolution at the level of tagged individual mitochondria revealed changes in mitochondrial size, membrane potential and displayed a fragile phenotype during viral infection of cells. thus, single-organelle and multi-parameter resolution allows to explore altered energy metabolism and antiviral defence by tagged mitochondria selectively in virus-infected cells and will be instrumental to identify viral immune escape and to develop and monitor novel mitochondrial-targeted therapies. mitochondria are crucial for cellular energy metabolism, critically involved in the coordination of signalling processes within cells and orchestrate induction of apoptotic cell death 1, 2 . besides this, cell-autonomous defence mechanisms during viral infection link innate immune sensing of infection and inflammation at the level of mitochondria 3, 4 . the research in the recent years has expanded our knowledge about the different roles of mitochondria. for the different functions mitochondrial shape and motility, but also size, are important and are highly dynamic processes 5 . mitochondrial shape and size are continuously changed during the dynamics of mitochondrial fusion and fission and mitochondrial turnover is controlled by mitophagy 5 . viruses modify the host cell to create an ideal ambience, which includes metabolic support for viral gene expression and replication. such modifications of cellular metabolism and structure of viruses can also affect mitochondria. there are more and more reports about viruses known to influence mitochondrial dynamics. viruses known to enhance mitochondrial fission are hepatitis b virus (hbv), hepatitis c virus (hcv) and epstein-barr virus [6] [7] [8] [9] . viruses, which interfere with or enhance mitophagy are hbv, hcv and measles virus [6] [7] [8] 10 . sars coronavirus is reported to enhance the fusion of mitochondria 11 . but the influence of viral infection on mitochondrial membrane potential and stress response has not been addressed in detail because of methodological constraints. so far, analysis of mitochondria and their functions relied mostly on bulk analysis of mitochondrial populations analysed ex vivo. in infected tissues where both, infected and non-infected cells are simultaneously present, it is very difficult to discriminate between mitochondria from infected versus healthy non-infected cells. this may be achieved by serial tissue sections analysed by electron microscopy, where viral particles could be visualized. however, this is a very time demanding process yielding results with little statistical power. we therefore aimed to develop a technology, where high numbers of single mitochondria and their function can be analysed in the context of viral infection in order to characterize changes induced by viral infection. we chose the liver, and more specifically hepatocytes, as viral infection increases size and mitochondrial fragility of liver mitochondria. we first aimed to determine the influence of viral infection of the liver on the size of liver mitochondria by flow cytometry. to that end, we established a reference curve using polystyrene microparticles with defined sizes (0.88 µm, 1,34 µm and 3 µm). forward scatter analysis of these polystyrene microparticles revealed clear demarcation of the differently sized microparticles and a direct linear correlation of forward scatter results with microparticle size (r 2 = 0.99) ( fig. 2a) , consistent with earlier reports that forward scatter measurements directly correlate with microparticle size down to 0.5 µm 20, 21 . the flow cytometric analysis revealed that mitochondria isolated from healthy non-infected liver ranged in size from 0.8 µm up to 1.4 µm (fig. 2b ) assuming that isolated mitochondria are spherical in morphology, which is indicated by electron microscopy (see fig. 1b ). since mitochondria from hepatocytes are much larger than those from non-parenchymal liver cells or immune cells, we assume that mitochondria ≥0.8 µm in size are derived from hepatocytes. mitochondria purified from virus-infected livers had a slightly higher mean size compared to healthy liver (1.04 ± 0.06 µm compared to 0.97 ± 0.04 µm, respectively) and ranged in size from 0.8 µm up to 3 µm (fig. 2b) . infection with recombinant replication-deficient adenoviruses is a well-established preclinical model system to study hepatotropic infections [22] [23] [24] . however, to confirm the results we repeated the experiments by infection with wildtype replication-competent lymphocytic choriomeningitis virus (lcmv). also after lcmv-infection, we detected an increase of mitochondrial size confirming the results obtained after adenoviral infection (supp. fig. 1a ). in order to investigate whether innate immunity generated during viral infection, was responsible for this increase in mitochondrial size, we induced a type i interferon response by application of poly i:c 25 . flow cytometric analysis of mitochondria isolated after poly i:c application did not reveal any differences in their size compared to the control groups suggesting other mechanisms (supp. fig. 1b) . the exact determination of the size of single mitochondria now opened the possibility to use this information for further analysis. next, we evaluated mitochondrial functionality by determining the mitochondrial membrane potential using the potentiometric dilc 1 (5) fluorescence dye. dose titration experiments of the dilc 1 (5) dye demonstrated a dose-dependent increase in fluorescence intensity in purified mitochondria (supp. fig. 1c ). upon addition of the electron chain uncoupling agent cccp, we found a profound reduction in dilc 1 (5) fluorescence (fig. 2c ) demonstrating that flow cytometric determination of changes in dilc 1 (5) fluorescence reflected mitochondrial membrane potential. by flow cytometric analysis we observed a significant decrease in the mitochondrial membrane potential of mitochondria isolated from virus-infected vs. healthy livers after either adenoviral or lcmv infection compared to healthy controls ( fig. 2d and supp. fig. 1d ). in contrast, we did not detect changes in the membrane potential after innate immune stimulation by poly i:c (supp. fig. 1e ). yet, the size of mitochondria may influence dilc 1 (5) signal intensity. indeed, we found a direct correlation between mitochondrial size and dilc 1 (5) staining ( fig. 2e and supp. fig. 1f ) suggesting that larger mitochondria purified from virus-infected livers should show higher dilc 1 (5) fluorescence intensity. we therefore compared mitochondria with the same size isolated from healthy or virus-infected livers. such direct comparison demonstrated that mitochondria of the same size from healthy vs. virus-infected livers showed a remarkable decrease in the membrane potential of mitochondria from infected livers (fig. 2f ) and suggested that viral infection caused changes in mitochondrial functionality. mitochondria also function to take up calcium from the cytosol and thereby coordinate cellular function 26 , which can also serve as a stress test. when challenged with high concentrations of calcium (100 µm), mitochondria isolated from virus-infected livers are much more fragile shown by time-dependent loss of membrane potential and change of their morphology indicated by decrease in side-scatter (fig. 2f ). this accurately detects mitochondrial swelling after loss of membrane potential following ca 2+ challenge which is also detected by bulk analysis with a classical stress test by adding ca 2+ and detection of loss of membrane potential by rh123-fluorescence and swelling by measuring optical density at 540 nm (supp. fig. 1g ) 18 . consistent with the loss of membrane potential and changes in side-scatter signals, we detected loss of mitochondrial integrity after www.nature.com/scientificreports www.nature.com/scientificreports/ calcium challenge. number of viable mitochondria detected per second by flow-cytometry declined after calcium challenge, consistent with loss of mitochondrial integrity, and did so much faster in samples from virus-infected livers (fig. 2f ). comparing mitochondria with different sizes, it became evident that larger mitochondria are more fragile and disappeared more rapidly after ca 2+ -challenge (fig. 2f ). taken together, here we detected an increase in size and a decrease in membrane potential as well as mitochondrial fragility of liver mitochondria after viral infection. however, since both, non-infected as well as infected hepatocytes are present in livers after adenoviral infection (see fig. 1b ), current protocols for isolation and analysis yield a mixture of mitochondria derived from healthy as well as infected hepatocytes. this makes it necessary to develop a methodology, by which mitochondria from healthy and virus-infected hepatocytes can be separated in order to characterize changes in mitochondrial function specifically in virus-infected cells. we generated a recombinant adenovirus expressing the fluorescent protein dsred fused to a mitochondrial localization sequence (ad-cmv-mitorl) that accumulates and selectively labels mitochondria within infected cells (supp. fig. 2 ). we combined this mitochondrial labelling in infected cells with a multispectral flow cytometric single organelle measurement of isolated mitochondria. upon infection of hepatocytes with ad-cmv-mitorl in vitro we detected mito-dsred-fluorescence in mitochondria using confocal microscopy (fig. 3a) . since ad-cmv-mitorl also codes for luciferase, we detected in vivo bioluminescence of the liver after infection, thus www.nature.com/scientificreports www.nature.com/scientificreports/ confirming successful infection of hepatocytes in vivo (fig. 3b ). this allowed us to test whether mitochondria from ad-cmv-mitorl-infected hepatocytes (mito-dsred + mitochondria) could be distinguished from those of non-infected hepatocytes (mito-dsred − mitochondria) within the same liver. after density-gradient purification, mitochondria isolated from virus-infected livers were counterstained with mitotracker green and analysed by flow cytometry allowing discrimination of mito-dsred + mitochondria from mito-dsred − mitochondria from the same liver (fig. 3c ). mito-dsred + mitochondria from virus-infected hepatocytes had a mean size of 1.19 ± 0.06 µm as compared to mito-dsred − mitochondria from healthy hepatocytes with a mean size of 0.96 ± 0.01 µm (fig. 3d ). this confirmed the results obtained from mitochondria isolated from non-infected livers and further demonstrated a more pronounced size difference when mitochondria from virus-infected could be distinguished at the single organelle level from those of healthy hepatocytes. this was most likely related to a relative underestimation of size for mitochondria from virus-infected livers due to contamination with mitochondria from non-infected cells that are smaller than hepatocyte mitochondria. yet, we cannot formally exclude that mito-dsred localizing to mitochondria after infection with ad-cmv-mitorl may have contributed to the size difference. the almost identical forward scatter results and size of mito-dsred − mitochondria compared to mitochondria isolated from non-infected livers (fig. 3d) indicated that there was no influence of viral infection in neighbouring hepatocytes on mitochondrial size after isolation. differences in size of mitochondria may have also an influence on other parameters detected by flow cytometry and we therefore systematically measured mitochondrial autofluorescence from 450 to 800 nm using a spectral flow cytometer. as expected, we detected increased fluorescence at 590 nm in mito-dsred + mitochondria, where the maximum of dsred fluorescence emission (590-650 nm) is expected 27 . interestingly, we detected higher autofluorescence signals between 500 and 550 nm as well as above 650 nm in mito-dsred + mitochondria (fig. 3e) . as the strength of autofluorescence may be influenced by the size of mitochondria, we analysed autofluorescence signals against the size of isolated mitochondria (fig. 3f ). we found that autofluorescence intensity between 430 and 550 nm directly correlated with mitochondrial size, which may explain the higher autofluorescence observed in larger mito-dsred + mitochondria. together, these data demonstrate the usefulness of single-organelle analysis by flow cytometry in combination with in vivo mitochondrial labelling in virus-infected hepatocytes to exactly determine physical parameters such as size or autofluorescence. mitochondrial crosstalk enables changes in membrane potential. since discrimination of mitochondria isolated from virus-infected compared to non-infected hepatocytes was reliably achieved using flow cytometry, we proceeded to test for changes in mitochondrial functionality upon infection. we assumed that the difference in membrane potential detected between mitochondria isolated from virus-infected livers compared to non-infected livers (see fig. 2 ) has previously been underestimated, and that our method would allow to more specifically discriminate mitochondria from virus-infected hepatocytes compared to non-infected hepatocytes. we determined whether mito-dsred + differed from mito-dsred − mitochondria with respect to dilc 1 (5) fluorescence intensity. to our surprise, we found that the dilc 1 (5) signal was similar for all sizes of mito-dsred + compared to mito-dsred − mitochondria (fig. 4a ). since dilc 1 (5) fluorescence was homogenous in all mitochondria isolated from ad-cmv-gol infected livers (see fig. 1 ), although they consisted of a mixture of mitochondria from infected and non-infected hepatocytes, we wondered whether there was an exchange of molecules between mitochondria. therefore, we mixed dilc 1 (5)-labelled mitochondria with non-labelled mitochondria and by time-dependent flow cytometric analysis found that dilc 1 (5) fluorescence decreased in pre-labelled and increased in un-labelled mitochondria reaching an equilibrium of intermediate fluorescence intensity within 30 seconds (fig. 4b) . however, mito-dsred was not exchanged between mitochondria, because we found clearly distinct dsred staining of mitochondria isolated from ad-cmv-mitorl-infected livers, and mito-dsred − mitochondria showed the same absent dsred fluorescence intensity as mitochondria isolated from non-infected livers. in order to further evaluate mitochondrial functionality, we challenged mitochondria with ca 2+ as stress test and performed time kinetic measurements of dilc 1 (5) fluorescence and side-scatter of mito-dsred + and mito-dsred − mitochondria isolated from ad-cmv-mitorl infected livers. remarkably, the differences in mitochondrial characteristics observed when comparing mitochondria isolated from infected livers to mitochondria from non-infected livers (see fig. 2f ) where not present any more when comparing mito-dsred + to mito-dsred − mitochondria originating from the same liver. in fact, loss of dilc 1 (5) fluorescence, decrease in side scatter and mitochondrial events were the same for mito-dsred + mitochondria as compared to mito-dsred − mitochondria (fig. 4c) . when in direct physical contact with mito-dsred + mitochondria, also mito-dsred − mitochondria showed the same fragility as mitochondria from virus-infected hepatocytes. there, was still a small difference in the large mitochondrial group after calcium stimulation and flow cytometric analysis of the ssc and dilc 1 (5) which could be explained by the fact that 5 to 10 minutes after calcium stimulation the number of events was drastically reduced. only approximately 10% from the initial number of events are still detectable (shown by number of events/s). because of the statistical variation the conclusions at later time points has to be taken with caution. interestingly, also mixing of dilc 1 (5) labelled mitochondria isolated from either ad-cmv-golor lcmv-infected with those from healthy uninfected livers yielded in rapid loss of mitochondrial membrane potential to that measured in mitochondria from infected livers (fig. 4d and supp. fig. 2 ) taken together these data demonstrate that mitochondria which are in close physical proximity exchange information leading to changes in mitochondrial membrane potential but not in mitochondrial size. here, we describe the influence of viral infection on the phenotype and function of mitochondria employing a new methodology combining spectral flow cytometry with virus-encoded markers to simultaneously evaluate multiple mitochondrial parameters at the level of single organelles. most studies involve confocal microscopy to detect mitochondria, which is also available in an automated manner to quantify large datasets of mitochondria 28 . www.nature.com/scientificreports www.nature.com/scientificreports/ while most of these microscopic studies are performed in cell cultures to explore mitochondrial dynamics at the level of single cells, there are only few reports specifically detecting tagged mitochondria in tissues for ex vivo or in vivo analysis 29, 30 . since in vivo microscopic analysis of mitochondria requires a complex experimental setup, is rather time consuming and does not allow for analysis of large numbers of mitochondria, we aimed to establish a methodology to evaluate mitochondria directly ex vivo following isolation from virus-infected tissue. so far, most of available methods analyse properties of mitochondria ex vivo at the level of mitochondrial populations, www.nature.com/scientificreports www.nature.com/scientificreports/ such as extracellular flux analysis, western blot analysis, calcium uptake or swelling assays. beyond visualization by microscopy, flow cytometry has emerged as technology to characterize mitochondria 18, 31, 32 . however, mitochondria isolated from virus-infected tissues can be derived from both, virus-infected cells as well as healthy cells, which may skew the experimental results. we therefore generated recombinant adenoviruses containing a mito-dsred expression cassette to selectively label mitochondria of infected cells. fusion of a fluorescent marker to mitochondrial target sequences has previously been reported to reliably and specifically label mitochondria as shown by confocal microscopy 33, 34 . we combined virus-encoded mito-dsred labelling of mitochondria to separate mitochondria of virus-infected cells from those originating from healthy cells, with the power of multi-parameter analysis by spectral flow cytometry. using this methodology, we provide evidence that mitochondria can be reliably separated from virus-infected cells and that viral infection led to an increase in size as well as a decrease of mitochondrial membrane potential. such changes in biophysical and functional properties of mitochondria were not triggered by innate immunity following recognition of infection through microbe-associated pattern recognition receptors indicating other reasons for these changes, which still have to be defined. time kinetic measurements of single mitochondria by flow cytometry further allowed us to detect a previously unknown mitochondrial cross-talk that involves rapid exchange of small molecules like the potentiometric dye dilc 1 (5) . such exchange of molecules among mitochondria required physical contact, occurred within seconds and did not include mitochondrial matrix-embedded proteins. this indicates a dynamic regulation of mitochondrial properties by cell autonomous mechanisms that require further investigation. taken together, the combination of mitochondrial labelling through mito-dsred together with single organelle analysis using spectral flow cytometry is ideally suited to further unravel biophysical and functional properties of mitochondria as well as mechanisms and consequences of mitochondrial interconnectivity in virus-infected cells. given the important role of mitochondria in cellular metabolism, anti-viral defence, cell signalling and cell death, the multiparametric analysis of single mitochondria opens new avenues to explore these complex mitochondrial functions in more detail in virus-infected cells. mice. c57bl/6 j mice were purchased from charles river (sulzfeld, germany). mice were maintained under specific pathogen-free (spf) conditions in the central animal facility of the klinikum rechts der isar, in accordance with the guidelines of the federation of laboratory animal science association. animal experiments were approved by the animal care commission of bavaria. male mice between the ages of 6-10 weeks were used. the expression cassette for cloning into recombinant adenovirus consists of the genes for the fluorescent protein dsred linked to a mitochondrial targeting sequence and cbg99-luciferase separated by p2a linker sites from the porcine teschovirus 1 followed by a bgh poly(a) signal. gene expression was driven by the ubiquitous minimal cmv-promoter (ad-cmv-mitorl). ad-cmv-gol generation has been reported before 23 . recombinant second generation serotype 5 adenoviruses were generated using the gateway ® technology from thermofisher as described before 23 . briefly, expression cassettes with cmv promotor, dsred linked to the mitochondrial targeting site, cbg99-luciferase and the bgh poly(a) signal were synthesized (eurofins genomics, germany) and cloned into gateway ® pentr ™ 11 dual selection vector (thermofisher scientific, germany). recombination of pentr ™ with expression cassette into pad/pl-dest ™ gateway ® vector (thermofisher scientific, germany) was performed in vitro via the lr clonase ® enzyme mix (thermofisher scientific, germany). the obtained pad/pl-dest ™ with expression cassette was linearized using the paci restriction enzyme and the resulting adenoviral dna was transfected with lipofectamine 2000 (thermofisher scientific, germany) into hek293 cells (crl-1573 ™ ; atcc, usa). cell debris and supernatant were harvested when complete detachment of the cells occurred. this suspension was freeze/thawed, centrifuged and used for further infection of hek293 cells. cells from several cell culture dishes were harvested and resuspended in tris-buffer and freeze/thawed three times. cell debris was removed by centrifugation and supernatant purified by a two-step cscl gradient ultracentrifugation. the band containing adenovirus was harvested and dialyzed. virus titer was determined via adenovirus hexon titration. hek293 cells were infected with serial dilutions of purified adenovirus. after 35 to 40 hours, cells were fixed with methanol, and virus infected cells were stained with anti-hexon antibody (anti-hexon 2297hrp, acris, germany) and detected via dab (dako, usa). the infected cells were counted and the titer was calculated. bioluminescence imaging. imaging of luciferase expression in infected mice was monitored by ivis lumina lt-series iii instrument (perkinelmer las, germany). five minutes before measurement mice have been anesthetized with 2.5% isofluran and treated intraperitoneally with 100 mg/kg bodyweight d-luciferin-k-salt (pjk gmbh, germany). isolation of mitochondria from murine liver tissue. heparin/nacl (300 u/150 µl) was injected i.p. into the mouse 5 minutes prior to preparation. mice were sacrificed and livers were perfused via portal vein for 1 minute with pbs to remove blood. liver was removed and weighed, and the liver was rinsed with isolation buffer www.nature.com/scientificreports www.nature.com/scientificreports/ (220 mm mannitol, 80 mm sucrose, 10 mm hepes, 1 mm edta, ph 7.4). the whole isolation procedure was performed on ice and in ice-cold isolation buffer. the tissue was rinsed with 1 ml isolation buffer and cut with a blunt end scissor into small pieces. the liver fragments were resuspended in 1 ml isolation buffer supplemented with 0.5% bsa and protease inhibitor (protease inhibitor cocktail, edta-free, roche, switzerland) per 0.1 gram of weighted organ and homogenized in a potter-elvehjem with 3 strokes at 800 rpm. the homogenate was transferred to cooled 50 ml falcon and centrifuged at 600 x g for 10 minutes to remove nuclei, intact cells and cellular debris. the supernatant was transferred to a glass tube and centrifuged at 4000 x g for 10 minutes to sediment mitochondria. the received crude pellet was gently dislodged with a glass pestle from the side of the glass tube. mitochondrial purification by density gradient centrifugation. mitochondria were purified as previously described 35, 36 . in brief, a discontinuous percoll density gradient was used for mitochondrial purification. crude mitochondria were resuspended in ip-buffer (300 mm sucrose, 5 mm tes, 0.2 mm egta, ph 6.9), loaded on a percoll density gradient (60%, 30% and 18% diluted in ipp buffer: 300 mm sucrose, 10 mm tes, 0.2 mm egta, 0.1% w/v bsa, ph 7.2) and separated at 9000 × g for 10 minutes. the phase containing mitochondria between 60% and 30% percoll-layer was recovered with a glass pipette and transferred to a 30 ml glass tube, resuspended in 15 ml ip-buffer and centrifuged for further 10 minutes at 9000 × g. the pellet was washed again in 10 ml ip-buffer and centrifuged at 9000 × g for 10 minutes to get rid of remaining percoll. the supernatant was removed and mitochondrial pellet was dislodged from the side of the glass tube. the received mitochondria were resuspended in 100 µl ip-buffer and kept on ice. determination of protein concentration. the protein content in the mitochondrial preparations was determined using the dc tm protein assay kit (bio rad laboratories, germany). the assay was performed according to the manufacturer´s protocol. four different bsa-dilutions reaching from 0.25 mg/ml to 1.5 mg/ml in ip-buffer were used as standards. the optical density was measured at 750 nm with a multiplate reader (infinitem100 pro, tecan, germany). determining mitochondria by flow cytometry. mitochondria were diluted to 10 µg protein per µl in ice-cold mitochondrial staining buffer msb (0.2 m saccharose, 10 mm mops-tris, 5 mm succinate, 1 mm phosphoric acid, 10 µm egta). the different mitochondrial probes were diluted in msb, mixed with the mitochondrial dilution in a 1:1 ratio and incubated at room temperature for 20 minutes. the cell permeable carbocyanine-based mitotracker green probe (mtg, 200 nm), which contains a mildly thiol-reactive chloromethyl moiety, was used to selectively stain all undamaged mitochondria regardless of the membrane potential. dilc1(5) (100 nm), a cationic carbocyanine dye, was used to measure the membrane potential of isolated mitochondria. mitochondria were pelleted at 9000 x g for 2 minutes and washed once in ice cold pbs. mitochondrial pellet was resuspended in msb to a final concentration of 10 µg/µl and stored on ice for analysis. immediately before analysis, samples were diluted in ice-cold and filtered pbs to the final analysis concentration of 0.05 µg/µl. samples were analysed using the spectral cell analyzer sp6800 (sony biotechnology inc, japan). the sample flow rate was set to record about 1500 events per second. as mitochondrial uncoupling by the protonophore cccp is well known to dissipate mitochondrial membrane potential (mmp), 5 µm cccp (sigma-aldrich, st. louis, missouri, usa) was used as a positive control for membrane potential dependence of diic 1 (5) (biotium, hayward, usa). the mitochondrial permeability transition (mpt), a process characterized by a large increase of permeability of the inner mitochondrial membrane (imm), leading to an influx of solutes with a molecular weight less than 1.5 kda and water into the mitochondrion, is a ca 2+ -induced process. the influx of solutes and water leads to swelling of mitochondria. in mpt-measurements 100 µm ca 2+ in msb was added to induce swelling and samples were analyzed immediately after administration and every following 5 minutes for 45 minutes in total. cyclosporina (sigma-aldrich, st. louis, missouri, usa) inhibiting mpt and thereby reversing the effect of ca 2+ , was added at a concentration of 5 µm. mitochondrial size was determined using polystyrene particle size standard beads (flow cytometry grade, spherotech) in three sizes: 0.88 μm, 1.34 μm and 3 μm. beads of each size were separated via ultrasound, vortexed and 20000 beads/size were added per ml filtered pbs. immediately before analysis, mitochondria were diluted in bead mixture to the final analysis concentration of 0,05 µg/ml. data were analysed using flowjo software (version 10, flowjo, oregon, usa). western-blot. 30 µg of protein per sample was loaded onto 4-20% mini-protean ® tgx stain-free ™ precast gels (bio rad laboratories, münchen) and separation was performed within a gel chamber filled with 1x sds electrophoresis buffer at 100 v for 1 to 2 hours. after separation, proteins were blotted using the trans-blot ® turbo ™ mini pvdf transfer packs (bio rad laboratories, germany). proteins were transferred onto membranes at 2.5 a for 30 minutes using the trans-blot turbo ™ (bio rad laboratories, germany). membranes were blocked with 10% milk in tbs-t (tbs + 0.1% tween-20) for 1 hour at room temperature, washed three times with tbs-t and incubated with primary antibodies in 5% bsa in tbs-t overnight at 4 °c. the membranes were washed three times with tbs-t and incubated for 4 hours at room temperature with hrp-coupled secondary antibodies in 10% milk powder in tbs-t. blots were washed three times and developed using cheluminate-hrp picodetect (applichem gmbh, germany), which was evenly distributed on the membrane. the luminescence was detected for up to 20 minutes using the imaging-system chemidoc tm xrs (bio rad laboratories, germany). to visualize www.nature.com/scientificreports www.nature.com/scientificreports/ several proteins on the same blot, primary and secondary antibodies were removed by incubating membranes for 45 minutes at 50 °c in stripping buffer containing ß-mercaptoethanol. subsequently membranes were washed three times with tbs-t and incubated as previously described with primary and secondary antibodies. following primary antibodies were used: adenine nucleotide translocator (ant) (santa cruz biotechnology usa), cytochrome-c-oxidase (cox iv), cytochrome-c (cyt-c), glyceraldehyde 3-phosphate dehydrogenase (gapdh), glucose-regulated-protein 78 (grp78), histon 2b (h2b), voltage dependent anion channel (vdac) (all cell signaling technology, usa), lysosome-associated membrane protein 2 (lamp2) (thermo fisher scientific, usa), peroxisomal membrane protein 70 (pmp70) (origene technologies, usa), following secondary antibodies were used: rabbit anti-goat hrp (santa cruz biotechnology, usa), mouse anti-rabbit hrp, goat anti-mouse hrp (jackson immunoresearch, uk). histology. mouse livers were fixed for 48 hours in 4% paraformaldehyde. dehydrated livers (leica asp300s, germany) were embedded in paraffin. serial 2 µm-thin sections were prepared with a rotary microtome (hm355s, thermofisher scientific, usa) and subjected to histological and immune-histochemical analysis. hematoxylin-eosin (he) staining was performed on deparaffinized sections with eosin and mayer's haemalaun according to standard protocol. immunohistochemistry was performed using a bondmax rxm system (leica, wetzlar, germany, all reagents from leica) with primary antibody against egfp (a-11122, diluted 1:500 in antibody diluent, invitrogen, thermofisher scientific, usa). slides were deparaffinized, pre-treated with epitope retrieval solution 1 for 30 minutes. bound antibody was detected with a polymer refine detection kit without post primary reagent and visualized with dab as a dark brown precipitate. counterstaining was done with hematoxyline. electron microscopy. tissues were fixed in 2.5% electron microscopy grade glutaraldehyde in 0.1 m sodium cacodylate buffer ph 7.4 (science services, munich, germany), postfixed in 2% aqueous osmium tetraoxide 37 , dehydrated in gradual ethanol (30-100%) and propylene oxide, embedded in epon (merck, darmstadt, germany) and cured for 48 hours at 60 °c. semithin sections were cut and stained with toluidine blue. ultrathin sections of 50 nm were collected onto 200 mesh copper grids, stained with uranyl acetate and lead citrate before examination by transmission electron microscopy (zeiss libra 120 plus, carl zeiss nts gmbh, oberkochen, germany). pictures were acquired using a slow scan ccd-camera and item software (olympus soft imaging solutions, münster, germany). statistics. student's t tests were calculated using graphpad prism software. significance was set at p < 0.05 and denoted as *p < 0.05, **p < 0.01, ***p < 0.001 and ***p < 0.0001. all results are expressed as the mean ± standard deviation (sd). the data within this manuscript are available from the corresponding author upon reasonable request. mitochondrial control of cellular life, stress, and death mitochondrial signaling pathways: a receiver/integrator organelle mechanisms of mavs regulation at the mitochondrial membrane identification and characterization of mavs, a mitochondrial antiviral signaling protein that activates nf-kappab and irf 3 mitochondria: dynamic organelles in disease, aging, and development hepatitis b virus disrupts mitochondrial dynamics: induces fission and mitophagy to attenuate apoptosis hepatitis c virus triggers mitochondrial fission and attenuates apoptosis to promote viral persistence hepatitis c virus induces the mitochondrial translocation of parkin and subsequent mitophagy epstein-barr virus latent membrane protein-2a alters mitochondrial dynamics promoting cellular migration mediated by notch signaling pathway mitophagy enhances oncolytic measles virus replication by mitigating ddx58/rig-i-like receptor signaling sars-coronavirus open reading frame-9b suppresses innate immunity by targeting mitochondria and the mavs/ traf3/traf6 signalosome living in the liver: hepatic infections correlated morphometric and biochemical studies on the liver cell. i. morphometric model, stereologic methods, and normal morphometric data for rat liver bioluminescence imaging allows measuring cd8 t cell function in the liver isolation of mitochondria from cultured cells and liver tissue biopsies for molecular and biochemical analyses analysis of mitochondria by flow cytometry real-time flow cytometry analysis of permeability transition in isolated mitochondria flow cytometric analysis of isolated liver mitochondria to detect changes relevant to cell death measurement of mitochondrial mass by flow cytometry during oxidative cell sizing: a light scattering photometer for rapid volume determination overcoming limitations of microparticle measurement by flow cytometry tnf-induced target cell killing by ctl activated through cross-presentation outcome of anti-viral immunity in the liver is shaped by the level of antigen expressed in infected hepatocytes perforin inhibition protects from lethal endothelial damage during fulminant viral hepatitis reduced type i interferon production by dendritic cells and weakened antiviral immunity in patients with wiskott-aldrich syndrome protein deficiency calcium uptake mechanisms of mitochondria biochemistry, mutagenesis, and oligomerization of dsred, a red fluorescent protein from coral deep analysis of mitochondria and cell health using machine learning multiparametric optical analysis of mitochondrial redox signals during neuronal physiology and pathology in vivo in vivo imaging of disease-related mitochondrial dynamics in a vertebrate model system flow cytometry of isolated mitochondria during development and under some pathological conditions why to compare absolute numbers of mitochondria analysis of mitochondrial dynamics and functions using imaging approaches strategies for imaging mitophagy in high-resolution and high-throughput a semi-automated method for isolating functionally intact mitochondria from cultured cells and tissue biopsies progressive stages of mitochondrial destruction caused by cell toxic bile salts a chrome-osmium fixative for electron microscopy this work was funded by the deutsche forschungsgemeinschaft (dfg, german research foundation) -projektnummer 272983813 -trr 179 to d.w and p.k. supplementary information accompanies this paper at https://doi.org/10.1038/s41598-019-44922-9.competing interests: the authors declare no competing interests.publisher's note: springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.open access this article is licensed under a creative commons attribution 4.0 international license, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the creative commons license, and indicate if changes were made. the images or other third party material in this article are included in the article's creative commons license, unless indicated otherwise in a credit line to the material. if material is not included in the article's creative commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. to view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. key: cord-315064-2mgv9j6n authors: escher, felicitas; pietsch, heiko; aleshcheva, ganna; bock, thomas; baumeier, christian; elsaesser, albrecht; wenzel, philip; hamm, christian; westenfeld, ralph; schultheiss, maximilian; gross, ulrich; morawietz, lars; schultheiss, heinz‐peter title: detection of viral sars‐cov‐2 genomes and histopathological changes in endomyocardial biopsies date: 2020-06-12 journal: esc heart fail doi: 10.1002/ehf2.12805 sha: doc_id: 315064 cord_uid: 2mgv9j6n aims: since december 2019, the novel coronavirus sars‐cov‐2 has spread rapidly throughout china and keeps the world in suspense. cardiovascular complications with myocarditis and embolism due to covid‐19 have been reported. sars‐cov‐2 genome detection in the heart muscle has not been demonstrated so far, and the underlying pathophysiological mechanisms remain to be investigated. methods and results: endomyocardial biopsies (embs) of 104 patients (mean age: 57.90 ± 16.37 years; left ventricular ejection fraction: 33.7 ± 14.6%, sex: n = 79 male/25 female) with suspected myocarditis or unexplained heart failure were analysed. emb analysis included histology, immunohistochemistry, and detection of sars‐cov‐2 genomes by real‐time reverse transcription polymerase chain reaction in the ikdt berlin, germany. among 104 embs investigated, five were confirmed with sars‐cov‐2 infected by reverse real‐time transcriptase polymerase chain reaction. we describe patients of different history of symptoms and time duration. additionally, we investigated histopathological changes in myocardial tissue showing that the inflammatory process in embs seemed to permeate vascular wall leading to small arterial obliteration and damage. conclusions: this is the first report that established the evidence of sars‐cov‐2 genomes detection in embs. in these patients, myocardial injury ischaemia may play a role, which could explain the ubiquitous troponin increases. emb‐based identification of the cause of myocardial injury may contribute to explain the different evolution of complicated sars‐cov‐2‐infection and to design future specific and personalized treatment strategies. in december 2019, a novel coronavirus with potential zoonotic origin, named severe acute respiratory syndrome coronavirus 2 (sars-cov-2), was identified as the causative agent of a cluster of suspicious pneumonia cases in wuhan, hubei, china. the incredible fast worldwide spread of the coronavirus disease 2019 (covid-19) prompt the world health organization (who) to declare covid-19 as a pandemic on 11 march 2020. 1 more than 1 776 867 confirmed cases of covid-19 and more than 111 828 fatalities in 185 countries have been attributed to sars-cov-2 as of 14 april 2020 (https://who.sprinklr.com/). molecular tests (real-time reverse transcriptase polymerase chain reaction, rt-qpcr) were generally used to confirm the clinical diagnosis of covid-19. a recent report showed that sars-cov-2 could be detected in different types of clinical specimens such as broncho alveolar lavage, sputum, nasal swabs, feces, blood, and urine. 2 the ubiquitous distribution of the main viral entry receptor angiotensin converting enzyme 2 (ace2) for sars-cov-2 entry into the target cells led to the hypothesis of the involvement of other potential target organs for sars-cov-2 besides the respiratory tract, for example, the heart, the liver, the brain, the pancreas, or the kidneys. 3 infection with the sars-cov-2 is associated with systemic illness by hyper-inflammation. 4 cardiovascular complications with embolism due to covid-19 have been reported recently. [5] [6] [7] [8] acute myocardial injury associated with covid-19 manifested as an increase of high-sensitivity cardiac troponin levels. 1 however, direct sars-cov-2 rna in the heart muscle has not been demonstrated so far. the damage caused by sars-cov-2 to the cardiovascular system and the underlying mechanisms remain to be investigated. accordingly, we prospectively analysed endomyocardial biopsies (embs) from a cohort of 104 samples of patients with suspected myocarditis or unexplained heart disease for the presence of sars-cov-2 rna by rt-qpcr and hints for histopathological injury. up to 8 embs each of 104 patients [mean age: 57.90 ± 16.37 years; left ventricular ejection fraction (lvef): 33.7 ± 14.6%, sex: n = 79 male/25 female] with suspected myocarditis or unexplained heart failure were analysed between 3 february and 26 march 2020 in german clinical centres in accordance with sars-cov2 spread in germany. embs were routinely taken from left ventricle. in 60.4% a hypertrophy was seen according possible due to a cardiac oedema. coronary artery disease was excluded angiographically in all patients prior to emb. the suspected diagnosis had been made by clinicians. embs were send for further diagnosis to the laboratory ikdt (institute for cardiac diagnostic and therapy berlin, germany). analysis included histology, immunohistochemistry, and molecular virology. following emb extraction, samples were transferred to formalin for histological analyses and to rnalater ™ solution (thermo fisher scientific, waltham, ma, usa) for immunohistological and molecular analyses. dna was extracted by puregene core kit a (qiagen, hilden, germany) according to manufacturer's instructions. total rna from one emb was isolated using trizol reagent ™ (thermo fisher scientific, waltham, ma, usa), solubilized in depc-h 2 o, and treated with dnase (peqlab, erlangen, germany) to remove any traces of dna followed by reverse transcription with high-capacity cdna reverse transcription kit (thermo fisher scientific, waltham, ma, usa). random hexamer primers (5 μm) were used in addition to specific primers targeting the e-gene of sars-cov2 (0.2 μm each). dna and cdna concentrations were measured by pcr-based quantifiler ™ human dna quantification kit (thermo fisher scientific, waltham, ma, usa) or by expression of housekeeping gene hprt, respectively. detection of other cardiotropic viruses (enteroviruses, adenoviruses, human herpesvirus 6, epstein-barr virus, parvovirus b19) using (rt-) qpcr or nested pcr was applied as described elsewhere. 9,10 commercially available rt-qpcr kits targeting the e-gene and rdrp-gene (tib molbiol, roche diagnostics, germany) and the assay n2 (n-gene) published by the cdc were chosen to initially screen samples for presence of sars-cov2 genomes. as aforementioned assays were proven to be the most robust, rdrp-gene assay was used for confirmation of results. 11 all rt-qpcr assays were performed using taqman universal pcr mastermix (thermo fisher scientific, waltham, ma, usa) in a 20 μl reaction mix consisting of 2× pcr buffer including enzyme mix, primers, and probes concentrations as recommended by manufacturers and 21.5 μl and 5 μl of cdna. thermal cycling was carried out as recommended by manufacturers on either abi quantstudio 12k flex or biorad cfx96 thermal cyclers. in brief, real-time rt-pcr was performed with 45 cycles using 1.5 μl of cdna. however, for validation of our pcr results additional pcr runs were performed with 5 μl of cdna not altering the results obtained by the 1.5 μl approach. synthetic in vitro rna of e-gene and rdrp-gene assays were diluted 1:10 prior to cdna synthesis and plasmid positive control of n-gene assay was diluted 1:104 prior to rt-qpcr to account for an expected low yield in total rna extracted from emb samples. histology was developed from formalin-fixed tissue by haematoxylin & eosin (he); azan, and periodic acid-schiff (pas) staining in light microscopy. for immunohistological evaluation, specimens were rnalater fixed, embedded in tissue tec (slee, mainz, germany) and immediately snap-frozen in methyl butane which had been cooled in liquid nitrogen and then stored at à80°c until processing. embedded specimens were cut into cryosections placed on 10% poly-l-lysine-precoated slides. myocardial inflammation was diagnosed by cd3 + tlymphocytes/mm 2 (dako, glostrup, denmark), cd11a + /lfa-1 + lymphocytes/mm 2 (immuno tools, friesoythe, germany), cd11b + /mac-1 + macrophages/mm 2 (immuno-tools, friesoythe, germany), cd45r0 + t memory cells (dako, glostrup, denmark), perforin + cytotoxic cells/mm 2 (bd bioscience, san jose, california). in addition, we stained intercellular adhesion molecules and mhc class ii cell surface receptor (cd54/icam-1 and hladr, immunotools, friesoythe, germany). staining were quantified by digital image analysis. 12 approval was not required. endomyocardial biopsy results of total patient cohort are summarized in table 1 . out of the 104 emb samples, five patients were positive for sars-cov-2 e-gene specific sequences indicating the first description of sars-cov-2 presents in a case series. besides latent infection with parvovirus b19, no other viral pathogens were detectable in sars-cov-2 positive samples. based on the clinical history, the clinicians expressed a suspicion of a previous covid-19 infection, but they were not tested with throat swab sample during admission to the hospital. the clinical courses of the five patients were different and showed highly acute to mild forms. patient 1 was a 48-year-old male with newly diagnosed heart failure and significantly reduced systolic function (ef 22%). suspected diagnosis was acute myocarditis. he described sudden onset of high-grade fever and dyspnoea within a few days. in addition, he suffered from thrombi and embolia. he reported a prior vacation in tyrol, austria. this patient showed a highly acute status was admitted to the intensive care unit (icu) and due to severe infection. the diagnosis of a small-vessel vasculitis was established, and cyclophosphamide and additional steroids were initiated. the patient recovered adequately. after receiving emb results, immunosuppressive treatment was stopped immediately. patient 2 was a 62-year-old male with mildly reduced ef (40%) and moderate lv-hypertrophy, and without respiratory infect. this patient had a new cardiac impairment of lv function since january 2020. the cause was unknown, so a possible myocarditis was assumed. with the exception of cardiac symptoms, this patient had a mild course and did not need to be monitored by icu. patient 3 was a 60-year-old female with heart failure symptoms but preserved ef (60%) with pronounced lvhypertrophy. initially, she was admitted to the icu with severe acute respiratory syndrome. blood tests revealed elevated levels of markers of myocyte injury (see table 2 ), which remained positive during the first days of her hospitalization. after respiratory improvement the emb was carried out 4 weeks after onset of syndromes. in this interesting case, the cardiac symptoms occurred with a pronounced relapse after the initial event. patient 4 was a 36-year-old male with a significantly reduced systolic function (ef 25%) with a history of mild respiratory infect 3 weeks ago. the clinical course developed without complications and icu surveillance. during hospitalization, the levels of troponin decreased laboratory values on day 15 were in reference range, and he recovered during this time. patient 5 was a 39-year-old male with heart failure symptoms but preserved ef with suspected diagnosis of acute myocarditis. the patient had a history of upper airway infection with headache and fever up to 4 weeks before admission. he suffered from shortness of breath, t-wave inversions in the anterolateral leads in ecg, elevated cardiac troponin i, and cardiac magnetic resonance imaging compatible with myocarditis. the course of this patient was acute and required icu treatment. in patients 2-5, treatment strategies were not modified after receiving the result of sars-cov-2 rt-qpcr in emb. they were treated symptomatically, in part with initiation of guideline-directed medication for heart failure. patient characteristics and emb results are summarized in table 2 . sars-cov-2 loads determined in the embs were low (ct values: 36.66 ± 1.99) corresponding to less than 100 to 500 viral copies/reaction. viral loads were determined from the internal sars-cov-2 positive control with a ct value of 32.73 ± 1.12 corresponding to approximately 10e + 4 copies/reaction while the ct values of sars-cov-2 negative samples were below 40 cycles and thus below detection limit. results from rt-qpcr are shown in table 3 . histological assessment of embs revealed an active myocarditis according to the dallas criteria in patient 1 13,14 ( figure 1a) . histological analysis could also show necrosis of myocytes and interstitial tissue and granulation tissue in the periphery of necrosis of the type observed after an infarction ( figure 1a) . immunohistochemical emb analysis confirmed pronounced intramyocardial inflammation. analysis of immune cell infiltrates of sars-cov-2 genome positive embs showed elevated number of t-cells, macrophages, lymphocytes, and t-memory cells (cd45r0) in four of the five patients ( figure 1a-c, e, f) . moreover, all sars-cov-2 patients exhibited an elevated number of cell adhesion molecules (cd54/icam-1). patient 2 showed inflammatory response on limit values. we could show that the inflammatory process in cardiac tissue seemed to permeate vascular wall. the inflammatory process was leading to arterial obliteration and damage (figure 1b-d) . the final mechanism of tissue damage in consequence of vascular obliteration appears to be similar to systemic forms of vasculitis leading to ischaemia. the neighbouring myocardium displayed vacuoles in myocytes as a sign of restricted metabolism. perivascular fibrosis with variation of fibre densities could be seen in cases 2 to 5 (not shown in figures). this phenomenon indicated relicts of previous damage. in this study, we established for the first time the evidence of sars-cov-2 genome detection in 5 of 104 embs of patients with suspected myocarditis or unexplained heart failure. after the first cases describing pneumonia of unknown origin in wuhan, china, sars-cov-2 rapidly spread worldwide with critical challenges for the public health and medical communities. cardiovascular involvement in covid-19 seems to be a notable complication. first single case reports could show viral particles in interstitial cytopathic macrophages and their surroundings in emb of a severe covid-19 shock patient by electron microscopic analyses. whether direct myocardial injury due to viral involvement or the effect of systemic inflammation appear to be the most common mechanisms responsible for cardiogenic shock situation needs to be further investigated. 19 in the analytic stage, real-time rt-pcr assays remain the molecular test of choice for the aetiologic diagnosis of sars-cov-2 infection. specificity of e-gene and rdrp-gene assays tested with clinical respiratory samples and sars-cov and mers-cov did not result in cross-reactivity and false positive results. high sensitivity of both assays as indicated by low pcr limit of detection for purified rna could also be confirmed for rna spiked into and extracted from swab samples. 15 however, direct sars-cov-2 rna detection in the myocardium has not been demonstrated so far. herein, we demonstrated by rt-qpcr that sars-cov-2 genomes is present in different cases. in this study, we described series of different histories of cardiovascular patients admitted to the hospital. one main clinical finding is that cardiac involvement with positive sars-cov-2 genomes in embs can either occur acutely or with latency after onset of symptoms of infection. based on the results of currently published research, it seems important to discuss the manifestations and characteristics of myocardial damage induced by covid-19. 16 herewith, we validated the direct cardiac involvement associated with intramyocardial inflammation in patients with sars-cov-2 genome positivity in embs. in patient 1, we could show an active myocarditis and in patient 5 a borderline-myocarditis according the dallas criteria. in the remaining patients, an inflammatory cardiomyopathy was determined. recent literature data have shown that cardiac troponin i concentration is increased in all patients with sars-cov-2 infection, and values exceeding the 99th percentile in the upper reference limit can be observed in 8-12% of positive cases. 17 moreover, patients with covid-19 are known to be at higher risk of acute pulmonary embolism, and elevated d-dimer levels on admission are predictive of adverse outcomes for patients with covid-19. 5 the first vascular sign has been referred to as 'vascular thickening' or 'vascular congestion' in the lung. bai et al. 18 reported vascular thickening to be significantly associated with covid-19 compared with non-covid-19 pneumonia (59% vs. 22%, p < 0.001). the physiopathologic mechanisms behind these changes remain unclear, but their role in diagnosis and possible future treatment strategies is substantial. in this regard, a very recent report showed that pericytes demonstrating high ace-2 expression might act as target cells for sars-cov-2, while pericyte injury can result in endothelial cell dysfunction. 22 recent reports showed that besides pericyctes ace-2 is expressed to different levels also in cardiomyocytes, endothelial cells, fibroblasts, and leucocytes. 23 however, ace-2 expression does not argue for permissive infection of a respective target cell by sars-cov-2. on the other hand, recent reports have demonstrated that sars-cov-2 genomes could be detected besides airway epithelium cells also in the intestinal enterocytes, spleen, liver, kidney, and heart. 2, 24 in addition, recent histologically post-mortem analyses in covid-10 positive patients revealed lymphocytic endotheliitis in different organs with evidence of direct viral infection, indicating endothelial dysfunction as a possible principle determination of microvascular dysfunction by shifting the vascular equilibrium towards more vasoconstriction with subsequent organ ischaemia and inflammation. 21 although nearly all organs seemed to be affected by covid-19, we currently do not know in-depth details about the organ-specific infection by sars-cov-2. in this regard, tavazzi and coworkers have shown recently in their case description using electron microscopy on embs of a patient with covid-19 in cardiogenic shock that sars-cov-2 particles could be localized to interstitial macrophages and their surroundings but not in cardiomyocytes. 19 as to whether this observation is due to a transient viraemia or infected macrophage migration from the lung has to be evaluated. our finding of sars-cov-2 genome detection in embs of patients suffering from myocarditis/inflammatory cardiomyopathy cannot rule out or confirm the infection of cardiac cells but revealed incremental insights into organ-specific infection of sars-cov-2 using possibly macrophage migration as a shuttle from the lung to the heart. in this study, we investigated histopathological changes in myocardial tissue in the series of sars-cov-2 positive embs. in line with the recently published study, we could show that the inflammatory process in embs seemed to permeate vascular wall leading to small arterial obliteration. the final mechanism of tissue damage in consequence of vascular obliteration appears to be similar to systemic forms of vasculitis. we therefore hypothesize that in these patients, myocardial injury ischaemia may play a role, which could explain the ubiquitous troponin increases. as a result, this ischaemia could trigger possible cardiac arrhythmias. a limitation of this study is that we did not had enough material for sars-cov-2 genome in depth analysis to certainly exclude cross reaction with other corona virus strains due to the limited material available by the embs. however, the high sensitivity and specificity of the used pcr systems to detect solely sars-cov-2 genomes have been demonstrated recently. 15 another limitation is that we cannot completely exclude that the detection of sars-cov-2 genomes in the heart might result from contamination of circulating blood. unfortunately, we have no blood samples to the corresponding embs on hand to analyse this aspect. however, sars-cov-2 load in blood seemed to be low in comparison with other clinical types of specimens. 2 nevertheless, sars cov-2 can potentially bind to its cellular ace2 receptor in heart tissue cells and can therefore be detected in the heart muscle. in this regard, a recent report showed that pericytes in the heart demonstrating high ace-2 expression might act as target cells for sars-cov-2 while pericyte injury can result in endothelial cell dysfunction. 20, 22 if sars cov-2 can replicate in these target cells of the heart, this has to be investigated in subsequent analysis. the low detection rate and low viral loads of sars-cov-2 genomes may be due to the limited number, size, and quantity of embs. heart tissue cells (e.g. pericytes) are not the main target cells of sars-cov-2 while specimens of the main target the lung of infected patients are easier and in larger quantity to obtain than embs and may contribute to the low detection rate in embs. however, we showed that sars-cov-2 is detectable in the heart muscle but can only speculate about the clinical relevance of sars-cov-2 infection of the heart. as to whether sars-cov-2 infection may induce myocarditis is questionable, however, may trigger an ongoing progress to myocarditis of other reason. in conclusion, in this study, we could show for the first-time evidence of sars-cov-2 genome detection in 5 of 104 patients with suspected myocarditis or unexplained heart failure with different history of symptoms and time duration. in addition to inflammation and consequential damage, one possible histopathological mechanism may be vascular involvement with arterial obliteration which can lead to ischaemia. a possible sars-cov-2 infection should therefore be considered in patients with acute unexplained heart failure or new cardiac arrhythmias. we believe that recognition by the scientific community of myocarditis as a possible complication associated with covid-19 may be helpful for strict monitoring of affected patients. emb-based identification of the cause of myocardial injury may contribute to explain the different evolution of complicated sars-cov-2-infection and to design future specific treatment strategies. an antiviral therapy is not yet available. based on our histopathological results, possible anticoagulant/antiaggregation therapy should be investigated. clinical features of patients infected with 2019 novel coronavirus in detection of sars-cov-2 in different types of clinical specimens preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov) in china, from 2019 to 2020: a data-driven analysis in the early phase of the outbreak hlh across speciality collaboration, uk. covid-19: consider cytokine storm syndromes and immunosuppression clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan covid-19 and the cardiovascular system cardiac involvement in a patient with coronavirus disease 2019 (covid-19) cardiovascular implications of fatal outcomes of patients with coronavirus disease 2019 (covid-19) therapeutic implications of a combined diagnostic workup including endomyocardial biopsy in an all-comer population of patients with heart failure: a retrospective analysis viral persistence in the myocardium is associated with progressive cardiac dysfunction large, stable, contemporary interspecies recombination events in circulating human herpes simplex viruses dilated cardiomyopathy myocarditis: the dallas criteria european society of cardiology working group on myocardial and pericardial diseases. current state of knowledge on aetiology, diagnosis, management, and therapy of myocarditis: a position statement of the european society of cardiology working group on myocardial and pericardial diseases detection of 2019 novel coronavirus (2019-ncov) by real-time rt-pcr potential effects of coronaviruses on the cardiovascular system: a review cardiac troponin i in patients with coronavirus disease 2019 (covid-19): evidence from a meta-analysis performance of radiologists in differentiating covid-19 from viral pneumonia on chest ct sepe sars-cov-2 genomes in endomyocardial biopsies 7 myocardial localization of coronavirus in covid-19 cardiogenic shock. myocardial localization of coronavirus in covid-19 cardiogenic shock the ace2 expression in human heart indicates new potential mechanism of heart injury among patients infected with sars-cov-2 endothelial cell infection and endotheliitis in covid-19 what is a pericyte? cell type-specific expression of the putative sars-cov-2 receptor ace2 in human hearts sars-cov-2 productively infects human gut enterocytes all nurses, clinicians, and infectious diseases specialists working hard in this difficult period are greatly acknowledged for their efforts and daily care for patients suffering from sars-cov-2 infection. this work was done within a profit grant of the investitionsbank berlin (profit no. 10169028, berlin, germany). for their excellent technical assistance, we thank k. winter, c. seifert, s. ochmann, c. liebig, and k. errami (ikdt berlin, germany). none declared. key: cord-252244-y5w9hjy8 authors: loeffler-wirth, h.; schmidt, m.; binder, h. title: covid-19 trajectories: monitoring pandemic in the worldwide context date: 2020-06-05 journal: nan doi: 10.1101/2020.06.04.20120725 sha: doc_id: 252244 cord_uid: y5w9hjy8 background: covid-19 pandemic is developing worldwide with common dynamics but also with partly marked differences between regions and countries. they are not completely understood, but presumably, provide one clue to find ways to mitigate epidemics until exit strategies to its eradication become available. method: we provide a monitoring tool available at www.izbi.de. it enables inspection of the dynamic state of the epidemic in 187 countries using trajectories. they visualize transmission and removal rates of the epidemic and this way bridge epi-curve tracking with modelling approaches. results: examples were provided which characterize state of epidemic in different regions of the world in terms of fast and slow growing and decaying regimes and estimate associated rate factors. basic spread of the disease associates with transmission between two individuals every two-three days on the average. non-pharmaceutical interventions decrease this value to up to ten days where complete lock down measures are required to stop the epidemic. comparison of trajectories revealed marked differences between the countries regarding efficiency of measures taken against the epidemic. trajectories also reveal marked country-specific dynamics of recovery and death rates. conclusions: the results presented refer to the pandemic state in may 2020 and can serve as working instruction for timely monitoring using the interactive monitoring tool as a sort of seismometer for the evaluation of the state of epidemic, e.g., the possible effect of measures taken in both, lock-down and lock-up directions. comparison of trajectories between countries and regions will support developing hypotheses and models to better understand regional differences of dynamics of covid-19. coronavirus disease arrived in 187 countries with 5.5 mio infections and more than 300,000 deaths worldwide so far (25 th may 2020). the disease affects almost all spheres of life, especially public health, economics and well-being. present situation and near future lasting from months to one-two years (in worst-case more, in best-case less) will require coexistence with the virus until effective pharmaceutical countermeasures (medication, vaccine) are available and applicable [1] . this coexistence requires adjustment of a balance between a controllable low level of infections and maximum-possible levels of public life and economics. controlling the infection requires feedback loops sensitive to early and robust indications of secondary outbreak waves. this includes permanent surveillance of epidemiologic and medical indicators by testing programs, monitoring of case numbers and symptoms and forecasting methods on one hand, and suited 'no-pharmacological intervention' (npis) strategies on the other hand, to held the case numbers low (ideally further decreasing) to prevent secondary outbreaks. various 'number-tracker' tools are active (e.g., [2] [3] [4] [5] ). they mostly plot case numbers (infected, recovered, death) over time, usually on a country-by-country (or region-by-region) basis. as an illustration, we show the number of current infections and of covid-19 related deaths as a function of time in selected countries ( figure 1 ). these 'epi-curves' reveal how the epidemic was expanding in time and space from china (end of 2019 and january 2020) via other asian countries (south korea, iran) and western europe towards eastern europe, amerika, and other parts of the world (february to april 2020). they also reveal different phases of epidemic, namely, an initial 'take-off stage', an 'exponential growing stage' followed by 'slowed growth', 'turning into a decline' and 'decline' [5] . charting the outbreak day by day in each country and comparing them, e.g. by setting an arbitrary starting threshold of, for example, 100 infections, illustrates the succession of events as a global story [2] . for a straightforward evaluation simple measures are typically used such as doubling time of cases, reproduction numbers (mean number of people infected by a typical case) or the number of new infections per 100,000 citizens in a certain region, which all provide a limited snapshot-view with pro's and con's in different states of epidemic. as a next, more elaborated level, standard epidemic models provide a theoretically well-founded description of dynamics of disease incidence in terms of rate constants for transmission and recovery of covid-19 and detailed infection-transmission 'serial interval' functions. different models, mostly assuming a series of diseases states such as the 'susceptible-infected-removed' (sir) types (see below) have been used to describe 'epi-curves' of selected countries and regions under consideration of i) spatial heterogeneous outbreak and transmission scenarios, and ii) the effect of npis [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] . in case of the latter, models have been applied not only in retro-perspective but also to forecast epidemic in dependence on measures taken. because of still limited knowledge about disease mechanisms and detailed data about its spread in the population forecasting either provides short-term extrapolations or hypothetical predictions of possible future scenarios as the result of different model assumptions. we here provide the covid-19 viewer, a monitoring tool which aims at bridging the temporal 'epicurve' and the modelling levels. our monitoring substitute the time-coordinate used in the epi-curves by infected cases (cumulative or current ones). the obtained trajectories then enable to visually estimate the dynamic state of epidemic in terms of simple shape characteristics such as slope, parallel shifts or turning points with direct relations to transmission and removal rates of the disease. comparative analysis between trajectories of different countries enables to judge different scenarios of npis, population size, and social factors. daily actualized data and interactive web-functionalities enable monitoring pandemic based on newest data. our trajectory-approach is complemented by a series of simple model calculation which visualize the obtained trajectories for comparison with real ones. the paper is organized as follows: in the results section we introduce and illustrate the different trajectories and plots available in the monitoring tool by showing examples from different countries of the world, which are thought to serve as worked examples referring to the actual state of pandemic in the second half of may 2020. the majority of plots shown in the publication were directly taken from the web-tool. the interested reader thus can actualize the data and/or chose countries of interest for similar views. we address the effect of nips in europe, the spread of epidemic in germany and compare mortalities between selected countries. the materials and methods section shortly explains the major functionalities. details of the methods, model simulations and fits as well as supplementary figures were provided in the supplement (appendix). figure 1 : covid-19 cases (left plot: currently infected, right plot: died individuals) in different countries as a function of date. the '100-cases per country' threshold is crossed between end of february and end of march for the countries shown (except china). the time courses reflect growing (e.g., us, rus, nl), slightly decaying (e.g., i, d, tk), strongly decaying (e.g., ch, rok) regimes of epidemic or indications of bi-or multiphasic growth (e.g. am, ir). the courses of the dead toll as a function of time reflect country-specific percentages of covid-19 victims. the plots were generated in the corona-viewer on a daily actualization-basis as described in the text. the trajectory-monitoring tool ('covid-19 viewer') was programmed as web application using the rpackage 'shiny' [22] . it processes the number of newly infected and of removed (sum of recovered and died) individuals from 187 countries (and of diamond princess cruise liner with 712 cases) as provided by the corona virus resource center of johns hopkins medical university ('world data': https://systems.jhu.edu/research/public-health/ncov/) and from robert-koch-institut ('germancountry' data: https://www.rki.de/de/content/infaz/n/neuartiges_coronavirus/fallzahlen.html). data are daily updated. the tool is available via the websites of izbi (www.izbi.de) and the leipzig health atlas (https://www.health-atlas.de/models/28). the 'covid-19 viewer' is an interactive tool to monitor the development of the pandemic in 187 countries and in the 16 german states using simple and intuitive plots ( figure 2 , appendix i). the tool is interactive and enables the user to select different presentations of data. the so-called 'rise-fall' trajectory was chosen as 'standard visualization'. it shows the newly confirmed covid-19 cases per country and per day (averaged over the past 7-days) as a function of accumulated total cases per country in double-logarithmic scale. the 'rise-fall' trajectory typically divides into a 'rising' exponential growth part reflecting growth of epidemic and a 'falling' decay regime due to counter measures and/or progressive immunization in the population. it allows estimating transmission and removal rates and reproduction numbers (appendix i). the time range can be chosen and, as an illustration, pressing the 'start animation' button generates a movie of the dynamics of epidemic in the selected countries in terms of progressing rise-fall trajectories. the user can chose 'custom' trajectories to combine different numbers (infected or removed cases, deaths, daily or cumulative counts, figure 1 ) along the coordinate axes for alternative views (use the hoover window for curve assignment and details such as date, numbers). trajectories can be generated for all countries, groups of countries (use left-handed table for selection) or single countries. german states can be selected by choosing 'germany-state codes'. in addition to the standard plot, conventional time series plots show the different numbers (infected, removed, recovered, died as cumulative or per-day) as a function of date. the viewer offers standard browsing functionalities (zooming in and out, image download). . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint figure 2 : covid-19 viewer: screenshot with major functionalities indicated (above) and example plots (below). the sir (susceptible-infected -removed) model provides a simple, adequate and straightforward interpretation of the data (see figure 3 for illustration and appendix ii). it describes the disease as a sequence of three states, s (susceptible), i (infected) and r (removed), where infection proceeds via interactions between s and i individuals. recovered individuals are assumed to get immunized. the respective numbers were reported by census systems, which can differ between countries, e.g. by counting only hospitalized individuals, counting died covid-19 positive cases as not covid-19 caused and/or referring to different test-frequencies. all case numbers must therefore be understood as 'visible', i.e. reported ones. the rise-fall trajectories enables classification of the type of the growth and identification of the epidemic threshold (no growth). custom trajectories allow to estimate time-dependent sir model parameters such as the effective transmission and removal rate factors, c e (t) and k(t), respectively. time courses of the rate factors were extracted from the local slopes of the trajectories (appendix i and ii). the ratio of the rate factors estimates the effective reproduction number r e (t) defined as the number of individuals who get contaminated by one infected person on the average. the timedependent rate factors depend, in addition to the intrinsic properties of covid-19 on a series of external factors such as public health measures (non-pharmaceutic interventions, npis) to slow down transmission of epidemics (affecting c e ) and effective medical services after infection (affecting k). in addition to the estimation of sir parameters as described above, we performed least-squared fits of the trajectories where the daily numbers of newly infected and removed cases were calculated as a function of the cumulative number as predicted by the sir model (appendix ii). the fits provide estimates of n max , the maximum cumulative number of infected cases, and of the rate constants. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint monitoring the state of epidemic using 'rise-fall' trajectories the 'rise-fall' trajectory plots the newly confirmed covid-19 cases (averaged over a running 7 day windows) as a function of accumulated total cases per country in double-logarithmic scale. the 'select all' function shows the trajectories of all countries considered (figure 4a ). overall, these doublelogarithmic trajectories reveal two basic features: an initially linear increase with a slope of unity indicates exponential growth of epidemic. this linear regime is followed for many countries by a downwards turn which indicates slowing down of growth owing to npis 'locking down' infections and/or possibly also to progressing immunization of the population in later phases of epidemic leading to the depletion of the reservoir of susceptible individuals and/or other factors. the 'rise-fall' plots use the cumulative number of cases n as a robust measure of progressing epidemic in a population. naturally, it is larger for countries with larger population sizes providing a larger overall reservoir for covid-19 infections compared with smaller countries. shape of the 'rise-fall' trajectories are however virtually independent of country size. the trajectories thus reflect intrinsic properties of epidemic in terms of its transmission and removal potential. the two sets of trajectories shown in the left and right part of figure 4a refer to situation at april 17th 2020 and about six weeks later, respectively. for most countries, among them france, italy, spain and germany, the trajectories turn into falling courses during this time and/or the falling parts further drop and intersects the '0.01 -slope' line referring to a more than tenfold reduction of the transmission rate of epidemic (see below). these trends thus indicate decay of pandemic after the npis taken in most of countries. on the other hand, brazil and russia emerged to the countries with most cumulative cases after usa, with still growing case numbers. most western european countries of larger and medium size reached the decaying part in the first week of april 2020 (except sweden and great britain) roughly two-three weeks after npis were taken in these countries. countries from different parts of the world such as austria, iceland, south korea, australia, new zealand and china reached low levels of new infections as indicated by strong vertical decays. larger countries (e.g. russia, india, brazil, pakistan) were in the rising part. some countries show a two-phasic growth as indicated by the parallel right shift of linear regions in their growing part (e.g. sweden, denmark, iran, ukraine, armenia) indicating that fast exponential growths are followed by slower phases due to reduced transmission rates (see below). singapore and japan show relatively slow growing phases with reduced rates and late turns into falling regimes while south korea's turn is very sharp presumably because of the 'crash down' measures taken there. is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 5, 2020. hence, the 'rise-fall' trajectories illustrate the current state of the epidemic and its developmental course with country-wise resolution. they enable monitoring the state in terms of differences and similarities between the countries and geographic regions revealing specifics and commons of epidemic spread: (i) a unique linear slope of most of the trajectories in the intermediate abscissa range is indicative for exponential growth in early phases of the outbreak of the pandemic (low level of immunity in the population). the nearly identical position of these lines refers to covid-19 typical pandemic spread rate and maximum basic reproduction numbers r 0 (appendix ii). (ii) parallel, downshifted lines suggest still exponential growth, however with reduced rates reflecting reduced effective reproduction numbers 1 < r e < r 0 . in these countries (e.g., sweden, iran), the epidemic is not stopped. (iii) the 'flattening' of slope and downwards curvature seen, e.g. for most european countries such as italy, spain or germany reflects slowing down growth owing to efficiency of npis and, possibly to a minor degree of progressive and significant immunization in the population. (iv) the sharp, virtually vertical drop of trajectories reflects the stop of epidemic observed, e.g. for china and south korea, and after may 1st for new zealand, australia, and also part of european countries. (v) the different qualitative features of the trajectories are virtually independent of (population) size of the countries. 'smaller' countries like island, cyprus, armenia or georgia show overall similar features such as linear rise, parallel shifts (armenia), a maximum and steep falling parts (e.g., island). . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint the 'rise-fall' trajectory uses cumulative cases n along the abscissa as a robust measure of the extent of the epidemic. this number doesn't consider the degree of recovery and thus it doesn't reflect the current amount of infected cases (i). custom trajectories make use of the independent number of removed cases (r) reported and plot cumulative, current and differential (per day) numbers in different combinations (appendix ii). using the current number of infected cases (i= n -r) as x-axis one sees whether the extent of infection increases or it decays. while the rise-fall trajectory, ï��n-vs-n, tends asymptotically towards a maximum cumulative number of infections (n max ) for each country, which reached the falling regime, the ï��n-vs-i trajectory turns from a growing i into a decaying branch at i max , the maximum number of infected individuals. these trajectories turn in clock-wise directions for most countries meaning that the rate factor of transmission of epidemic, c e (t), strongly decays (appendix i and ii). for example, austria and japan show full turns while the turns of sweden and usa remain incomplete leading to less pronounced decays of the respective c e (t)-courses (figure 5a, b) . in contrast, the ï��r-vs-i trajectories turn typically in counter-clockwise direction referring to an increase of the removal rate factor as explicitly seen in the respective k(t) plots. the ratio of the effective transmission and of the removal rates then estimates the effective reproduction number as a function of time, r e (t) (figure 5b ). the trajectories of the countries selected for illustration reflect different types of trends such as strong and straight repression and stop of epidemic via reduction of transmission in austria, reduced growth but still expanding epidemic in usa and sweden or indications of a second wave of expanding epidemic in iran. here, the respective trajectories and plots of rate factors and of r e (t) show different aspects of the dynamic of the epidemic. for example, s and j are characterized by relatively low levels of rate factors compared with a and ir, a difference seen also in the parallel shifts of the respective trajectories. in appendix ii we find analogous differences between western and south european countries (e, f, i, figure s 3) compared with middle european ones (d, a, ch), which suggest differences in the spread mechanism of covid-19 and, possibly, also in the recovery dynamics. the removal rate obtained depends on the time-delay between infection and recovery, which is neglected our simple trajectory-approach (see also epicurves in figure 5a ). 'cumulative balance' and 'current case' custom trajectories complete the visualization options: lower levels of transmission and removal rates associate with such trajectories running closer to the diagonal. overall, the trajectories enable tracing an epidemic in terms of case numbers reported directly be the census agencies of the respective countries. derived numbers such as the rate factors and reproduction numbers 'translate' these numbers into features more directly describing the dynamics of the epidemic. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint effective reproduction numbers as shown in figure 5b provide suited summary measures of the case numbers with a well-defined epidemiological meaning. their value defines the transmission potential in the population in terms of the mean number of individuals who are infected by one infectious person on the average. for the comparison of all or a selection of the countries available, the monitoring tool generates a ranked boxplot of their actual reproduction numbers. presently, the epidemic is not stopped in roughly 50% of all countries because their r e is still larger than unity ( figure 6 ). the tool also generates the respective plot for r e -values obtained two and four weeks before. at the latter date about 70% of countries show r e > 1, which demonstrates the presently decaying trend. time courses of a selection of countries illustrate different types of decays which eventually relate to the type of npis taken. for example, early, consequent eradication of epidemic in island and croatia result in fast and steep decays. slower but monotonous decays were observed in russia, spain and portugal. also wave-like changes before the final decay (japan, singapore) or even worsening of situation (armenia, sweden until middle of may) were found. presently (may, 25 th ) sweden shows the highest reproduction numbers among all countries studied. note, that r e is a relative measure considering daily changes and current numbers of infections and recoveries (appendix i), meaning that restricted outbreak clusters affecting only relatively small numbers of individuals suggest spread of epidemic in a larger, not affected population. hence, a combination of charcteristic numbers should be used to characterize dynamic of epidemic, namely transmission rate factor (or doubling time of cases) more at the beginning, effective reproduction numbers more in the phase of vast spread of epidemic and absolute numbers of new cases in the phase of mitigation and near eradication. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint next, we asked how the npis taken in middle and western europe and scandinavia in the first three weeks of march 2020 affected the dynamics of the epidemic. the rise-fall trajectories of countries selected from [9] reveal that they now are mostly in the falling regime however with modifications such as parallel downwards shifts, wave-like decays and even lacking decays as already discussed above (figure 7fehler! verweisquelle konnte nicht gefunden werden.a) . in figure 7fehler ! verweisquelle konnte nicht gefunden werden.b we re-plot the trajectories separately for each country together with marks indicating which measure was taken when along the trajectories. in most cases, trajectories start turning downwards about two weeks after a complete lockdown in the respective country. before this, one often finds slowing down of the exponential growth as indicated by small differences compared with the trajectory of us referring to exponential growth. in norway, denmark, and also sweden one observes a relatively strong first slowing down as indicated by the parallel downwards shift of the trajectories which roughly refers to a reduction of the transmission rate constant by about 30 % (figure 7d ). sweden, without complete lockdown measures, but also great britain show weakest decay of the trajectories and largest values of the effective reproduction numbers r e > 1 in contrast to all other countries except belgium (figure 7c ). comparison of the reproduction numbers two and four weeks earlier indicates consistent high values in britain and sweden and also a delayed decay in italy, spain and france, the european countries, which were heavily hit by covid-19 in february and march. the time courses of the reproduction numbers r e (t) respond nearly immediately on the measures in many cases showing, at least, small drops in support of a recent study [9] which assumes that the reproductive number -a measure of transmissionimmediately responds to interventions being implemented ( figure 7d , the first measure and complete lockdown were indicated). consistent decays to values r e < 1 after about two weeks were seen in scandinavia (except sweden) and austria, switzerland and germany while in belgium, france, italy and spain the decays last roughly four weeks until they fall below the epidemic threshold. in sweden and great britain, virtually unchanged levels of r e above the et were observed. a recent model analysis of the effect of npis in germany applies a sir model with changed rate constants at so-called 'change points' which are assumed to take place when measures were applied [23] . we found a decay of the transmission rate during the time when measures were applied which drops overall by 60 -70% in rough agreement with [23] (figure 7d , right part). interestingly, japan showed a similar resonse to npis as the european countries, namely a slow, but instantaneous growth of epidemic turned into the falling regime at the beginningf may ( figure 5 ), two-three weeks after npi measures were intensified at april 10 th . overall, our simple analysis reveals that npis were followed by drops of the reproduction number mainly due to a decay of the transmission rate factor and by halt of epidemic after two to four weeks after complete lock down. sweden (and partly gb) shows also a drop of r e and the transmission rate which however overall are insufficient until end of may to stop epidemic. both, the time-course of reproduction number and the rise-fall trajectory are sensitive to detect the slowing down and the halt of epidemic. the available country-wise numbers used do not allow to analyse the observed effect assuming heterogeneous effects of npi on different subpopulations which, in principle, could explain steps and wavelike changes in the courses of the trajectories as an alternative to alterations of the rate factors in a homogeneous population assumed here. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint figure 7 : the effect of non-pharmaceutical interventions across ten european countries selected in analogy with [9] . the trajectory of us is shown for comparison. a) rise-fall trajectories of selected countries mostly decay thus indicating marked decrease of epidemic in most cases. b.) country-by-country plots of the rise-fall trajectories together with marks assigning the nips (dates and assignments were taken from [9] ) show that the trajectories turn downwards about two weeks after lockdown in most cases (the grey box refers to the 'two weeks after the last measure' date). exceptions are sweden (no complete lockdown) and united kingdom. the two green boxes indicate the data obtained at march 10 th (mostly before measures) and may 1th. c) the effective reproduction numbers are still clearly above the critical value of r e =1 for sweden and great britain. italy and france show the strongest decay of re over the last 4 weeks. d) courses of the effective reproduction number as a function of time indicate a marked drop of re(t) immediately after the lock down in most countries. also the first measure taken is indicated. for germany all 5 measures were indicated together with the courses of the rate factors. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint countries across the world differ in many factors related to covid-19 epidemic such as the particular npi measures, social behaviour, family structure and education systems with differing school rules, population densities, urban structure, transport system and also age distribution. the heterogeneity of these factors is assumed to be smaller inside each of the countries than between them. for germany, the covid-19 viewer provides 'rise-fall' trajectories for all sixteen german states, which cover population sizes between about 0.7 mio (bremen) up to 18 mio inhabitants (nordrhein-westfalen). they include three city-states (hamburg, bremen, berlin), while the other states are 'area'-states include countryside regions and towns of different sizes. the trajectories overall express very similar courses of the epidemic across germany (figure 8a) , which suggest relatively similar dynamics of the epidemic in different parts of the country and, particularly, that germany-wide npis 'locked-down' epidemics in the different states in a similar way. analysis of the maximum cumulative number of infected individuals, n max , using fits of the 'rise-fall' trajectories however reveals considerable differences especially between the south and west of germany and its east and north (figure 8b ). in bavaria, which is located in the south of germany, roughly eight-times more people are infected on relative scale than in mecklenburg-vorpommern located in the north-east. in general, 'area' states from the west and south of germany were more affected by epidemic than states in the east and north. this difference associates with an earlier outbreak in the former states with higher amounts of infected individuals (figure 8c ). npis were taken germany-wide at the same time between 9 th and 23 th of march, which suggests that delayed measures with respect to the outbreak will increase the burden of infections. in summary, germany-wide the trajectories reflect similar dynamics of epidemic where however earlier outbreaks especially in the west and south and in larger cities gives rise to increased numbers of infected persons, possibly because of the delay of npi. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint figure 8 : covid-19 in germany: a) 'rise-fall' trajectories across german states: the trajectories of german states resemble that of whole germany indicating similar dynamics of covid-19 across germany. trajectory of us is shown for comparison. b) the relative maximum cumulative number of infected cases (per 1,000 residents of the respective states divides clearly into states from west and south germany and states in the east and north of germany. city states (be, hh, hb) are found in the former group. c) epi-curves (cumulative case numbers as a function of time) reveal that epidemic arrived earlier in western and southern states mostly by a few days compared with the eastern and northern ones. the curve of the city state bremen (hb) slightly differs from that of the other ones. mortality is an important endpoint of covid-19 epidemic related to a series of factors such as the intrinsic severity of the virus [24] in first instance, but also age, sex, genetic and immunological predisposition [25] , disease history and also co-morbidities of the patients [26] , as well as the effectivity of medical measures such as icu services [27] , the capacity of health care systems and also socio-economic factors. censing of deaths, e.g. by counting covid-19 positively tested deaths as covid-19 caused or not, is another factor affecting the reported numbers. so far we subsumed the numbers of death cases together with recovered individuals as removed ones. separate counting shows that, overall, the dead toll of covid-19 ranges from less than 1% up to more than 10% of counted infections, depending on country and time, when the data were registered (see below). the 'custom trajectory' page provides 'mortality trajectories' in terms of cumulative death cases versus cumulative infections . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint (alternatively one can choose daily cases). constant percentages refer to parallel diagonal lines as indicated ('iso-percentage' lines). for illustration we selected groups of countries in figure 9 for comparison with part of the 'rise-fall' trajectories in figure 4b . larger-size west-european countries (great britain, france, spain, italy) all show similar mortality trajectories referring to about 10% of the (visible) infected individuals. mortality of germany and austria is smaller (about 4%), possibly due to the smaller mean age of infected persons at the beginning of epidemic. the respective mortalitytrajectories however slowly grow in direction of the level of the other european countries with increasing number of infections. note that the slopes of the trajectories of the latter countries (e.g. france, italy, spain) is slightly steeper than that of the iso-percentage lines which indicates slowly growing mortalities across in these countries. presently, mortality in europe is largest in sweden, belgium, netherlands and great britain with further increasing trends. relative small mortality is found in russia and belarus possibly caused by governmental-control about covid-19 related death-census. mortalities in ukraine and estonia and in east asia (china, japan) are comparable with mortality in us, where the latter asian countries and also south korea show an increasing trend of mortality. in south america, one finds higher mortalities than in us with further increasing trends. overall, comparison of the mortality trajectories reveals systematic differences and trends, which need further analysis for interpretation. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint we here presented the 'covid-19 trajectory viewer', which generates a series of trajectories and plots based on public available covid19 data. it enables the comparison between epidemic development with country-wise resolution worldwide. trajectories are based on two types of counts, namely the number of infected and of removed (recovered and died) individuals. plots use either these counts directly, their cumulative values or increments per day and combine them in different ways, which allows to inspect the actual state of the epidemic from different perspectives. in addition, the monitoring tool enables calculation and visualization of derived parameters, namely the effective transmission and recovery rate factors and the effective reproduction number. they estimate the transmission and removal 'power' as basic characteristics showing whether epidemic growths or declines. changes of these parameters during epidemic development reflect different factors affecting the dynamic of epidemic, namely (i) the possible consequences npis, (ii) eventually growing immunity due to decaying numbers of susceptible individuals, and, (iii) also differences in the methods of counting and reporting data between different countries. our monitoring metric is sensitive for subtle alterations of the dynamics of the epidemic making it suitable to estimate the effectivity of npis and to serve as 'seismometer' for secondary outbreaks to early indicate such events ( figure 10 ). three possible future pandemic scenarios for covid-19 dynamics have been suggested based on previos influenca courses [1] , firstly, 'peaks and valleys' where the first big wave in spring 2020 is followed by repetetive smaller waves with geographic specifics depending on local npis; secondly, the 'fall peak' suggesting a large secondary peak in fall, winter 2020; and, third, a 'slow burn' of ongoing transmission and case occurrence, but without a clear wave pattern, again with geographic variations affected by the degree of mitigation measures in place in various areas. one or none of them, or even all three in parallel in different countries will be possible, where trajectories and rate factor curves will provide an instrument to distinguish the different scenarios. thereby, one has to keep in mind that these are data on visible, symptomatic covid19 cases. unsymptomatic cases remain usually undetected and can exceed the number of symptomatic ones considerably. a recent publication shows that more than 80% of all positively tested covid-19 cases on a cruise liner did not show any symptoms, raising questions about the true prevalence of "silent" infections [28] with possible consequences for the immunization dynamics in a population. moreover, our simple monitoring does not explicitly consider heterogeneities of the spread of the epidemic in a population (e.g. cities versus countryside, elderly versus younger, hospitalized versus non-hospitalized, symptomatic versus asymptomatic, highly exposed professions versus less exposed ones, etc.). such effects are hidden in the data and can be considered in terms of the trajectory approach by using more detailed data, e.g. by stratifying populations geographically, with respect to professions, age, symptoms etc. and/or by applying more elaborated models. our visualization in terms of trajectories and derived rate factors and their interpretation is based on the simple sir model dividing the visible population into three types of individuals. such three-state models have been widely and successfully used in many areas of sciences to describe different kinds of dynamics, ranging from elementary reaction kinetics in chemistry to photo-physics, molecular transformations in biology and many other fields. the basic assumption behind the sir model is the mass action law, claiming that changes of the population of a state directly relates to its population number. the different trajectories visualize this relationship by plotting changes of newly infected or . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint removed individuals as functions of the number of cumulative or currently infected individuals. the double logarithmic scaling of the axes accounts for the fact that the solution of the ordinary differential equations behind the sir model predicts exponential dynamics in important limiting regimes such as the early or late outbreak limits, which in turn, suggest linear courses of the trajectories. this way the obtained trajectories reflect a virtually common maximum transmission rate in the exponential growth phase in many countries suggesting that each infected individual infects another one every two-three days (figure 10a ). the initial growth is followed by down-steps and parallel shifted lines indicative for exponential growth with reduced transmission rate (e.g., transfer of infection between two individuals every five days). downturns of different sharpness indicate markedly reduced spread dynamics, and also halt of the epidemic in terms of falling courses if transmission frequency reaches a level of more than one per ten days. the close temporal relatedness between slowing down of the transmission dynamics and the dates when measures of the npi-type were taken suggests causal relations and shows that an associated 'falling' regime can be monitored using the trajectory approach. the npi result in dropping transmission rates and reproduction numbers where the steepness of decay in europe is larger for countries such as austria and germany, which were hit by the main infection wave a few weeks later than italy, france and spain showing slower decays. early nips on a relative time scale with respect to growth dynamics obviously facilitate faster slowing down afterwards. so-called 'complete lockdown' measures seems to be an essential measure for stopping epidemic despite considerable differences between countries, e.g. in handling go-out restrictions ('ausgangssperre', relatively moderate rules in germany versus strong ones in italy, spain and france). the swedish model seems to fail regarding transmission dynamics conceding further expanding epidemic and high death toll (figure 10a ). our trajectories show that lowering a of transmission rates by more than 50-70% compared with its maximum, intrinsic value, is required to stop epidemic and to turn it into the decaying regime. joint plotting of trajectories using the covid-19 viewer shows that at present majority of east asian (china, south korea, singapore) and european countries are in the falling regime, while most american countries are in the exponential growth phase. epidemic seems virtually eradicated in the island states new zealand, iceland but also other small countries such as croatia in a similar way as observed at 'diamond princess' cruise liner held under isolation (figure 10b ). it shows that isolation in combination with strong npis effectively stop epidemic. on the contrary, slowing down but still exponential growth are seen in other small and relatively isolated countries such as armenia (surrounded by mountains and closed borders to part of neighbouring countries) reflecting inefficiency of measures taken. wavelike up and down as seen for iran indicate repeated waves of growing epidemic (figure 10c ). new outbreak clusters become evident as spiked upturns in the falling regime as indicated presently for south korea (figure 10d ). the removal rate factor is a second, important characteristic of covid-19 dynamics, which additively composes of recovery and death rates, where the former number is dominating. removal rates can differ by a factor of two-to-ten between different countries (e.g. germany and austria versus spain and france, figure s 3) by unknown reasons. possible explanations are specifics of the recovery process due to healthcare measures applied and/or epidemiological factors such as age-and/or health-risk of the respective populations. also counting criteria of recovered individuals are another, possibly more relevant factor, which can differ between countries. often census agencies apply recovery counting algorithms (e.g. by assuming recovery two weeks after infection if no other information is available in germany) presumably biasing estimation of removal rate factors. moreover, also counting of deaths is census-dependent. on the other hand, the initially low but afterwards increasing mortality rates in austria and germany can be rationalized by the increasing age of infected individuals (disease was initially spread in communities of younger persons). thus, comparing trajectories supports detection . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june 5, 2020. . https://doi.org/10.1101/2020.06.04.20120725 doi: medrxiv preprint of differences of recovery and mortality rates between countries for subsequent analysis of the possible reasons. figure 10 : example trajectories indicating different dynamic regimes of covid-19: a) basic rise and falling regimes refer to transmission intervals of 3-4 and more than 10 days, respectively. they were observed in european countries under complete lock down such as austria. incomplete lock down as applied in sweden only slowed down spread of epidemic. it associates with roughly two times more infections and a more than four-fold deathtoll. b) eradication of epidemic can be expected in island states (iceland, new zealand) and other relatively small countries (e.g. croatia) showing disappearance of new cases two to three months after the outbreak (see epicurves in the insertion). another example of eradication is covid-19 spread at the princess diamond cruise liner with about 760 infections. c) wave-like up and downs of epidemic were observed in armenia and iran. the trajectories transform into wave-like oscillations of the effective reproduction number (insertion). d) a new spike of cases is seen in the trajectory of south korea. the trajectory for us is shown for comparison. covid-19 pandemic develops in different phases around the world ranging from exponential growth to decaying regimes and even eradication from region to region and from country to country. it is characterized by high dynamics, which necessitate prompt monitoring to evaluate the outcome of npi measures in either, 'lockdown' or 'lock up' direction to indicate improvement or worsening in terms of suited metrics such as increasing or decreasing numbers of cases, rate factors or reproduction numbers. the covid-19 viewer provides this information in the worldwide context on a daily actualized basis. we understand our report as a worked example reflecting aspects of the pandemic in may 2020, which supports future monitoring using the covid-19 viewer as a sort of working instruction. many aspects of the covid-19 pandemic are not completely understood. this includes dark figures of infections, detailed spreading mechanisms and associated socio-economic, politic and health factors. here more studies reasoning differences between regions and countries are required. the trajectory approach complements epi-curve reporting by bridging the gap to modelling methods. inspection and comparison of the trajectories and of the time courses of rate factors extracted are expected to inspire development of substantiated hypotheses and elaboration of improved models to better understand mechanisms of epidemic spread and decay and theirs specific in different countries and regions. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june 5, 2020. . covid-19: the cidrap viewpoint: part 1: the future of the covid-19 pandemic: lessons learned from pandemic influenza coronavirus pandemic (covid-19) coronavirus tracked: the latest figures as countries fight to contain the pandemic the covid tracking project mitigation and herd immunity strategy for covid-19 is likely to fail a first study on the impact of current and future control measures on the spread of covid-19 in germany projecting the spread of covid19 for germany imperial college covid-19 response team estimate of the development of the epidemic reproduction number rt from coronavirus sars-cov-2 case data and implications for political measures based on prognostics quantifying the effect of quarantine control in covid-19 infectious spread using machine learning covid-19 spread: reproduction of data and prediction using a sir model on euclidean network sequential data assimilation of the stochastic seir epidemic model for regional covid-19 dynamics effective containment explains subexponential growth in recent confirmed covid-19 cases in china estimating effects of physical distancing on the covid-19 pandemic using an urban mobility index a time-dependent sir model for covid-19 with undetectable infected persons. eprint arxiv viola priesemann: inferring change points in the covid-19 spreading reveals the effectiveness of interventions autocatalytic model for covid-19 progression in a country using phenomenological models for forecasting the extended sir prediction of the epidemics trend of covid-19 in italy and compared with hunan evaluation of the secondary transmission pattern and epidemic prediction of covid-19 in the four metropolitan areas of china shiny: web application framework for r. r package version inferring change points in the spread of covid-19 reveals the effectiveness of interventions sars-cov-2 (covid-19) by the numbers a global effort to define the human genetics of protective immunity to sars-cov-2 infection factors associated with hospitalization and critical illness among 4,103 patients with covid-19 disease features of 16,749 hospitalised uk patients with covid-19 using the isaric who clinical characterisation protocol covid-19: in the footsteps of ernest shackleton estimating epidemic exponential growth rate and basic reproduction number the disease-induced herd immunity level for covid-19 is substantially lower than the classical herd immunity level estimating individual and household reproduction numbers in an emerging epidemic time-dependent sir model for covid-19 with undetectable infected persons. arxivorg 2020 key: cord-270948-qfsjtflv authors: klosterhalfen, stephanie; kotz, daniel; kuntz, benjamin; zeiher, johannes; starker, anne title: waterpipe use among adolescents in germany: prevalence, associated consumer characteristics, and trends (german health interview and examination survey for children and adolescents, kiggs) date: 2020-10-22 journal: int j environ res public health doi: 10.3390/ijerph17217740 sha: doc_id: 270948 cord_uid: qfsjtflv waterpipe (wp) use is popular among youth worldwide, but epidemiological data from germany are scarce. we aimed to describe prevalence rates of wp use (current, last 12 months, ever) and analysed correlates and trends among 11to 17-year-olds in germany. analyses were based on data from the “german health interview and examination survey for children and adolescents” study during 2014–2017 (n = 6599). changes in wp use prevalence compared with 2009–2012 were used to describe trends. associations with sociodemographic characteristics and cigarette smoking were assessed with multivariable logistic regression models. prevalence of current wp use among adolescents was 8.5% (95% confidence interval (ci) = 7.5–9.6), use in the last 12 months was 19.7% (95% ci = 18.3–21.2), and ever use was 25.8% (95% ci = 24.2–27.5). high prevalence rates were particularly found among 16–17-year-olds. during 2009–2012, these prevalence rates were 9.0%, 18.5%, and 26.1%, respectively. wp use was associated with older age, male sex, migration background, lower educational level, and current smoking status. among current wp users, 66.2% (95% ci = 60.0–71.9) identified themselves as non-smokers, and 38.1% (95% ci = 32.5–44.0) had used wp ≥ three times in the last month. wp consumption is popular among german youth, and prevalence rates have not changed over time. specific prevention strategies to reduce harmful wp consumption among youth should be implemented. in recent decades, there has been a worldwide increase in the prevalence of waterpipe (wp) use among young people. historically, the popularity of wps spread from india, across continents, until its consumption became accepted in the western world as an alternative form of tobacco smoking. regular consumption of wps by broad sections of the population is a phenomenon that was not observed prior to the end of the 20th century [1] [2] [3] . although the name (hookah, shisha, narghile, argileh, boory, goza, or hubble bubble), size, and design of wps vary from region to region, they all function in the same way. the characteristic of this time-consuming (average duration of 47 min) method of tobacco smoking is that the smoke passes through water before being inhaled into the lungs once cooled [4] . figure 1 shows the required components of a wp. to fill the tobacco head, a special, mostly sweet and flavored wp tobacco called maassal can be used, as well as alternative tobacco-free products such as steam stones [5] . to heat the tobacco, wp charcoal (or alternatively, an electronic heat source [6] ) is used. see: figure 1 . components of a waterpipe. int. j. environ. res. public health 2020, 17, x 2 of 16 through water before being inhaled into the lungs once cooled [4] . figure 1 shows the required components of a wp. to fill the tobacco head, a special, mostly sweet and flavored wp tobacco called maassal can be used, as well as alternative tobacco-free products such as steam stones [5] . to heat the tobacco, wp charcoal (or alternatively, an electronic heat source [6] ) is used. see: figure 1 . components of a waterpipe. wp use differs from conventional cigarette use not only with respect to the length of a smoking session; wp tobacco tastes often sweeter due to the added flavors, and the inhalation of cooled smoke seems less irritating to the mucosae and lungs. in addition, wps can be smoked as a group, e.g., at a party, and can therefore create a social experience [7] . these aspects provide insight into why wp use is popular among adolescents, why many wp wp use differs from conventional cigarette use not only with respect to the length of a smoking session; wp tobacco tastes often sweeter due to the added flavors, and the inhalation of cooled smoke seems less irritating to the mucosae and lungs. in addition, wps can be smoked as a group, e.g., at a party, and can therefore create a social experience [7] . these aspects provide insight into why wp use is popular among adolescents, why many wp users do not perceive themselves as "conventional smokers" [8] , and why some users underestimate the health risks of wp consumption [9] [10] [11] [12] . first experiences with the consumption of tobacco typically take place during the period of experimentation during adolescence. the most frequent first tobacco product tried by young people is the cigarette (followed by cigar, smokeless tobacco, and wp) [13] . during this period, adolescents are at special risk of developing dependency, and the risk of early deterioration of health increases [14] . different cultural and socioeconomic backgrounds as well as use of other tobacco products can be determinants regarding the consumption of wp by adolescents [15] [16] [17] . the aromatic taste of wp tobacco (e.g., apple, cherry, melon) appeals to young people and can be associated with a more pleasant, longer smoking experience which leads to increased nicotine exposure and dependence potential [18] [19] [20] . furthermore, the consumption of wp is associated with other harmful health effects similar to those associated with cigarette smoking [21] . in addition to the increased risk of carbon monoxide poisoning, which can result from combustion of the wp charcoal [22] , smoking wp can cause acute to chronic impairment [23] , negative impacts on executive brain function, or carcinogenic changes in various organs including the lungs and cardiovascular system [24] [25] [26] . sharing a wp among different people can also increase the risk of transmission and infection with bacterial or viral diseases [27] , which is particularly relevant during times of acute pandemic such as the present global novel coronavirus disease (covid-19) pandemic. the number of shisha bars (almost 6000) and the consumption of wp tobacco have risen in germany [28] . the increasing number of wp cafés can influence societal acceptance, and these serve as a place of social exchange for adolescents, just like pubs in former generations [12, 29] . in germany, there are legislative measures at the both state and the federal level to regulate wp consumption (bundesnichtraucherschutzgesetz ("federal non-smoker protection act"), jugendschutzgesetz ("youth protection act"), tabakerzeugnisgesetz ("tobacco products act"), nichtraucherschutzgesetz ("non-smoker protection act")). the german tobacco products act regulates ingredients, emission levels and information requirements for tobacco and related products. in 2016, the ingredients of wp tobacco changed (% content of glycerin). the youth protection act regulates the distribution of tobacco products. in 2007, the age limit for the consumption of tobacco products in public has been raised from 16 to 18 years. it is not permitted to sell tobacco products to minors. children and adolescents under the age of 18 are not allowed to smoke in publicly accessible rooms in places open to the public and otherwise in public places. these measures were accompanied by a tobacco prevention program. purchase of wp tobacco and accessories or the entry to a shisha bar are not permitted to people under 18 years of age. apart from regional studies, there are only a few population-based studies on the prevalence of wp consumption among adolescents in germany. the german health interview and examination survey for children and adolescents (kiggs) study and studies of the federal centre for health education (bzga) such as the drug affinity study have collected data on awareness about and use of wp, differentiated according to migration background, frequency of consumption, and combined consumption of tobacco cigarettes, wps, e-products, and tobacco heaters [16, 30] . national and international study findings indicate that male adolescents or youth with a migration background use wp more often than girls or people without a migration background [3, 16, 30] . regarding socioeconomic or educational factors, there seems to be a relationship between wp use and lower educational levels in germany, whereas international studies have reported opposite findings [3, 16, 30] . a study by the german health insurance dak ("dak-präventionsradar") has collected prevalence figures of wp consumption among school children [31] . prevalence rates of 6-14% for current and 22-44% for ever use of wps are reported for adolescents in germany under 18 years of age [16, 27, [30] [31] [32] . regarding international prevalence rates, current wp consumption varies widely, from 2.2% in romania to 36.9% in lebanon [15, 33] . several studies from the united states (us) reported increasing rates of wp use among 11-to 18-year-olds between 2009 and 2017 [34] . smoking a wp is a common form of tobacco use among adolescents in the us [12] . however, little is currently known about the factors associated with wp use. the influence of a one-or both-sided migration background, the socioeconomic status (ses) of the family, and sex, have not yet specifically been investigated in germany. data are also missing on the percentage of wp users who perceive themselves as smokers or non-smokers. this is an important issue, which can influence the perception of health risks of wp tobacco consumption and the creation of prevention programs. we, therefore, aimed to evaluate wp use and associated factors among german adolescents. more specifically, based on data of the second wave of the german health interview and examination survey for children and adolescents (kiggs wave 2), in the present study, we aimed to (i) investigate the prevalence of wp consumption among 11-to 17-year-old boys and girls; (ii) describe the frequency of wp use and the self-assessed smoking status; (iii) examine the associations between sociodemographic factors, smoking status and wp consumption among adolescents; and (iv) to monitor trends between the previous and the current wave of the kiggs study. due to a large study sample, the kiggs study-in contrast to other population-wide studies conducted in germany-allows the surveillance of prevalence figures more detailed (e.g., one-or both-sided migration backgrounds, survey of 11-year-olds, survey 12-month prevalence) and to include statements on self-assessed smoking status. these data can help in the identification of different risk profiles to develop targeted group-specific and gender-sensitive prevention strategies. the kiggs study is part of health monitoring conducted by the robert koch institute (rki) on behalf of the federal ministry of health in germany. kiggs focusses on health status, health behavior, living conditions, protective and risk factors, and healthcare among children, adolescents, and young adults living in germany. cross-sectional data have been collected at three time points: the kiggs baseline study (2003) (2004) (2005) (2006) , kiggs wave 1 (2009-2012) and kiggs wave 2 (2014-2017). the response rate (according to aapor response rate 2) of kiggs wave 2 was 40.1% in total [35] . a multi-step approach was used to include people with a migration background in kiggs wave 2. the share of children and adolescents of non-german nationality in kiggs wave 2 corresponds to the population figures from the federal statistical office [36] . the concept, methodology, and analyses of kiggs are described in detail elsewhere [35, [37] [38] [39] . comparable to the kiggs baseline study, respondents for kiggs wave 2 were selected randomly based on the population registers of 167 representative german municipalities and cities (two steps sampling process). the study population of kiggs wave 1 consists of re-invited participants from the baseline study supplemented by newly invited children aged 0-6 years. kiggs wave 2 (like kiggs baseline study) was comprised of an interview and examination part, whereas kiggs wave 1 was conducted as a telephone interview survey [37] [38] [39] . to achieve an optimal number of respondents and sample composition, a variety of measures were applied (e.g., phone calls or home visits) [35, 36] , resulting in a total of 15,023 respondents aged 0-17 years. the analyses of wp consumption were restricted to data from 11-to 17-year-old respondents (n = 6599), collected using a written questionnaire. to identify trends in comparison with the previous wave, the results from wave 1 were compared with the currently collected prevalence rates from wave 2. the study was approved by the ethics committee of hannover medical school (no. 2275-2014). the prevalence of wp use was assessed with the question "have you ever smoked a waterpipe or shisha?" respondents who affirmed having used a wp were defined as "ever wp user" and were further asked "have you smoked a waterpipe or shisha in the last 12 months?" (yes defined as "last-12-month wp user") and "if you think about the last 30 days, on how many days did you smoke a waterpipe or shisha?" (response options: ≥1 day, defined as "current user" or "none in the past 30 days"). regarding the frequency of use during the past month, we classified responses according to one, two, or ≥three times. to determine the ses of the family, an index was generated based on information of the parents' level of education, occupational status, and income (equivalized disposable income). thus, respondents were classified as belonging to a family with "low", "medium", or "high" ses [40] . school type was surveyed by asking the parents "which type of school does your child go to?", with nine response options: "primary school", "secondary school", "middle school", "school with secondary and middle educational program", "integrated comprehensive school", "academic secondary school", "technical secondary school", "special school", and "other". due to its federal structure, there is no uniform school system in germany. as some federal states now have a two-tier school system, we categorize for the following analyses, two groups for secondary school: "secondary/middle/comprehensive school" and "technical/academic secondary school". young people who no longer attended school were assigned to the corresponding category based on the highest level of education they achieved [41] . to assess migration background, all respondents were asked about their own and their parents' country of origin: "in which country were you born?" and "in which country were your parents born?" a one-sided migration background meant that one parent was not born in germany or had no german citizenship; a both-sided migration background meant that the child himself/herself migrated to germany and had at least one parent who was not born in germany or both parents were born abroad [42] . to assess smoking status, respondents were asked "do you currently smoke?", with the following response options: "no", "daily", "several times a week", "once a week", or "less than once a week". all respondents who answered in the affirmative were defined as a "current smoker". the data collected for kiggs wave 2 are available from the rki research data center (https: //www.rki.de/en/content/health_monitoring/public_use_files/public_use_file_node.html). the descriptive analyses of wp use patterns (current, last 12 months, ever) stratified by sociodemographic characteristics and smoking status are presented, differentiated for female and male respondents, as percentages with 95% confidence intervals (cis). weighting with regard to age, sex, federal state, german citizenship, and the child's parents' level of education was applied to ensure representative data for children and adolescents living in germany. comparison of current prevalence figures and those obtained between 2009 and 2012 was based on descriptive statistics and is presented as percentage with 95% ci. three multivariable logistic regression models were applied to explore associations between different wp use patterns and sociodemographic characteristics and smoking status for girls and boys: model i = current wp use vs. never wp use, model ii = last 12 month wp use vs. never wp use and model iii = ever wp use vs. never wp use. respondents with missing data were excluded from the regression analyses. data were analyzed using stata 15.1 (stata corp., college station, tx, usa). stata's survey procedures were applied to account for the clustered sampling design. the prevalence of current wp use among 11-to 17-year-old adolescents in germany was 8.5% (95% ci = 7.5-9.6; n = 446) in the period 2014-2017. almost every fifth adolescent had used wp within the last 12 months (19.7%, 95% ci = 18.3-21.2; n = 1101), and 25.8% (95% ci = 24.2-27.5; n = 1415) were ever wp users (weighted data). table 1 presents prevalence of different wp use patterns, sociodemographic characteristics, and smoking status, stratified by sex (weighted data, missing data regarding ses (n = 145), education (n = 710), migration background (n = 33), and current smoking status (n = 852)). the pattern of missing values showed a higher amount of missing values among boys with migration background, boys with lower ses and lower education level, and among girls with lower ses and multivariable analyses showed that the odds of missing values are especially high among boys with a both-sided migration background (data not shown). boys were more likely than girls to report current (10.6% vs. 6.3%), last 12-month (22.1% vs. 17.3%), and ever (28.1% vs. 23.4%) wp use. respondents with a migration background and current smokers reported using wp more often than those without a migration background or non-smokers (current, last 12 month, and ever wp use). the results of the three multivariable regression analyses regarding sociodemographic characteristics, current smoking status, and wp consumption are presented in table 2 . the adjusted odds ratios (ors) of current vs. never wp use (model i) were higher in adolescents with older age and current smokers (girls: or = 1.97, 95% ci = 1.69-2.29 and or = 48.27, 95% ci = 24.12-96.59; boys: or = 2.20, ci = 1.92-2.52 and or = 67.57, 95% ci = 18.02-253.32). concerning migration background, we found that boys with a one-sided migration background used wp more often than boys without a migration background (or = 3.03, 95% ci = 1.36-6.77). we found similar associations when comparing wp use in the last 12 months vs. never wp use (model ii). in addition, girls with a both-sided migration background showed a lower or for wp use than girls without a migration background (or = 0.38, 95% ci = 0.22-0.65), and girls with a lower educational level showed a higher or for wp use than girls with higher educational levels (or = 1.82, 95% ci = 1.32-2.51). we also found the above-mentioned associations when comparing ever vs. never wp use (model iii), except that the adjusted or was also higher in girls from a family with low ses compared with girls belonging to a family with high ses (or = 1.66, 95% ci = 1.02-2.71). the numerator for the calculation refers to the total number in the corresponding series (e.g., 50.6% of 17-year-old girls report wp ever use). bold printed indicates the prevalence for the respective group. defined as using wp in the last 30 days. • one-sided indicates children and adolescents having one parent not born in germany or without german citizenship; two-sided indicates children and adolescents who themselves migrated to germany and have at least one parent who was not born in germany, and children and adolescents whose parents were both born in a country other than germany or non-german nationals. * socioeconomic status generated as a household characteristic based on parental levels of education, occupational status, and income. german equivalents to school types: secondary school = hauptschule; middle school = realschule; comprehensive school = gesamtschule; technical secondary school = fachoberschule (fos); academic secondary school = gymnasium. 1 † all listed covariates were included in models i-iii. data are presented as odds ratio (or) 95% confidence interval (ci). * p < 0.05; ** p < 0.01; *** p < 0.001. > age was treated as a continuous variable in the regression analyses. • one-sided indicated children having one parent not born in germany or without german citizenship; both-sided indicates children who themselves migrated to germany and have at least one parent who was not born in germany and children and adolescents whose parents were both born in a country other than germany or non-german citizens. defined as using wp in the past 30 days. ‡ socioeconomic status generated as a household characteristic based on parental levels of education, occupational status, and income. german equival ents to school types: secondary school = hauptschule; middle school = realschule; comprehensive school = gesamtschule; technical secondary school = fachoberschule (fos); academic secondary school = gymnasium. the prevalence rates of wp use in wave 2 (2014-2017) were similar to those identified earlier in wave 1 (2009 wave 1 ( -2012 , as shown in figure 2 . among german 11-to 17-year olds surveyed in the period 2014-2017, 8 .5% reported being current wp users and about 26% reported being ever users. the use of wp seems to be most common in the age group of 16-17-year-olds. a considerable proportion (62%) of current wp users had smoked a wp twice or more in the last month. only one-third of wp users considered themselves smokers. we found positive associations of wp use with older age, male sex, and current smoking status. regarding the associations between wp consumption and education level or migration background, an inverse relationship was observed for both genders in some analyses. as shown in table 2 , the association between lower educational level and the use of wp was more pronounced among girls, whereas the association between the migration background and the use of wp is found primarily among boys. the prevalence rates did not differ much from those obtained during 2009-2012. the prevalence rates found in the present study are highly congruent with data collected in 2015 by the bzga [43] . the two nationwide surveys yielded comparable prevalence rates for both current use (kiggs wave 2 (11-to 17-year-olds): 8.5% vs. drug affinity study (12-to 17-year-olds): 8.9%) and ever use (25.8% vs. 27.3%). the prevalence identified in the european school survey project on alcohol and other drugs (espad) in austria was strikingly higher: in 2019, 21% of 14-to 17-year-olds reported current and 51% reported ever wp use [44] . a possible reason for the difference may be the difference in age groups, as prevalence increases with age. this may also explain the comparatively high prevalence rates for young people (14-to 16-year-olds) living in the german state of bavaria (current wp use: 20.1%; ever use: 48.9%) who also participated in the espad study in 2015 [45] . comparing the prevalence rates reported in germany with those in the us (2009-2017), nationally representative estimates indicate lower prevalence figures (current use among high school students (grades 9 to 12): 4.8%, ever use: 14.3%); however, representative state-wide estimates showed comparable figures (current use: 11.6%; ever use: 22.5%) [34] . within the present study we aimed to explore the frequency of current wp consumption and self-assessed smoking status. most current wp users reported a wp use frequency of no more than twice in the past 30 days. this consumption pattern is also seen in previous studies [32, 46] . reasons for the difference in consumer behavior, for example, in comparison with (daily) cigarette consumption, could be owing to the inflexibility of the stationary tobacco use method and its time-consuming nature. most current wp users identified themselves as non-smokers. thus, wp consumption is not perceived as smoking, a result which has been also reported elsewhere [8] . the results of the kiggs study showed variation in wp use according to sex, age, migration background, and current smoking status. we found higher ors for current and ever use among respondents who were male, older, and who had a one-sided migration background (boys). these findings are in line with prior national and international studies [30, 33, 34, 47] . migration background is a known correlate of wp use described in previous kiggs waves and other studies. whereas in the first wave of the german health survey for children and adolescents (kiggs wave 1, 2009 wave 1, --2012 [48] , boys with a both-sided migration background were found to use wps more often (current and ever) than those without a migration background, we found counterintuitively low prevalence for wp use with a both-sided migration background but high prevalence with a one-sided migration background among boys in kiggs wave 2. hence, we speculate that the particular high amount of missing values among boys with a both-sided migration background might explain their low prevalence of wp use. the case of girls was reversed; we found an association of a both-sided migration background and lower ors for current and ever wp use. similar results have been described for smoking adults (over 18 years) in germany [49] . our findings also point out that young people who regard themselves as current smokers were up to 68 times more likely to use wp than non-smokers. associations regarding this kind of dual use have been reported in other studies [33, 47] . concerning the trend in prevalence figures, our study found stable figures over time. for 12to 17-year-old boys, the bzga reports similar trends in the figures for current wp use. first, these figures decreased from 2007 (16.3%) to 2011 (9.8%), but then remained at this level until 2015. for 12to 17-year-old girls, a similar trend can be seen over time. the prevalence figures for the current use of wp ranged from 7.4% (2011) to 6.4% (2015) [50] . the present study entails the following limitations. owing to the cross-sectional design, it was not possible to make conclusive statements about causality with respect to the results. responses given in kiggs wave 2 are self-reported data, which are always associated with biases. respondents may remember of the corresponding answer categories inaccurately (recall bias) or may give socially acceptable answers (social desirability bias). as there are different terminologies for wp, the use of pictures within the questionnaire would probably have been preferable to ensure that all respondents have the same understanding of the tobacco product. to be able to assess the health risks arising from the consumption of wp tobacco, the ingredients of wp tobacco play an integral part. unfortunately, the composition of wp tobacco or the number of puffs during a session could not be investigated in this study. over the course of the kiggs study, there has been a change in methods: kiggs wave 2 was conducted using self-report questionnaires and kiggs wave 1 using telephone interviews, which are more susceptible to socially desirable response behavior [51] . as with all surveys, the possibility of bias owing to selective non-participation also exists. it is assumed that people who participate in a health study also have greater health awareness and therefore differ from the general population in terms of smoking behavior (selection bias) systematic identification of patterns of missing items was not feasible, but could help to interpret results more accurately in further studies. the described selection effects were partially corrected by weighting. thus, the observed results may be generalizable to 11-to 17-year-olds in germany, which is a strength of the kiggs study. furthermore, it was possible to identify different wp consumption patterns (current, in the last 12 months, and ever), the frequency of wp consumption, and the combined consumption of tobacco cigarettes and wps, as well as the association of wp use with sociodemographic characteristics and cigarette smoking status. older age, male sex, migration background, lower educational level, as well as current cigarette smoking were found to be associated with wp use among german adolescents. wp consumption is popular among adolescents but does not seem to have increased substantially in recent years. continuous monitoring of trends in prevalence and use behavior is important to yield an evidence basis for developing targeted group-specific and gender-sensitive prevention approaches within public health prevention strategies. in addition to preventive programs within schools, it would be also useful to provide information about the health hazards and addiction of wp use in sports clubs or on preferred social networks (e.g., youtube, facebook, twitter) visited by young people. a targeted gender-specific approach could also be made here. the law for the protection of youth, which has been adapted since 2016 and prohibits the sale of wps by mail order to minors, is an important step to reduce the illegal sale to minors. a consistent and frequent age control in shisha bars should continue to be carried out by public authorities. information campaigns (also for parents) may help to decrease the private use of wps. the ban on marketing tobacco with characteristic flavors (e.g., menthol) implemented in germany by § 5 of the tobacco products act in 2020 is an important step to prevent young people from consuming flavored wp tobacco. a further ban on the advertising of tobacco products or combined warnings (consisting of pictures and text) are planned for wp tobacco in germany from may 2024, which will help to increase the awareness about health hazards connected to wp use. further research should explore why many adolescent wp users do not see themselves as smokers, that is, the beliefs and motives that underlie this. more research is needed on the consumption patterns (e.g., number of puffs, duration of a wp session) and on the type of wp use (e.g., types of wp tobacco, use of charcoal). moreover, the association between the consumption of wp and other substances, e.g., cigarettes, should be investigated more in detail. we thank analisa avila, els, of edanz group (https://en-author-services.edanzgroup.com/ac) for editing a draft of this manuscript. the authors declare no conflict of interest. advisory note: water-pipe tobacco smoking: health effects, research needs and recommended actions by regulators estimating the beginning of the waterpipe epidemic in syria the global epidemiology of waterpipe smoking tobacco smoking using a waterpipe: a re-emerging strain in a global epidemic waterpipes. facts about smoking tobacco-free waterpipes can also be a health hazard self-assessment of adolescents regarding water pipe consumption health effects of waterpipe tobacco use: getting the public health message just right adolescents' perceptions of health risks, social risks, and 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wave 2 has been completed socioeconomic status and subjective social status measurement in kiggs wave 2 trends in educational inequalities in smoking among adolescents in germany: evidence from four population-based studies health interview and examination survey for children and adolescents the drug affinity of young people in the federal republic of germany 2015. smoking, alcohol consumption and use of illegal drugs: current prevalence and trends survey of 9th and 10th grade students in bavaria expert panel on waterpipe assessment in epidemiological, studies. consensus statement on assessment of waterpipe smoking in epidemiological studies waterpipe tobacco smoking trends among middle and high school students in the united states from smoke on the water distribution and patterns of tobacco consumption in germany the decline in cigarette consumption by adolescents and young adults in germany and the increasing importance of hookahs, e-cigarettes and e-shishas empirische sozialforschung key: cord-345834-l2e5v39s authors: anacleto, m.a.; brito, f.a.; de queiroz, a.r.; passos, e.; santos, j.r.l. title: diffusive process under lifshitz scaling and pandemic scenarios date: 2020-08-20 journal: physica a doi: 10.1016/j.physa.2020.125092 sha: doc_id: 345834 cord_uid: l2e5v39s we here propose to model active and cumulative cases data from covid-19 by a continuous effective model based on a modified diffusion equation under lifshitz scaling with a dynamic diffusion coefficient. the proposed model is rich enough to capture different aspects of a complex virus diffusion as humanity has been recently facing. the model being continuous it is bound to be solved analytically and/or numerically. so, we investigate two possible models where the diffusion coefficient associated with possible types of contamination are captured by some specific profiles. the active cases curves here derived were able to successfully describe the pandemic behavior of germany and spain. moreover, we also predict some scenarios for the evolution of covid-19 in brazil. furthermore, we depicted the cumulative cases curves of covid-19, reproducing the spreading of the pandemic between the cities of são paulo and são josé dos campos, brazil. the scenarios also unveil how the lockdown measures can flatten the contamination curves. we can find the best profile of the diffusion coefficient that better fit the real data of pandemic. in december 2019, the world started to face a new type of severe pneumonia which appeared in wuhan, china. only two months later the international committee on taxonomy of viruses named the virus responsible for these pneumonia cases as severe acute respiratory syndrome coronavirus 2 or sars-cov-2, whose disease was popularly known as coronavirus disease 2019, or simply covid-19 [1] . such disease was classified as a public health emergency of international concern at the end of january 2020, by the world health organization. up to now, sars-cov-2 has spread all over the world, presenting more than 3.5 million of cases, taken approximately 247107 lives, and has a new epicenter in the united states of america which has reported almost one-third of the total amount of cases [2] . few places in the world were able to fully control the pandemic of covid-19. in europe, for instance, italy and spain were for a long time the world's two worst-hit countries by the covid-19. now, the numbers of active cases in these two countries are slowly decreasing and they are facing the final stage of the pandemic. one of the best countries in europe to adopt measures against covid-19 so far is germany, who is also entering in the controllable phase of the pandemic. behind the success of germany are measures of social distance or lockdown procedures, and a large number of people tested for sars-cov-2 [3] . after spreading in asia and europe, now covid-19 is a challenge for the usa, as well as for low and middle-income countries, such as brazil. there is a serious concern on the international scientific community about the behavior of sars-cov-2 in such countries, since they face other severe problems such as poverty, food security, economic growth, besides other diseases like human immunodeficiency virus, tuberculosis, and malaria [4] . so far, several scientific works and reports based on numerical simulations have been published, lighting the evolution of the pandemic in different countries and reflecting the actions as well as the strategies of each country to mitigate the effects of covid-19. some of these studies can be found in references [4] [5] [6] [7] [8] . among recent works on this subject, we also highlight an interesting proposal of an age-structured model presented by canabarro et al. [9] , a model based on hospital infrastructure developed by pacheco et al. [10] , and a study to predict covid-19 peaks around the world based on active cases curves, introduced by tsallis et al. [11] . in this work we intend to collaborate with the current investigations by proposing a model which can describe the evolution of the pandemic through the solutions of a modified version of the diffusion equation. the standard diffusion equation describes the macroscopic behavior due the effect of many micro-particle bodies, as it is observed in a brownian motion, for instance [12] . an interesting modification of this equation was proposed in the seminal paper of petr horava [13] , in his studies about quantum gravity, where he extended the definition of spectral dimension to theories on smooth spacetimes in anisotropic or lifshitz scaling. in our investigation, we introduce a new version of the diffusion equation inspired by horava's work, and we use it to fit real active cases data of covid-19 from germany, spain and brazil. the diffusion equation with the lifshitz scalling and the equation of motion for the diffusion coefficient are going to be introduced in section ii. in section iii we are going to show different solutions for the diffusion equation which can be used to fit the evolution of covid-19. the availability of our models are carefully discussed in section iv. the spreading of the pandemic between two different cities is modeled in section v. then, we present our final remarks and perspectives in section vi. the first issue to describe a pandemic evolution consists in choosing an appropriate diffusion process. the complexity of a virus transmission such as sars-cov-2, demands a diffusion process characterized by a probability density ρ = ρ(x, τ ; x , τ ; σ) measuring the diffusion from a time τ to a time τ , and from a space coordinate x to x at a diffusion time σ. notice that σ and τ are two different types of time, τ would be understood as the standard time variation of the pandemic, while σ would control the collective response to the pandemic, such as social distance measures, for instance. besides, as each country can adopt several strategies to mitigate the pandemic effects, it is expected that the diffusion process would account for different degrees of anisotropy. a general continuous diffusion equation that attends such criteria was introduced by horava in his seminal work [13] , whose form is here τ is the so-called euclidean time and z is the lifshitz critical exponent, which measures the anisotropic scaling of a given model [13, 14] . the lifshitz critical exponent is essential to determine the spectral dimension, which can be applied to several geometric objects presenting fractal behavior [13] . the relative sign (−1) z+1 concerns the requirement of ellipticity of the diffusion operator valid for integer z, but the results can be analytically continued for any positive real z [13, 14] . an extra relevant ingredient to proper modeling a pandemic spread is a diffusion coefficient, which can account for the transmission rate of the virus. therefore, this discussion suggests that a pandemic scenario is governed by the following anisotropic diffusion equation where φ(τ ) is a dynamic diffusion coefficient. we are going to show that a proper balance between φ and z yields to distributions that can fit real pandemic data. let us also constrain the diffusion coefficient φ(τ ) with the standard lagrangian where the negative kinetic part stands for the euclidean time. therefore, the equation of motion for the diffusion coefficient is such that by integrating the previous equation once, we find the first-order differential equation where we considered the function w is known as superpotential in analogy with the bosonic sector of a super symmetric field theory. the diffusion equation (2) has the general solution where ρ 0 stands for the initial probability density subject to the pandemic (or to the diffusion process). in this work, we consider ρ as the probability density of active cases of covid-19 to make a parallel between our model and real pandemic data. the number of active cases of covid-19 is defined as follows [3] active cases = total cases − total deaths − recovered , therefore, it represents the current number of patients detected and confirmed as infected with sars-cov-2. the number of active cases is also a relevant metric for public health and primary care functions, as it allows measuring capacity versus hospitalization needs. such a number is used to plot the distributions of active cases of covid-19 for different countries as we see in [3] , and it was used to predict the pandemic peaks in different countries as one can see in [11] . before starting to make numerical integrals of eq. (7) to depict the active cases curves, let us comment on the dimensionality of the model. a (spatial) bi-dimensional model seems most natural to discuss the diffusion process in the population. this usually is captured by the bi-dimensional networks with persons being nodes and relation being links [15] . moreover, one particular feature of the transmission of this virus is that it occurs by contact between persons [1] . this feature is captured by a nearest-neighbor interaction between the nodes. it can be argued that one can project down this nearest-neighbor interaction bi-dimensional network into a long-range interaction chain (one-dimensional chain) with appropriate boundary conditions. thus in the passing to the continuum model we can in a reasonable approximation consider a d = 1 model with x ranging from −∞ to +∞. for the numerical integration in the reciprocal space, we can take therefore −∞ ≤ ω ≤ ∞, and −∞ ≤ k ≤ ∞. moreover, we choose evaluate ρ at x = x indicating that the probability density is measured in the same spatial location after the evolution of the diffusion process. the simplest model that we can analyze consist in where the diffusion coefficient is normalized. this first model will enable us to observe the influence of the critical exponent and of the diffusion time in our curves. the fig. 1 shows four different behaviors for the solution of the diffusion equation. the diffusion time and the critical exponent z are competing parameters. particularly in the top left curve, with a same diffusion time large values of z ≥ 1 makes the gaussian flattened, whereas bottom right for z < 1 the gaussian tends to blow up even for sufficiently large diffusion time. the best scenario in the sense of flattening the gaussian curve seems to be the increasing of both diffusion time and critical exponent z (top right). the features of σ presented in the previous scenarios yield us to indeed understand the diffusion time as equivalent to a lockdown period. in this work we adopted the lockdown definition introduced by flaxman et al. [5] , which means a scenario where regulations and laws regard strict social interaction. these regulations/laws include the banning of any non-essential public gatherings, closure of educational, public and cultural institutions, and ordering people to stay at home apart from exercise or essential tasks. in this example we are going to consider the following superpotential where λ and α are real constants. such superpotential leads us to which is known as λ φ 6 potential, and it is depicted in the left panel of fig. 2 . the minima or vacua values of v correspond to φ v = 0, and φ v = ± √ 2 α. the region between these different minima is called a topological sector, and it mediates the transmission rate in our pandemic model. this potential was applied in subjects like higher-order phase transitions in ginzburg-landau theory [16, 17] , modeling domain walls in ferroelastic transitions [18] , and in new physics beyond the standard model of particles at high energies scales [19, 20] . the previous definition of w yields to the first-order differential equation whose analytic solutions are exhibiting anti-kink and kink-like profiles as one can see in figure 2 . once φ(τ ) can be interpreted as the transmission rate of the virus, in fig. 2 , we observe that for τ τ 1 the virus is not transmitted, however its transmission increases until an approximately constant rate (φ v = √ 2 α) as τ gets bigger than τ 1 . the applicability of such a model is going to be carefully discussed later, in section iv. as a next example, let us deal with a more complex model for the diffusion coefficient. such a model is derived from this potential is known as double sine-gordon model and it is applied to study ultra short optical pulses in he 3 [21, 22] , in decaying of false vacuum and phase transitions in field theory [22, 23] . the left panel of fig. 3 shows part of the periodic form of potential v (14). there we can see one topological sector between vacua φ v = ± n π/(2 κ). an interesting feature about this model is that the parameter β can deform this potential at φ = 2 π n/κ. such deformation is responsible for the double (anti)kink profiles observed in the right panel of fig. 3 , and it is also related to the variation of the transmission rate of our pandemic model. the previous potential yields to the first-order differential equation which is satisfied by the analytic solutions for s = ±1, and n = 0, ±1, ±2, ... . the behavior of these analytic solutions v can be appreciated in fig. there it is shown that φ(τ ) has three different regimes of transmission rate, the first one for τ τ 1 where φ v = (2 n − 1) π/(2 κ), the second regime occurs when τ ≈ τ 1 and φ ≈ π n/κ, and the third one appears for τ τ 1 and φ v = (2 n+1) π/(2 κ). these regimes can lead us to distributions with different waves of contagious, as we are going to show below. in the next section we are going to analyze the viability of model iii and compare the numerical curves of ρ derived from it with those obtained through model ii. as it is known, the active cases data can present a high level of uncertainty once it depends on the number of the tests performed by each country and also the countries' transparency in reporting the tests. the data set used to depict the graphics of this section were taken up to may 02, 2020. therefore, some discrepancies between our predictions and the pandemic evolution are expected. to depict active cases curves that could j o u r n a l p r e -p r o o f journal pre-proof reproduce the existent data and able to predict the behavior of the pandemic, we decided first to test our model against a now well-established data set, and for that, we choose data from germany. nowadays germany is the 6th leading country in the world in numbers of covid-19 cases, accumulating a total of 164967 cases up to may 02 [24] . moreover, germany is the third leading country in the total number of tests, reporting a total amount of 2547052 tests for sars-cov-2, which corresponds to 30400 tests per million of population (considering the data up to may 02) [24] . therefore, to constraint some free parameters in our model, we use the data from germany as guidance. despite this procedure, we still have other free parameters to represent the particular features of each country's strategy to deal with the pandemic. we present the features of our models against real active cases data from germany, brazil, and spain below. in this first scenario we shown in figs. 4, and 5, the active cases curves for germany integrated from model ii and iii, respectively. there, the black solid curves are the numerical solutions generated from eq. (7), which best fitted the real data depicted in blue dots. the parameters constrained in the fitting process were ρ 0 = 10 7 (for fig 4) , ρ 0 = 10 5 (for fig. 5) , and time scaling t = 2 τ representing the number of days of pandemic. moreover, we also used σ = 28 (for figs. 4, and 5), referring to the number of lockdown days in germany [25] . we also depicted the active cases data from germany (blue dots), since february 15, 2020 (day 1), until may 02, 2020 (day 78) [24] . the left panels of figs. 4, and 5 predict that the pandemic of covid-19 would be fully controlled in germany after day 102 of infection (or after may 26, 2020), when the number of active cases is less than 1000 people. besides, the active cases curves unveil that the kink and the double anti-kink solutions, eqs. (13) , and (16) deform the standard gaussian curve. by comparing the right panels of figs. 4, and 5, we realize that the double anti-kink solution yields us to a better fitting of real data, reproducing a change in the decreasing of the number of active cases at t ≈ 60 day. the graphics of figs. 6, and 7 shown the currently infected people by sars-cov-2 in spain. at the present moment, spain reported an amount of 245567 cases of covid-19, which makes it the second leading country in the world pandemic rank [26] . the active cases data for spain are depicted as blue dots in figs. 6, and 7, and to plot our numerical curves we considered σ = 43 lockdown days [25] . we can observe that the black solid curves are in good agreement with the pandemic data, and they predict that the active cases of covid-19 would be fully controlled in spain after day 120 (june 11, 2020), where the number of infected people is less than 1000. moreover, in this scenario the kink and the double anti-kink like solutions eqs. (13) , and (16), strongly deform the standard gaussian curve. as in the case of germany, the double anti-kink curve leads us to a better fitting of real data, reproducing a second wave of contagious after day 50. the pandemic of covid-19 starts in brazil eleven days after spreads in europe. despite this few difference in time, the evolution of the contamination in brazil was deeply different from germany and spain, as we can see in the graphics of figs. 8, and 9. the numerical solutions presented in figs. 8, and 9 were depicted using the same values for ρ 0 and t from germany curves and the same value for z from spain curves. moreover, we derived two possible scenarios of lockdown measures, the black solid curves show a model with σ = 30 lockdown days while the red solid curves were depicted with σ = 90 lockdown days. furthermore, we also included the active cases data from brazil as blue dots [27] . the real data from brazil reveal an abrupt change of contamination which started on day 48 (april 13, 2020) and developed to a new increasing rate after day 56 (april 26, 2020). along this period, besides the pandemic, brazil has been facing a political crisis, which would explain the behavior of the covid-19 infection here observed. another problem with brazil's data is its high degree of uncertainty. up to may 02, 2020, brazil reported a total of 97100 cases of covid-19, figuring at the 9th leading country in the world pandemic rank [3] . however, brazil has performed only 339552 tests of covid-19, representing a total of 1597 per million of people [3] . for these reasons, it is challenging to make any prediction about the evolution of the pandemic in brazil. although, our curves seem to be in good agreement with the active cases data so far, and we also can realize that a long time social distance flatten the curves of the active cases. the peaks of the two active cases curves from figs. 8, and 9 have considerable differences about 115000, and 141000 cases, respectively. moreover, the peaks are predicted to happen on days 92 (may 27, 2020), and 86 (may 21, 2020) for black and red solid curves from fig. 8 , and on days 95 (may 30, 2020), and 110 (june 04, 2020) for black and red curves from fig. 9 . it is relevant to mention, that up to may 02, 2020, brazil can attend in maximum 32703 patients with needs for icu [28] .the solutions from fig. 8 predict that the pandemic in brazil would not be fully controlled earlier than day 131 (june 22, 2020). in the longer predicted scenario, observed in the red solid curve of fig. 9 , the pandemic would be fully controlled after day 198 (august 28, 2020), when the number of active cases is less than 1000. we also realize that the double anti-kink like solutions are able to fit better the real data than the single kink-like ones, reproducing the increasing in the number of active cases after day 48. . the peaks of black and red curves are approximately 268000 and 153000 cases, respectively. we also depicted the active cases data from brazil (blue dots), since february 26 (day 1), 2020 until may 02, 2020 (day 67) [27] . as it is known the primary mechanism used by covid-19 to spread is through person-to-person contact. consequently, big cities favor the spreading of the virus to small centers, once they facilitate the mixing of people from different areas. moreover, their strategical positions close to airports and crossed by state roads, make such cities susceptible to rapidly spread the virus to innermost regions. this phenomenon of advancing of covid-19 into the countryside happened in several places in the world, such as around new york city and close to several metropolises from brazil. it was also modeled in several regions of brazil using a markov chain approach as one can see in the work of costa et al. [29] . in this section, we adapted our diffusion equation to describe the dissemination of the virus around different cities. in order to reproduce such a scenario, we rewrite our diffusion equation as (17) where n is the number of the cities, and j i (σ) are free sources of the diffusion process. the previous equations present the following general analytic solutions and the free sources should obey the conservation constraint the simplest definition for the sources is to work with j i (σ) = constant. in this application we are going to understand such sources as proportional to the basic reproductive rate at the beginning of the pandemic, commonly known as r 0 [30] . the basic reproductive rate is a non-dimensional quantity which measures the secondary cases of contamination produced by one case introduced in susceptible populations [31] . such a rate is a key ingredient in several mathematical models to describe pandemic scenarios, and any attempt to estimate its value is a real challenge. consequently, by working with an equivalence between j i and r 0 , our model suggests that the basic reproductive rate is changed between different cities as the pandemic evolves in a given region. to exemplify our methodology, let us consider two cities from brazil which experienced the phenomenon of the spreading of sars-cov-2 to innermost regions. the cities here considered are são paulo, and são josé dos campos. these two cities have about 12 million and 721 thousand of inhabitants, respectively, and they are approximately 100 km distant apart. they are experiencing the so-called yellow-phase of the reopening plan designed by the state of são paulo government, where people have access to public places such as parks, restaurants, and cultural events with limited capacity [32] . the pandemic started in são paulo at february 25 (day 1), and up to august 02, 2020 it accumulated more than 200000 cases with more than 9600 fatalities [33] . the first case of covid-19 in são josé dos campos was reported in march 18, 2020 and the city has been registered more than 17000 cases, besides 204 deaths up to august 02, 2020 [33] . moreover, the most recent basic reproductive rate estimated for the state of são paulo in the beginning of the pandemic is r 0 = 9.24 [34] . in such an j o u r n a l p r e -p r o o f application, the best model to fit the cumulative cases data from the two cities was model ii, therefore, the asymptotic behavior of ρ in eq. (18) is going to be proportional to the product j i φ v , corresponding to a kink like profile for the density distribution. so, in the following application, we choose to test our model against the cumulative cases data. then, let us consider n = 2 as the number of the cities, and whereρ 0 is a proportionality constant and r 0 is the basic reproductive rate. taking the previous ingredients into eq. (18) yield us to depict the graphics presented in fig. 10 . there, we consider labels i = 1, and i = 2 to describe são paulo and são josé dos campos, respectively, and we worked with σ = 6 lockdown days, corresponding to the anticipation of holidays in the city of são paulo [35] . such anticipation of holidays was planned to increase the social distancing, attempting to reduce the spreading of covid-19. we can observe that our model successfully reproduces the evolution of the pandemic in theses two cities if we consider z = 50, which is the same value used to fit spain and brazil's active cases curves in the previous section. moreover, the fact that j 2 = −r 0 means that the basic reproduction rate was passing from são paulo to são josé dos campos between february 25 and march 18, as the pandemic spreading evolves. x = x , ρ 0 = 10 2 , α = 2.90 × 10 3 , s = 1, λ = 0.72 × 10 −1 , z = 50, τ = 50, τ 1 = 69, j 1 = 9.24,ρ 0 = 1, and σ = 6 (black solid curve). we also depicted the cumulative cases data from the city of são paulo (blue dots), since february 25 (day 1), 2020 until august 02, 2020 (day 160) [33] . in the right panel we present the cumulative cases solutions for model ii with t = 2τ (time in days), d = 1, x = x , ρ 0 = 10, α = −117.38, s = 1, λ = 0.82 × 10 −1 , z = 50, τ = 85, τ 1 = 77.5, j 2 = −9.24,ρ 0 = 1, and σ = 6 (red solid curve). besides, we depicted the cumulative cases data from the city of são josé dos campos (blue dots), since march 18 (day 1), 2020 until august 02, 2020 (day 137) [33] . in this work we introduced a modified version of the diffusion equation, mediated by a lifshitz scaling together with the diffusion coefficient φ(τ ). the diffusion time σ is analogous to the so-called fictitious time in stochastic quantization theories [36] . we were able to find an analytic solution for this diffusion equation, and to use the standard gaussian curves to interpret σ as the lockdown time, if such an equation is applied to model pandemic cases. therefore, we investigate two possible models with φ(τ ) having (anti)kink, and double (anti)kink-like profiles. these models were used to fit real active cases data of covid-19 from three different countries (germany, spain, and brazil). we successfully depicted the active cases curves for germany and spain up to may 02, 2020, and use them to constraint some of our free parameters to generate curves for brazil. then, we predicted four scenarios for the advance of the pandemic in brazil, based on 30 and 90 lockdown days. these scenarios alerted for a potential escalation of the pandemic in brazil if no lockdown measure is taken. moreover, the solution which best fitted the active cases data up to may 02, 2020, is the red curve from fig. 9 , where it was considered 90 lockdown days. such a solution predicted that the pandemic would be fully controlled after day 198 (august 28, 2020). from the previous analyses we are able to observe how crucial the lockdown measures are to flatten the active cases curves and to control the pandemic spread, corroborating with the remarks from [9] . we also applied our model in a new phase of the pandemic, where the virus is moving towards innermost regions of the countries. in this application we considered several diffusion processes interacting through free sources. each one of these diffusion processes corresponds to the spreading of sars-cov-2 in a given city. as a simplest case to model, we worked with constant sources and understood them as proportional to the so-called basic reproductive rate at the beginning of the pandemic (r 0 ). in order to exemplify our model we built the cumulative cases curves of two cities from brazil -são paulo and são josé dos campos, and compare them with real data. our results unveil that this pandemic model can be successfully applied in the context of coupled spreading of covid-19. it is relevant to point that the lifshitz scaling exponent was essential to depict the numerical curves here studied. moreover, we also verified that the double (anti)kink-like profiles were able to fit better the real active cases data than the single (anti)kink-like solutions. consequently, we can conjecture that multiple anti(kink)-like models, like those introduced in [37] , would improve the level of precision of our active cases curves, and would enable us to model multiple pandemic phases. another interesting perspective consists in investigate solutions for the diffusion equation derived from models with multiple lump like solutions, such as those presented in [38] . moreover, the methodology here adopted can be applied to other pandemics, as well as to other covid-19 data set like new daily cases, for instance. covid-19 dashboard the potential impact of the covid-19 epidemic on hiv, tb and malaria in low-and middle-income countries report 13 -estimating the number of infections and the impact of non-pharmaceutical interventions on covid-19 in 11 european countries contacts in context: large-scale setting-specific social mixing matrices from the bbc pandemic project expected impact of covid-19 outbreak in a major metropolitan area in brazil data-driven study of the covid-19 pandemic via age-structured modelling and prediction of the health system failure in brazil amid diverse intervention strategies coronavirus disease 2019 (covid-19) dynamics considering the influence of hospital infrastructure double sine gordon model, in solitons, topics in current physics germany: active coronavirus cases what are the lockdown measures across europe? spain: active coronavirus cases brazil: active coronavirus cases ministério da saúde covid-19 info metapopulation modeling of covid-19 advancing into the countryside: an analysis of mitigation strategies for brazil evaluating reduction in covid-19 cases by isolation and protective measures in são paulo state, brazil, and scenarios of release stochastic quatization we inform the credit statements about the preparation of this manuscript bellow • m.a. anacleto conceptualization, writing -review & editing, and brito conceptualization, investigation, writing -original draft, writing -review & editing, resources, supervision, and project administration de queiroz conceptualization, investigation, writing -original draft, writing -review & editing, and project administration passos conceptualization, writing -review & editing, and project administration we would like to thank cnpq, capes and pronex/cnpq & paraiba state research foundation (grants no. 165/2018 and 0015/2019), for partial financial support. maa, fab, ep and jrls acknowledge support from cnpq (grant nos. 306962/2018-7, 312104/2018-9, 304852/2017-1 and 420479/2018-0, respectively). the authors also would like to thank the anonymous referees for thoughtful comments which undoubtedly raised the quality of this work. key: cord-257940-12nf27j4 authors: schwendicke, falk; krasowski, aleksander; gomez rossi, jesus; paris, sebastian; kuhlmey, adelheid; meyer-lückel, hendrik; krois, joachim title: dental service utilization in the very old: an insurance database analysis from northeast germany date: 2020-09-30 journal: clin oral investig doi: 10.1007/s00784-020-03591-z sha: doc_id: 257940 cord_uid: 12nf27j4 objectives: we assessed dental service utilization in very old germans. methods: a comprehensive sample of 404,610 very old (≥ 75 years), insured at a large statutory insurer (allgemeine ortskrankenkasse nordost, active in the federal states berlin, brandenburg, mecklenburg-western pomerania), was followed over 6 years (2012–2017). our outcome was the utilization of dental services, in total (any utilization) and in five subgroups: (1) examinations and associated assessment or advice, (2) restorations, (3) surgery, (4) prevention, (5) outreach care. association of utilization with (1) sex, (2) age, (3) region, (4) social hardship status, (5) icd-10 diagnoses, and (6) german modified diagnosis-related groups (gm-drgs) was explored. results: the mean (sd) age of the sample was 81.9 (5.4) years. the utilization of any dental service was 73%; utilization was highest for examinations (68%), followed by prevention (44%), surgery (33%), restorations (32%), and outreach care (13%). utilization decreased with age for nearly all services except outreach care. service utilization was significantly higher in berlin and most cities compared with rural municipalities, and in individuals with common, less severe, and short-term conditions compared with life-threatening and long-term conditions. in multi-variable analysis, social hardship status (or: 1.14; 95% ci: 1.12-1.16), federal state (brandenburg 0.85; 0.84–0.87; mecklenburg-western pomerania: 0.80; 0.78–0.82), and age significantly affected utilization (0.95; 0.95–0.95/year), together with a range of co-morbidities according to icd-10 and drg. conclusions: social, demographic, regional, and general health aspects were associated with the utilization of dental services in very old germans. policies to maintain access to services up to high age are needed. clinical significance: the utilization of dental services in the very old in northeast germany showed significant disparities within populations. policies to allow service utilization for sick, economically disadvantaged, rural and very old populations are required. these may include incentives for outreach servicing, treatment-fee increases for specific populations, or referral schemes between general medical practitioners and dentists. electronic supplementary material: the online version of this article (10.1007/s00784-020-03591-z) contains supplementary material, which is available to authorized users. for decades, interventions to improve dental health have been focused on children and adolescents, with widely acknowledged success in many high-income countries. while adults and older individuals also benefitted from a general improvement in oral health, showing a reduced number of restored or missing teeth [1, 2] , data on the resulting treatment needs in these populations are scarce. especially for the very old, defined as those aged 75 years or older, there is very limited knowledge on their needs for and utilization of dental service. this group of very old, notably, is the only growing one in many high-income countries, with remarkably complex oral health dynamics: retaining an increasing number of teeth up to such high age, this group is, oftentimes suddenly, affected by general health deterioration, impacting on the capability for oral self-care as well as the physical abilities to utilize in-office dental care [3] [4] [5] [6] . in a previous study and building on claims data, we found a disparate utilization of prosthetic services in the very old, with those aged 85 years or older, those living rural, and those with severe general health conditions utilizing prosthetic services, by large, to a lower degree than younger, urban living and only limitedly sick seniors [7] . the only service the former group used more often was maintenance of existing prosthetics. notably, claims data come with a range of possible limitations, e.g., selection bias, confounding bias, or misclassification bias. however, employing claims data allows to investigate groups which are otherwise hard to represent, e.g., the very old, the sick, and the rural living ones. claims data also come with robust sample sizes and represent everyday care. they also suffer from limited risks of recollection or reporting bias and have a high generalizability for their respective healthcare setting [8, 9] . in the present study, we used claims data from a large health insurance in northeast germany to assess dental service utilization in the very old. we hypothesized that utilization differed according to age, general health, socioeconomic status, and place of living. for reasons of comparability, the design and conduct of this study largely aligns with that of a previous publication on prosthetic treatment patterns in the same population [7] . the investigated cohort was evaluated based on routinely collected claims data from a statutory (public) health insurance in germany. individuals aged 75 years or older from one large insurer, the aok nordost, were followed over 6 years (2012 to 2017). the aok nordost is a regional branch of the allgemeine ortskrankenkasse (aok), acting mainly in the northeast of germany in the federal states of berlin, brandenburg, and mecklenburg-western pomerania. our reporting follows the record statement [10] . the aok nordost insures around 1.8 million individuals from the described three federal states. insured individuals may, however, also move into other areas of germany, which is why for our geographic analyses only individuals living in these federal states between 2012 and 2017 were included. the area of interest encompasses the german capital, berlin, and two rural states, brandenburg and mecklenburg-western pomerania, with only few larger cities (> 70,000 inhabitants). all three states are considered economically weak in comparison with other parts of germany. data for this study were claims data, including claims from 1 january 2012 to 31 december 2017. data were routinely collected and provided under ethical approval in a pseudonymized form using a data protection cleared platform via the scientific institute of the aok nordost, the gewino. a comprehensive sample of very old, aged 75 years or above, insured with the aok nordost in 2012, was drawn and followed over 6 years. no further eligibility criteria were defined. variable ascertainment was only possible via insurance base data and claims data. the database had been curated for plausibility at gewino and once more by the study team. no formal sample size estimation was performed given this being a comprehensive sample. our outcome was the relative utilization (in % of the population) of dental services. within the statutory german insurance, dental services are provided on a fee-per-item basis using fee items catalogs of the statutory or private german insurance [11, 12] . the vast majority (88%) of patients are statutorily insured. for the statutory insurance, all items are drawn from the fee item catalog bewertungsmaßstab (bema), which contains a large range of granular items comprising (1) examinations, assessment and advice, radiographic evaluations etc. (examinations); (2) restorative dentistry (restorations), note that within german insurance coding, crowns are not subsumed under "restorations" and hence there is no overlap between this service group and our previous analysis on prosthetic dentistry; (3) oral surgery and medicine (surgery); (4) prevention (for adults, the only preventive measure available until 2015 was removal of calculus; in 2015, further fee items (focusing on oral hygiene measurement, and oral hygiene plan, denture cleaning, and fluoride application) were introduced but these were not available for the present analysis); and (5) outreach care. further items include, for example, periodontal treatment, prosthetic therapies, and adjunct measures. we here report on any utilization in bema (min 1 item claimed/year) as well as stratified along the item blocks 1-5. as this is the first detailed analysis on dental service utilization in the very old in northeast germany, we provide largely descriptive analyses. the utilization of dental services was assessed according to following independent variables: (1) sex (male/female); (2) age (in years) in each year of follow-up; (3) region, we used municipalities as regional units, mainly as on a lower (more granular) spatial level only few individuals were retained in some areas. municipalities included the capital berlin (with over 3.5 million inhabitants), medium-sized cities (70,000-200,000 inhabitants), and rural areas. further analyses were performed on federal state level; (4) social hardship status (income < 1246 euro/month per capita in 2019); (5) icd-10 diagnoses, derived from outpatient diagnostic data; (6) inpatient hospital diagnoses and treatments, derived from german modified diagnosis-related groups (gm-drgs). the gm-drgs classify diseases in groups of similar pathogenesis, characteristics, and treatment complexity, and are mainly used for reimbursement reasons. only the 25 most frequently recorded icd-10 and gm-drg codes were used. the data used for this study were provided by the gewino using a data protection approved storage and analysis platform after cleaning and consistency controls. data were pseudonymized and included individuals' age, sex, social hardship status, spatial code of their place of living (allowing classification into municipalities), all bema items claimed per year as well as icd-10 codes and gm-drgs for each year, among further variables. comparability of data between different years and data consistency was given. a comprehensive sample had been used, and neither participants nor providers were aware that the collected claims data will be used for routine data analyses later on. the data collection is not prone to selection and detection bias. however, given this being claims data from only one insurance, the overall population of very old germans differs and data may be affected by biases associated with claims data, as laid out above and in the discussion. no further measures against these biases could be taken. the statistical analysis was performed on a sample (n = 404,610) of the database provided by aok nordost. the only inclusion criterion was that an individual had to be insured in the year 2012 and had to be aged 75 years or above at this point. for the descriptive analysis of utilization of dental services, we considered an individual to have consumed a particular service if at least once during the period 2012 to 2017 the provision of such a service was claimed. descriptive statistics of age groups were computed based on the age distribution in 2012. an individual was assigned to having a social hardship if the individual was assigned to this status at least once during the period 2012 to 2017. for geographical analysis, we excluded all individuals that relocated from one of the federal states (berlin, brandenburg, and mecklenburg-western pomerania) to another federal state, thereby decreasing the sample size to 390,044. however, we did not correct for relocations within the three federal states during the observational period. for each particular outpatient diagnosis (icd-10 codes) and inpatient hospital diagnosis and treatment (gm-drgs), we summed up all claims and ranked them from most to least frequent. we then selected the 25 most frequent diagnoses each (in total 50) and computed for each of them the number of individuals that were assigned to having a diagnosis, respectively, treatment, during 2012 to 2017. we applied logistic regression, a method to model a binary outcome variable as a linear combination of predictor variables. the response variable was the utilization of any type of dental services claimed by an individual at least once in the year 2012. as predictor variables we included age, sex, being deceased, social hardship status, federal state (note that we allowed the category "other" for relocated individuals), and the described outpatient and inpatient hospital diagnosis variables, all of them referring to the year 2012. all analyses, modeling, and visualization were performed using python (version 3.7, available at http://www.python.org) and auxiliary modules from its scientific computing ecosystem. overall, 404,610 very old (75 years or older) individuals were followed over a period of up to 6 years (173,733 of these did not survive follow-up). the mean (sd, median, min, max) age of the sample was 81.9 (5.4, 81, 75, 109) years. the population comprised significantly more females than males and those aged 75-84 years old than those aged 85 years or older. about one-third lived in berlin, and the other two-thirds in the more rural brandenburg and mecklenburg-western pomerania. social hardship status was claimed by nearly half of the population at least once during the follow-up period (table 1 ). our sample was overall more female and much older and claimed far more hardship status than the national average. the utilization of any dental service was 73%; utilization was highest for examinations (68%), followed by prevention (44%), surgery (33%), and restorative (32%) and outreach care (13%). utilization decreased with age for nearly all services except outreach care (fig. 1) . utilization of restorations, surgery, and prevention decreased by 75-80% (in relative terms, e.g., from 36% to 6% for restorations) between age 75 and 95 years; the decrease after age 95 years was limited. a slightly less pronounced, but nevertheless consistent, decrease was found for examinations. in contrast, outreach care increased and was, at age 95 years or above, the main service (together with examinations, which one would assume is the minimum consequence of outreach care). utilization was further different between regions ( table 1 , fig. 2 ). utilization of any dental service was generally higher in cities than rural areas, and highest in berlin and three other urban municipalities (rostock, potsdam, schwerin). utilization further differed geographically according to specific services. utilization of restorations was nearly 50% increased in certain cities and one rural southwestern municipality compared with most other rural areas. surgical services were provided more often in berlin and the south as well as cities in general; a similar pattern was observed for preventive services. for outreach care, no such strict pattern was observed; certain cities as well as a stretch of municipalities along the coastline showed higher utilization. utilization of any dental service was assessed according to icd-10 codes (table 2) . utilization was higher for the majority of codes, e.g., for eye conditions (e.g., presbyopia, cataract, astigmatism), gonarthrosis, cox-arthrosis, benign hypertension, anti-coagulants therapy, varicose, prostate hyperplasia, osteoporosis, hyperlipidemia and hypercholesterinemia and unspecified chronic pain. a similar pattern was found for most specific services. notably, individuals with dementia showed a similar utilization with regard to any services, but mainly received examinations, not restorative or surgical care. the same was found for patients with urinary incontinence. for outreach care, an opposite pattern was observed, with higher utilization by those with dementia and incontinence, and lower utilization by those with eye conditions, for example ( table 2) . we further assessed the utilization of any dental service stratified according to different gm-drgs (table 3) . utilization of any service was higher in participants hospitalized for non-severe gastrointestinal ulcerations, non-severe arrhythmia, bronchitis, non-severe hypertension, syncope, non-severe renal insufficiency, and non-complicated cardial diagnostics or eye operations. utilization was lower in patients with severe gastrointestinal ulcerations as well as severe heart insufficiency. these trends of higher or lower utilization were similar for other services, except outreach care, where a different pattern emerged: utilization was higher in patients with non-severe but also severe ulcerations, paraplegia/tetraplegia, non-severe hypertension, infections, head or skin injuries, joint operations, apoplexy, and geriatric rehabilitation. it was lower in patients with bronchitis (table 3) . in multi-variable analysis, social hardship status (or: 1.14; 95% ci: 1.12-1.16), federal state (brandenburg 0.85; 0.84-0.87; mecklenburg-western pomerania: 0.80; 0.78-0.82) and age significantly affected utilization (0.95; 0.95-0.95/year), together with a range of co-morbidities according to icd-10 and gm-dgrs (table 4, table s1 ). pseudo-r 2 indicated that the model generally had limited explanatory power (r 2 = 0.15). understanding dental service utilization in specific populations and groups may allow to increase access to the right services for every individual, thereby improving health and services' efficiency and equitability [13] . the present study tried to evaluate how factors driving services' needs (age, sex, general health) and access on patient level (income and financial means, place of living) and system level (physical and organizational) impact on utilization [14, 15] . we hypothesized that the utilization of dental services in the very old was associated with an individual's age, general health status, place of living, and social status. moreover, we assumed to find service-specific disparities. we confirm these hypotheses; social, demographic, regional, and general health aspects were associated with the utilization of dental services in very old germans. a number of aspects should be discussed. first, utilization in this specific group was comparably high; in general, dental service utilization in germany is higher than that in most other countries, likely due to the setup of the service provision, with most services being available at no costs at all to the patient [16]. moreover, regular consumption of dental services is incentivized using a bonus scheme, with patients getting a discount on their out-of-pocket expenses for prosthetic services in case they can demonstrate a history of regular yearly checkups. such incentive will be especially efficacious in old individuals, who either have or expect to have prosthetic services with higher likelihood than younger ones. we also found only minimal changes in the age-specific utilization over the 6-year period; that is, seniors of similar age did not show considerably increased utilizations in 2012 compared with 2017, for example. the only detectable increase occurred between 2012 and 2013, most likely associated with a general policy shift in dental healthcare in germany (an entry fee existing until 2012, with patients paying 10 euro to the practice-which passed it on to the insurer-whenever entering the practice for the first time in a quarter of a year had been abolished in 2013). these findings of rather constant utilization over the first half of the last decade as well as the increase in utilization of dental services from 2012 and 2013 are in line with previous research [17, 18] . our findings are in so far relevant, as a number of major policy shifts targeting the very old requiring care assistance have been introduced between 2013 and 2015, the effects of which our analysis did not capture (so far). this might be as we only included individuals aged 75 years or older in 2012 and followed them for 6 years (i.e., those entering this group later on were not included), but also as we did not focus on those requiring care assistance, i.e., probably "diluted" their relevance in our analysis. it would be relevant to re-assess this cohort, expanding it to individuals aged 75 years or older in 2018 and focusing on only those receiving care assistance. we find a drastic and only limitedly service-specific decrease in utilization with age; individuals aged 85 years, for example, consumed only a fraction of services compared with those age 75 years. notably, from age 95 years onwards utilization was fairly stable, indicating a possible "survivor" effect. the only exception from these observations was outreach care, as discussed below. age is associated with an increasing prevalence of chronic and severe diseases or hospitalization [19] . in line with our previous analysis on prosthetic services, such severe general health conditions (e.g., severe gastrointestinal ulcerations as well as severe heart insufficiency) were found to significantly decrease utilization. notably, for most other (especially icd-10 coded) conditions, the overall utilization was unaffected. this might be as icd-10 codes were derived from ambulatory assessments, where individuals need to attend their general practitioners and hence show some kind of mobility and self-capability. moreover, individuals with dementia (and incontinency) showed reduced utilization of therapeutic services (but not examinations). this might be as these individuals do not accept more intense (and time consuming) care for treatment. we further assessed the impact of social hardship status on utilization. such status is a proxy for low income. it has been found associated with increased utilization of prosthetic services, as individuals with this status usually pay very low or no additional fee at all for any prosthetic service; that is, financial utilization barriers for this type of dental treatment are very low or absent [7] . for the present analysis, hardship status was used only as a social marker, as the analyzed dental services (examination, restorations, surgery, prevention, outreach care) are coming at no costs for all statutorily insured individuals, regardless of their age. [29] this is a remarkable difference of the german compared with many other healthcare systems, where retirement oftentimes means loss of professionally supported health insurance [20] [21] [22] and a subsequent collapse of service utilization [23] . it is noteworthy that utilization for those with hardship status was found significantly increased in multivariable analysis (in bivariate analyses this was less clear, indicating possible confounding by age, place of living, or health status, for example). as those with low social status are also likely to show the poorest oral and general health [24], it is highly relevant to find them to consume services more often, too. it is beyond this study to elucidate the reasons underlying this utilization. notably, though, existing public policies to support healthcare utilization in vulnerable groups in germany, e.g., those with chronic diseases [25] , do not capture those with economic constraints and poor oral health, i.e. cannot be at the heart of this association. independently of the found increased utilization, policy makers may want to revisit such policies and to strengthen dental service utilization for the very old, the very sick, and the very poor. we also found an association between utilization and place of living [13] . such association has been assumed to be grounded in rural areas being underserviced due to workforce shortages while urban areas suffer from provider clustering and associated supply-side-induced demand [26, 27] . we confirm such ruralurban disparities for any service utilization in the very old. the two rural federal states in our study, brandenburg and mecklenburg-western pomerania, show much lower dentist densities than berlin [28] , possibly explaining our findings. notably, utilization in the whole population (not only the very old) has been found to follow the opposite pattern, with higher utilization in the two rural states than in berlin [17] . hence, the observed inequalities seem to be moderated by age: older individuals seem to seek care more often, but are not able to physically access it in rural areas, while younger individuals could access it more easily in urban areas, but are not seeking care. we want to highlight that our analyses on smaller spatial level (municipalities) showed a more nuanced picture, with some rural areas showing high utilization of specific (but not all) services. we are so far unable to entangle possible reasons underlying this observation, which may be grounded in local dentist densities (some municipalities show surprisingly high densities) or a locally increased proportion of dentists with specific contractual agreements with care homes (thereby increasing access to care for the very old). more in-depth analyses seem warranted to first confirm and then explain such peculiar patterns, as they may allow to identify local best practices which could be translated to regional or national level. we identified service-specific utilization patterns not only across regions, as described, but also age. our findings of a generally decreasing utilization between age 75 years and 95 years have been identified before, with utilization of dental therapeutic services decreasing by around 50% along this age span in a national sample [17] . in the national sample, restorative care was provided far more often than surgical care, while we found restorative care being consumed to a similar degree like surgical care. this might be as our sample was generally older and also represented a different target population (see below). we assume that these two factors drive a treatment concept where maintaining teeth (using restorative care) is deprioritized while achieving an overall pain free status (by removing teeth, for example) is getting more important (and usually also being the only available option). notably, prevention (which was only calculus removal in the present study) continued to be provided up to high age (albeit to a lower intensity). the only service where utilization was increasing with age was outreach care, while this seemed to allow for only very limited provision of therapies. it is relevant to understand the drivers behind treatment patterns in outreach care, and it may not be sufficient to only incentivize outreach visits, but also support outreach management or referral concepts for those requiring more complex care. in light of the covid-19 pandemic and the near-global shutdown of any dental visits (except for emergencies) to care homes (also in germany), outreach care is likely to be re-evaluated with regard to its benefits and risks. overall, our study calls for a range of possible policy and research initiatives: first, healthcare policy and decision makers should install incentives to provide services to the high needs elderly population. this may come by increasing single treatment fees for this group, or more generally by making outreach services more attractive. the latter may be realized by increasing fees once more or trialing and allowing different kinds of servicing, e.g., involving task delegation to assistance personnel. outreach care should further be provided not only to individuals in long-term care centers (nursing homes) but also to those residing at home (which is the vast majority of elderly). similarly, referral schemes between general medical practitioners and dentists may be helpful to identify high-risk individuals; mandatory follow-ups after such referrals may make sure that sick and remote older individuals (who seldom proactively seek care) are not plainly overlooked by standard dental healthcare. integrated service models (for example oral and dental hygiene enforcement for patients at risk for pneumonia) should further be strengthened. dental research, on the other hand, is called to action to develop applicable concepts fig. 2 regionally specific utilization of dental services, stratified in services blocks, in northeast germany. relative (in %) any utilization and specific service utilization is shown. larger cities with an increased or decreased utilization compared with the surrounding municipalities are further highlighted by arrows table 2 utilization of dental services according to international disease classification (icd-10, german modification) codes by the very old in northeast germany. any and specific service utilization (in %) is shown icd-10-gm *categories z00-z99 are intended for cases in which facts are indicated as "diagnoses" or "problems" which cannot be classified as disease, injury or external cause under categories a00-y89 **this chapter includes (subjective and objective) symptoms, abnormal results of clinical or other investigations, and inaccurately identified conditions for which there is no classifiable diagnosis elsewhere table 3 utilization of dental services according to german modified diagnosis-related groups (gm-drgs encompassing effective management of dental diseases at optimal infection and transmission control measures. right now, servicing is at a minimal level due to fears of infection and it can be expected that infection control will remain a highly relevant topic in this vulnerable population even when covid-19 is finally brought behind us. moreover, dental research should develop and evaluate the described complex care models involving delegation or cooperation. a number of initiatives are currently underway in germany in this direction (e.g., https://innovationsfonds.g-ba.de). further, primary and secondary prevention models in this group should be enhanced; currently prevention concepts in the elderly are by large identical with those in younger individuals. policy makers may want to revisit such age-group-specific prevention concepts when they are available. generally, we see a great need to emphasize prevention in this group (based on our findings, prevention was near-absent for the very old in the northeast). dentists and dental bodies may want to actively participate in such research and also the implementation of possible policies, especially considering that with the very old, there is a growing group with high needs who can truly benefit from dental care. this study has a number of strengths and limitations. first, this is one of few longitudinal studies evaluating dental service utilization in very old individuals. our cohort involved over 400,000 individuals from three federal states spanning an area of similar size as austria or the netherlands and belgium combined. second, we evaluated a range of demographic, social, general health, and regional factors, some of which (drgs, icd-10) have not routinely been employed when evaluating dental healthcare. third, and as a limitation discussed above, claims data suffer from a range of biases. provided and claimed treatment cannot be equated with needs or morbidity. exploring causality is only limitedly possible, and within the present (largely descriptive) analyses, this was also not within our scope (the available longitudinal data may permit some more in-depth analyses in the future). any identified bivariate association may suffer from confounding bias, and even the performed multivariable analysis showed only limited explanatory value, likely as further relevant factors (e.g., medication, care status) were not available and accounted for, or as available factors (e.g., social hardship status, place of living) came with very limited granularity. fourth, individuals insured by aok nordost are not fully representative for other individuals from the same target area or even the whole of germany: more affluent people are often not statutorily insured (there is a minimum income level defined as entry barrier into private insurances in germany). this may affect the individual's health status and his or her utilization behavior (reflecting health literacy, but also specific incentives set by insurers towards seeking or avoiding care) as well as the number and type of services provided by the dentists (as services are remunerated differently). the northeast of germany is overproportionally old and, as mentioned, economically comparably weak (notably, there is a significant economic disparity within the northeast, too, which our data reflect on). the rural parts of the northeast suffered from emigration to other areas of germany especially after the reunification, while berlin experienced an over-proportional immigration in the 1960s from aboard as well as the last 20 years from within germany. these specifics will impact service utilization but may not be found to this degree in other areas of germany. future studies on the present dataset may explore them in detail, if possible, to better understand what impact on utilization they have. in conclusion, and within the limitations of this study, social, demographic, regional, and general health aspects were associated with the utilization of dental services in very old germans. we identified consistent and considerable disparities in utilization between populations. policies to allow service utilization also for the sick, economically disadvantaged, rural, and very old should be developed, tested, and employed. competing interests the authors declare that they have no competing interests. ethical approval and informed consent all experiments were carried out in accordance with relevant guidelines and regulations. data collection was ethically approved by the ethics committee of the aok nordost. no informed consent was required for this study given that data were pseudonymized. open access this article is licensed under a creative commons attribution 4.0 international license, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the creative commons licence, and indicate if changes were made. the images or other third party material in this article are included in the article's creative commons licence, unless indicated otherwise in a credit line to the material. if material is not included in the article's creative commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. to view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. global burden of severe tooth loss: a systematic review and meta-analysis trends in caries experience in the permanent dentition in germany 1997-2014, and projection to 2030: morbidity shifts in an aging society our current geriatric population: demographic and oral health care utilization ageing, dental caries and periodontal diseases elder's oral health crisis. the journal of evidence-based dental practice zahnverlust und prothetische versorgung prosthetic treatment patterns in the very old: an insurance database analysis from germany the limitations of using insurance data for research misclassification in administrative claims data: quantifying the impact on treatment effect estimates the reporting of studies conducted using observational routinely-collected health data (record) statement befundbezogene festzuschüsse als innovatives steuerungsinstrument in der zahnmedizin defining and targeting health care access barriers societal and individual determinants of medical care utilization in the united states barriers to and enablers of older adults' use of dental services can we predict usage of dental services? an analysis from germany dental visits among older u.s. adults, 1999: the roles of dentition status and cost disparity in dental coverage among older adult populations: a comparative analysis across selected european countries and the usa dental care utilization and retirement oral health conditions of community-dwelling cognitively intact elderly persons with disabilities versorgungsprävalenzen bei älteren senioren mit pflegebedarf bekanntmachung eines beschlusses des gemeinsamen bundesausschusses über eine änderung der chroniker-richtlinie accessibility of general practitioners and selected specialist physicians by car and by public transport in a rural region of germany vertragszahnärztlichen versorgung von pflegebedürftigen und menschen mit behinderungen, kzbv/bzäk zahnarztdichte in deutschland nach bundesländern im jahr der wirtschaft: trend zu festsitzenden versorgungen hält an acknowledgments we thank the gewino for providing access to the data within.author contributions the study was conceived by fs. fs, akr, and jk planned the analyses. fs, akr, and jk performed the analyses. all authors interpreted the data. fs wrote the manuscript. all authors read and approved the manuscript.funding open access funding enabled and organized by projekt deal. this study was funded by the bundesministerium für bildung und forschung (bmbf tailohr, az 01gy1802).data availability data used in this study cannot be made available by the authors given data protection rules, but may be requested at the gewino. publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. key: cord-289285-aof7xy13 authors: michaelis, martin; geiler, janina; naczk, patrizia; sithisarn, patchima; leutz, anke; doerr, hans wilhelm; cinatl, jindrich title: glycyrrhizin exerts antioxidative effects in h5n1 influenza a virus-infected cells and inhibits virus replication and pro-inflammatory gene expression date: 2011-05-17 journal: plos one doi: 10.1371/journal.pone.0019705 sha: doc_id: 289285 cord_uid: aof7xy13 glycyrrhizin is known to exert antiviral and anti-inflammatory effects. here, the effects of an approved parenteral glycyrrhizin preparation (stronger neo-minophafen c) were investigated on highly pathogenic influenza a h5n1 virus replication, h5n1-induced apoptosis, and h5n1-induced pro-inflammatory responses in lung epithelial (a549) cells. therapeutic glycyrrhizin concentrations substantially inhibited h5n1-induced expression of the pro-inflammatory molecules cxcl10, interleukin 6, ccl2, and ccl5 (effective glycyrrhizin concentrations 25 to 50 µg/ml) but interfered with h5n1 replication and h5n1-induced apoptosis to a lesser extent (effective glycyrrhizin concentrations 100 µg/ml or higher). glycyrrhizin also diminished monocyte migration towards supernatants of h5n1-infected a549 cells. the mechanism by which glycyrrhizin interferes with h5n1 replication and h5n1-induced pro-inflammatory gene expression includes inhibition of h5n1-induced formation of reactive oxygen species and (in turn) reduced activation of nfκb, jnk, and p38, redox-sensitive signalling events known to be relevant for influenza a virus replication. therefore, glycyrrhizin may complement the arsenal of potential drugs for the treatment of h5n1 disease. highly pathogenic h5n1 influenza a viruses are considered to be potential influenza pandemic progenitors [1] [2] [3] [4] [5] [6] . at least for the first wave of an h5n1 pandemic, no sufficient amounts of adequate vaccines will be available [1] [2] [3] [4] [6] [7] [8] . therefore, antiviral therapy for influenza a viruses including highly pathogenic h5n1 virus strains remains of great importance for the first line defense against the virus [1] [2] [3] [4] 6, 9] . the neuraminidase inhibitors oseltamivir and zanamivir as well as the adamantanes amantadin and rimantadin that interfere with the influenza m2 protein are licensed for the treament of influenza [1] [2] [3] [4] 6] . however, the use of both drug classes is limited by the emergence of resistant virus strains. in seasonal influenza strains, the majority of h3n2 viruses and a great proportion of h1n1 viruses in humans are now considered to be amantadine-and rimantadine-resistant [10] [11] [12] [13] . moreover, a drastic increase in oseltamivir-resistant h1n1 viruses has been reported during the 2007/2008 influenza season in the northern hemisphere [14] [15] [16] [17] . preliminary data from the united states predict a further rise for the 2008/2009 season, possibly resulting in more than 90% of the circulating h1n1 strains to be oseltamivir resistant [14] . h5n1 virus strains appear to be generally less sensitive to antiviral treatment than seasonal influenza a virus strains and treatment-resistant h5n1 strains emerge [1] [2] [3] [4] 6, [18] [19] [20] [21] . more-over, parenteral agents for the treatment of seriously ill patients are missing. glycyrrhizin, a triterpene saponine, is a constituent of licorice root. it has been found to interfere with replication and/or cytopathogenic effect (cpe) induction of many viruses including respiratory viruses such as respiratory syncytial virus, sars coronavirus, hiv, and influenza viruses [22] [23] [24] [25] [26] [27] [28] . moreover, antiinflammatory and immunomodulatory properties were attributed to glycyrrhizin [26] . the severity of human h5n1 disease has been associated with hypercytokinaemia (''cytokine storm'') [29, 30] . delayed antiviral plus immunomodulator treatment reduced h5n1-induced mortality in mice [31] . therefore, antiinflammatory and immunomodulatory effects exerted by glycyrrhizin may be beneficial for treatment of h5n1. also, glycyrrhizin is a known antioxidant [26] and antioxidants were already shown to interfere with influenza a virus replication and virus-induced pro-inflammatory responses [32] [33] [34] . stronger neo-minophagen c (snmc) is a glycyrrhizin preparation (available as tablets or parenteral formulation) that is approved in japan for the treatment of chronic hepatic diseases and is marketed in japan, china, korea, taiwan, indonesia, india, and mongolia. here, we investigated the influence of snmc on h5n1 replication, on h5n1-induced cytokine expression, on h5n1-induced cellular oxidative stress, and on critical h5n1-induced cellular signalling events in human pneumocytes (a549 cell line). glycyrrhizin (stronger neo minophagen c) was obtained from minophagen pharmaceuticals co., ltd. (tokyo, japan). the influenza strain a/vietnam/1203/04 (h5n1) was received from the who influenza centre (national institute for medical research, london, uk). the h5n1 influenza strain a/thailand/ 1(kan-1)/04 was obtained from prof. pilaipan puthavathana (mahidol university, bangkok, thailand). virus stocks were prepared by infecting vero cells (african green monkey kidney; atcc, manassas, va) and aliquots were stored at 280uc. virus titres were determined as 50% tissue culture infectious dose (tcid 50 /ml) in confluent vero cells in 96-well microtiter plates. a549 cells (human lung carcinoma; atcc: ccl-185, obtained from lgc standards gmbh, wesel, germany) were grown at 37uc in minimal essential medium (mem) supplemented with 10% fbs, 100 iu/ml of penicillin and 100 mg/ml streptomycin. human monocytes were isolated from buffy coats of healthy donors, obtained from institute of transfusion medicine and immune haematology, german red cross blood donor center, johann wolfgang goethe-university, frankfurt am main. after centrifugation on ficoll (biocoll)-hypaque density gradient (biochrom ag, berlin, germany), mononuclear cells were collected from the interface and washed with pbs. then, monocytes were isolated using magnetically labeled cd14 microbeads (miltenyi biotec gmbh, bergisch gladbach, germany) following the manufacturer's instructions. monocytes were cultivated in imdm supplemented with 10% pooled human serum, 100 iu/ml of penicillin, and 100 mg/ml streptomycin. the cellular viability was assessed on confluent cell layers with celltiter-gloh luminescent cell viability assay (promega gmbh, mannheim, germany) according to the manufacturers' protocol. cell viability was expressed as percentage of non-treated control. to determine intracellular np localisation, h5n1-infected a549 were fixed 8 hours p.i. for 15 min with ice-cold acetone/ methanol (40:60, mallinckrodt baker b.v., deventer, the netherlands) and stained with a mouse monoclonal antibody (1 h incubation, 1:1000 in pbs) directed against the influenza a virus nucleoprotein (np) (millipore, molsheim, france). an alexa fluor 488 goat anti-mouse igg (h&l) (invitrogen, eugene, oregon, usa) was used (1 h incubation, 1:1000 in pbs) as secondary antibody. nuclei were stained using 49,6-diamidino-2phenylindole (dapi) (sigma-aldrich chemie gmbh, munich, germany). fluorescence was visualised using olympus ix 1 fluorescence microscope (olympus, planegg, germany). for flow cytometric analysis, the same antibodies were used. the cytopathogenic effect (cpe) reduction assay was performed as described before [34] . confluent a549 cell monolayers grown in 96-well microtitre plates were infected with influenza a strains at the indicated multiplicities of infection (mois). after a one hour adsorption period, cells were washed to remove non-detached virus. the virus-induced cpe was recorded at 24 h post infection (p.i.). unless otherwise stated, a549 cells were continuously treated with glycyrrhizin starting with a 1 h pre-incubation period. for time-ofaddition experiments, glycyrrhizin was added exclusively during the 1 h pre-incubation period, exclusively during the 1 h adsorption period, or after exclusively after the wash-out of input virus. total rna was isolated from cell cultures using tri reagent (sigma-aldrich, munich, germany). real time pcr for h5 was performed using described methods [35] . the following primers were used: sense 59 acg tat gac tac ccg cag tat tca g 39; antisense 59 aga cca gcy acc atg att gc 39; probe 6-fam-tca aca gtg gcg agt tcc cta gca-tamra. the fraction of cells with fractional dna content (''sub-g1'' cell subpopulation) indicates cytotoxicity. sub-g1 cells are considered to be dead (usually apoptotic) cells. cells were fixed with 70% ethanol for two hours at 220uc. the cellular dna was stained using propidium iodide (20 mg/ml) and analysed by flow cytometry (facscalibur, bd biosciences, heidelberg, germany). caspase activation was measured using the caspase-glo 8, 9, or 3/7 assays (promega, mannheim, germany) following the manufacturer's instructions. cell culture supernatants were collected and frozen at 280uc. cytokines/chemokines were quantified by specific elisa duo sets (r&d systems gmbh, wiesbaden, germany) following the manufacturer's instructions. nfkb activity was investigated in h5n1 (moi 0.01)-infected cells by quantification of the nfkb subunits rel a (p65) and nfkb1 (p50) from nuclear extracts using the transam tm transcription factor dna-binding elisas (active motif, rixensart, belgium). nuclear extract were prepared using the nuclear extract kit (active motif, carlsbad, ca, usa) following the manufacturer's instruction. cell culture supernatants were investigated for chemotactic activity by measurement of the activity to induce monocyte migration through membrane inserts in 24-well plates (pore size 8 mm; bd biosciences, heidelberg, germany). monocytes (1610 6 in 100 ml of imdm with 10% pooled human serum) were added into the cell culture inserts (upper chamber) and cell culture supernatants (300 ml), were added to the lower chamber of the well. after a 48 h incubation period, cells were fixed with 4% paraformaldehyde and permeabilised with pbs containing 0.3% tritron x-100. then, nuclei were stained with 49,6-diamidino-2phenylindole (dapi). the upper side of the membrane was wiped with a wet swab to remove the cells, while the lower side of the membrane was rinsed with pbs. the number of cells at the lower side of each membrane was quantified by counting of cells from three randomly chosen sections (3.7 mm 2 ) using an olympus ix 1 fluorescence microscope (olympus, planegg, germany). cells were lysed in triton x-sample buffer and separated by sds-page. nuclear extract were prepared using the nuclear extract kit (active motif, carlsbad, ca, usa) following the manufacturer's instruction. proteins were detected using specific antibodies against bactin (sigma-aldrich chemie gmbh, munich, germany), jnk, phosphorylated jnk, p38, or phosphorylated p38, (all purchased from new england biolabs gmbh, frankfurt am main, germany) and were visualised by enhanced chemiluminescence using a commercially available kit (amersham, freiburg, germany). reactive oxygen species (ros) were detected using the image-it live green reactive oxygen species kit (molecular probes, distributed by invitrogen, karlsruhe, germany). two groups were compared by t-test. more groups were compared by anova with subsequent student-newman-keuls test. the a549 cell line, derived from a human pulmonary adenocarcinoma, is an established model for type ii pneumocytes [36] , and commonly used for the investigation of the effect of influenza viruses on this cell type [see e.g. 6,37,38]. if not otherwise stated, glycyrrhizin was continuously present in cell culture media starting with a 1 h preinfection period. glycyrrhizin 200 mg/ml (the maximum tested concentration) did not affect a549 cell viability (data not shown) but clearly decreased cpe formation in a549 cells infected with the h5n1 influenza strain a/thailand/1(kan-1)/04 at mois of 0.01, 0.1 or 1 ( figure 1a ). similar results were obtained in a549 cells infected with strain a/vietnam/1203/04 (h5n1) (suppl. figure 1a) . staining of a549 cells for influenza a nucleoprotein 24 h after infection with strain h5n1 a/thailand/1(kan-1)/04 indicated that glycyrrhizin 200 mg/ml significantly reduces the number of influenza a nucleoprotein positive cells ( figure 1b) . to examine the influence of glycyrrhizin on virus progeny, a549 cells were infected with the h5n1 influenza strain a/ thailand/1(kan-1)/04 at moi 0.01 or moi 1 and infectious virus titres were determined 24 h post infection ( figure 1c ). while glycyrrhizin in concentrations up to 50 mg/ml did not affect h5n1 replication, moderate effects were exerted by glycyrrhizin 100 mg/ ml and more pronounced effects by glycyrrhizin 200 mg/ml (moi 0.01: 13-fold reduction, moi 1: 10-fold reduction). next, influence of glycyrrhizin on h5n1 replication was confirmed by the detection of viral (h5) rna using quantitative pcr. only glycyrrhizin concentrations $100 mg/ml significantly reduced figure 1b) or h5n1 a/vietnam/1203/04-infected (suppl. figure 1c ) a549 cells (moi 0.01) 24 h post infection. time-of-addition experiments revealed that maximal effects were achieved when glycyrrhizin was continuously present starting with a 1 h pre-incubation period ( figure 1d ). addition of glycyrrhizin post infection showed reduced antiviral effects while pre-incubation alone or glycyrrhizin addition during the adsorption period did not significantly affect h5n1 replication. for investigation of h5n1-induced cytokine expression, five pro-inflammatory genes were chosen that had been correlated to severity of influenza disease: cxcl10 (also known as interferon-cinducible protein 10, ip-10), interleukin 6 (il6), interleukin 8, (il8; also known as cxcl8), ccl2 (also known as monocyte chemoattractant protein 1, mcp-1), and ccl5 (also known as rantes). a549 cells were infected with h5n1 a/thailand/ 1(kan-1)/04 or h5n1 a/vietnam/1203/04 at moi 0.01, 0.1, or 1. glycyrrhizin treatment was performed with 25, 50, 100, or 200 mg/ml. cytokine expression was detected 24 h post infection by elisa. glycyrrhizin did not affect cytokine expression of noninfected cells (data not shown) but inhibited expression of all cytokines investigated in h5n1-infected cells in a dose-dependent manner (figure 2, figure 3a ). effects were more pronounced at lower mois. notably, expression of all cytokines except il8 was significantly inhibited after treatment with glycyrrhizin 50 mg/ml figure 3a ) although these glycyrrhizin concentrations had no effect on h5n1 replication in a549 cells (figure 1, figure s1 ). cytokine expression by influenza a virus-infected respiratory cells causes recruitment of peripheral blood monocytes into the lungs of patients where they differentiate to macrophages which are thought to contribute to influenza a virus pathogenicity [5, 39] . in a chemotaxis assay, the influence of glycyrrhizin was investigated on migration of monocytes towards supernatants of h5n1 a/thailand/1(kan-1)/04 (moi 0.1)-infected a549 cells through 8 mm filters. monocyte migration towards supernatants of h5n1-infected cells was strongly increased relative to migration towards supernatants of non-infected cells. treatment of h5n1infected cells with glycyrrhizin 100 mg/ml clearly suppressed chemoattraction activity of supernatants ( figure 3b ). influenza viruses including h5n1 have been shown to induce caspase-dependent apoptosis in airway cells and this apoptosis has been correlated to the virus pathogenicity [40, 41] . glycyrrhizin concentrations up to 200 mg/ml did not affect caspase activation in non-infected cells ( figure 4a-c) . glycyrrhizin concentrations $100 mg/ml inhibited h5n1 a/thailand/1(kan-1)/04 (moi 0.01)-induced activation of the initiator caspases 8 and 9 as well as of the effector caspases 3/7 in a549 cells as determined 24 h post infection ( figure 4a-c) . lower glycyrrhizin concentrations did not affect h5n1-induced apoptosis. the detection of cells in sub-g1 phase resulted in similar findings ( figure 4d ). substances that inhibit h5n1-induced caspase 3 activation including caspase 3 inhibitors cause nuclear retention of rnp complexes [34, 42] . in accordance, glycyrrhizin also interfered with nuclear export rnp at moi 1 ( figure s2 ). similar results were obtained in moi 0.01 h5n1 a/thailand/1(kan-1)/04infected cells ( figure s3 ). influence of glycyrrhizin on h5n1-induced activation of nuclear factor kb (nfkb), p38, and on h5n1-induced cellular reactive oxygen species (ros) formation activation of nfkb, p38, and jnk have been associated with influenza a virus replication and virus-induced pro-inflammatory gene expression [34, [43] [44] [45] [46] [47] . while glycyrrhizin did not influence nfkb activity in non-infected a549 cells in the tested concentra-tions (data not shown), glycyrrhizin inhibited nfkb activation in h5n1-infected cells ( figure 5a ). moreover, glycyrrhizin inhibited h5n1-induced phosphorylation of the mapks p38 and jnk ( figure 5b ). in addition to their roles during influenza a virus replication and virus-induced cytokine/chemokine expression, nfkb, p38, and jnk are constituents of redox-sensitive signalling pathways [48] [49] [50] [51] . antioxidants had been already found to interfere with influenza a virus-induced signalling through nfkb, p38, and jnk, with influenza a virus replication, and with influenza a virus-induced pro-inflammatory gene expression [32] [33] [34] . since glycyrrhizin is known to exert antioxidative effects [26] we speculated that glycyrrhizin may interfere with h5n1-induced ros formation. indeed glycyrrhizin exerted clear antioxidative effects in h5n1 (moi 0.01)-infected cells ( figure 5c ) causing significant reduction of ros formation already at a concentration of 25 mg/ml ( figure 5d ). here, we show that glycyrrhizin inhibits the replication of highly pathogenic h5n1 influenza a virus, h5n1-induced apoptosis, and h5n1-induced expression of pro-inflammatory cytokines in lung-derived a549 cells. after intravenous administration, achievable plasma concentrations of glycyrrhizin have been described to be about 100 mg/ml [52] . therefore, the glycyrrhizin concentrations found to interfere with h5n1 replication and h5n1-induced pro-inflammatory gene expression in the present report are in the range of therapeutic plasma levels. notably, although higher glycyrrhizin concentrations were needed to interfere with sars coronavirus replication [22] than with h5n1 replication, beneficial results were reported in glycyrrhizin (snmc)-treated sars patients in comparison to sars patients who did not receive glycyrrhizin [23] . notably, investigation of different glycyrrhizin derivatives against sars coronavirus led to the identification of compounds with enhanced antiviral activity [53] . therefore, glycyrrhizin might also serve as lead structure for the development of novel anti-influenza drugs. experimental results suggested that glycyrrhizin might be able to affect seasonal influenza a virus disease by antiviral and immunomodulatory effects [26, 27] . mice were prevented from lethal h2n2 infection by glycyrrhizin although no influence on virus replication was detected. the mechanism was suggested to be induction of interferon-c in t-cells by glycyrrhizin [54] . moreover, glycyrrhizin was shown to influence seasonal influenza a virus replication through interaction with the cell membrane [25, 28] . however, these effects were observed only in concentrations $200 mg/ml when glycyrrhizin was added during the virus adsorption period. since glycyrrhizin addition during the adsorption period did not influence h5n1 replication in our experiments it appears not likely that membrane effects contribute to anti-h5n1 effects detected here in lower concentrations. our results rather suggest that glycyrrhizin interferes with h5n1-induced oxidative stress. influenza a virus (including h5n1) infection induces ros formation. antioxidants were found to inhibit influenza a virus replication and influenza a virus-induced pro-inflammatory gene expression [32] [33] [34] and glycyrrhizin is known to exert antioxidative effects [26] . here, glycyrrhizin interfered with h5n1-induced activation of nfkb, p38, and jnk representing redox-sensitive signalling events [48] [49] [50] [51] involved in influenza a virus replication and influenza a virusinduced cellular cytokine/chemokine production [34, [43] [44] [45] [46] 55] . glycyrrhizin 50 mg/ml significantly reduced h5n1-induced activation of nfkb. in addition, glycyrrhizin concentrations as low as 25 mg/ml effectively interfered with h5n1-induced ros formation and with phosphorylation of the redox-sensitive mapks p38 and jnk. in our model, activation of p38 appears to be critical for h5n1-associated redox signalling since p38 inhibition had been shown before to mimick effects of the antioxidant n-acetyl-cysteine (nac) [34] . interestingly and in contrast to glycyrrhizin, nac failed to inhibit h5n1 replication or h5n1-induced cytokine/chemokine expression in therapeutically relevant concentrations. glycyrrhizin diminished h5n1-induced cellular cytokine/ chemokine production in concentrations (#50 mg/ml) that did not interfere with h5n1 replication although redox-sensitive signalling pathways have been described to be involved in both processes. therefore, h5n1-induced proinflammatory gene expression appears to be more sensitive to inhibition of ros formation than h5n1 replication. indeed, influenza viruses had been shown to induce cellular pathways through replicationdependent and -independent events [56] . in a previous report, we could show that similar glycyrrhizin concentrations like those investigated here interfered with h5n1-induced pro-inflammatory gene expression but not with h5n1 replication in human monocyte-derived macrophages [57] . in addition, other immunomodulatory treatment regimens that did not influence h5n1 replication reduced mortality in h5n1-infected mice [31, 58] . therefore, glycyrrhizin represents a potential additional treatment option that interfers with both h5n1 replication and h5n1induced expression of pro-inflammatory cytokines in lung cells. interference with immune responses may also result in the loss of control of virus replication by cytotoxic immune cells including natural killer cells and cytotoxic cd8 + t-lymphocytes. global immunosuppressants like corticosteroids failed to protect from lethal influenza virus infection [59] . moreover, antiviral drugs may interfere with cytotoxic cells that control virus replication as demonstrated for ribavirin that was shown to hamper nk cell cytolytic activity [60] . in this context, glycyrrhizin had already been shown not to affect natural killer cell activity in the concentrations used here [57] . in conclusion, we show in this report that therapeutic concentrations of glycyrrhizin (used as clinically approved parenteral preparation snmc) interfere with highly pathogenic h5n1 influenza a virus replication and h5n1-induced proinflammatory gene expression at least in part through interference with h5n1-induced ros formation and in turn reduced activation of p38, jnk, and nfkb in lung cells. since we used the clinical formulation snmc effects of other ingredients like glycin or cystein cannot be excluded. vaccines and antiviral agents will fail to meet global needs at least at the beginning of a severe influenza a virus pandemic [61] . anti-inflammatory and immunomodulatory agents are considered to be important candidates as constituents of anti-influenza treatment strategies that may save lives in an influenza pandemic situation [61] . therefore, glycyrrhizin may complement the arsenal of potential drugs for the treatment of h5n1-caused disease. the threat of avian influenza a (h5n1). part i: epidemiologic concerns and virulence determinants the threat of avian influenza a (h5n1): part ii: clues to pathogenicity and pathology the threat of avian influenza a (h5n1). part iii: antiviral therapy the threat of avian influenza a (h5n1). part iv: development of vaccines pathogenesis of emerging avian influenza viruses in mammals and the host innate immune response of chickens and men: avian influenza in humans vaccines for pandemic influenza. the history of our current vaccines, their limitations and the requirements to deal with a pandemic threat the pandemic influenza vaccine challenge antiviral drugs for the control of pandemic influenza virus surveillance of resistance to adamantanes among influenza a(h3n2) and a(h1n1) viruses isolated worldwide high prevalence of amantadine-resistance influenza a (h3n2) in six prefectures, japan, in the 2005-2006 season increased incidence of adamantane-resistant influenza a(h1n1) and a(h3n2) viruses during the 2006-2007 influenza season in japan epidemiologic study of influenza infection in okinawa, japan, from 2001 to 2007: changing patterns of seasonality and prevalence of amantadine-resistant influenza a virus infections with oseltamivir-resistant influenza a(h1n1) virus in the united states oseltamivirresistant influenza viruses a (h1n1), norway, 2007-08 use of oseltamivir in 12 european countries between 2002 and 2007-lack of association with the appearance of oseltamivir-resistant influenza a(h1n1) viruses global transmission of oseltamivir-resistant influenza distribution of amantadine-resistant h5n1 avian influenza variants in asia reduced sensitivity of influenza a (h5n1) to oseltamivir h5n1 transmission and disease: observations from the frontlines human infection with highly pathogenic avian influenza virus (h5n1) in northern vietnam glycyrrhizin, an active component of liquorice roots, and replication of 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infection antiviral activity of glycyrrhizic acid derivatives against sars-coronavirus glycyrrhizin, an active component of licorice roots, reduces morbidity and mortality of mice infected with lethal doses of influenza virus acetylsalicylic acid (asa) blocks influenza virus propagation via its nf-kappabinhibiting activity global impact of influenza virus on cellular pathways is mediated by both replication-dependent and -independent events glycyrrhizin inhibits highly pathogenic h5n1 influenza a virus-induced proinflammatory cytokine and chemokine expression in human macrophages tnf/inos-producing dendritic cells are the necessary evil of lethal influenza virus infection inhibition of the cytokine response does not protect against lethal h5n1 influenza infection a novel immunomodulatory mechanism of ribavirin in suppressing natural killer cell function confronting the next influenza pandemic with antiinflammatory and immunomodulatory agents: why they are needed and how they might work the authors thank mrs. kerstin euler, mrs. gesa meincke, and mrs. christina matreux for technical support. key: cord-292380-ulsejzqt authors: iwanejko, jakub; wojaczyńska, elżbieta; turlej, eliza; maciejewska, magdalena; wietrzyk, joanna title: octahydroquinoxalin-2(1h)-one-based aminophosphonic acids and their derivatives—biological activity towards cancer cells date: 2020-05-22 journal: materials (basel) doi: 10.3390/ma13102393 sha: doc_id: 292380 cord_uid: ulsejzqt in the search for new antitumor agents, aminophosphonic acids and their derivatives based on octahydroquinoxalin-2(1h)-one scaffold were obtained and their cytotoxic properties and a mechanism of action were evaluated. phosphonic acid and phosphonate moieties increased the antiproliferative activity in comparison to phenolic mannich bases previously reported. most of the obtained compounds revealed a strong antiproliferative effect against leukemia cell line (mv-4-11) with simultaneous low cytotoxicity against normal cell line (mouse fibroblasts-balb/3t3). the most active compound was diphenyl-[(1r,6r)-3-oxo-2,5-diazabicyclo[4.4.0]dec-4-yl]phosphonate. preliminary evaluation of the mechanism of action showed the proapoptotic effect associated with caspase 3/7 induction. at present, our attention is focused on the covid-19 pandemic and there is a tendency to neglect the civilization diseases which however remain the main reason for mortality worldwide. in particular, recently published data have shown that cancers are some of the leading causes of death in poland, with prostate cancer (almost 20% of patients) and lung cancer as the most common in the male population. the third cause of male mortality is colorectal (colon and rectum) cancer. in the female population, lung cancer dominates, followed by breast and colorectal cancer. among young poles, leukemias, lymphomas and brain cancers predominate and account for about 56% of cases [1] . anticancer drug design is a challenging field with a continuous demand for new, selective and non-toxic agents for treatment [2] . among various classes of compounds, aminophosphonic acids and their derivatives meet these requirements. due to their similarities to α-amino acids and a wide range of applications, α-aminophosphonic acids are continuously gaining importance in organic synthesis. so far, a number of applications such as antiviral [3, 4] or cytotoxic agents [5, 6] , enzyme inhibitors [7, 8] immune system activators [9] or antibacterial activities [10] have attracted considerable attention. the importance of these acids and their derivatives in the search for new pharmaceutical uses has been extensively discussed in numerous review articles [11] [12] [13] [14] . the α-aminophosphonic acid and its derivatives pose a crucial role in a variety of biological activities (figure 1 ), including cytotoxic properties. ampa (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor antagonist [15] ; (b) antimicrobial aminophosphonate [16] ; (c) anti-hiv agent [17] ; (d) cytotoxic agent against human cervical carcinoma [18] . aminophosphonates bearing an n-heterocyclic fragment have received particular attention over the last years among other potential anticancer agents [19] [20] [21] [22] . α-amino acids and their esters are considered versatile pharmacophores, known for antitumor activity [23] . the group of nikalje successfully coupled indole-2,3-diones with α-aminophosphonates, which led to new selective, antiproliferative compounds, analogues of commercially available drugs, orantinib and sunitinib [24] . in another noteworthy example, huang and co-workers proved that the incorporation of an aminophosphonate moiety to irinotecan, a chemotherapeutic agent, increased the cytotoxicity against certain cancer cell lines [25] . the fact of their negligible mammalian toxicity [12] testifies to the usefulness of these compounds in drug discovery research. a convenient route to this class of compounds is the pudovik reaction-a nucleophilic addition of dialkyl phosphites to imines [26] . another approach, kabachnik-fields one-pot three-component protocol, requires an amine, a carbonyl compound and an alkyl phosphite, however, it fails with electron-deficient amines [27] . most of the reported reactions are base-or acid-catalyzed, and noncatalyzed procedures remain scarce [28] . a recent review covers the reactions and synthetic methods for aminophosphonates [29] . in our previous research, we reported on the synthesis and antiproliferative action of novel phenolic adducts of bicyclic imine 1 (scheme 1) [30] . two phenolic mannich bases were found to be comparatively active to cisplatin with a noticeable increase of selectivity against cancer cell lines (one of them shown on the scheme). the tested compounds exhibit a resemblance to bioactive diketopiperazines in their bicyclic fragments. our new goal was to synthesize phosphorus analogs of these structures and evaluate their cytotoxicity against cancer cell lines. among a variety of synthetic methods for heterocyclic aminophosphonates formation [31] , our group has focused on a convenient nucleophilic addition of dialkyl phosphites to a cyclic imine. bearing in mind the remarkable precedents of improving the efficacy of cytotoxicity against cancer cell lines by insertion of aminophosphonate moiety and the results of our previous research, we directed our examinations toward the evaluation of antiproliferative properties of the phosphonic derivatives of octahydroquinoxalin-2(1h)-one. [15] ; (b) antimicrobial aminophosphonate [16] ; (c) anti-hiv agent [17] ; (d) cytotoxic agent against human cervical carcinoma [18] . aminophosphonates bearing an n-heterocyclic fragment have received particular attention over the last years among other potential anticancer agents [19] [20] [21] [22] . α-amino acids and their esters are considered versatile pharmacophores, known for antitumor activity [23] . the group of nikalje successfully coupled indole-2,3-diones with α-aminophosphonates, which led to new selective, antiproliferative compounds, analogues of commercially available drugs, orantinib and sunitinib [24] . in another noteworthy example, huang and co-workers proved that the incorporation of an aminophosphonate moiety to irinotecan, a chemotherapeutic agent, increased the cytotoxicity against certain cancer cell lines [25] . the fact of their negligible mammalian toxicity [12] testifies to the usefulness of these compounds in drug discovery research. a convenient route to this class of compounds is the pudovik reaction-a nucleophilic addition of dialkyl phosphites to imines [26] . another approach, kabachnik-fields one-pot three-component protocol, requires an amine, a carbonyl compound and an alkyl phosphite, however, it fails with electron-deficient amines [27] . most of the reported reactions are base-or acid-catalyzed, and non-catalyzed procedures remain scarce [28] . a recent review covers the reactions and synthetic methods for aminophosphonates [29] . in our previous research, we reported on the synthesis and antiproliferative action of novel phenolic adducts of bicyclic imine 1 (scheme 1) [30] . two phenolic mannich bases were found to be comparatively active to cisplatin with a noticeable increase of selectivity against cancer cell lines (one of them shown on the scheme). the tested compounds exhibit a resemblance to bioactive diketopiperazines in their bicyclic fragments. our new goal was to synthesize phosphorus analogs of these structures and evaluate their cytotoxicity against cancer cell lines. among a variety of synthetic methods for heterocyclic aminophosphonates formation [31] , our group has focused on a convenient nucleophilic addition of dialkyl phosphites to a cyclic imine. bearing in mind the remarkable precedents of improving the efficacy of cytotoxicity against cancer cell lines by insertion of aminophosphonate moiety and the results of our previous research, we directed our examinations toward the evaluation of antiproliferative properties of the phosphonic derivatives of octahydroquinoxalin-2(1h)-one. in our studies of the aminophosphonic acids and aminophosphonates mv4-11 (b phenotypic myelomonocytic) cell line carrying translocation t(4;11) was used. mv4-11 corresponds to aml m5b (according to the previously used french-american-british (fab) classification based on the morphology features of the cells). such an aml subtype is characterized by a tendency to occupy the gums, lymph nodes and skin [32] . mv4-11 cell line growth in suspension has about 50 h doubling time that makes it a good and a sensitive model for searching for new synthesized compounds against leukemia cells. all the reagents and solvents were purchased from commercial suppliers and used without further purification. melting points were carried out on the apotec ® schmelzpunktbestimmer melting point apparatus and are uncorrected. 1 h, 13 c and 31 p nmr spectra were collected on jeol 400yh and bruker avance ii 600 instruments. nmr spectra were recorded in cdcl3, unless specified otherwise. the temperature of the samples was 298 k. fourier-transform infrared spectra were measured using the perkin elmer 2000 ftir spectrometer. the principle peaks and their assignments are listed in table 1 . the high-resolution mass spectra (hrms) measurements were performed using the waters lct premier xe tof instrument. optical rotations were measured at ambient temperature on optical activity ltd. model aa-5 automatic polarimeter; [α] d values are given in 10 −1 deg cm 2 g −1 . column chromatography was performed on silica gel 60 (particle size 0.063-0.200 mm). thin-layer chromatography was conducted with the merck silica gel 60 pre-coated plates (f254) and visualized with uv light and/or iodine vapors. (1r,6r)-3-oxo-2,5-diazabicyclo [4.4 .0]dec-4-ene (1). typical procedure (1r,2r)-trans-diaminocyclohexane (4.00 mmol, 456 mg, 2.00 equiv) was dissolved in 2-proh (8 ml). to the stirred solution ethyl glyoxylate solution (50% solution in toluene, 2.00 mmol, 0.420 ml, 1.00 equiv) was added and the mixture was stirred for 24 h at room temperature (293 k). the solvent was removed in vacuo and the product was purified by silica gel column chromatography (eluent: in our studies of the aminophosphonic acids and aminophosphonates mv4-11 (b phenotypic myelomonocytic) cell line carrying translocation t(4;11) was used. mv4-11 corresponds to aml m5b (according to the previously used french-american-british (fab) classification based on the morphology features of the cells). such an aml subtype is characterized by a tendency to occupy the gums, lymph nodes and skin [32] . mv4-11 cell line growth in suspension has about 50 h doubling time that makes it a good and a sensitive model for searching for new synthesized compounds against leukemia cells. all the reagents and solvents were purchased from commercial suppliers and used without further purification. melting points were carried out on the apotec ® schmelzpunktbestimmer melting point apparatus and are uncorrected. 1 h, 13 c and 31 p nmr spectra were collected on jeol 400yh and bruker avance ii 600 instruments. nmr spectra were recorded in cdcl 3, unless specified otherwise. the temperature of the samples was 298 k. fourier-transform infrared spectra were measured using the perkin elmer 2000 ftir spectrometer. the principle peaks and their assignments are listed in table 1 . the high-resolution mass spectra (hrms) measurements were performed using the waters lct premier xe tof instrument. optical rotations were measured at ambient temperature on optical activity ltd. model aa-5 automatic polarimeter; [α] d values are given in 10 −1 deg cm 2 g −1 . column chromatography was performed on silica gel 60 (particle size 0.063-0.200 mm). thin-layer chromatography was conducted with the merck silica gel 60 pre-coated plates (f 254 ) and visualized with uv light and/or iodine vapors. [(1r,6r)-3-oxo-2,5-diazabicyclo [4.4 .0]dec-4-yl]-phosphonic acid (3a). procedure: the imine 1 (1.00 mmol, 152 mg, 1.00 equiv) was dissolved in ch 2 cl 2 (15 ml) followed by the addition of the tris (trimethylsilyl) phosphite (1.00 mmol, 0.334 ml, 1.00 equiv). the reaction was kept at ambient temperature for 24 h, with magnetic stirring. the solvent was removed under reduced pressure and the residue dissolved in methanol (15 ml) followed by stirring overnight at ambient temperature. methanol was removed under reduced pressure and the acid was separated by crystallization (anhydrous etoh/et 2 o 1:5 v/v) which led to the product as a colorless solid. the ftir analysis was conducted to additionally confirm the structures of the products. in the spectrum of imine 1, the strong band at 1622 cm −1 has been assigned to the double-bonded imino group [33] . this stretching vibration was not present in the other products which confirmed the addition of phosphorus nucleophiles. moreover, these compounds exhibited signals in the range of 1416-1453 cm −1 (c-n), characteristic for secondary cyclic amines, which corresponds to the spectra of aminophosphonates known in the literature [34] . absorption in the region of 3100-3400 cm −1 has been attributed to the n-h stretching from the lactam group. the differences are observed for acids 3a and 3b, due to the possible intermolecular hydrogen bond formation. the p=o stretch was found at 1166-1349 cm −1 , in accordance to the literature [35] . the other essential signals between 909 and 1122 cm −1 were assigned to p-o and p-ar bonds as identified in tusek-bozic's work [36] . . balb/3t3 cell line was cultured in dmem (gibco, scotland, uk) supplemented with 2 mm l-glutamine and 5% fbs). all the culture media contained antibiotics: 100 u/ml penicillin (polfa tarchomin sa, warsaw, poland) and 100 µg/ml streptomycin (sigma-aldrich chemie gmbh, steinheim, germany)). all the cell lines were cultured in a humid atmosphere at 37 • c and in 5% co 2 . twenty four hours before adding the tested compounds, each of the cell lines was seeded in 96-well plastic plates (sarstedt, numbrecht, germany) in an appropriate medium at a density (10 4 cells/well), except a549 cell line (0.25 × 10 4 /well), and mcf7 cell line: (0.75 × 10 4 /well). the selected cell lines were exposed to each of the tested chemical compounds at four different concentrations in the range of 100 to 0.1 µg/ml for 72 h. as a reference, cisplatin (teva pharmaceuticals, poland) was used, and dmso (sigma-aldrich chemie gmbh, steinheim, germany) served as a solvent control at concentrations corresponding to these present in the dilutions of the tested compounds. for adherent cells, a sulforhodamine b assay (srb), and for leukemic-an mtt assay was performed. after 72 h of incubation, cells were fixed in situ by gently adding of 50 µl per well of ice-cold 50% tca (trichloroacetic acid, poch, gliwice, poland) and were incubated at 4 • c for one hour. afterwards, wells were washed five times with water and 50 µl of 0.4% solution of srb (sulforhodamine b, sigma-aldrich chemie gmbh, steinheim, germany) in 1% acetic acid (poch, gliwice, poland) was added to each well and plates were again incubated at rt for 30 min. the unbound dye was removed by washing plates five times with 1% acetic acid, while stained cells were treated with 10 mm tris (tris base, sigma-aldrich, chemie gmbh, steinheim, germany). the absorbance in each well was read using the elisa plate reader (biotek synergy h4, swindon, uk) equipped with gen5 software at the 540 nm wavelength [37] . the percentage of proliferation inhibition of leukemia cells by the tested compounds was determined by an mtt assay. briefly, 20 µl of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide solution (sigma-aldrich, chemie gmbh, steinheim, germany) was added to each well and plates were left for 4 h at 37 • c. then, plates were centrifuged for 5 min, at 88× g, at 4 • c, the supernatant was thrown out and 200 µl of dmso per well (poch, gliwice, poland) was added. the plates were left in rt for 10 min and the absorbance in each well was read using the elisa plate reader (biotek synergy h4, swindon, uk), equipped with gen5 software at the 570 nm wavelength [38] . the results are presented as mean ic 50 values (the concentration of the compound, that inhibits cell proliferation by 50%) ± standard deviation. ic 50 values were assessed by the prolab-3 system based on cheburator 0.4, software developed by nevozhay [39] . at each concentration, chemical compounds were tested in triplicates in a single experiment. each experiment was repeated at least three times independently. for the cell cycle analysis, mv4-11 cell line was used. the cells were seeded in 24-well plastic plates (sarstedt, darmstadt, germany) at a density of 0.25 × 10 6 cells/1 ml. next, after 24 h, the tested compounds at the final concentration ic 50 and 2 × ic 50 , were added in a volume of 1 ml to the cells. the cells were exposed to the tested compounds for 48 h. next, the cells growing in suspension were collected, counted with the trypan blue solution (sigma-aldrich chemie gmbh, steinheim, germany), centrifuged for 5 min at +4 • c, 5 min, at 324× g, resuspended in 1 ml of 70% ice-cold ethanol (poch, gliwice, poland) and frozen at −20 • c for at least 24 h. after that, the cells were transferred to 5 ml propylene tubes (dedicated for flow cytometry analysis), washed in pbs (iiet, pas, wroclaw, poland) and centrifuged (+4 • c, 10 min, 324× g). then, the rnase solution (in pbs, 8 µg/ml) (life technologies, carlsbad, ca, usa) was added (500 µl for 0.5 × 10 6 cells) and the cells were incubated for 60 min at 37 • c with gentle mixing. after that, the cells were placed on ice, a propidium iodide (pi) solution (sigma-aldrich chemie gmbh, steinheim, germany) (in concentration 0.1 mg/ml) was added to the cells for 30 min. next, the flow cytometry analysis of the cell cycle was performed using bd lsr ii fortessa (becton dickinson, san jose, ca, usa), equipped with facs diva version 6.1. software (bd). the analysis of the obtained results was performed using flowing software version 2.5.1 developed by perttu terho. for each sample, the percentage of cells in each cell cycle phase was determined. each experiment was performed three times independently. the mv-4-11 cell line was seeded at the density of 0.25 × 10 6 cells/ml (total 1 × 10 6 cells) in a culture medium on 24-well plastic plates (sarstedt, numbrecht, germany) and was exposed to the chemical compounds at the concentration of ic 50 and 2 × ic 50 for 48 h. as a solvent control, dmso (poch, gliwice, poland) was used at a concentration corresponding to the highest concentration of compounds. after 48 h of incubation, the cells were collected, washed in pbs (324 g, 10 min, 4 • c) and counted. the cells (0.5 × 10 6 /ml) were diluted in a 0.5 ml annexin binding buffer (10 mm hepes/naoh; 140 mm nacl, 2.5 mm cacl 2 : iiet pas, wrocław, poland), diluted in distilled water at a ratio of 1:4. 5 µl of annexin v conjugated with apc (bd bioscience, san jose, ca, usa) was added to each 195 µl of cell suspension. after 15 min of incubation at room temperature in the dark, and pbs washing, the pi solution at 0.5 mg/ml (sigma-aldrich gmbh chemie, steinheim, germany) was added to the samples. the data were processed using bd lsrii fortessa, equipped with diva 6.1 software. the data were analyzed using flowing software version 2.5.1., developed by perttu terho and described as: double negative (live), double-positive (late apoptotic), annexin v positive-propidine iodine negative (early apoptotic)-and annexin v negative-propidine iodine positive (necrotic). each experiment was repeated 4-5 times. the mv-4-11 cells were seeded at the density of 0.25 × 10 6 cells/ml in culture medium on 24-well plastic plates (sarstedt, numbrecht, germany). after a 48 h exposition to the compounds at the concentration of ic 50 and 2 × ic 50 and incubated for 48 h, cells were collected and washed in pbs. as a solvent control, dmso was used at the concentration corresponding to the highest concentration of the compounds. camptothecin (sigma-aldrich gmbh chemie, steinheim, germany) was used as a positive control. the appropriate volume of lysis buffer ph 7.5 (50 mm hepes, 10% sucrose, 150 mm nacl, 1% triton x-100) (iiet, pas, wroclaw, poland) with the addition of 1% of dtt (dl-dithiotreithol, sigma-aldrich gmbh chemie steinheim, germany) was prepared. the reaction buffer ph 7.5 (20 mm hepes, 10% sucrose, 100 mm nacl) iiet pas, wrocław, poland with the dtt addition and with 10 µm of caspase-3 substrate (ac-devd-amc, cayman chemicals, ann arbor, mi, usa) was prepared and warmed to 37 • c before using. after incubation time the cells were centrifuged (324× g, 10 min, 4 • c), 50 µl of the lysis buffer was added to each sample and the probes were left at 4 • c for 30 min. then 40 µl of lysates were added to white 96-well plates (perkin-elmer, waltham, ma, usa) in triplicate, 160 µl of a pre-warmed reaction buffer was added to each well and the fluorescence was read out using a fluorescence plate reader (biotek synergy h4, swindon, uk) equipped with gen5 software the measurements were performed at 355 nm and 460 nm for 2 h every 10 min at 37 • c. at the same time, an mtt test was performed in order to normalize results. based on the results obtained, an mfi (mean fluorescence intensity) vs. reaction time curve was plotted and the vmax (reaction rate) values were determined. after normalization, the values obtained for the tested samples were compared to the control to assess how many times caspase-3 activity in tested probes is higher/lower than in control. each experiment was conducted at least 4-5 times. the mv-4-11 cell line was seeded at the density of 0.25 × 10 6 cells/ml in a culture medium on 24-well plates (sarstedt, numbrecht, germany). the cells were exposed to the compounds at the concentration of ic 50 and 2 × ic 50 for 48 h. then, the cells were collected, washed in pbs and counted in a trypan blue solution. the collections of 0.2 × 10 6 cells/sample were centrifuged (300× g, 5 min, room temperature) and pellets were suspended in a jc-1 solution (cayman chemicals, ann arbor, mi, usa) in a warm culture medium (final concentration 2.5 µg/ml). after 10 min of incubation at 37 • c in the dark, cells were centrifuged (300× g, 5 min, room temperature) and pellets were suspended in 200 µl of pbs (iiet, pas, wrocław, poland). as a solvent control, dmso was used at the concentration corresponding to the highest concentration of the compounds. valinomycin (sigma-aldrich gmbh chemie, steinheim, germany) was used as a positive control. the results were read using bd lsrii fortessa (becton dickinson, san jose, ca, usa), equipped with facs diva 6.1. software and were analyzed with flowing software 2.5.1, developed by perttu terho in dot plots presenting jc-1 monomers to aggregates. the mv-4-11 cells were seeded at a density of 0.25 × 10 6 cells/ml in culture medium on 24-well plates (sarstedt, numbrecht, germany). the cells were exposed to the compounds at the concentration of ic 50 and 2 × ic 50 and incubated for 48 h. as a solvent control, dmso was used at a concentration corresponding to the highest concentration of the compounds. tamoxifen (sigma-aldrich gmbh chemie, steinheim, germany) was used as a positive control. after 48 h of incubation, the cells were collected and washed in pbs (324 g, 10 min, 4 • c). for this purpose, 96-well black plates were used (perkin elmer, walthman, ma, usa). 100 µl of propidine iodine (pi) (final concentration: 10 µg/ml) was added to each sample, except the probes intended for background measurement. after 2 min of room temperature incubation, the cells were centrifuged (400× g, 5 min, room temperature), pellets were suspended in 100 µl of pbs (iiet pas, wrocław, poland) and again centrifuged. next 100 µl of 0.05 mmol/l dansyl cadaverine (sigma aldrich gmbh chemie, steinheim, germany) was added to each sample and the samples were incubated at 37 • c for 10 min. next, the cells were centrifuged and washed with pbs. finally, the obtained pellet was suspended in 300 µl of pbs and transferred into the appropriate wells. each sample was made in triplicate. autophagic vacuole staining intensity was detected at the excitation wavelength of 335 nm and emission of 512 nm, and the degree of cell death at excitation wavelength 536 nm and emission of 617 nm. each experiment was conducted at least 4-5 times. the mv-4-11 cell line was seeded at the density of 0.25 × 10 6 cells/ml in a culture medium on 24-well plastic plates (sarstedt, germany) to the final volume of 2 ml. the cells were exposed to the compounds at the concentration of ic 50 and 2ic 50 and incubated for 48 h. as a solvent control, dmso was used at the concentration corresponding to the highest concentration of the compounds. after 48 h of incubation, the cells were collected, washed in pbs (324 g, 5 min, room temperature) and counted. the collection of 0.2 × 10 6 cells were stained with 10 µg/ml of acridine orange (ao) (sigma aldrich gmbh chemie, steinheim, germany) for 20 min at 37 • c, washed two times with pbs and read using bd lsr ii fortessa (becton dickinson, san jose, ca, usa), equipped with facs diva 6.1. software and were analyzed with flowing software 2.5.1, developed by perttu terho. each experiment was performed at least 4 times. the presented compounds were synthesized using the previously published methods [40, 41] . a cyclic imine 1, derived from optically pure trans-(r,r)-1,2-diaminocyclohexane was reacted with h-phosphonates or phosphine oxides to give compounds 2a-f with good yields as mixtures of epimers (table 2) . a single epimer 2g of p-taddol derivative (taddol = α,α,α ,α -tetraaryl-2,2-disubstituted 1,3-dioxolane-4,5-dimethanol) was obtained by crystallization from mixture 2f. nmr spectra of products 1 and 2a-g are shown in the supplementary materials (figures s1-s8 ). the presented compounds were synthesized using the previously published methods [40, 41] . a cyclic imine 1, derived from optically pure trans-(r,r)-1,2-diaminocyclohexane was reacted with hphosphonates or phosphine oxides to give compounds 2a-f with good yields as mixtures of epimers (table 2) . a single epimer 2g of p-taddol derivative (taddol = α,α,α′,α′-tetraaryl-2,2disubstituted 1,3-dioxolane-4,5-dimethanol) was obtained by crystallization from mixture 2f. nmr spectra of products 1 and 2a-g are shown in the supplementary materials (figures s1-s8 ). in a modified protocol, we obtained aminophosphonic acids 3a and 3b (scheme 2). an addition of tris(trimethylsilyl)phosphite and further methanolysis yielded product 3a (supplementary materials, figure s9 ). when a ketimine (x = ph) was used in the reaction, an additive of bromotrimethylsilane was required for the reaction to complete. an activation of c=n bond was necessary, since c-substituted imines are less reactive. the diastereoselectivity of the reactions was improved, especially in the case when a sterically hindered phenyl ketimine was used. the dr values provided in table 2 represent the compositions of the epimeric mixtures used in further studies and were determined by 31 p nmr and confirmed by 1 h nmr spectroscopy. in the case of compound 3b (supplementary materials, figure s10 ), only traces of the second epimer were detected at the level of in a modified protocol, we obtained aminophosphonic acids 3a and 3b (scheme 2). an addition of tris(trimethylsilyl)phosphite and further methanolysis yielded product 3a (supplementary materials, figure s9 ). when a ketimine (x = ph) was used in the reaction, an additive of bromotrimethylsilane was required for the reaction to complete. an activation of c=n bond was necessary, since c-substituted imines are less reactive. the diastereoselectivity of the reactions was improved, especially in the case when a sterically hindered phenyl ketimine was used. the dr values provided in table 2 represent the compositions of the epimeric mixtures used in further studies and were determined by 31 p nmr and confirmed by 1 h nmr spectroscopy. in the case of compound 3b (supplementary materials, figure s10 ), only traces of the second epimer were detected at the level of the accuracy of nmr technique (ca. 2%). in a modified protocol, we obtained aminophosphonic acids 3a and 3b (scheme 2). an addition of tris(trimethylsilyl)phosphite and further methanolysis yielded product 3a (supplementary materials, figure s9 ). when a ketimine (x = ph) was used in the reaction, an additive of bromotrimethylsilane was required for the reaction to complete. an activation of c=n bond was necessary, since c-substituted imines are less reactive. the diastereoselectivity of the reactions was improved, especially in the case when a sterically hindered phenyl ketimine was used. the dr values provided in table 2 represent the compositions of the epimeric mixtures used in further studies and were determined by 31 p nmr and confirmed by 1 h nmr spectroscopy. in the case of compound 3b (supplementary materials, figure s10 ), only traces of the second epimer were detected at the level of the accuracy of nmr technique (ca. 2%). all compounds were evaluated according to their antiproliferative activity towards human acute myeloid leukemia (aml-m5b) cell line (mv4-11) and three adenocarcinoma cell lines of different origin: lung (a549), colorectal (lovo) and breast (mcf-7). the results were compared with those obtained on the normal murine fibroblasts cell line (balb/3t3). among the modified compounds, only derivatives 2f and 2g (similarly to 1) exert antiproliferative activity against all the cancer cell lines tested, however in contrast to compound 1 their activity towards balb/3t3 cells was visibly lower as compared to the cancer cells (table 3) . on the other hand, 2b and 3a were most active towards leukemia cells, though they were not toxic neither for solid tumors cell lines nor murine fibroblasts. a preliminary sar (structure-activity relationship) analysis reveals a few conclusions about structural features that result in the desired activity. among the tested phosphonates, phenyl derivative 2b performed better than benzyl (2c), methyl (2a) and taddol esters (2f). however, the latter derivative bearing a substituent introducing a big steric hindrance was found to be more versatile and acted on all of the investigated cell lines. comparison of diastereomeric mixture (2f) and isolated single isomer (2g) reveals no significant differences between epimers with opposite configurations of the stereogenic center c-4. therefore, the separation of phosphonate diastereomers for biological tests seems unnecessary. remarkably, h-phosphinate 2d was practically inactive, while phosphine oxide 2e exhibited a moderate activity in comparison to the majority of the tested phosphonates. this indicates the directions of further modifications, which should be focused on esters of aminophosphonic acids. the acid itself (3a) exhibited high cytotoxicity, but only toward leukemia cells; comparison of compounds 3a and 3b suggests that complete substitution of a stereogenic center decreases the antiproliferative activity. compounds 2b, 2e and 2f were selected for further studies. for evaluation of the impact of the selected compounds on cell cycle distribution, we analyzed the percentage of cells in each of the cell divisions upon incubation with selected compounds. analyzing cell cycle distribution (figure 2a-d) , we could only observe a decrease of cells in the s phase after 48 h incubation with 2e. in parallel, the tendency to increase the percentage of cells in g0/g1 phase was observed. cisplatin used as a control of the test increased cells percentage in the g2m phase. analysis of dead cells (subg1) showed a significant increase in dead cells caused by 2f used in higher concentrations. next, we decided to analyze apoptotic and necrotic cells using annexin v/pi staining ( figure 2e-g) , as well as the activity of caspase 3/7 in the treated cells ( figure 2h ). compound 2b increased the level of early apoptotic cells with an increase of caspase 3/7 activity. compound 2f increased the percentage of necrotic cells (but also the tendency to increase the level of apoptotic cells: early and late, was observed) and also increased the activity of caspase 3/7. in the case of compound 2e, an increased percentage of late apoptotic cells was accompanied by an increase of caspase 3/7 activity. the drop of the percentage of cells with high mitochondrial membrane potential (∆ψ) was observed in mv4-11 cells incubated with compound 2f and 2e ( figure 2i ). for labeling autophagic vacuoles, two techniques with dansyl cadaverin and with acridine orange were used. in both methods, compound 2f increased the level of acidic autophagic vacuoles ( figure 2j,k) . increased the activity of caspase 3/7. in the case of compound 2e, an increased percentage of late apoptotic cells was accompanied by an increase of caspase 3/7 activity. the drop of the percentage of cells with high mitochondrial membrane potential (δψ) was observed in mv4-11 cells incubated with compound 2f and 2e ( figure 2i ). for labeling autophagic vacuoles, two techniques with dansyl cadaverin and with acridine orange were used. in both methods, compound 2f increased the level of acidic autophagic vacuoles ( figure 2j ,k). in this study, we prepared aminophosphonic acids and their derivatives based on octahydroquinoxalin-2(1h)-one scaffold via pudovik reaction. the syntheses proceeded efficiently giving stable products in case of all types of h-phosphonates, phosphine oxides and phosphite used. since no significant differences of antiproliferative activities for a diastereomeric mixture (2f) and a single epimer (2g) were observed, further studies were conducted for mixtures of both stereoisomers of each compound. compound 2b, which was found to be the most active in proliferation inhibition of the mv4-11 cells, induces apoptosis of these cells with an increased caspase 3/7 activity. compound 2f, which inhibited the proliferation of all neoplastic cell lines, tends to decrease the percentage of cells in the g2m phase and increases the percentage of dead cells, including cells undergoing necrosis. this compound increases the activity of caspases 3/7 and reduces the mitochondrial potential of cells. a long-lasting drop or rise of ∆ψ from control levels may induce a loss of cell viability. the higher is the level of intracellular atp, the more stable are the ∆ψ values, making atp a compound buffering mitochondrial ∆ψ [42] . however, compound 2f can also enhance autophagy. this phenomenon may not be beneficial from the point of view of cancer therapies, although there are different opinions, as well as it may depend on specific mechanisms of action of studied compounds [43] . derivative 2e reduces the percentage of cells in the s phase of the cell cycle, increases the percentage of cells in late apoptosis and necrotic cells, increases caspase 3/7 activity, and reduces mitochondrial potential, so it works as a pro-apoptotic agent. a similar mechanism of action was reported by huang's group in the paper on the synthesis of potential anticancer candidates for the use in the therapy of ovarian cancer cells [25] . the tested compounds, with the emphasis put on 2b, 2e and 2f, could be used as promising scaffolds in further antiproliferative drug design. supplementary materials: the following are available online at http://www.mdpi.com/1996-1944/13/10/2393/s1, figure s1 . 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an effective route to new bicyclic compounds: aminophosphonates, enamines and imines aminophosphonates and aminophosphonic acids with tetrasubstituted stereogenic center: diastereoselective synthesis from cyclic ketimines mitochondrial membrane potential the roles of autophagy in cancer funding: this research received no external funding. the authors declare no conflict of interest. key: cord-264526-bxpzo2xu authors: aydin, malik; naumova, ella a.; paulsen, friedrich; zhang, wenli; gopon, felix; theis, christian; lutz, sören; ehrke-schulz, eric; arnold, wolfgang h.; wirth, stefan; ehrhardt, anja title: house dust mite exposure causes increased susceptibility of nasal epithelial cells to adenovirus infection date: 2020-10-11 journal: viruses doi: 10.3390/v12101151 sha: doc_id: 264526 cord_uid: bxpzo2xu adenovirus (adv) infections in the respiratory tract may cause asthma exacerbation and allergic predisposition, and the house dust mite (hdm) may aggravate virus-induced asthma exacerbations. however, the underlying mechanisms of whether and how adv affects asthmatic patients remains unclear. to address this question, we investigated nasal epithelial cells (naepcs) derived from a pediatric exacerbation study cohort for experimental analyses. we analyzed twenty-one different green-fluorescent proteinand luciferase-tagged adv types in submerged 2d and organotypic 3d cell culture models. transduction experiments revealed robust transduction of adv type 5 (adv5) in naepcs, which was associated with an increased uptake of adv5 in the presence of hdm. in healthy and asthmatic naepcs exposed to hdm before infection, we observed a timeand dose-dependent increase of adv5 uptake associated with upregulation of entry receptors for adv5. furthermore, electron microscopic and histologic analyses of 3d cell cultures revealed an impairment of the respiratory cilia after hdm exposition. this ex vivo pilot study shows the impact of adv infection and hdm exposition in a primary cell culture model for asthma. currently, more than 100 human adenoviruses (adv) (http://hadvwg.gmu.edu/) have been identified. they have been phylogenetically divided into seven species (a to g) based on hemagglutination features, oncogenic potential in rodents, dna homology, and genome organization [1, 2] . adenoviruses are non-enveloped viruses, which contain a double-stranded dna viral genome of an approximate length of 26-46 kbp [3] . the capsid consists of 252 capsomeres, and the virus shape is icosahedral with 240 hexon-, 12 penton-, and fiber proteins including shaft and knob [4] . for adv cell entry, several cellular receptors have been described, including the coxsackie andadenovirus receptor (car), cd46, sialic acid, desmoglein-2 (dsg-2), and heparan sulfate proteoglycan (hspg) [4] . adv are known as pathogens, but they have also been explored as viral vectors in gene therapeutic applications. in clinics, human adv have become increasingly important in recent years. they cause different clinical symptoms in a wide range of diseases, e.g., pneumonia, conjunctivitis, gastroenteritis, or myocarditis [5] [6] [7] [8] . threatened groups include children younger than five years of age or immune-deficient patients after transplantation. in addition, adv have also been causatively associated with pneumonia outbreaks in us-military bases [9] . several adv can be isolated from patients with lung infections [8] , and here we addressed the question of whether this is associated with asthma exacerbation. there is strong evidence that asthma exacerbations are associated with virus-mediated upper and/or lower respiratory infections [10] , and therefore there is a broad interest in studying the role of viruses in asthma pathogenesis and exacerbation [11] [12] [13] [14] . it was described that predominantly rhinovirus (rv), and other viruses, particularly adenoviruses (adv), cytomegalovirus, bocavirus, coronavirus, herpes simplex virus, influenza virus, parainfluenza virus, respiratory syncytial virus, or enteroviruses, may be involved in asthma development [15] . in addition to viruses, house dust mite (hdm) as a major allergen is strongly associated with asthma and presents an important risk factor for virus-induced asthma exacerbation [12, 13] . although various studies have investigated the molecular roles of some respiratory viruses in allergic pathways [14, 15] , the relationship between adv infection and hdm sensitization in asthma exacerbation has not been sufficiently analyzed. here, we aimed at analyzing this relationship in primary nasal epithelial cells (naepcs) as an ex vivo cell culture model, to better study allergies and the immunology of asthma [16] [17] [18] . to analyze adv infection in the context of hdm sensitization, we utilized primary nasal naepcs derived from our pediatric exacerbation study cohort in submerged 2d and organotypic 3d cell culture models. for this approach, we applied twenty-one previously described green-fluorescent protein (gfp)-and luciferase-tagged adv types [19] , encompassing adv of all seven species. moreover, we performed electron microscopic and histologic analyses of 3d cell cultures to study the impairment of respiratory cilia after hdm exposure. we found that hdm exposure may increase adv5 infection in vitro, and that major adv surface receptors may play a role. we established a pediatric exacerbation study network in two children's hospitals in germany. participating study centers were wuppertal (witten/herdecke university, germany) and niederberg/velbert (teaching hospital of the university hospital essen, germany). pediatric subjects with a chronic bronchitis/wheeze (3 months to ≤5 years of age) or asthma (>6 years to 17 years of age) suffering from acute exacerbation episodes were recruited. in addition, healthy controls (age range >3 months to 65 years of age) were recruited for comparison. a detailed study description and protocol is currently in preparation for publication. for the experimental approach used here, only naepcs from asthmatics and healthy donors were used (n = 3 per each group as biologic with each n = 3 technical replicates). for the control experiments, cells from healthy donors were compared with cells from asthmatic subjects (treated and untreated). only asthmatics with an hdm sensitization (released ige levels in serum, positive immunocap ® results for dermatophagoides pteronyssinus, cap class >3) were chosen for this work. furthermore, only healthy donors without any positive sensitization to dermatophagoides pteronyssinus were selected. clinically, asthmatic patients showed an immunologic reaction to dermatophagoides pteryonossinus, and the healthy donors did not present any allergic reactions. for this prospective study, all analyzed biomaterials and data involving human participants were collected in concordance with the ethical standards and with the 1964 helsinki declaration and its later amendments or comparable ethical standards. ethics approval was obtained from the local ethics committees (witten/herdecke university (158/2017) and medical chamber (ärztekammer nordrhein, nr 2019312), germany). the study was retrospectively assigned the human study at german clinical trials register (drks) with the registration number drks00015738. all study cohort relevant data analyses were pseudonymously performed. all participated subjects or their legal custodians/parents provided a written informed consent. this article does not contain any animal studies. the naepcs were obtained by performing a nasal brushing (cytobrush eswab ® copan italia) from both nostrils, resuspended in warm begm ® medium (purchased from lonza, basel, switzerland), and shaken for 30 s. approximately, 150,000-250,000 cells per nasal brushing procedure (including both nostrils) were collected, the total number was approximately 1 × 10 6 cells at passage 2 (p2). to eliminate possible contamination with erythrocytes and fibroblasts, lysing procedures were performed before experimental set-up. after centrifugation at 350× g for 8 min, the cell number was calculated using a neubauer counting chamber. cells were incubated in collagen i pre-coated t75 flasks (greiner bio-one, austria) for up to a maximum of two passages (p2) at 37 • c and 5% co 2 atmosphere. at p2, the cells were seeded using an organotypic 3d air liquid interface (ali) cell culturing technique adapted to the instructions of stemcell tm technologies (https://www.stemcell.com/). for this, 25,000 cells were seeded in collagen i pre-coated transwells using pneumacult tm ali proliferation medium added to the basal and apical chambers, and the medium was changed every single day. at day 4, the medium in both chambers were removed, and the cells received pneumacult tm ali differentiation medium at the basal chamber. the medium was changed every 2 to 3 days assuring airlifting for up to 4 weeks until the pseudostratified morphology was reached, which was confirmed by ciliary beats and production of mucus (pneumacult tm ali and differentiation medium were purchased from stemcell tm technologies, canada). naepcs were characterized through flow cytometry using cd45-apc (miltenyi biotec, germany), cd326 (epcam)-pe (miltenyi biotec, germany), and anti-cytokeratin-fitc (miltenyi biotec, germany), followed by fixation and permeabilization using inside stain kit (miltenyi biotec, germany) according to manufacturer's instructions. the selected antibodies for the characterization of naepcs were adapted in a previously published study [20] . the adv receptors, cd46-apc (miltenyi biotec, germany), cxadr/car-pe, and dsg-2-pe (affymetrix, thermo fisher scientific) were chosen for flow cytometry analyses. the specimens were fixed with 0.1 m cacodylate buffer containing 2.5% glutaraldehyde, 2% polyvinylpyrrolidone, and 75 mm nano 2 for 30 min. at 4 • c. samples were washed in 0.1 m cacodylate buffer without glutaraldehyde and subsequently incubated in a solution containing 2% arginine-hcl, glycine, sucrose, and sodium glutamate for 18 h at room temperature (rt). the specimens were rinsed in distilled water, followed by immersion in a mixture of each 2% tannic acid and guanidine-hcl for 6 h at rt. the samples were rinsed again in 0.1 m cacodylate buffer and incubated in a 1% oso 4 solution for 30 min at rt. after three rinsing steps with 0.1 m cacodylate buffer, the specimens were dehydrated, dried in liquid co 2 , and finally examined with a zeiss sigma sem (zeiss, oberkochen, germany) scanning electron microscope using 2 kv acceleration voltage after sputtering with gold palladium. as detectors, the in-lens and se detectors were used. the specimens were processed for tem according to a previously published protocol [21] . in brief, samples were fixed in ito's fixative (2.5% glutaraldehyde, 2.5% paraformaldehyde, and 0.3% picric acid) dissolved in phosphate buffered saline (pbs) (ph = 7.3) and embedded in epon. semi-thin sagittal sections of 1 µm were cut with a microtome (ultracut e; reichert jung, vienna, austria) and subsequently stained with toluidine blue. sections were viewed with an epifluorescence microscope (aristoplan; ernst leitz, wetzlar, germany) and photographed (keyence biorevo bz9000 microscope). ultrathin sections were stained with uranyl acetate and lead citrate and viewed with a transmission electron microscope (em109; carl zeiss meditec gmbh, oberkochen, germany). the naepcs were seeded in collagen coated 96 wells (day 0). at day 1, the culture medium was changed. for exposition experiments, dermatophagoides pteronyssinus (citeq biologics, netherlands, product code: 02.01.64) was used in different concentrations (1 µg/ml, 10 µg/ml, and 100 µg/ml) for two time points. the first time point included an exposition duration of 24 h. the read-out parameters will be presented in the course of the manuscript. after 24 h exposition with dermatophagoides pteronyssinus, the supernatant was removed, fresh begm ® cell culture medium was added, and naepcs were incubated for 24 h. after this incubation time, a second exposition with dermatophagoides pteronyssinus was performed for 24 h, and after that, the read-out parameters were measured (see below). these two time points were presented as 24 h and 72 h throughout the manuscript. in addition, to easily follow the manuscript, the term hdm was used for dermatophagoides pteronyssinus throughout the manuscript. we used different recombinant adv types deleted for the early gene region e3, which was replaced by a transgene expression cassette encoding the reporter genes luciferase and gfp [19] . in brief, recombinant viruses were amplified in permissive cell lines and purified using cesium-chloride gradients as described before [19] . we explored n = 21 different adv types derived from different species to transduce naepcs. twenty-four hours before transduction, we seeded 1 × 10 4 naepcs per well in collagen i pre-coated 96 wells plates. gfp and luciferase expressing adv types were added to each well using 50 viral particles per cell (vpc). twenty-four hours post transduction of naepcs, we determined luciferase activity within the transduced cells using the nano-glo ® luciferase assay system from promega. to perform the luciferase assay, we removed 100 µl supernatant, added nano-glo ® luciferase assay substrate and nano-glo ® luciferase assay buffer (dilution: 1:50) to cells, and incubated for up to 10 min at 37 • c and 5% co 2 until cells were detached. subsequently, luciferase expression levels were quantified using a tecan elisa reader. statistical analyses were performed using graphpad prism version 8.3.0 for windows, graphpad software, la jolla california usa, www.graphpad.com. data were presented as mean and standard error of the mean (sem) or as absolute values with percentages or fold changes (n = 3 to 5). comparisons between two groups were performed with unpaired/paired, two-tailed, and t-tests. comparisons between more than two groups were performed with one-way-anova and holm-sidak's multiple comparison posttest. the significance levels were set at * p < 0.05, ** p < 0.01, and *** p < 0.001. to prove the purity of the cultured cells derived from our pediatric exacerbation study cohort, flow cytometric analyses were performed for each culture. as presented in figure 1a , the isolated cells were cd45 neg epcam pos pan-cytokeratin pos . in addition, the morphology of the cultured cells was analyzed through raster electron microscopy (rem) as well as histology, which revealed the purity of the cultures (figure 1b,c) . to address the question whether naepcs were submissive to adv infection, we transduced cultured naepcs in a monolayer with 21 different luciferase and gfp expressing adv types ( figure 2 ) at 50 vpc. twenty-four hours post-transduction, the luciferase activity of infected cells was determined. permeabilization, anti-cytokeratin-fitc was used for intracellular staining. (b) after passage 2 (p2), the cells were seeded for organotypic 3d air-liquid interface cultures. nasal mucus secretion and ciliary beats were observed through light microscopy after 6 to 8 weeks of culturing. final specimens were then processed for raster electron microscopic imaging. (c) histologic analyses confirmed the morphology of the nasal epithelial cell population (10x magnification). to address the question whether naepcs were submissive to adv infection, we transduced cultured naepcs in a monolayer with 21 different luciferase and gfp expressing adv types ( figure 2 ) at 50 vpc. twenty-four hours post-transduction, the luciferase activity of infected cells was determined. as shown in figure 3 , adv type 5, followed by 9, 21, 3, and 35, showed the highest transduction rates in naepcs if directly compared to other adv types. therefore, adv5, as a common respiratory virus and the most analyzed virus in terms of gene therapeutic approaches, was then used for further analyses. to determine the infections rates of adv5 in naepcs, we transduced naepcs with adv5 using different vpc and measured the luciferase expression level and visualized gfp pos cells through immunofluorescence microscopy. twenty-five hours post-transduction, there was a clear correlation as shown in figure 3 , adv type 5, followed by 9, 21, 3, and 35, showed the highest transduction rates in naepcs if directly compared to other adv types. therefore, adv5, as a common respiratory virus and the most analyzed virus in terms of gene therapeutic approaches, was then used for further analyses. to determine the infections rates of adv5 in naepcs, we transduced naepcs with adv5 using different vpc and measured the luciferase expression level and visualized gfp pos cells through immunofluorescence microscopy. twenty-five hours post-transduction, there was a clear correlation between the virus dose, the luciferase expression levels, and the gfp + -expressing cell numbers. a cytopathic effect of infected cells associated with adenovirus infection was not observed (figure 4a,b) . it is assumed that patients with allergies and asthma suffer from increased virus infections [22] . therefore, we studied the virus transduction efficiency of adv5 in hdm-provoked naepcs. different concentrations of hdm (1 µg/ml, 10 µg/ml, and 100 µg/ml) were used to provoke naepcs ex vivo, and the schematic outline of this experiment is shown in figure 5 . between the virus dose, the luciferase expression levels, and the gfp + -expressing cell numbers. a cytopathic effect of infected cells associated with adenovirus infection was not observed (figure 4a,b) . between the virus dose, the luciferase expression levels, and the gfp + -expressing cell numbers. a cytopathic effect of infected cells associated with adenovirus infection was not observed (figure 4a,b) . it is assumed that patients with allergies and asthma suffer from increased virus infections [22] . therefore, we studied the virus transduction efficiency of adv5 in hdm-provoked naepcs. different concentrations of hdm (1 μg/ml, 10 μg/ml, and 100 μg/ml) were used to provoke naepcs ex vivo, and the schematic outline of this experiment is shown in figure 5 . during the nasal brushing procedure, we collected the cells in cell culture medium, centrifuged at 350x g for 8 min, and washed with pbs. the cell pellet was resuspended in cell culture medium, and the cells were seeded in collagen i pre-coated t75 flasks. after passage 2 (p2) was reached, naepcs were collected and seeded in collagen i pre-coated 96 well plates. different hdm concentrations were used (1 μl/ml, 10 μg/ml, 100 μg/ml). the transduction concentration of adv5 was set at 10 virus particle per cell (vpc). this figure was generated using biorender.com luciferase assays were performed one and three days post-transduction correlating with adv transduciton rates. there was a trend of increased adv transduction in healthy control cells and in cells derived from asthmatics. especially on day 3 after hdm exposure, we observed an enhanced adv mediated luciferase activity in hdm-provoked naepcs from asthmatics, compared to naepcs derived from healthy cells ( figure 6 ). during the nasal brushing procedure, we collected the cells in cell culture medium, centrifuged at 350× g for 8 min, and washed with pbs. the cell pellet was resuspended in cell culture medium, and the cells were seeded in collagen i pre-coated t75 flasks. after passage 2 (p2) was reached, naepcs were collected and seeded in collagen i pre-coated 96 well plates. different hdm concentrations were used (1 µl/ml, 10 µg/ml, 100 µg/ml). the transduction concentration of adv5 was set at 10 virus particle per cell (vpc). this figure was generated using biorender.com luciferase assays were performed one and three days post-transduction correlating with adv transduciton rates. there was a trend of increased adv transduction in healthy control cells and in cells derived from asthmatics. especially on day 3 after hdm exposure, we observed an enhanced adv mediated luciferase activity in hdm-provoked naepcs from asthmatics, compared to naepcs derived from healthy cells ( figure 6 ). to shed light on the underlying mechanism for enhanced adv5 uptake, major adv receptor expression levels, in particular, car, cd46, and dsg-2, were characterized on naepcs through flow cytometry. in comparison to hdm-provoked naepcs, we observed a significant increase of car and cd46 expression levels on naepcs of asthmatics as well as on naepcs of healthy donors. thus, we speculate that an increased adv receptor expression level may explain the enhanced adv5 transduction efficiency of naepcs after hdm exposition (figure 7a,b) . in contrast, there was no figure 6 . the effect of hdm stimulation and adv5 infection on naepcs. naepcs were stimulated at different time points (day 1 and day 3) with different hdm concentrations (1 µg/ml, 10 µg/ml, and 100 µg/ml), and the cells were subsequently transduced with adv5 at 10 virus particle numbers per cell (vpc). twenty-four hours post-transduction, luciferase assays were performed. we observed an increased adv5 transduction efficiency in pre-stimulated naepcs with hdm, particularly at day 3 in asthmatic specimens. this was in contrast to samples of healthy controls. values were normalized and presented as fold change given as mean and standard error of mean (sem). to shed light on the underlying mechanism for enhanced adv5 uptake, major adv receptor expression levels, in particular, car, cd46, and dsg-2, were characterized on naepcs through flow cytometry. in comparison to hdm-provoked naepcs, we observed a significant increase of car and cd46 expression levels on naepcs of asthmatics as well as on naepcs of healthy donors. thus, we speculate that an increased adv receptor expression level may explain the enhanced adv5 transduction efficiency of naepcs after hdm exposition (figure 7a,b) . in contrast, there was no significant difference in the expression level of dsg-2 on hdm-treated naepcs, compared to healthy naepcs controls (figure 7c ). the mean-pe values for car were set as absolute numbers. as shown, the asthmatic group had significant differences at car expression levels after hdm stimulation, particularly at day 3 compared to day 1. (b) the mean-apc values for cd46 were set as absolute numbers. as shown, the healthy control group showed significant differences between time points and concentration levels, compared to the asthmatic group (c) desmoglein-2-pe was not significantly different in terms of time points and concentration levels in healthy controls and asthmatics. to analyze whether hdm influences the barrier function on naepcs that may lead to enhanced adv transduction, we provoked 3d naepcs cultures with hdm and performed raster-em on days 1 (d1) and day 3 (d3). raster-em scan provided interesting insights into the irritated epithelium after high dosage of hdm, in particular at d3 (figure 8a ). measuring the lengths and thickness of the ciliary, there was no statistical differences for the different groups (figure 8b) . histologic analyses confirmed an increased mucus production and an irritated basal layer after hdm treatment (figure 8c ). furthermore, we observed a different tight junction conformation in organotypic 3d naepcs cultures of asthmatics compared to healthy controls. the tight junction conformation in untreated asthmatic samples was tightly packed and was presented in a higher number than the untreated control samples (figure 8d,e) . here, we characterized the effects of hdm exposition on adv infection in an ex vivo cell culture models of naepcs of exacerbated pediatric asthmatics and healthy controls from our pediatric exacerbation study. with this experimental approach, we successfully characterized the effects of hdm exposition on human adv infection in naepcs ex vivo. using a library of 21 luciferase-and gfp-tagged advs, we analyzed adv infection rates in naecps in the presence of hdm as a common allergen. we found that adv luciferase expression levels were significantly increased 3 days after hdm exposure in asthmatics, compared to healthy controls, hinting towards the hypothesis that replication of adv may be influenced by hdm stimulation. however, this hypothesis needs to be further analyzed by performing adv genome replication studies in naecps. it was described previously that virus infection can synergize with allergens in the induction of asthma exacerbations. the first study describing the interaction between rv infection and hdm exposure was performed by bossios et al. (2008) [23] . they observed an increase in cytokine levels in immortalized human bronchial epithelial cell line when rv and hdm were applied or when cells were provoked with hdm before rv infection [23] . interestingly, akbarshahi et al. (2018) found a similar effect by showing that hdm exposure affected the antiviral response provoked by virus infections [12] . furthermore, golebski et al. (2014) described a relationship between hdm and poly i:c stimulation in terms of gene and protein expression [24] . the results of our study broaden the preceding findings, as we have observed an increased uptake of adv5 after hdm stimulation potentially mediated by enhanced major adv receptor expression. our results represent the first in vitro evidence that hdm stimulation may increase susceptibility to adv infections. adenovirus receptors, including car, cd46, or dsg-2, are required for uptake of adv into the respective target cell. adv5 mostly interacts with car, whereas cd46 and dsg-2 receptors are used by adv3, 7, 14, and others. car is localized on the basolateral and apical surface of the epithelial cells. lung epithelial cells are interconnected by tight junctions. by this formation, the basolateraly-located car receptors may protect the cell from the interaction with adv [25] [26] [27] . the flow cytometric analyses of hdm-provoked naepcs showed higher levels of car on naepcs. in contrast to the work of excoffon et al., our data do not include the analyses of a car localization shift but include the adenoviral susceptibility of hdm-provoked cells [27] . we speculate that an upregulation of adv receptors upon hdm inhalation may lead to increased susceptibility to adv infection in patients with allergic rhinitis or asthma exacerbation in vivo. however, to support this hypothesis, additional in vivo experiments are needed. we furthermore noticed a low but measurable increase of cd46 receptor expression levels on naepcs after hdm exposition. contrary to our results, tsai and colleagues (2018) observed decreased cd46 levels and increased apoptosis in primary nasal mucosa samples from adult mild asthmatics when cultured with hdm extracts [28] . naepcs gained increased attention as a model to study asthma development, to study immune responses during virus infection in asthma patients, and to define biomarkers specific for asthma and virus infections [29] [30] [31] . their innate immune reactions such as toll-like receptor pathways, secretion of il-33, or thymic stromal lymphoprotein boost adaptive immune responses and start a broad range of stimulation processes, e.g., activation of naïve t cells [18] . by using naepcs from healthy and allergic subjects, vroling et al. showed that both groups had differences in the chemokine, growth factor, and transcription factor levels [16, 17] . thus, naecps represent a valuable alternative as an ex vivo model, compared to tracheal or bronchial epithelium of the small airways. this further supports the use of naecps in our study to explore the relationship between asthma development, hdm exposure, and adv infections. future studies should analyze immune responses in these cells after hdm exposure and adv infection. note that the used set-up of the present study was completely based on a primary human biomaterial database. this is in contrast to other published studies, which exemplarily used cancer cell lines to correlate their experimental findings with clinical observations. in summary, this work provides novel insights into the mechanism of adenoviruses on the airway epithelium of asthmatics. to the best of our knowledge, this is the first ex vivo study presenting the impact of hdm sensitization on adv infection in an in vitro exposition model. our study may open new paths for the interaction between allergens and virus infections, and may provide a basis for further potential gene therapeutic approaches in treatment of childhood asthma exacerbation. this work analyzed the interaction of the hdm exposition in the presence of adv infection in an in vitro model based on naepcs. we demonstrate that a pre-stimulation with hdm may induce an increased adv infection rate at least partially mediated by increased car receptor expression. moreover, electron microscopy and histologic imaging revealed an effect on the cilia in organotypic 3d cell cultures when exposed to hdm that may be 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studies we thank the center for biomedical education and research, school of life sciences (zbaf), and its members for their intellectual input during seminars and lectures of the zbaf ph.d. program. we thank manuela besser for the technical preparation of few 3d cultures for histologic analyses. we appreciate the support of susanne haussmann from the witten/herdecke university, germany; elke kretschmar from the friedrich-alexander-university erlangen, germany; and the colleagues, including nurses, physicians, and technicians of the emergency room of the children's hospital of the helios university medical hospital of the witten/herdecke university, germany. in addition, we thank the children and parents who participated in this study. finally, figure 5 was created with biorender.com. funding: this research received funding from the internal research promotion of the faculty of health at witten/herdecke university, germany (iff 2019-13). the funding organizations had no role in the design and conduction of the study; sample collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; or decision to submit the manuscript for publication. the authors declare that the research was conducted in the absence of any commercial or financial relationships that could be constructed as a potential conflict of interest. the authors have declared that they have no competing interests. this work has not been published before, and it is not under consideration for publication elsewhere. the manuscript has been approved for publication by all co-authors. key: cord-329900-lq91rb8c authors: seiffert, moritz; brunner, fabian j.; remmel, marko; thomalla, götz; marschall, ursula; l’hoest, helmut; acar, laura; debus, eike s.; blankenberg, stefan; gerloff, christian; behrendt, christian-alexander title: temporal trends in the presentation of cardiovascular and cerebrovascular emergencies during the covid-19 pandemic in germany: an analysis of health insurance claims date: 2020-08-04 journal: clin res cardiol doi: 10.1007/s00392-020-01723-9 sha: doc_id: 329900 cord_uid: lq91rb8c aims: the first reports of declining hospital admissions for major cardiovascular emergencies during the covid-19 pandemic attracted public attention. however, systematic evidence on this subject is sparse. we aimed to investigate the rate of emergent hospital admissions, subsequent invasive treatments and comorbidities during the covid-19 pandemic in germany. methods and results: this was a retrospective analysis of health insurance claims data from the second largest insurance fund in germany, barmer. patients hospitalized for acute myocardial infarction, acute limb ischemia, aortic rupture, stroke or transient ischemic attack (tia) between january 1, 2019, and may 31, 2020, were included. admission rates per 100,000 insured, invasive treatments and comorbidities were compared from january–may 2019 (pre-covid) to january–may 2020 (covid). a total of 115,720 hospitalizations were included in the current analysis (51.3% females, mean age 72.9 years). monthly admission rates declined from 78.6/100,000 insured (pre-covid) to 70.6/100,000 (covid). the lowest admission rate was observed in april 2020 (61.6/100,000). administration rates for st-segment elevation myocardial infarction (7.3–6.6), non-st-segment elevation myocardial infarction (16.8–14.6), acute limb ischemia (5.1–4.6), stroke (35.0–32.5) and tia (13.7–11.9) decreased from pre-covid to covid. baseline comorbidities and the percentage of these patients treated with interventional or open-surgical procedures remained similar over time across all entities. in-hospital mortality in hospitalizations for stroke increased from pre-covid to covid (8.5–9.8%). conclusions: admission rates for cardiovascular and cerebrovascular emergencies declined during the pandemic in germany, while patients’ comorbidities and treatment allocations remained unchanged. further investigation is warranted to identify underlying reasons and potential implications on patients’ outcomes. graphic abstract: [image: see text] electronic supplementary material: the online version of this article (10.1007/s00392-020-01723-9) contains supplementary material, which is available to authorized users. since its outbreak in wuhan, hubei province, china, in december 2019, the novel sars coronavirus (sars-cov-2) has spread rapidly, causing an outbreak of acute and severe respiratory illness worldwide [1] . the first disease outbreak news from the world health organization (who) had been issued january 5, 2020. after a rapid spread of sars-cov-2 in italy [2] and other european regions, several countries issued strict infection control measures. elective in-hospital procedures were widely cancelled or postponed to provide additional capacities for the treatment of covid-patients in germany, starting in march 2020 [3, 4] . while an association between acute viral respiratory disease and subsequent cardiovascular events had been described for other diseases (e.g., influenza) [5, 6] , several centers reported a decline in hospital admissions for acute cardiovascular and cerebrovascular emergencies during the covid pandemic [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] . since acute cardiovascular and cerebrovascular diseases remain leading causes for morbidity and mortality, further investigation of this concerning trend is warranted to identify potential implications for both health-care professionals and regulators. this analysis sought to determine trends in admission rates, invasive treatments, and comorbidities of inpatients treated for cardiovascular and cerebrovascular emergencies during the sars-cov-2 pandemic in germany. this was a retrospective analysis of routinely collected health insurance claims data. based on their primary or admission diagnosis, we included all patients with inpatient treatment between january 1, 2019, and may 31, 2020, for cardiovascular and cerebrovascular emergencies. these included (1a) st-segment elevation myocardial infarction (stemi), (1b) non-st-segment elevation myocardial infarction (nstemi), (2) acute limb ischemia, (3) acute aortic rupture, (4a) acute stroke and (4b) transient ischemic attack (tia) (for detailed coding see supplemental table 1 ). data collected during the pandemic (covid: january through may 2020) were compared to a control period in the previous year (pre-covid: january through may 2019). the primary study end point was the absolute number of monthly hospitalizations and the corresponding admission rate per 100,000 insured inhabitants. secondary end points included the absolute number and proportion of invasive procedures provided to these patients (for detailed coding see supplemental table 1) , as well as all-cause mortality during the hospital stay and the proportion of relevant comorbidities and socio-demographic variables. the longitudinal data of germany's second-largest insurance fund, barmer, includes the outpatient and inpatient medical care provided to up to 9.4 million (from 2008 to 2020) german citizens (13.2% of germany's population) involving more than 24 million hospitalizations between january 1, 2008, and may 31, 2020. the barmer cohort is similar to western european countries and has been widely used for research projects before [20, 21] . a regular random sample validation of internal and external validity is performed by the medical service of the health funds (mdk) in germany, and various peer-reviewed validation studies have been published before [22, 23] . the diagnoses and comorbidities routinely collected in health insurance claims data follow the commonly accepted international standard for reporting diseases and health conditions using world health organization (who) international classification of diseases in its 10th revision of the german modification (icd-10-gm) and operations and procedures codes (ops) as a german adaptation of the international classification of procedures in medicine (icpm) by who. the primary diagnosis of the hospital case was used to discriminate between the cardiovascular or cerebrovascular emergencies. in approximately 0.6% of the most current hospitalizations (in may 2020), the admission diagnosis was utilized on a supplementary basis if no primary diagnosis was available. in addition to age (in years) and gender (dichotomized), we used the following icd-10 codes to identify diabetes (e10*, e11*, e12*, e13*, e14*), hypertension (i10*, i11*, i12*, i13*, i14*, i15*), heart failure (i50*), atrial fibrillation (i48*), chronic ischemic heart disease (i25*), obesity (e66*), chronic renal disease (n18*), chronic obstructive pulmonary disease (copd, j44*), and cancer (c00-97*) as comorbidities among the study sample. all-cause mortality was provided during the index hospital stay. we summarized the baseline characteristics of the patients with means for age and with percentages and 95% confidence interval (ci) for discrete variables. a comparison of 95% ci and chi square test was used to test for differences. for table 1 , we compared symmetric samples from january 01, 2019, to may 31, 2019 (pre-covid), vs. january 01, 2020, to may 31, 2020 (covid), to adjust for seasonal effects. missing data (0.6%) were handled by exclusion. as additional sensitivity analysis, we compared the study variables using shorter time periods (e.g., march 2019 vs. march 2020, april 2019 vs. april 2020, may 2019 vs. may 2020). besides, we determined the admission rates using either both primary and admission diagnosis vs. only primary diagnosis (only reimbursed cases). data processing was performed with software sas version 9.04 (sas institute, north carolina, usa) and spss version 25 (ibm corporation, new york, usa), visualization was performed with software adobe illustrator version 24.1.2 (adobe, california, usa). we identified 115,720 hospitalizations (mean age 72.9 years, 51.3% females, 95% ci 51.0% to 51.6%) for cardiovascular or cerebrovascular emergencies between january 1, 2019, and may 31, 2020 (monthly mean: 6,807 patients) ( table 1) . among all hospitalizations, a total of 8,202 deaths occurred. the monthly hospital admission rate for cardiovascular or cerebrovascular emergencies declined from a maximum of 83.8 per 100,000 in january 2019 to a minimum of 61.6 per 100,000 in april 2020, which increased to 67.1 per 100,000 in may 2020 (mean: 75.2 per 100,000). comparing pre-covid to covid time frames, overall monthly admission rates declined from 78.6 per 100,000 to 70.6 per 100,000. this was observed across all strata ( fig. 1) : admission rates per 100,000 during covid compared to pre-covid decreased for stemi (7.3 vs. 6.6, − 12.2% percentage points, p.p.), nstemi (16.8 vs. 14.6, − 15.2% p.p.), acute limb ischemia (5.1 vs. 4.6, − 12.4% p.p.), stroke (35.0 vs. 32.5, − 8.9% p.p.), and tia (13.7 vs. 11.9, − 14.6% p.p.). no relevant differences were observed for aortic ruptures (0.6 vs. 0.5) ( fig. 1 and table 1 ). the lowest admission rates were noted in april 2020 (61.6 per 100,000) with declines in stemi (− 16.3%), nstemi (− 21.5%), acute limb ischemia (− 22.5%), stroke (− 17.8%), and tia (− 30.2%) compared to the respective rates in april 2019. for may 2020, slowly recovering admission rates were observed for nstemi, stemi, ali, stroke, and tia compared to april 2020 (fig. 1 ). the admission rates of nstemi and stemi and the corresponding numbers of daily sars-cov-2 infections in germany from january through may 2020 are depicted in fig. 1a . comorbidities, cardiovascular risk profiles and sociodemographic variables were similar among patients admitted during covid compared to pre-covid eras (table 1) . besides patients admitted for stroke (8.5-9 .8%), the inhospital mortality was similar among patients admitted during covid compared to pre-covid eras (table 1) . table 1 admission rates and baseline characteristics and comorbidities of pre-covid vs. covid groups (january to may 2019 vs. january to may 2020) proportions for comorbidities are presented as % with 95% confidence interval in parentheses # statistically significant differences (p < 0.05). n.s. the percentage of patients admitted for cardiovascular or cerebrovascular emergencies, who underwent interventional or open-surgical procedures during the hospital stay, were similar between pre-covid and covid periods for stemi (84.7-86.3%), nstemi (58.0-60.5%), acute limb ischemia (81.9-82.8%), aortic rupture (51.5-56.7%), stroke (18.4-19.1%), and tia (2.1-2.2%) (fig. 2 and table 1 ). all sensitivity analyses were confirmative (not shown). this analysis of a large dataset of routinely collected health insurance claims demonstrated a marked decrease in hospital admission rates for several cardiovascular and cerebrovascular emergencies during the covid-19 pandemic in germany. these patients' comorbidities and the percentage of them, who were treated invasively, remained unchanged. a concerning decline of more than 40% in hospital admissions for acute coronary syndromes after the covid-19 outbreak had been reported in smaller series of severely affected regions [9, 11-14, 18, 24] . we observed reductions of 12.2% in patients presenting with stemi and 15.2% with nstemi in a large representative sample of the german population during a longer phase of observation (january through may 2020). the maximum decline of nstemi presentations was detected in april 2020 (− 21.5% compared to 2019), followed by a slow recovery in may 2020, essentially mirroring sars-cov-2 infection rates in germany. these observations were of particular interest asopposed to other countries-germany was not affected as strongly by the covid-19 pandemic and a significant limitations of health-care resources did not become evident. this may explain why we found a milder decline compared to regions heavily affected by the disease outbreak [25] and was in line with reports from other less-affected areas reporting reductions of approximately 25% in acute cases. interestingly, admissions for several cardiovascular and cerebrovascular emergencies started to increase again in may, suggesting a potential recovery after a significant drop in new daily covid-19 cases and a liberalization of public restrictions in germany. similar trends were observed for patients with acute cerebrovascular and peripheral vascular diseases. using surrogate markers for the quantity of care, a large recent analysis reported a decrease of 39% in march 2020 in patients presenting with acute ischemic stroke to us hospitals [8] . the results of the current study confirmed declines in strokes and tia during the pandemic in germany, albeit less severe. consistent with these observations, we detected a marked decline in the admission rates for acute limb ischemia during the pandemic. whether this translates into increased disease severity and worse outcomes as others have suggested [26] will need to be investigated. additional information on age, gender, and comorbidities revealed patient populations to be similar before and during the pandemic, arguing against the notion that milder affected patients might particularly refrain from seeking medical care, thus shifting the severity of diseases. likewise, treatment allocation of the patients admitted remained unchanged. furthermore, in the current study, patients presenting to the emergency departments with acute cardiovascular or cerebrovascular disease had a similar chance to receive interventional or open-surgical therapy before and during the pandemic in germany. this seems to be an indicator for an ongoing high-level medical therapy during this time period. since rapid diagnosis and treatment of acute coronary syndromes are important to avoid further complications [27, 28] , recently published results from italy are alarming reporting a delay in coronary revascularization and increasing rates of case fatality and major complications in patients suffering from acute myocardial infarction during covid-19 [14] . to guide the management of acute coronary syndromes and cardiovascular disease during the covid-19 pandemic and to contain collateral damage, the european association of percutaneous cardiovascular interventions and german cardiac society recently issued comprehensive expert documents [29, 30] . the root causes for the observed decline in acute admissions for cardiovascular and cerebrovascular diseases remain unclear and may be multifactorial: avoidance of medical care due to patient-based anxiety and fear of contagion during the pandemic may play an important role. however, an attitude toward increased deferrals of less urgent cases by health-care personnel and lifestyle changes among other confounders during the time of extensive social restrictions need to be evaluated as well. patient information and public education will be of paramount importance to contain collateral damages caused by delayed medical treatment for acute cardiovascular and cerebrovascular diseases. most previous reports on this topic used either surveys [31], selective multi-center data, or surrogate parameters (e.g., use of imaging software) [8] to quantity patient care. population-based data investigating emergency admissions in this setting validly remain scarce. nevertheless, the following limitations merit consideration. first, health insurance claims data were not primarily collected for research purposes and retrospective observational studies are unsuitable to prove underlying causal relationships. however, data from health insurance claims, as used in this analysis, may help to identify potential implications for both healthcare professionals and regulators at an early stage. second, while longitudinal data were available between 2008 and today, pandemic measures in germany began in february 2020 with no relevant follow-up available. therefore, future analyses investigating patients' outcomes are required. this is particularly important for mortality, albeit differentiating covid-19-related mortality from mortality due to other causes in the light of covid infection will remain complex from insurance claims data. third, admission diagnoses were used for current analyses in a small share of cases in may 2020 (0.6%) if the main diagnosis was not yet submitted. however, comorbidities were only analyzed for individuals with complete datasets available to avoid classification bias. last, the barmer sample included a relevant proportion of the entire population in germany. a selection bias appeared unlikely and the barmer cohort was comparable to other european countries in terms of comorbidities, age, and gender. in contrast to clinical registries or administrative data, the barmer cohort was less affected by selection bias and includes all age groups, all hospitals, and all medical specialties. however, spatial analyses aiming for regional differences were not feasible in the existing dataset. in this large-scale retrospective analysis of health insurance claims, we observed a marked decrease of in-hospital admission rates for acute cardiovascular and cerebrovascular emergencies including myocardial infarction, acute limb ischemia, stroke, and transient ischemic attack during the covid-19 pandemic in germany. no changes were seen in these patients' comorbidities and treatment allocations. the underlying root cause for these developments and subsequent implications on patient outcomes warrant further investigation. public education will be important to contain collateral damage caused by delayed treatment for acute cardiovascular and cerebrovascular diseases. ted work. dr. gerloff reports personal fees from amgen, bayer vital, bristol-myers squibb, boehringer ingelheim, sanofi aventis, abbott, and prediction biosciences outside the submitted work. dr. behrendt and dr. debus report grants from the german federal joint committee and grants from german stifterverband outside the submitted work. the other authors declare no conflicts of interest. ethics approval several review boards have determined that using anonymized data from claims or national statistics retrospectively is not human subject research because de-identified datasets were used. consent to participate all analyses were following the european union general data privacy regulation (eu-gdpr), considering the theoretical concept of k-anonymity. thus, patient informed consent was not obtained for this retrospective secondary data analysis [31] . availability of data and material (data transparency) the data will be shared on reasonable request to the corresponding author. open access this article is licensed under a creative commons attribution 4.0 international license, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the creative commons licence, and indicate if changes were made. the images or other third party material in this article are included in the article's creative commons licence, unless indicated otherwise in a credit line to the material. if material is not included in the article's creative commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. to view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/. a novel coronavirus outbreak of global health concern pattern of vascular disease in lombardy, italy, during the first month of the covid-19 outbreak cardiovascular disease and surgery amid covid-19 pandemic the global impact of covid-19 on vascular surgical services role of acute infection in triggering acute coronary syndromes acute myocardial infarction after laboratory-confirmed influenza infection 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time-series analysis in a tertiary greek general hospital where have the stemis gone during covid-19 lockdown? an increased severity of peripheral arterial disease in the covid-19 era esc guidelines for the management of acute myocardial infarction in patients presenting with st-segment elevation: the task force for the management of acute myocardial infarction in patients presenting with st-segment elevation of the european society of cardiology (esc) accf/aha guideline for the management of st-elevation myocardial infarction: a report of the american college of cardiology foundation eapci position statement on invasive management of acute coronary syndromes during the covid-19 pandemic coronavirus disease 2019 (covid-19) and its implications for cardiovascular care: expert document from the german cardiac society and the world heart federation acknowledgment open access funding provided by projekt deal. key: cord-337339-0vkigjv2 authors: osterrieder, nikolaus; bertzbach, luca d.; dietert, kristina; abdelgawad, azza; vladimirova, daria; kunec, dusan; hoffmann, donata; beer, martin; gruber, achim d.; trimpert, jakob title: age-dependent progression of sars-cov-2 infection in syrian hamsters date: 2020-07-20 journal: viruses doi: 10.3390/v12070779 sha: doc_id: 337339 cord_uid: 0vkigjv2 in late 2019, an outbreak of a severe respiratory disease caused by an emerging coronavirus, sars-cov-2, resulted in high morbidity and mortality in infected humans. complete understanding of covid-19, the multi-faceted disease caused by sars-cov-2, requires suitable small animal models, as does the development and evaluation of vaccines and antivirals. since age-dependent differences of covid-19 were identified in humans, we compared the course of sars-cov-2 infection in young and aged syrian hamsters. we show that virus replication in the upper and lower respiratory tract was independent of the age of the animals. however, older hamsters exhibited more pronounced and consistent weight loss. in situ hybridization in the lungs identified viral rna in bronchial epithelium, alveolar epithelial cells type i and ii, and macrophages. histopathology revealed clear age-dependent differences, with young hamsters launching earlier and stronger immune cell influx than aged hamsters. the latter developed conspicuous alveolar and perivascular edema, indicating vascular leakage. in contrast, we observed rapid lung recovery at day 14 after infection only in young hamsters. we propose that comparative assessment in young versus aged hamsters of sars-cov-2 vaccines and treatments may yield valuable information, as this small-animal model appears to mirror age-dependent differences in human patients. emerging coronaviruses have caused serious global public health concerns in the past two decades and cause infections that lead to severe respiratory and occasionally systemic disease [1] . these include severe acute respiratory syndrome (sars)-cov as well as middle east respiratory syndrome (mers)-cov, both of which resulted in high morbidity and mortality in infected humans [2, 3] . similar to other emerging cov, the novel sars-cov-2 likely arose from an ancestor in bats and amplified in a yet unknown animal reservoir before making its jump into the human population [4] . sars-cov-2 has pushed global health systems to the brink of breakdown. the remarkably fast and unexpected spread of sars-cov-2 can be attributed to efficient replication in the upper respiratory tract and robust human-to-human transmission. while covid-19 is primarily a respiratory syndrome, it can induce quite variable clinical signs including fatigue, headache, and gastrointestinal symptoms, which can in severe cases result in fatality [5] . it has become evident that differences in the type and severity of sars-cov-2-induced disease and its sequelae seem to be strongly correlated with the age of patients and exacerbated by pre-existing medical conditions (e.g., chronic obstructive pulmonary disease, heart disease, diabetes, obesity) [1, [6] [7] [8] . the availability of reliable animal models is of critical importance for pathogenesis studies as well as the development and preclinical evaluation of vaccines and therapeutics [2, 9, 10] . for sars-cov-2, the susceptibility of several animal species was predicted by in silico analysis based on comparisons of the entry receptor for sars-cov and sars-cov-2, angiotensin converting enzyme 2 (ace2). these predictions are of relevance because the ace2 sequence is deemed an important factor governing susceptibility [11] . more specifically, the interaction of the viral spike (s) glycoprotein receptor binding domain with its ace2 counterpart was examined [12, 13] , and in some cases confirmed in vivo [9] . productive sars-cov-2 infection was shown in non-human primates, which developed respiratory disease recapitulating moderate disease as observed in humans [14] [15] [16] [17] . mice are not naturally susceptible to sars-cov-2, but mouse-adapted virus strains have been developed and used in balb/c mice [18, 19] . moreover, transgenic mice expressing human ace2 represent a lethal sars-cov-2 infection model resulting in significant weight loss and permitting robust virus replication in the respiratory tract including the lungs [20] . ferrets have provided valuable data in the case of sars-cov [21, 22] , and two studies describe the infection of ferrets with sars-cov-2 and successful transmission to in-contact animals without clinical signs [23, 24] . first and preliminary studies also focused on the assessment of a syrian hamster model that had previously been used successfully in sars and mers research [21, 22, 25, 26] . it was suggested that hamsters are highly susceptible, although they were reported to show no or only moderate respiratory signs and body weight losses. however, it is important to note that only young male hamsters of 4 to 5 weeks of age were used in these studies [27, 28] . we sought to explore age-related differences in the course of sars-cov-2 infection in syrian hamsters and to establish a small-animal model that resembles the more severe sars-cov-2-infection observed particularly in elderly patients. we conducted all animal work in compliance with relevant national and international guidelines for care and humane use of animals. the animal use protocol for the experiments reported here was approved by the landesamt für gesundheit und soziales in berlin, germany (approval number 0086/20; approved on 30.04.2020). virus stocks were prepared from a previously published sars-cov-2 isolate (betacov/germany/bavpat1/2020) [29] , which was kindly provided by drs. daniela niemeyer und christian drosten, charité berlin, germany. the isolate, referred to as sars-cov-2 münchen (sars-cov-2m) [30] , was handled under the appropriate safety precautions in a bsl-3 facility (freie universität berlin, institut für virologie) and propagated on vero e6 cells (atcc crl-1586) in minimal essential medium (mem; pan biotech, aidenbach, germany) supplemented with 10% fetal bovine serum (pan biotech), 100 iu/ml penicillin g and 100 µg/ml streptomycin (carl roth, karlsruhe, germany). thirty-six 6-or 32-to-34-week-old female and male syrian hamsters (mesocricetus auratus; breed rjhan:aura, janvier labs, saint-berthevin, france) were kept in individually ventilated cages (ivcs; tecniplast, buguggiate, italy) in an approved bsl-3 facility. ivcs were equipped with enrichment (carfil, oud-turnhout, belgium). all animals had unrestricted access to food and water and were allowed to acclimate to the conditions for seven days prior to infection. cage temperatures and relative humidities were recorded daily and ranged from 22-24 • c and 40-55%, respectively. the 6-week-old hamsters were randomly distributed into two groups: mock (n = 12, 6-week-old) and young infected (n = 12, 6-week-old). the third group represents the aged infected hamsters (n = 12, 32-34-week-old). iptt-300 transponders (biomedic data systems, seaford, de, usa) were subcutaneously implanted into all hamsters 2 days prior to infection to allow the identification and monitoring of body temperatures. animals were mock-infected with 60 µl medium from uninfected vero e6 cells or infected with 1 × 105 pfu sars-cov-2m in 60 µl by intranasal instillation. for transponder implantation, hamsters were sedated with butorphanol (2.5 mg/kg; cp-pharma, burgdorf, germany) and midazolam (2 mg/kg; braun, melsungen, germany). for infections, hamsters were sedated with ketamine (25 mg/kg; serumwerk bernburg, bernburg, germany) and midazolam (2 mg/kg; braun). on 2, 3, and 5 days post-infection (dpi), three randomly assigned hamsters of each group were euthanized by exsanguination under medetomidine (0.15 mg/kg; pharma-partner, hamburg, germany), midazolam (2 mg/kg), and butorphanol (2.5 mg/kg) anesthesia [31] . blood, nasal washes, bucco-laryngeal swabs, lungs (left and right), kidneys, spleens, duodenums, and blood sera were collected for (histo)pathological examinations and/or virus titrations, rt-qpcr, and serological examination. during the 14-day experiment, body temperatures, body weights, and clinical signs of all animals were monitored twice daily. animals that had a body weight loss of more than 10% weight over a 72 h period were euthanized in compliance with the animal use protocol. such humane termination applies to the two hamsters euthanized 7 dpi. for histopathology and in situ hybridization (ish), the left lung lobe was carefully removed, immersion-fixed in formalin, ph 7.0, for 48 h, embedded in paraffin, and cut in 2 µm sections. for histopathology, slides were stained with hematoxylin and eosin (he) after dewaxing in xylene and rehydration in decreasing ethanol concentrations. lung sections were microscopically evaluated in a blinded fashion by a board-certified veterinary pathologist to assess the character and severity of pathologic lesions using lung-specific inflammation scoring parameters as described for other lung infection models before [32] . three different scores were used that included the following parameters: (1) lung inflammation score including severity of (i) interstitial pneumonia (ii) bronchitis, (iii) epithelial necrosis of bronchi and alveoli, and (iv) hyperplasia of type ii-alveolar epithelial cells; (2) immune cell infiltration score taking into account the presence of (i) neutrophils, (ii) macrophages, and (iii) lymphocytes in the lungs as well as (iv) perivascular lymphocytic cuffing; and (3) edema score including (i) alveolar edema and (ii) perivascular edema. ish was performed as reported previously [33] using the viewrna™ ish tissue assay kit (invitrogen by thermo fisher scientific, darmstadt, germany) following the manufacturer's instructions with minor adjustments. probes for the detection of n gene rna of sars-cov-2 (ncbi database nc_045512.2, nucleotides 28,274 to 9533, assay id: vpnkrhm) and the mouse housekeeping gene eukaryotic translation elongation factor-1α (ef1a; assay id: vb1-14428-vt, affymetrix, inc., santa clara, ca, usa), which shares 95% sequence identity with the syrian hamster orthologue, were designed. lung sections (2 µm thickness) on adhesive glass slides were dewaxed in xylol and dehydrated in ethanol. tissues were incubated at 95 • c for 10 min with subsequent protease digestion for 20 min. sections were fixed with 4% paraformaldehyde in phosphate-buffered saline (alfa aesar, thermo fisher, kandel, germany) and hybridized with the probes. amplifier and label probe hybridizations were performed according to the manufacturer's instructions using fast red as the chromogen, followed by counterstaining with hematoxylin for 45 s, washing in tap water for 5 min, and mounting with roti ® -mount fluor-care dapi (4, 6-diaminidino-2-phenylindole; carl roth). for negative and morphologically intact controls, lungs from uninfected hamsters of each group (n = 4) were included. in addition, an irrelevant probe for the detection of pneumolysin was used as a negative control for unspecific reactions. he-stained and ish slides were analyzed and images were taken using an olympus bx41 microscope with a dp80 microscope digital camera and the cellsens™ imaging software, version 1.18 (olympus corporation, münster, germany). for the display of overviews of whole lung lobe sections, slides were automatically digitized using the aperio cs2 slide scanner (leica biosystems imaging inc., vista, ca, usa), and image files were generated using the image scope software (leica biosystems imaging inc.). the percentages of lung tissues affected by inflammation were determined histologically by an experienced board certified experimental veterinary pathologist (k.d.) as described previously [34] . lung inflammation scores were determined as (0) absent, (1) minimal, (2) mild, (3) moderate, or (4) severe, and quantified as described previously [35] . immune cell influx scores and edema scores were rated from (0) absent to (1) sporadic, (2) mild, (3) moderate, or (4) severe. ish signals were digitally quantified on scanned whole slides of each animal using the aperio positive pixel count algorithm (leica biosystems imaging inc.) with minor adjustments. specifically, a positivity score encompassing the number of positive pixels in relation to the total number of pixels per tissue scan as well as the total intensity of positive pixels were determined ( figure s3 ). for an assessment of virus titers from 25 mg of lung tissue, tissue homogenates were serially diluted and plated on vero e6 cells in 12-well cell culture plates (sarstedt, nümbrecht, germany). at 3 dpi, cells were fixed in 4% formalin, stained with 0.1% crystal violet (in 25% methanol), and plaques were counted. rna was extracted from nasal washes and tracheal swabs with the rtp dna/rna virus mini kit (stratec, birkenfeld, germany) according to the manufacturer's instructions. the innuprep virus dna/rna kit (analytic jena, jena, germany) was used for rna extractions from tissue samples. viral rna was quantified using a one-step rt qpcr reaction with the neb luna universal probe one-step rt-qpcr (new england biolabs, ipswitch, ma, usa) and the 2019-ncov rt-qpcr primers and probe (e_sarbeco) [36] on a steponeplus realtime pcr system (thermo fisher scientific, waltham, ma, usa) according to the manufacturer's instructions. viral rna copies were then normalized to cellular rpl18 as previously described [37] . all primers and probes are listed in table s2 . standard curves for absolute quantification were generated from serial dilutions of sars-cov-2 rna obtained from a full-length virus genome cloned as a bacterial artificial chromosome and propagated in e. coli or from serial dilutions of the purified hamster rpl-18 pcr product. the latter was generated by pcr using rpl-18 qpcr-primers (table s2 ) and a cdna template obtained from hamster lung tissue. in lung tissue, viral rna copies were calculated per 1×10 5 hamster rpl-18 transcripts. for serum neutralization assays, 50 µl of medium containing 103.3 tissue culture infectious doses 50 (tcid 50 ) of sars-cov-2m were mixed with 50 µl of diluted serum. each sample was tested in triplicate. after 1 h incubation at 37 • c, the mixture was transferred to confluent vero e6 cells in a 96-well plate (sarstedt, nümbrecht, germany). viral replication was assessed after 3 days by the detection of cytopathic effects. statistical analyses were performed using graph-pad prism v8 (graphpad software inc., san diego, ca, usa). the statistical details of all analyzed experiments can be found in the respective figure legend. for our experiments, we used a total of 36 female and male syrian hamsters (mesocricetus auratus), which were either 6 (n = 24) or 32 to 34 weeks old (n = 12). hamsters were kept in individually ventilated cages (ivcs) and randomly assigned to three groups: mock (n = 12, 6-week-old), young infected (n = 12, 6-week-old) and aged infected (n = 12, 32-to 34-week-old). animals were mock-infected with supernatants of cell culture medium taken from uninfected vero e6 cells or infected with 1 × 10 5 plaque-forming units of sars-cov-2 münchen (sars-cov-2m; betacov/germany/ bavpat1/2020) [30] . during the 14-day experiment, body temperatures, body weights, and clinical signs were recorded daily. animals were euthanized and sampled at different time points after infection to assess virus titers in various organs and to examine pathological changes in the lungs (figures 1 and 2) . each group (n = 3 for 2, 3, and 5 dpi, n = 1 for 7 dpi and n = 2 for 14 dpi; bar = 0.5 cm) (b) affected areas of inflammation were identified histologically for each lung and compared between the groups. (c) lung inflammation score taking into account (i) severity of pulmonary inflammation; (ii) bronchitis (iii) bronchial and alveolar necrosis; iv) hyperplasia of alveolar epithelial cells type ii. (d) immune cell influx score taking into account the infiltration of lung tissue with (i) neutrophils; (ii) macrophages; (iii) lymphocytes; (iv) perivascular lymphocytic cuffing; and (e) edema score including (i) alveolar and (ii) perivascular edema. scores and parameters in c to e were graded as absent (0), minimal (1), mild (2), moderate (3), or severe (4) as described [35] . (f) time-dependent distribution of sars-cov-2 rna signals in young and adult hamsters representative of each group as detected by in situ hybridization (group sizes as in a; for digital image analysis of the differences, see figure s3 ; bar = 0.5 cm). first, we observed age-dependent sars-cov-2-induced body weight losses, with more pronounced weight reductions in aged compared to young hamsters ( figure 1a-c) . mean body weight losses peaked at 6 to 7 days post-infection (dpi), with partial recovery until 14 dpi in both infected groups. there were no differences in body temperatures between the infected groups or between infected and mock-infected animals ( figure 1d ). next, we determined viral titers and sars-cov-2 rna copy numbers in various tissues by rt-qpcr [36, 37] and performed virus titrations from lung homogenates using vero e6 cells ( figure 1e -h). results were similar between age groups and confirmed high viral loads in respiratory samples at early time points after infection, but a relatively rapid clearance of infection. while we did not identify any other sex-specific differences, it seems important to note that the rt-qpcr of blood samples revealed viremia in two male individuals from both age groups with viral rna copy numbers of >10 5 at 5 and 7 dpi, respectively ( figure 1i ). in these individuals, we also detected relatively high levels of viral rna in the spleen, kidneys, and duodenum, indicating a systemic spread of sars-cov-2 in some cases (table s1 ). to further investigate the potential dissemination of infection, we tested the aforementioned organs from all animals sacrificed at 5 dpi and found them to be either negative for sars-cov-2 rna or to contain only low levels of viral rna (table s1 ). viral loads in bucco-laryngeal swabs and nasal washes appeared to be a reliable surrogate of the presence or absence of virus in the lungs in both age groups. the average loads ranged between 10 4 and 10 7 copies, respectively, at early times after infection, indicating that these sampling techniques can be used to monitor sars-cov-2 replication in syrian hamsters ( figure 1g,h) . at 14 dpi, hamsters had mounted a humoral immune response as evidenced by relatively high titers of neutralizing antibodies. it is worth noting that antibody titers appear to be higher in young when compared to aged hamsters in the animals tested (table s1) . histopathology revealed clear age-dependent differences, with young hamsters launching an earlier and stronger immune cell influx into the lungs associated with a faster recovery than their aged counterparts (figure 2a-e) . at 2 dpi, young hamsters developed a marked necro-suppurative bronchointerstitial pneumonia with strong alveolar and interstitial influx of neutrophils and macrophages as well as perivascular lymphocytic cuffing, which was much milder or absent in the aged group ( figure s1a, right panel) . in contrast, only aged animals developed pronounced alveolar and perivascular edema indicating vascular leakage at 3 dpi ( figure 2e and figure s2c) . a more diffuse, severe bronchointerstitial pneumonia was similarly present in both groups at 5 dpi with an onset of tissue regeneration, including hyperplasia of the bronchial epithelium ( figure s1c , arrowhead) and type ii alveolar epithelial cells. only at the 5 dpi time point was the arterial and venous endothelium of animals in both groups swollen and vacuolated, with necrotic endothelial cells separated from the underlying basement membrane by the presence of subendothelial lymphocytes and neutrophils ( figure s2c, left) , which was consistent with what has been described as endothelialitis in human sars-cov-2 infection [38] . at 7 dpi, recovery as indicated by the marked hyperplasia of bronchial epithelial cells and type ii alveolar epithelial cells were seen in both groups ( figure s2a ). interestingly, lung tissues had almost recovered in young hamsters at day 14, while the aged animals still had persistent tissue damage and active inflammation ( figure s2b ). from 2 dpi onwards, sars-cov-2 rna was detected by in situ hybridization in bronchial epithelial cells, debris in the bronchial lumen, alveolar epithelial cells type i and type ii, as well as macrophages in both groups, again with clear age-dependent differences over time ( figure 2f , figures s2d and s3) . young animals had high amounts of viral rna in numerous bronchial epithelial cells and within the bronchial lumen that was accompanied by marked spreading through the lung parenchyma on 2 and 3 dpi. in contrast, aged animals had less virus rna present in the bronchi. we detected only a scattered pattern of infected bronchial epithelial cells and sporadic areas of parenchymal infection at 2 and 3 dpi. at 5 dpi, viral rna was undetectable in the bronchi of young hamsters, and only small infected areas containing low levels of rna with a patchy distribution were detected. it is noteworthy that aged animals, at the same time after infection, had increased numbers of infected areas with a similarly patchy distribution throughout the lungs as well as copious amounts of viral rna associated with cellular debris in the bronchial lumen. using this technique, no viral rna was detected at 14 dpi in either group. in summary, our study examined the suitability of a small animal model to study sars-cov-2 infections and expands on determining the role that age might play in the differences with respect to disease progression. intranasal infection of syrian hamsters resulted in weight loss and robust virus replication in the upper and lower respiratory tract. a limitation of this study is the lack of an age-matched mock group for the older hamsters, which we are unable to include for legal reasons as we are bound under german law to follow the 3r principle. we further demonstrate that aged 32-to 34-week-old hamsters experienced higher and more consistent weight loss after intranasal infection, while body temperatures and virus replication in upper airways and lungs were similar between both age groups. furthermore, we show that, using in situ hybridization, viral rna was detectable in bronchial epithelial cells, type i and type ii alveolar epithelial cells, and macrophages. all these cell types are potential targets of sars-cov-2 in human lung tissue; hence, the infection of hamsters of different ages seems to closely reflect what has been reported for human patients [28, 39] . in contrast to sars-cov-2 titers, histopathological changes differed markedly between young and aged syrian hamsters over time: younger animals launched more severe reactions at early time points after infection, while lesions and inflammation in the lungs became more pronounced and widespread at later time points in the elderly. notably, age-related differences of sars-cov-2 infections have also been observed in non-human primates [17] , and while this manuscript was under revision, in hamsters [40] . the study by imai et al. also describes infections of syrian hamsters of different age groups, and they also observed more robust body weight losses in older hamsters [40] . based on the data presented here, we propose that comparative preclinical assessments of sars-cov-2 vaccines and other treatment options in young versus aged hamsters may yield valuable and relevant results, as this small animal model appears to mimic age-dependent differences in humans. the development of a humoral immune response emphasizes that hamsters are likely suitable for vaccination trials. our observations also confirm that body weight loss is a readily quantifiable parameter that has proven very useful to measure disease severity in sars-cov-2 infection of syrian hamsters. this makes the difference in body weight loss between age groups with more consistent losses in aged hamsters only more important as it provides an objective way to judge clinical efficacy of antiviral therapy or vaccination. association between age and 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real-time rt-pcr validation of assays to monitor immune responses in the syrian golden hamster (mesocricetus auratus) tropism, replication competence, and innate immune responses of the coronavirus sars-cov-2 in human respiratory tract and conjunctiva: an analysis in ex-vivo and in-vitro cultures syrian hamsters as a small animal model for sars-cov-2 infection and countermeasure development this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license the authors acknowledge the excellent technical assistance by ann reum, annett neubert, and simon dökel. we would like to thank carfil inc. for their generous support of our animal husbandry. the authors declare no conflict of interest. key: cord-342160-snfm62js authors: panait, luciana cătălina; stock, graham; globokar, majda; balzer, jörg; groth, bernhard; mihalca, andrei daniel; pantchev, nikola title: first report of cytauxzoon sp. infection in germany: organism description and molecular confirmation in a domestic cat date: 2020-07-17 journal: parasitol res doi: 10.1007/s00436-020-06811-3 sha: doc_id: 342160 cord_uid: snfm62js cytauxzoonosis is described as an emerging tick-borne disease of domestic and wild felids caused by protozoans of the genus cytauxzoon. while in the americas the condition is described as a fatal disease, in europe, reports on the clinical expression of the infection are scarce. this study describes the first case of cytauxzoon sp. infection in germany, in a domestic cat. a 6-year-old male domestic cat living in saarlouis (saarland) was presented with anorexia, lethargy and weight loss. the cat had an outdoor lifestyle and had not travelled abroad. serum clinical chemistry analysis revealed azotaemia with markedly increased symmetric dimethylarginine, hypercreatinemia, hyperphosphatemia and hypoalbuminemia. moreover, a mild non-regenerative anaemia was present. approximately 1 year prior to these findings, the domestic cat was diagnosed with a feline immunodeficiency virus (fiv) infection. these results pointed toward a decreased glomerular filtration rate, presumably as a result of kidney dysfunction. round to oval signet ring–shaped intraerythrocytic organisms, morphologically suggestive for a piroplasm, were revealed during blood smear evaluation with a degree of parasitaemia of 33.0%. pcr analyses and sequencing of a region of the 18s rrna gene confirmed the presence of a cytauxzoon sp. infection, with 99–100% nucleotide sequence identity with previously published cytauxzoon sp. isolates. as this is the first molecularly confirmed cytauxzoon sp. infection in a domestic cat in germany, these findings suggest that cytauxzoonosis should be considered as a differential diagnosis in cases of anaemia in outdoor domestic cats, particularly in areas where wild felid populations are present. in recent years, cytauxzoon felis, a tick-borne pathogen of felids endemic in north america, is gaining clinical importance. domestic cats infected with c. felis generally develop a peracute and highly fatal disease . furthermore, other closely related piroplasms infecting domestic and wild felids have been reported. cytauxzoon manul was described in naturally infected pallas's cats (otocolobus section editor: leonhard schnittger manul) from mongolia (ketz-riley et al. 2003; reichard et al. 2005) . in europe, an unnamed species of cytauxzoon was reported not only in domestic cats from spain (criado-fornelio et al. 2004; díaz-regañón et al. 2017) , france (criado-fornelio et al. 2009; legroux et al. 2017) , italy (carli et al. 2012 (carli et al. , 2014 , portugal (alho et al. 2016) and switzerland (nentwig et al. 2018 ) but also in wild cats (felis silvestris) in spain (barandika et al. 2016; león et al. 2017) , romania (gallusová et al. 2016) , italy (veronesi et al. 2016) and bosnia and herzegovina (hodžić et al. 2018) , iberian lynx (lynx pardinus) in spain (luaces et al. 2005; millán et al. 2007 millán et al. , 2009 meli et al. 2009; garcía-bocanegra et al. 2010) and eurasian lynx (lynx lynx) in romania (gallusová et al. 2016) . studies on cytauxzoon sp. in europe show different infection rates depending on countries and host species involved. while the infection rate in domestic cats is ranging from 0.8% in france (criado-fornelio et al. 2009 ) to 23% in italy (carli et al. 2012) , in wild felids, the assessed prevalence is generally higher than 50% in romania (gallusová et al. 2016) , bosnia and herzegovina (hodžić et al. 2018) and spain (barandika et al. 2016; león et al. 2017) . the european isolates of cytauxzoon seem to be less virulent than c. felis, and the clinical manifestations appear to be associated with immune-mediated diseases or secondary infections (díaz-regañón et al. 2017; nentwig et al. 2018) . however, reports of cytauxzoon sp. infections in europe are scarce and most of them refer to subclinical cases. nonspecific clinical signs such as lethargy, anorexia, anaemia, fever, weight loss, tachycardia, tachypnoea, diarrhoea and vomiting have also been described (carli et al. 2012 (carli et al. , 2014 alho et al. 2016; legroux et al. 2017) . the present paper reports the first molecular confirmation of cytauxzoon sp. infection in germany and provides a detailed clinical picture of the disease in association with feline immunodeficiency virus (fiv) infection. in march 2017, a 6-year-old male domestic cat was referred to a veterinary facility in saarlouis (49.31°n, 6.75°e), a small city located in saarland (south-western germany), with anorexia and lethargy. the cat had an outdoor lifestyle and had never travelled abroad. according to the owner, the patient had refused to eat in the last 3 days and lost approximately 1.5 kg in the previous few weeks. episodes of vomiting could not be excluded due to the outdoor lifestyle of the cat. the patient received supportive therapy for 5 days with maropitant citrate (cerenia®, 1 mg/kg, sc), metamizole (novalgin®; 35 mg/kg, im), amoxicillin (betamox® long acting 150 mg/ml, 15 mg/kg, sc) and fluids (lactated ringer's solution, 15 ml/kg, sc) . despite the therapy, the cat was euthanized on the 5th day, due to the worsening of the clinical state, being presented in a lateral decubitus with severe lethargy and ataxia. nevertheless, the owner elected against necropsy. no information regarding the history of tick infestation or previous antiparasitic treatments was available. in march 2017, a complete blood count and serum clinical biochemical analysis (including the assessment of liver, kidney and pancreatic parameters) were performed at idexx reference laboratory in ludwigsburg, germany (table 1) . symmetric dimethylarginine (sdma) was measured using a commercially available high-throughput immunoassay (idexx sdma test, idexx laboratories inc.; ernst et al. 2018) . no urine examination was performed. approximately 1 year prior to these investigations (january 2016), a blood sample from the same patient was sent to idexx laboratories for similar haematologic and clinical biochemical analysis ( table 1 ). at that time, the blood sample was also tested for feline leukaemia virus (felv) antigen (p27; petchek felv, idexx laboratories inc.), as well as for antibodies against fiv (p24/gp40; petchek plus anti-fiv, idexx laboratories inc.) and feline coronavirus (fcov) (fcov elisa cat, afosa, germany). in march 2017, may-grünwald-giemsa-stained blood smears were prepared from peripheral blood and were evaluated for the presence of blood pathogens. the degree of parasitaemia was estimated by counting the number of infected erythrocytes per 2000 erythrocytes with an olympus bx61 microscope at × 1000 magnification. the measurement of the well-defined organisms (with a characteristic shape, n = 100) was assessed with a dp72 camera and cell^f software (olympus corporation, japan). total nucleic acids were extracted using the qiaamp dna blood biorobot mdx kit (qiagen, hilden, germany) following the manufacturer's instructions. a polymerase chain reaction (pcr) assay for piroplasmida targeting the 18s rrna gene was performed according to carret et al. (1999) and katargina et al. (2011) . furthermore, a nested and a conventional pcr protocol were used for the amplification of a part of the 18s rrna gene of the phylum apicomplexa using primer pairs bth-1f/bth-1r, gf2/gr2 and 7549/7548, respectively, following previously published reaction procedures and protocols (reichard et al. 2005; hrazdilová et al. 2019) . pcr products were visualized by electrophoresis in a 2% agarose gel. after purification, the amplicons were submitted for sequencing on both strands (macrogen, the netherlands). consensus sequences were compared with sequences available in genbank™ dataset by basic local alignment search tool (blast) analysis. in march 2017, the haematological analyses revealed a z o t a e m i a w i t h m a r k e d l y i n c r e a s e d s d m a , hypercreatinemia, as well as hyperphosphatemia and hypoalbuminemia. furthermore, a mild non-regenerative anaemia was present. abnormal laboratory findings are shown in table 1 . the results indicated decreased glomerular filtration rate that suggested the presence of kidney disease. urinalysis was not performed to assess specific gravity, protein concentration or sediment. in january 2016, the haematological and clinical chemistry variables had been within normal limits. felv and fcov tests were negative, but a positive fiv antibody test was obtained. blood smear examination in march 2017 revealed morphologically inconspicuous leukocytes, and erythrocytes displayed no significant anisocytosis or polychromasia. blood smear evaluation revealed round to oval signet ringshaped organisms inside the erythrocytes, with a light blue cytoplasm and a blue nucleus usually located in an eccentric position (fig. 1) . one to four merozoites were observed within individual red blood cells. the mean length of the well-defined forms was 1.2 ± 0.2 μm, and the measured width was 1.0 ± 0.2 μm. the intensity of parasitaemia was estimated at 33.0%. the intracellular parasites were morphologically suggestive for a piroplasm. moreover, the typical signet ring-shaped organisms could be clearly differentiated from feline haemotropic mycoplasma due to their evident large nuclear area . microscopic examination of a blood smear in january 2016 had revealed no blood cell morphologic abnormalities and no microorganisms. the presence of cytauxzoon sp. dna was confirmed by positive pcr results in all three protocols and subsequent sequencing. the longest consensus sequence available (1010 bp) was submitted to genbank™ under the accession number mn629916. blast analysis of the sequenced 18s rrna gene region revealed 99.9% nucleotide sequence identity with a genbank™ sequence of cytauxzoon sp. (legroux et al. 2017; nentwig et al. 2018 ). the study reported herein describes the clinical picture, laboratory findings and diagnostic procedures of a cytauxzoon sp. clinical infection in a domestic cat from germany. a previous piroplasmid fatal infection was described in a captive bengal tiger from a zoo in germany, when parasitic inclusions resembling cytauxzoon spp. were visualized in histological sections of various tissues, the largest number being found in blood vessels of lymph nodes and spleen. even though there was no evidence of tick infestation of the tiger, three bobcats (lynx rufus) originating from an american zoo were incriminated as a possible source of the infection (jakob and wesemeier 1996) . the cat patient in the current report was also diagnosed with a fiv infection, being presented in a critical condition a few days following clinical examination due to suspected kidney disease. since clinical cases of canine babesiosis and theilerioses are associated with acute or chronic nephropathy or glomerulonephritis (camacho-garcía 2006; solano-gallego et al. 2016), the renal disturbances observed in this patient could have been attributed to the piroplasmid infection to fiv or both. moreover, in c. felis infection, several cases of concomitant kidney disorders have been described in domestic and wild felids (meier and moore 2000; peixoto et al. 2007; lewis et al. 2012) . previous studies have also confirmed that fiv infection can induce the accumulation of immune complexes in renal tissue; therefore, a causative relationship between fiv infection and glomerulonephritis has been posited (reinacher and frese 1991; poli et al. 1995; harley and langston 2012; hosie et al. 2009 ). in the light of this information and the laboratory results (hypoalbuminemia pointing toward a renal loss of protein, increased creatinine and phosphate values as well as a very high sdma value), one could postulate that the patient had glomerular disease due t o i m m u n e -c o m p l e x d e p o s i t i o n i n t e r m s o f a membranoproliferative glomerulonephritis. other potential causes of hypalbuminaemia in this patient would include decreased production, other causes of loss (i.e. blood loss and protein-losing enteropathy) or haemodilution. in cases of renal injury, sdma serum concentration increases earlier than creatinine, remaining elevated also in cases of chronic kidney fig. 1 may-grünwald-giemsa stained peripheral blood smear (× 1000). cytauxzoon sp. appears as single or paired signet ring-shaped organisms (arrows) within erythrocytes. a high parasitaemia can be observed disease (on average with 40% reduction of glomerular filtration rate, compared with up to 75% reduction needed to increase the creatinine value) (relford et al. 2016) . regarding the pathogenesis of fiv infection, cats remain subclinically infected for several years until functional immunodeficiency (by increasing the susceptibility to secondary infections and neoplasia) and/or immune-mediated diseases will eventually translate into clinical manifestation around 4 to 6 years of age or older (hosie et al. 2009 ). in the present case, the cat did not display any noticeable clinical signs at 5 years of age, approximately 1 year before merozoites resembling cytauxzoon sp. were detected in high numbers in the blood smear. therefore, it can be presumed that, as a result of immunosuppression caused by fiv, the piroplasm contributed as an opportunistic factor triggering the clinical picture. furthermore, an increased pathogenicity in association with immunosuppression induced by concurrent diseases has been previously suggested in cytauxzoon sp. infection (carli et al. 2012; díaz-regañón et al. 2017 ). however, the clinical role of cytauxzoon sp. in domestic cats without immunosuppression and coinfections remains debatable, as the information about pathogenesis and clinical involvement is limited. although some cases of clinical illness and fatal outcome have been described (alho et al. 2016; legroux et al. 2017; nentwig et al. 2018) , the majority of cytauxzoon sp. infected cats were apparently healthy, with only few animals showing mild anaemia (carli et al. 2012 (carli et al. , 2014 díaz-regañón et al. 2017; nentwig et al. 2018) . microscopic examination of the blood smear revealed a degree of parasitaemia of 33%. other clinical studies showed lower levels of parasitaemia (luaces et al. 2005; carli et al. 2012 carli et al. , 2014 legroux et al. 2017) , while similar percentages of piroplasminfected erythrocytes were observed in the blood smear of three cats with cytauxzoonosis from switzerland (nentwig et al. 2018) . as the molecular confirmation of cytauxzoon sp. infection was established post-mortem, no specific anti-piroplasm treatment was applied. although, in c. felis infection, the recommended therapeutic protocol consists of atovaquone and azithromycin (cohn et al. 2011) , the optimal therapy for cytauxzoon sp. infection remains unknown due to the lack of controlled clinical studies. in a recently published case report, three 2-month-old kittens infected with cytauxzoon sp. were treated with a combination of atovaquone and azithromycin, with a putative success (nentwig et al. 2018) . also, previously published cytauxzoon sp. infections in domestic cats have been medicated with various antiprotozoal drugs, including imidocarb dipropionate and doxycycline (carli et al. 2012 (carli et al. , 2014 alho et al. 2016; legroux et al. 2017) . clinical studies in europe reported that a single imidocarb dipropionate administration was not successful in treating cytauxzoonosis, although the addition of doxycycline cleared parasitaemia in another patient (carli et al. 2014; legroux et al. 2017 ). based on the sequencing results performed on the 18s rrna gene amplification product, cytauxzoon sp. detected in the present case revealed a high homology (99-100%) with cytauxzoon sp. reported in european domestic felids (legroux et al. 2017; nentwig et al. 2018 ) and with cytauxzoon manul (99.8%) described from pallas's cats from mongolia (reichard et al. 2005) . in contrast, the sequence displayed a more distant identity of 95% to c. felis 18s rrna partial sequences deposited in genbank®. a significant association between the detection of cytauxzoon sp. dna in european domestic cats and outdoor lifestyle has been reported, particularly in rural areas (carli et al. 2012; díaz-regañón et al. 2017) . in agreement with these reports, the cat from the present study showed an outdoor lifestyle, which entails a higher risk of infection due to exposure to tick vectors and wildlife reservoirs. for c. felis infections of domestic cats, the american bobcat (l. rufus) is assumed to act as the main reservoir (kier et al. 1982) and amblyomma americanum and dermacentor variabilis are the confirmed tick vectors (blouin et al. 1984; reichard et al. 1991) . however, for the european isolates of cytauxzoon sp., little is known about vectors and routes of transmission. in europe, high prevalences of cytauxzoon sp. infection were found in felis silvestris in romania (gallusová et al. 2016) , italy (veronesi et al. 2016) , bosnia and herzegovina (hodžić et al. 2018) and spain (barandika et al. 2016; león et al. 2017) . moreover, germany has one of the biggest european populations of f. silvestris, which is concentrated in the low altitude mountain areas (balzer et al. 2018) . studies on wild animal distribution suggest that saarlouis city is surrounded by an abundant wild cat population (steyer et al. 2016) . consequently, considering that they might live in close proximity to urban and rural areas and crossbreed with domestic cats, it is possible that wild cats play a central role in the transmission of cytauxzoon sp. in west germany as well as in other european countries. ixodes ricinus is the most commonly found tick in germany (petney et al. 2012) , and it has been hypothesised to be a possible vector for cytauxzoon sp. (gallusová et al. 2016) . this study describes, to the best of our knowledge, the first case of molecularly confirmed cytauxzoon sp. infection in germany. this case provides a new geographical record of cytauxzoon sp. infection in domestic cats in central europe and describes the clinical and laboratory findings in association with fiv infection. results advocate that cytauxzoonosis should be considered as a differential diagnosis in cases of anaemia in domestic cats with an outdoor lifestyle, particularly in areas where populations of wild felids are present. additional studies are required to identify the possible arthropod vectors which may be involved in the transmission and to clarify the relationship between cytauxzoon sp. infection in cats and the presented clinical signs. code availability not applicable. data availability all data generated or analysed during this study are included in this published article. conflict of interest the authors declare that they have no conflict 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silvestris) first detection of cytauxzoon spp. infection in european wildcats (felis silvestris silvestris) of italy publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations key: cord-254169-sjoiv70c authors: nakano, katsuyuki title: future risk of dengue fever to workforce and industry through global supply chain date: 2017-03-16 journal: mitig adapt strateg glob chang doi: 10.1007/s11027-017-9741-4 sha: doc_id: 254169 cord_uid: sjoiv70c the primary vector of the dengue fever virus, the aedes aegypti mosquito, is distributed across the tropical and sub-tropical latitudes; however, the area at risk of infection has been expanding steadily. this study aimed to identify the industries most vulnerable to the effects of dengue fever by 2030. the assessment was done by considering the international supply chain, with aspects such as the labor intensity, and the relevant geographical and socioeconomic aspects being taken into account. in addition, multi-regional input-output tables were employed to analyze the ripple effects of productivity losses resulting from workers contracting the disease. the results indicate that more than 10% of the workers involved in the supply chain of all the major industries in the united states (usa), china, japan, and germany could be considered at risk of contracting dengue fever by 2030. moreover, the risk was even higher in india and brazil, namely, more than 70%. the effect of widespread dengue fever infection could influence industrial activities severely, not only in the regions most at risk (india and brazil) but also in the other regions (usa, japan, and germany). labor-intensive industries, such as agriculture, fisheries, and the distribution sector are particularly at risk and will have to consider appropriate contingency measures. it is recommended that the downstream side of the supply chain, the industries in the usa, japan, and germany, supports the introduction of worker’s health management system against the infectious disease into their business partners. this study employed limited data and only estimated the possible effects of the disease by 2030. further comprehensive analysis is required with more data modeled for the future to verify and enhance the reliability of the present results. dengue fever is a systemic viral infection transmitted to humans by various types of mosquito, such as the aedes aegypti. after infection, the symptoms typically appear after an incubation period of 3 to 7 days (simmons et al. 2012 ). in the initial febrile phase, the patients suffer from high temperature (≥38.5°c), headaches, vomiting, myalgia, and joint pain, often accompanied by a transient macular rash. this phase lasts for 3 to 7 days, after which most patients recover without any complications (simmons et al. 2012) . however, in a small number of cases, the condition of the patient deteriorates and dengue hemorrhagic fever could develop. this condition could be fatal without proper medical care. in december 2015, the first dengue vaccine was licensed; however, currently, it is not available widely and treatment therefore remains supportive (pitisuttithum and bouckenooghe 2016; world health organization 2016) . at present, the dengue virus is found across the tropical and sub-tropical latitudes (simmons et al. 2012) , and the annual rate of infection is estimated at 390 million (95% credible interval 284-528), of which 96 million (95% credible interval 67-136) of those infected develop symptoms at different levels of severity (bhatt et al. 2013) . the increase in the incidence of dengue fever has been ascribed to the changing human ecology, demography, and globalization, and probably climate change (world health organization 2012). for example, for the first time in metropolitan france, two cases of autochthonous dengue fever were diagnosed in september 2010 (la ruche et al. 2010) . furthermore, after 70 years with no confirmed autochthonous cases of dengue fever in japan, 19 cases were reported in tokyo during august and september 2014 (kutsuna et al. 2015) . it has been predicted that climate change would contribute to an expansion at the fringes of the current distribution of dengue fever, with 4.39 billion people being at risk of contracting the disease by 2030 (hales et al. 2014) . the mortality rate resulting from the disease can be reduced to almost zero by implementing timely and appropriate clinical management (world health organization 2012). for example, suaya et al. (2009) conducted a survey of 1695 patients, with no fatalities occurring. although dengue fever is normally not a critical illness, the more severe cases of infection do need a specialized treatment. on average, ambulatory and hospitalized patients lose 6.6 and 9.9 days of work, respectively. absence from work often results in economic losses (suaya et al. 2009 ), and the estimated total annual cost (i.e., direct and indirect medical costs) associated with the disease amounted to us$2.1 billion in the americas for the period 2000 -2007 (shepard et al. 2011 . it has been calculated that these costs were mostly related to productivity losses induced by non-fatal dengue fever cases, whereas the deaths resulting from the disease accounted for only a small proportion (2.6%) of the total costs (shepard et al. 2011) . such productivity losses appeared as stagnation of the production activities and increased production costs. as industries are often interlinked locally and internationally, a mishap occurring in one industry could easily affect the other industries. for example, the floods suffered in thailand in 2011 damaged not only the thai economy but also that of other asian countries (haraguchi and lall 2015) . furthermore, the progress of climate change is expected to have a detrimental effect on industrial activities. in view of the above, a consideration of the future risks to the supply chain and the introduction of countermeasures to sustain industrial activities are required. life cycle assessment (lca) (iso 2006) has been employed to assess the environmental effects throughout the product supply chain. this method enables the quantification of environmental effects such as carbon dioxide (co 2 ) emissions and the consumption of resources. a number of databases have been developed to support lca, e.g., ecoinvent (wernet et al. 2016) and gabi (think step 2015) . in addition, multi-regional input-output tables (mrios) such as exiobase (wood et al. 2015) and eora ) have been developed to assess the environmental effects of the international supply chain of industrial activities. the quantification of the consumption of scarce resources by the supply chain (wiedmann et al. 2013) has indicated that the resource supply could be at risk. nakatani et al. (2015) assessed the risk of water shortages, whereas norris et al. (2014) employed input-output tables to assess the social risks associated with supply chains. nakano (2015a) extended the lca method to evaluate the effects of environmental change on the product supply chain, and evaluated the effects of climate change on the international supply chain of japan (nakano 2015b) . santos et al. (2013) analyzed the economic losses and inoperability that could result from an influenza epidemic by employing the input-output tables of the united states (usa). industries and governments have limited capacity to introduce adaptive actions to risks, and such studies support the introduction of efficient countermeasures by identifying the weak points in the system. however, no studies evaluating the effects of infectious diseases on all industrial activities through the international supply chain have been conducted before, to my knowledge. to establish an effective adaptive plan, improved understanding is needed of the effects of climate change on humans (ebi et al. 2006 ). therefore, this study aims to propose a method to evaluate the effects of an infectious disease on industrial activities by utilizing a method that indicates the priorities for considering countermeasures. the study focused on the dengue virus because predictions indicate an increasing risk of infection owing to climate change and the vaccine not being available widely. widespread infection of workers and/or their families by a virus such as dengue and the consequent absences from work would result in inevitable productivity losses. moreover, it is clear that labor-intensive industries are relatively more at risk to such losses. in addition, geographical aspects have to be considered, as the virus-bearing mosquitos favor areas that have high temperatures and water available. furthermore, socioeconomic aspects are important, as developed countries have a greater capacity to provide appropriate treatment smoothly. therefore, the labor intensity of an industry and the geographical and socioeconomic aspects should be taken into account to identify regions where the risk of dengue virus infection is high. the intergovernmental panel on climate change (ipcc) has indicated that risk results from the interaction of hazard, vulnerability, and exposure (ipcc 2014). the life cycle assessment framework for adaptive planning (lca-ap) to climate change adopted this concept and is able to evaluate the potential climatic effects on industries throughout the supply chain (nakano 2015a) . this method quantifies inputs (e.g., water and workforce) to industrial activities that could be affected by climatic factors. such inventory analysis results indicate the risk of exposure to the infection (nakano 2015a) . in lca-ap, the inventory analysis results are adjusted by accounting for the geographical aspect (hazard) and the socioeconomic aspect (vulnerability). furthermore, lca-ap is able to utilize the wellestablished lca database. lca-ap was therefore used in this study to evaluate the risk to the industry of dengue infection through the international supply chain. the potential effects of dengue infection were calculated by multiplying the inventory analysis result and a factor accounting for the country-specific climate hazard, as well as the socioeconomic vulnerability characteristics, as follows: where ci is the category indicator (potential impact from dengue), exp is the inventory analysis result (expressing exposure), haz is the hazard of dengue, and vul is the vulnerability. figure 1 shows the assessment procedure. the population at risk of dengue per value of production of each industrial sector (direct effect) was calculated from the portion of the population at risk of dengue infection in 2030 owing to climate and socioeconomic change, and the number of workers per value of production of each industrial sector. to quantify the indirect effect (upstream part of the supply chain), the mrio was used, which expresses international trade among the industrial sectors of each country. data below explains the detail of the assessment method. various methods have been proposed to predict the distribution of the risk of dengue infection in the future (messina et al. 2015) . in such calculations, the environmental change induced by climatic change, as well as other factors, such as socioeconomic change, have to be considered (messina et al. 2015) . hales et al. (2014) estimated the population at risk of dengue infection in 2030 by taking into account the future climate, population, and the gross domestic product (gdp) of each country and region. the gdp was used to evaluate the vulnerability of each country and region (hales et al. 2014) , with the study utilizing the data from these countries portion at risk of dengue under climate and socioeconomic change in 2030 (hales et al. 2014) number of workers per value of production of each industrial sector (wood et al. 2015) number of workers at risk of dengue per value of production of each industrial sector (direct impact) multi-regional input-output (mrio) tables (wood et al. 2015) number of workers at risk of dengue per value of production of each industrial sector (direct and indirect impact) (table 1) was used as f(haz, vul) in eq. (1). it was predicted that more than 90% of the population in southeast asia and latin america (tropical) would be at risk by 2030. in addition, a relatively high risk was indicated for south asia, the caribbean, and central sub-saharan africa. on the other hand, no risk was indicated for europe, whereas the highincome countries in asia pacific and north america had a small risk. input-output tables statistically express trade among all the industrial sectors in monetary value. analysis employing input-output tables is able to determine the environmental and wider sustainability effects of traded goods and services (hendrickson et al. 1998; wiedmann et al. 2011) . for example, the usa input-output tables were used to analyze the economic losses and inoperability caused by the 2009 h1n1 pandemic in the national capital region of the usa (santos et al. 2013) . mrios, such as exiobase (wood et al. 2015) , eora , and the global trade analysis project (gtap) (aguiar et al. 2016 ) have been developed to analyze the international supply chain. these mrios can quantify the monetary data, greenhouse gas emissions, and the labor force of each industrial sector in each country and region. in particular, the focus of exiobase (wood et al. 2015 ) is on environmentally relevant activities and the detail modeling of the industrial sectors that have more pronounced effects on the environment. in addition, eora has also been used for environmental analysis. the quality of eora is comparable with that of exiobase (geschke et al. 2014) . in this study, (wood et al. 2015 ) was adopted, comprising a matrix of 163 industrial sectors in 48 countries and regions. to quantify the involvement of workers throughout the supply chain (exp), the following equation was used: where w d is a diagonal matrix of direct workforce input (person/million euro (person/m eur)), i is an identity matrix (dimensionless), a is a technical coefficient matrix (dimensionless), k′ is a column vector expressing the final demand (m eur), and (i − a) is known as the leontief inverse matrix (miller and blair 2009 ). the leontief inverse matrix of exiobase, (i − a) −1 , is a square matrix of 7824 × 7824. to analyze the potential effect of each industry in each country per one monetary unit (1 m eur), the k′ of the target industry in the target country was set to 1 m eur and the others were set to 0. to assess the magnitude of the risk of dengue infection for one industry, the portion of workers at risk of contracting dengue infection (r impact ) was calculated by eq. (3), as follows: where ci is the category indicator (number of workers at risk/m eur) and exp is the inventory analysis result (number of workers/m eur). an industry for which a higher r impact is indicated has a higher potential risk relevant to the workers and the supply chain of the industry. such industries would be advised to establish countermeasures to dengue infection to safeguard their industry and supply chain. in addition, to clarify the dengue risk distribution in a supply chain, a portion of indirect influence (upper part of the supply chain) (r indirect ) is calculated by eq. (4): where ci indirect is the category indicator of the upstream part of the supply chain (number of workers at risk of contracting dengue fever/m eur). an industry indicating higher r indirect has a higher potential risk relevant to the workers in their upstream side of the supply chain. such an industry would be advised to establish relevant countermeasures to the risk beyond the border of the organization and/or the national border. the granularity of exiobase is 163 industries for 48 countries, enabling the calculation of exceptionally large results. the study intended to clarify major impacts of production losses to global economy due to disabled workforce; therefore, the focus was on the major industries in major countries. major countries, usa, china, japan, germany, india, and brazil, were selected by descending gross domestic product (gdp) values. the uk, france, and italy have larger gdps than brazil; however, these countries were excluded based on the similarity of their geographical and socioeconomical characteristics to germany. the selection of industry was based on the characteristics of industries such as classification of the industrial sector, economic scale, and labor intensity. from the primary sector of the economy, the fish product sector was selected for their highest labor intensity (wood et al. 2015) . from the primary and the tertiary sectors of economy, industries with higher labor intensities (fish products and hotels and restaurants) were selected. from the second sector of economy, industries with high supply values were selected from each segment (such as raw material). therefore, the major industries analyzed in this study include food products, fish products, textiles, plastics, chemicals, iron and steel, motor vehicles, construction, and hotels and restaurants. note that this study followed the exact definitions for each industrial sector name and boundary, as defined in exiobase (wood et al. 2015) . 3 results and discussion 3.1 proportion of workers at risk of contracting dengue infection table 2 shows the portion of workers at risk of contracting dengue infection in the supply chain (r impact ) of the countries and industrial sectors included in the analysis. as indicated by the table, more than 70% of the workers in all the major industries in india and brazil would be at risk in 2030. in the usa, 63% of workers in the fish product sector would be at risk, whereas in china, japan, and germany, the risk would be less than 50% for the workers in the major industries. however, more than 30% of the workers in the supply chain of the basic plastic and chemical industries in these countries would be at risk. moreover, more than 10% of the workers in all the major industries in all major countries would be at risk of contracting the virus; therefore, the activities of all the major industries could potentially be affected by the consequences of dengue virus infection. the portion of indirect effects (r indirect ) was calculated for the major industries in the major countries (table 3 ). the calculations indicated that 0% of the population would be at risk of contracting dengue fever in germany in 2030 (hales et al. 2014) ; therefore, the risk indicated in all the major industrial sectors in germany would be induced by indirect effects. parts of the usa and japan were classified as regions at risk of dengue infection; therefore, slight direct effects were observed for these countries. in contrast, the direct effects were significant in china, india, and brazil. in particular, in the construction sector in india and brazil, the textile sector, and the hotel and restaurant sector in brazil, more than half of the effects were induced by local industrial activities. however, in all the industries, indirect effects should not be ignored. the relation between the production value (billion euro (b eur)/year) and the effect (number of workers at risk of contracting dengue fever (person/m eur)) is illustrated in fig. 2 . an industrial sector located in the upper right side of the graph has higher production value and a large number of workers at risk of contracting dengue fever; therefore, this industry would be specifically advised to introduce countermeasures to manage the effects of the disease. note that the scales of the vertical and horizontal axes of fig. 2 are different among the countries to express the economic size and the effects relevant to each country. an extremely significant effect (342 person/m eur) was indicated for the fish product sector in the usa. similarly, significant effects were indicated for the fish product sector in the other countries, whereas the production values of this sector were small. in china, the textile, food product, and hotel and restaurant sectors showed relatively higher production values and effects. in japan, the motor vehicle sector had the largest production value, whereas the effect was small. in germany, the plastic sector showed a relatively higher production value and effect. however, the scale of the vertical axes of the graphs for both germany and japan was smaller by 1 digit in comparison with the other countries. no major industrial sectors in japan or germany were located in the upper right side of the graphs; therefore, no critical sectors were identified in either of these countries. in brazil and india, the construction sector showed relatively higher production values and effects. most of the effects were induced by the local construction industries (table 3 ) and, as this industry is labor intensive, appropriate countermeasures would have to be introduced in these two countries. the major emerging countries, such as china, brazil, and india showed significant effects relevant to the food product and hotel and restaurant sectors, whereas the production values were not significant ( table 4 ). the effects indicated for india (person/m eur) were relatively more significant for the major industries of the country in comparison with those of the other countries. this result is ascribed to india being located in southeast asia, which is more at risk of dengue fever infection, and to the labor intensity of the country being higher than in the developed countries. therefore, industries located in the bottom area in fig. 2 (e.g., the chemical, motor vehicle, and steel industries) would be advised to consider improving their health care systems to counteract the effects of dengue fever infection. in order to study the countermeasures for dengue fever infection in practice, an activity that has a greater effect in the supply chain has to be identified. therefore, the supply chains of nine major industrial sectors were analyzed for which relatively higher effects and production values had been indicated (fig. 3) . wood et al. (2015) the induced effects in the usa were found insignificant (less than 1%), whereas the effects of imports from asia-pacific and african countries were significant. the fish product sector in the usa purchased fish amounting to 474 m eur locally, 825 m eur from south american countries, 1 692 m eur from asia-pacific countries, 2 and 269 m eur from african countries 3 (wood et al. 2015) . these exporting countries have a higher percentage of population at risk of contracting dengue fever (table 1) . furthermore, the labor intensity of the fishing sector in the usa is 8.6 workers/m eur, whereas it is 2841 workers/m eur in the asia-pacific countries, and 444 workers/m eur in the african countries (wood et al. 2015) . the risk in the asia-pacific and african countries was significant, with 63% of workers classified as being at risk of contracting dengue fever (table 2 ). in view of these findings, it would be advisable for the fish product industry in the usa to promote risk management in their international supply chain. the textile sector in china (direct effect) contributed 13% of the effect, with 56% of the effects being induced locally in the country. the plant-based fiber sector accounted for 38% of the effects, namely, 10% in china, 15% in african countries, and 13% in asia-pacific countries. the plant-based fiber sector provides the main materials to the textile sector, such as cotton (gossypium spp) and jute (corchorus capsularis). the textile sector in china purchases 20,532 m eur from the chemical sector and 8497 m eur from the local plant-based fiber sector in china in 2007 (wood et al. 2015) . the purchase amount of the chemical sector exceeded that of the plant-based fiber sector; however, the labor intensity of the chemical sector (14.7 workers/m eur) was much lower than was that of the plant-based fiber sector (762 workers/m eur) (wood et al. 2015) , and the plant-based fiber sector was therefore identified as a significant sector. as the textile sector is labor intensive, it is important to strengthen the risk management in this sector. moreover, the plant-based fiber sector provides materials (e.g., cotton) to the textile sector; consequently, there is a need to reinforce the risk management for dengue fever infection. most of the effects (94%) were induced in china. the food product sector (direct effect) contributed 11% of the total, whereas the effects of indirect activities, such as the vegetable sector (17%), the cereal grain sector (13%), the wheat sector (12%), and the paddy rice sector (11%), contributed more than 50%. the economic scale of the food product sector in china is large (225 b eur) (wood et al. 2015) , and the proportion of workers in the supply chain at risk of contracting dengue fever is significant (27%, as shown in table 2 ); therefore, it is important to consider appropriate countermeasures to dengue fever infection. 1 south american countries except brazil and mexico 2 asia pacific countries except japan, china, south korea, india, taiwan, indonesia, and australia 3 african countries except south africa (d) hotels and restaurants in japan although the direct effect was not actually 0%, as the risk of dengue fever infection does exist in japan, most of the indicated effects were induced abroad. food imports from the asia-pacific countries had significant effects, namely, 23% from the fish product sector and 10% from the vegetable sector. the hotel and restaurant sector in japan purchased 8252 m eur from the local food product sector, 7750 m eur from the local beverage sector, and 1041 m eur from the fish product sector in the asia-pacific countries (wood et al. 2015) . although the value of the products purchased from the asia-pacific countries was smaller than was that of the local purchases, there was significant risk (18%) of the asia-pacific workers in the supply chain contracting the dengue virus (table 2) . japan imports various foods from asian countries, such as shrimp (e.g., penaeus indicus) from southeast asia, and appropriate risk management relevant to these foods would have to be considered. no workers in germany were predicted at risk of contracting dengue fever, the domestic effects were zero, and all the effects indicated were induced in asia, africa, and other countries. a number of sectors, such as the vegetable sector in asia-pacific countries (2%) and the crop sector in the african countries (2%) contributed to the effects. no significant industry contributed to the result. as regards the direct transactional value relevant to the motor vehicle sector in germany, the value of the fabricated metal product sector in germany was 12,424 m eur and that of the rubber and plastic product sector was 7606 m eur. in contrast, the value of both the vegetable sector in the asia-pacific countries and the crop sector in the african countries was less than 1 m eur (wood et al. 2015) . the supply chain of the motor vehicle sector is complex and includes agricultural activities. for example, vegetable oil is a raw material of chemicals, such as surfactants, and the starch produced by the crop sector is a component of the surface-sizing agents used in the paper manufacturing process. the motor vehicle sector in germany purchased 147 m eur from the paper and paper product sector (wood et al. 2015) . the absolute amount of these agricultural inputs to the motor vehicle sector is small; however, these agricultural industries indicated relatively higher impacts. significantly, 23% of the workers in the supply chain were classified at risk of contracting dengue fever (table 2) . therefore, the motor vehicle sector in germany would be advised to analyze the components for which agricultural products from asia and africa are used in order to have appropriate contingency measures in place. similar to the motor vehicle sector, no effects were predicted for the plastic industry in germany. relevant to the international supply chain, no sectors showed a clear and significant contribution to the result; however, the wholesale sector (5%) and the vegetable sector in the asia-pacific countries (4%) were indicated in the result. labor intensity in these countries is high, and 38% of workers in the supply chain were at risk of contracting dengue fever (table 2 ). similar to the motor vehicle sector in germany, it is recommended that the components be examined that use agricultural products from asia and africa. in india, 96% of the effects are derived locally, including the direct effect of the iron and steel industry (26%). the service sectors, such as the retail trade sector (16%) and the wholesale trade sector (5%) contributed to the result in the supply chain. in addition, the effects of raw material acquisition activities, relevant to the coal and lignite sector (10%) and the iron ore sector (2%), were detected in the result. as shown in table 2 , 71% of workers were at risk of contracting dengue fever; therefore, proactive risk management is required in this sector and its supply chain. direct effects accounted for 57% of the effects in the construction sector in india. the construction sector is labor intensive (223 workers/m eur) compared with other sectors in india, such as the plastic sector (30 workers/m eur) and the paper sector (93 workers/m eur) (wood et al. 2015) . the sectors providing materials to the construction sector, such as the wood product sector (5%) and the forestry sector (3%) had significant effects on the supply chain. in addition, the service sectors, such as the retail trade sector (6%) and the land transport sector (3%) contributed to the result. the effects induced locally in india contributed 97% to the total effects indicated for the country. the production value of this sector is large (135 b eur) (wood et al. 2015) , and the effects per monetary unit are significant (297 workers/m eur). consequently, this sector should consider countermeasures to the consequences of dengue fever infection. the domestic effect accounted for 83% of the total, including a direct effect of 27%. in the supply chain, service sectors, such as the retail trade sector (8%) and the wholesale trade sector (6%), and agricultural sectors, such as the sugar cane sector (11%) and the forestry sector (2%), were indicated in the results. the chemical sector in brazil purchased 2.8 b eur from the local sugar cane and beet sector and 2.7 b eur from the local naphtha sector (wood et al. 2015) . sugar cane has been used to produce ethanol as an alternative source of energy for motor vehicles in brazil. the international supply chain contributed 17% to the effects; however, no significant effect was indicated from any sector in brazil. however, the chemical sector would be advised to enhance risk management in their own sector and their supply chain, especially the sugar cane industry and the trade sectors. this study indicated that the effects of dengue fever could influence other countries through the international supply chain. the dengue infection data in 2030 (hales et al. 2014 ) considered current-level countermeasures according to gdp. therefore, the results indicated that further introduction of countermeasures are required to deduce the risk. the regions where dengue fever is not prevalent, such as the usa, japan, and germany, should consider appropriate countermeasures, as a percentage of workers involved in the supply chain of these countries have been classified as at risk of contracting the disease. in particular, industries that are reliant on labor (e.g., agriculture and the distribution industry) would have to consider adaptation measures carefully. worldwide, various adaptation actions have been introduced (lesnikowski et al. 2013) . bowen et al. (2014) suggested that reducing the health risks induced by climate change, cross-sectoral partnerships should be improved and influential organizations in the development of mitigation and adaptation measures should be identified. the downstream side of the supply chain has buying power, whereas the adaptive activities of the upstream side are influenced by the attitude of costumers (berkhout et al. 2006; fleming et al. 2014) . therefore, the downstream side of the supply chain, such as industries in the usa, japan, and germany, could contribute to promoting a health management system in industries at risk of dengue fever infection. the organization for economic co-operation and development (oecd) guidelines for multinational enterprises (oecd 2011) recommend avoiding bthe foreseeable environmental, health, and safety-related impacts associated with the processes, goods, and services of the enterprise over their full life cycle.^for example, ajinomoto incorporated company advises their suppliers to provide a regular healthcare management to their workers (ajinomoto 2013) . these guidelines and activities could lead to support introduction of countermeasures to infectious disease to business partners and reduce business risk. however, a number of enterprises still do not implement such activities. therefore, it is recommended that international initiatives, such as the united nations global compact (united nations 2017), clearly advice companies to support introduction of worker's health management systems to their business partners. these activities reduce business risks (godfrey et al. 2009 ); therefore, i recommend that investors positively evaluate such risk management activities. a comprehensive and systematic framework is needed to study a policy option for the formulation of robust, pro-development climatic measures and effective health management (chalabi and kovats 2014) in order to counteract the effects of widespread diseases. however, this study focused only on the risk of dengue fever infection, with other diseases (e.g., malaria) and disasters (e.g., extreme weather conditions) not being taken into account. furthermore, the results of this study include uncertainty. this is ascribed to the study having to model the predicted population at risk of dengue fever infection in 2030 on the actual industrial structure and international supply chain in 2007. the situation in 2007 was adopted because of the difficulty of predicting the future economic situation. however, as the textile industry has been relocating to a country where labor cost is lower, the industrial structure and the international supply chain have been changing. therefore, the future economic situation has to be considered in order to increase the reliability of the study. in this study, only the supply side was evaluated, although, typically, infectious diseases would affect the demand side as well. for example, the pandemic of severe acute respiratory syndrome (sars) in hong kong, from november 2002 to august 2003, significantly affected local consumption and the travel industry (siu and wong 2004) . therefore, future study would have to consider the effects of infectious diseases on the demand side as well. the primary vector of dengue fever, the urban-adapted a. aegypti mosquito has been distributed across the tropical and sub-tropical latitudes (simmons et al. 2012 ), but the total area at risk of dengue infection has been expanding (hales et al. 2014) . the study clarified the effects of dengue fever infection on various global industries by projections for 2030, taking into account the international supply chain. the results indicated that more than 10% of workers involved in the supply chain of all the major industries in the usa, china, japan, and germany would be at risk of contracting dengue fever by 2030, whereas more than 70% of the workers in india and brazil would be at risk by that time. the effects of dengue fever could influence industrial activities in the regions at risk (e.g., india and brazil) and in the other regions (e.g., usa, japan, and germany) through the supply chain. in particular, industries that are highly labor intensive (agriculture, fishery, and the distribution industry) would be advised to consider adequate adaptation measures. it is recommended that the downstream side of the supply chain, such as industries in the usa, japan, and germany, identify processes at risk of infectious disease in the supply chain where worker's health management systems should be introduced. this study indicated that implementation of such systems would reduce business risks and improve shareholder value (godfrey et al. 2009 ); therefore, i recommend that such interventions to upstream side of the supply chain be included in investment criteria. as the study focused only on the effects of dengue fever in 2030, with limited data being available, comprehensive analysis with data modeled for the future could 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footprint analysis dengue vaccine research world health organization (2012) global strategy for dengue prevention and control 2012-2020. world health organiszation conflict of interest the author declares that there is no conflict of interest. key: cord-348495-pa6iqc83 authors: perrotta, d.; grow, a.; rampazzo, f.; cimentada, j.; del fava, e.; gil-clavel, s.; zagheni, e. title: behaviors and attitudes in response to the covid-19 pandemic: insights from a cross-national facebook survey date: 2020-05-15 journal: nan doi: 10.1101/2020.05.09.20096388 sha: doc_id: 348495 cord_uid: pa6iqc83 in the absence of medical treatment and vaccination, the mitigation and containment of the ongoing covid-19 pandemic relies on behavioral changes. timely data on attitudes and behaviors are thus necessary to develop optimal intervention strategies and to assess the consequences of the pandemic for different demographic groups. we developed a rapid response monitoring system via a continuously run online survey (the "covid-19 health behavior survey") across eight countries (belgium, france, germany, italy, the netherlands, spain, the united kingdom, the united states). the survey was specifically designed to collect key information on people's health status, behaviors, close social contacts, and attitudes in response to the covid-19 pandemic. we developed an innovative approach to recruit participants via targeted facebook advertisement campaigns in order to generate balanced samples for post-stratification. in this paper, we present results for the period from march 13-april 19, 2020. we estimate important differences by sex: women show a substantially higher perception of threat along with a lower level of confidence in the health system. this is paralleled by sex-specific behaviors, with women more likely to adopt a wide range of preventive behaviors. we thus expect behavior to serve as a protective factor for women. our findings also show a higher level of awareness and concern among older respondents, in line with the evidence that the elderly are at highest risk of severe complications following infection from covid-19. while across all the samples respondents were less concerned for themselves than for their country or for the world, we also observed substantial temporal and spatial heterogeneity in terms of confidence in institutions and responses to non-pharmaceutical interventions. the ongoing coronavirus disease 2019 (covid-19) outbreak started in wuhan city, china, in december 2019 and quickly spread globally, soon reaching pandemic proportions [1] . by mid-april 2020, the virus had already caused over 1.6 million cases and over 100,000 deaths worldwide [2] , placing a substantial burden on national healthcare systems and posing unprecedented challenges for governments and societies. as yet, governmental responses to mitigate the coronavirus epidemic have varied considerably across countries. non-pharmaceutical interventions, specifically intended to reduce sustained local transmission by reducing contact rates in the general population, have so far ranged from moderate containment measures, such as school closures and cancellations of public gatherings, to drastic measures, such as travel bans and nationwide lockdowns [3] . in western democracies, individual behaviors, rather than governmental actions, are potentially crucial to control the spread of covid-19 [4] . human behavior is in fact a key factor in shaping the course of epidemics [5] . individuals may spontaneously modify their behaviors and adopt preventive measures in response to an epidemic when mortality or the perception of risk is high, and this may in turn change the epidemic itself by reducing the likelihood of transmission and infection [6, 7, 8] . however, a key problem is a lack of data to assess people's behavior and reactions to epidemics. decision-making and the evaluation of non-pharmaceutical interventions require specific, reliable, and timely data not only about infections, but also about human behavior. especially in the ongoing covid-19 pandemic, where medical treatment and vaccination are still only remote options, mitigation and containment mainly rely on massive and rapid adoption of preventive measures [9] . understanding how the members of different demographic groups perceive the risk, and consequently adopt specific behaviors in response to it, is therefore key to measure the effectiveness of non-pharmaceutical interventions, design more realistic epidemic models, and enable public health agencies to develop optimal control policies to contain the spread of covid-19. we seek to narrow this data gap by monitoring individual behaviors and attitudes in response to the covid-19 pandemic in multiple countries. in march 2020, we launched a crossnational online survey, called the "covid-19 health behavior survey" (chbs), to collect timely data on people's health status, behaviors, close social contacts, and attitudes related to covid-19. we recruit respondents through advertisement campaigns on facebook, that we created via the facebook advertising manager (fam). this novel approach to recruiting respondents allows us to combine the flexibility of online surveys for rapid data collection, with the controlled environment of targeted advertisement. this makes it possible to recruit a balanced sample across demographic groups, that is approximately representative of the general population, after applying appropriate post-stratification weights [10, 11, 12] . other similar online initiatives have emerged recently [13, 14, 15, 16] , but to the best of our knowledge, this is the first cross-national study addressing multiple key factors, ranging from individual behaviors and attitudes to health-related indicators to social contact patterns. moreover, our sampling approach and continued data collection allows us to compare people's behaviors across countries that are at different stages of the covid-19 pandemic, and to assess changes in behaviors after pivotal events, such as nationwide lockdowns. in this paper, we present first results based on survey data collected over the period march 13 to april 19, 2020 in belgium, france, germany, italy, the netherlands, spain, the united kingdom, and the united states. over this period, a total of 66,266 participants completed the questionnaire. our goal in this paper is to provide insights into the relation between participants' demographic characteristics and (i) the threat they perceive covid-19 to pose to various levels of society, (ii) the confidence they have in the preparedness of different national and international organizations to handle the current crisis, and (iii) the behavioral measures (preventive measures and social distancing measures) they have taken to protect themselves from the coronavirus. from a public health perspective, this information is key to understand the behaviors and attitudes of specific demographic groups in different countries and help guide the decision-making process to design adequate policies to contain the spread of covid-19. in the following sections, we outline our methodological approach and discuss the innovative aspects of participant recruitment through facebook advertising campaigns, as well as the statistical adjustments needed to approximate a sample representative of the general population. then we describe the main features of our sample and present results of the first analyses regarding behaviors and attitudes in response to covid-19. we close with a discussion and an outlook for the next steps in our broader project. the chbs is designed to collect information on respondents' health behaviors and attitudes related to covid-19. participation in the survey is anonymous and voluntary. respondents can stop participating at any time and can skip questions they feel uncomfortable answering. the questionnaire consists of four topical sections: (i) socio-demographic indicators (age, sex, country of birth, country of residence, level of education, household size and composition); (ii) health indicators (underlying medical conditions, flu vaccination status, pregnancy, symptoms experienced in the previous seven days); (iii) opinions and behaviors (perceived threat from covid-19, level of trust in institutions, level of confidence in sources of information, preventive measures taken, disruptions to daily routine); (iv) social contact data, i.e. the number of interactions that respondents had the day before participating in the survey in different settings (at home, at school, at work, or in other locations). to facilitate validation and warrant comparability with existing surveys, we included standard questions from several sources, such as the european social survey (ess) [17] regarding socio-demographic characteristics, ipsos [18] regarding opinions on the coronavirus outbreak, and the polymod project [19] regarding social contacts. note that we ask respondents about their behavior and attitudes related to the coronavirus outbreak only if they indicated that they were aware of it. in more detail, we asked respondents how much, if at all, they had seen, read or heard about the coronavirus outbreak, with the answer options "a great deal", "a fair amount", "not very much", "nothing at all", and "prefer not to answer". respondents who indicated that they knew nothing at all, or that they preferred not to answer, were not asked any further questions related to the outbreak. we created the questionnaire first in english, and then translated it into the different official languages of the countries in our study, with support from professional translators. we considered country-level differences when adjusting the questionnaire for different countries, where applicable (e.g. differences in the educational system). in the online implementation, the questionnaire is available in both english and the national language(s) of the respective country in which respondents are located. the questionnaire was implemented in the online survey tool limesurvey (version 3.22.8+20030) and hosted by the society for scientific data processing (gwdg). the full english questionnaire (as used in the united states) is reported in appendix a. the link to the questionnaire is distributed through advertisement campaigns that we created via the fam. facebook is currently the largest social media platform, with 2.45 billion monthly active users worldwide as of september 2019 [20] . in the united states, about 69% of adults used facebook in 2019 [21] , with similar penetration rates in europe, ranging from 56% in germany to 92% in denmark [22] . the fam enables advertisers to create advertising campaigns that can be targeted at specific user groups, as defined by their demographic characteristics (e.g. sex and age) and a set of characteristics that facebook infers from their behavior on the network (e.g. interests). an increasing number of studies explore the use of facebook in demographic and health research to recruit participants for online surveys [23, 24, 25] . two main advantages of this approach are rooted in facebook's wide reach and the possibility to directly target members of different demographic groups. two concerns that are often raised are that in online samples self-selection might lead to bias in results, and that online sub-populations may not be representative of the general population. however, there is increasing evidence that samples obtained from facebook do not significantly differ from samples obtained from more traditional recruitment and sampling techniques in central demographic and psychometric characteristics, especially if post-stratification weights are applied adequately [10, 12, 26, 27] . we created one advertising campaign per country and stratified each campaign by sex (male and female), age group (18-24, 25-44, 45-64 , and 65+ years), and region of residence (largely following the nuts classification in europe and the census regions in us; see table s4 in the supplementary material), resulting in 24 to 56 strata per country, further stratified using six different ad images. figure s1 in section 1 of the supplementary material illustrates the structure of our facebook advertising campaigns in the united states. note that we aggregated the different regions of residence into larger macro-regions, to keep the number of strata in facebook manageable (see table s4 for the exact mapping). we launched the campaigns on march 13, 2020, in italy, the united kingdom, and the united states. we added germany and france on march 17, spain on march 19, the netherlands on april 1, and belgium on april 4, 2020. in the period 21-26 march, we were unable to recruit a significant number of participants due to technical issues with the fam which prevented the delivery of our advertisements. we select participants for our analysis in three steps. first, we include only participants who reported that they lived in the country that the respective advertising campaign and countryspecific questionnaire targeted, and who reported their sex, age, and region of residence (the central variables in our post-stratification weighting approach, see details below). second, when analysing responses to a given question, we exclude respondents who chose the options "don't know" or "prefer not to answer". in the analysis reported here, this particularly affects the question about awareness of the coronavirus outbreak (see section 2.1); however, as table s2 in the supplementary material shows, the share of respondents to whom this applies is less than 1% across countries. third, given that in calendar week 12 we were only able to collect a small number of completed questionnaires in spain (less than 100), we excluded these data from our analysis as the sample size would render our analysis unreliable for this period. note that all period references consider local time zones across countries and regions. after participant selection, we apply post-stratification weights to the final data set in order to correct for potential issues with non-representativeness in our sample. we use a standard procedure in survey research, in which appropriate weights are computed based on population information from more traditional data sources (e.g. census data). here we use population data from eurostat (2019) [28] and the us census (2018) [29] . specifically, for each stratum i (given by each combination of sex, age, and macro-region) in each country, we compute the fraction p i andp i of, respectively, the true population counts n i and the sample countsn i , compared to the total population i n i and the total sample size ini . the weights w i are then defined as w i = p i /p i , thus giving less weight to groups which are over-represented (w i < 1) and more weight to groups which are under-represented (w i > 1) in the sample. we provide more details about our approach to post-stratification in section 3 of the supplementary material. in our analysis, we focus on (i) perception of threat from covid-19, (ii) confidence in the preparedness of different national and international organizations to respond to this threat, and (iii) behavioral measures taken to protect oneself from the virus. all our analyses are based on the weighted sample, whereas the reported sample sizes refer to the unweighted sample. we asked respondents to rate the threat they perceived covid-19 to pose for different levels of society (i.e. to themselves, their family, their local community, their country, and the world) on a 5-point likert-type scale (1 = very low threat, 5 = very high threat), including the options "don't know" and "prefer not to answer", which are treated as missing values (table s3 in the supplementary material reports the corresponding sample size for each item). for comparison, we asked respondents to answer the same questions also for the seasonal flu. we normalized respondents' answers to each item to the range 0-1, meaning that values around 0.5 correspond to moderate perceived threat, whereas 0 and 1 correspond to low and high perceived threat, respectively. in a similar way, we asked respondents to rate the confidence they had in the preparedness and ability of different organizations to effectively deal with the covid-19 pandemic (i.e. doctors and healthcare professionals in their community, hospitals in their local area, health care services in their country, the world health organization, their local government, and their national government) on a 4-point likert-type scale (1 = not confident at all, 4 = very confident), also including the options "don't know" and "prefer not to answer", which are treated as missing values (see table s3 in the supplementary material). we normalized answers to the range 0-1, and aggregated responses related to the local health system (doctors and healthcare professionals in respondents' community and hospitals in their local area) by averaging them across items within respondents. finally, we asked respondents which measures, if any, they had taken to protect themselves from the coronavirus. for this, we showed a list of actions, from which they can choose all that apply. this list includes preventive measures (e.g. washing hand more often), measures of social distancing (e.g. avoided social events), measures of reduced mobility (e.g. avoided public transportation), panic buying (e.g. stockpiling of food), and potential discriminatory actions (e.g. avoided eating in asian restaurants). see the questionnaire in the appendix a for the full list of actions. in the analysis, we consider the shares of participants who reported having adopted specific behaviors in response to covid-19, including: (i) the stockpiling of food and/or medicine; (ii) the use of a face mask; (iii) the increased use of hand sanitizer; (iv) the increased washing of hands; (v) social distancing (if participants selected at least one of the following: avoided shaking hands, avoided social activities, and avoided crowded places); and (vi) the reduced use of transportation (if participants selected at least one of the following: avoided travelling by public transportation, and avoided travelling by taxi). in our analyses, we used non-parametric tests for median comparisons (wilcoxon test to compare two groups and kruskall-wallis test to compare three or more groups) and considered p-values of less than 0.05 to be significant. data analysis was performed with the programming language python (version 3.7). . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 15, 2020. . https://doi.org/10.1101/2020.05.09.20096388 doi: medrxiv preprint 3 results a total of 66,266 participants completed the survey in belgium (n=5,520), france (n=6,216), germany (n=11,030), italy (n=9,310), the netherlands (n=4,711), spain (n=7,145), the united kingdom (n=8,412), and the united states (n=13,922) in the period between march 13, 2020 (calendar week 11) and april 19, 2020 (calendar week 16). as table 1 shows, participation by week was high in all countries, with a median number of 1,610 participants per week in belgium, 1,490 in france, 1,646 in germany, 1,810 in italy, 1,743 in the netherlands, 1,842 in spain, 1,114 in the united kingdom, and 2,498 in the united states. table 1 also shows the demographic characteristics of the participants in each country, based on the unweighted sample. the sex ratio is somewhat skewed towards females compared to the overall population, ranging from 63% female in germany to 71% female in france. in terms of age, older respondents tend to be over-represented, with a median age of 48 years (iqr 31-62) in belgium, 45 years (iqr 29-61) in france, 40 years (iqr 27-56) in germany, 39 years (iqr 26-56) in italy, 55 years (iqr 38-64) in the netherlands, 49 years (iqr 36-60) in spain, 56 years (iqr 41-65) in the united kingdom, and 55 years (iqr 37-65) in the united states. when it comes to education, there is some variation across countries. more specifically, in belgium (46%), france (71%), spain (59%), the united kingdom (46%), and the united states (60%) most respondents attained university-level education, whereas in germany (62%), italy (50%), and the netherlands (58%) most respondents attained secondary-level education. after applying post-stratification weights, the bias described above is reduced and the sample approximates the shares reported in nationally representative surveys in terms of sex, age, and educational attainment, as shown in figure s3 in the supplementary material. for more details, see section 3 of the supplementary material. the perception of threat: higher for the elderly and for women, while everyone is less concerned for oneself than for the country as a whole in all countries, there is significant variation in threat perceptions across levels of society (p < 0.001). in particular, the perception of threat increases sharply from the personal sphere (oneself and the family) to more distal contexts, i.e. the local community, the country, and, ultimately, the world 1 . considering specifically the perceived threat to oneself and to the world, the latter is on average 32% greater, whereas this difference ranges from 24% in italy to 37% in the united states. apart from these variations at the country level, the threat perception posed by covid-19 is both age-and sex-specific. as shown in figure 1b, 7 . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 15, 2020. . overall, the perceived threat increases with age, with few notable exceptions, including the perceived threat to the family in germany, the netherlands, spain, and the united states, the perceived threat to the local community in the netherlands, spain, and the united states, and the perceived threat to the country and to the world in the united states (all p > 0.06). importantly, as figure 1c shows, the perceived threat is significantly higher among women than among men 2 . the development of threat perceptions over time shows different temporal patterns across countries, as can be seen in figure 1d . in particular, there is significant variation over time in germany (p < 0.001), and the united states (p < 0.001). in germany the perceived threat shows a negative trend, with the median value compared to that of week 12 decreasing by about 4% in week 13, 9% in week 14, 15% in week 15, and 18% in week 16. in the united states the trend changes over time, with the median value compared to that of week 11 increasing by about 20% in week 12, 28% in week 13, and 31% in week 14, but then dropping to being only 17% higher in week 15, and 15% higher in week 16. in france, italy, and the united kingdom, the temporal pattern is more mixed, with significant variation over time across levels of society (p < 0.02), except for the perceived threat to oneself in france (p = 0.5), italy (p = 0.6), and 2 all p < 0.01, except in spain for the perceived threat to oneself (p = 0.06), to the family (p = 0.2), and to the local community (p = 0.05) 8 . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 15, 2020. finally, figure 2 compares the threat perception for seasonal influenza (panel a) with that for covid-19 (panel b). the perceived threat posed by covid-19 is significantly higher than the perceived threat posed by influenza (all p < 0.001). in more detail, the perceived threat to oneself is on average 51% higher (ranging from 41% in germany to 61% in belgium), the threat to the family is 46% higher (40% in the netherlands to 51% in the united states), the threat to the local community is 44% higher (33% in france to 54% in the united kingdom), the threat to the country is 64% higher (51% in germany to 71% in belgium), and the threat to the world is 55% higher (47% in italy to 62% in belgium). more details about the perceived threat posed by influenza can be found in section 5 of the supplementary material. landscape, men have higher confidence in local and national health systems in all countries, there is significant variation across organizations (all p < 0.001). first, respondents' confidence in the national health system tends to be lower than their confidence in the local health system 3 . considering the median values, respondents' confidence in the national health system is about 13% lower than their confidence in the local health system in belgium, 19% lower in france, 6% lower in germany, 6% lower in 3 all p < 0.007, except italy (p = 0.2) and the united kingdom (p = 0.9) . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 15, 2020. . the netherlands, 2% lower in spain, and 14% lower in the united states. second, respondents' confidence in local and national governments differs substantially in all countries (p < 0.04). in particular, their confidence in the national government is about 3% lower than their confidence in the local government in germany, it is 26% lower in france, 12% lower in spain, and 31% lower in the united states. by contrast, it is about 1% higher in belgium, 7% higher in italy, 6% higher in the netherlands, and 8% higher in the united kingdom. apart from this variation, several other patterns stand out in the level of confidence by age group and sex. as shown in figure 3b , overall the elderly tend to be more confident in the preparedness of the various organizations, with the exception of the who, in which young adults aged between 18 and 24 years show instead greater confidence. additionally, the level of confidence is sex-specific across organizations, as can be seen in figure 3c . male respondents are more confident in the local or national health systems 4 , whereas female respondents are more confident in the who and in the local government 5 . as for the national government, instead, confidence is higher among female respondents in germany (p < 0.001), and spain (p = 0.01), but it is higher among male respondents in the united states (p < 0.001). figure 3d shows the development of the level of confidence over time. similarly to the perceived threat shown in figure 1d , the temporal patterns vary across countries. in particular, 4 all p < 0.02, except for the netherlands, spain, and the united kingdom 5 as for the who, all p < 0.002, except for belgium, france, and italy, while for the local government, all p < 0.02, except belgium, italy, and the united states . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 15, 2020. . there is significant variation across weeks in germany (p < 0.01), italy (p < 0.03), the united kingdom (p < 0.01), and the united states (p < 0.01). while in germany and in the united kingdom, the trend is positive with the median value in week 16 being about 7% and 21% higher compared to the first week, on the contrary, in italy this trend is negative with the median value in week 16 being about 12% lower than in week 11. in the united states, instead, the temporal pattern is more variable, with the level of confidence in the health systems increasing, whereas the level of confidence in the different levels of government diverges. it is higher for the local government (about 8% higher in week 16 than in week 11), while for the national government the trend changes over time, with the median value compared to that of week 11 decreasing by about 3% in week 12, 17% in week 13, and 12% in week 14, but then increasing to being only 7% lower in week 15, and 5% lower in week 16. on the other hand, the temporal pattern in france shows significant variation, except for the local health system (p = 0.09), whereas there is no significant variation in the level of confidence over time in belgium (all p > 0.07), the netherlands (all p > 0.08), and spain (all p > 0.5). moreover, looking at the level of confidence in the who separately, this consistently shows a negative trend in france (about 14% lower in week 16 compared to week 13), germany (about 13% lower in week 16 compared to week 12), italy (about 12% lower in week 16 compared to week 11), the united kingdom (about 7% lower in week 16 compared to week 11), and the united states (about 24% lower in week 16 compared to week 11). figure 4 shows the self-reported behaviors broken down by country (panel a), age group (panel b), sex (panel c), and week (panel d). as shown in figure 4a , the least frequently reported behavior is the stockpiling of food and/or medicine, ranging from about 18% of respondents (iqr [16] [17] [18] [19] [20] [21] in the netherlands to about 31% (iqr 24-33) in germany. secondly, the share of participants who reported wearing a face mask ranges from about 6% (iqr 4-9) in the netherlands to about 57% (iqr 54-61) in italy. as for hand hygiene, the share of participants who increased the use of hand sanitizer ranges from about 49% (iqr 46-54) in germany to about 70% (iqr 68-77) in the united states, while the share of participants who increased washing their hands ranges from about 89% (iqr 85-91) in germany to about 94% (iqr 91-96) in spain. finally, the most frequently reported behaviors are, respectively, increased social distancing, which ranges from about 93% (iqr 90-95) in the united kingdom to about 98% (iqr 97-99) in italy, and the reduced use of transportation, which ranges from about 72% (iqr 68-75) in the united states to about 82% (iqr 78-85) in france. moreover, the share of participants adopting specific behaviors related to covid-19 shows a variable pattern across age groups in all countries, as shown in figure 4b . in particular, significant variations in the age distribution is observed in respondents who stockpiled food and/or medicine, increased the use of hand sanitizer, and reduced the use of transportation 6 . however, there is no significant variation in the age distribution in terms of respondents who engaged in social distancing, increased hand washing, and worn a face mask 7 . . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 15, 2020. . fig. 4 . proportions of participants who reported having adopted specific behaviors in response to covid-19 broken down by country (a), age group (b), sex (c), and week (d). behaviors include the stockpiling of food and/or medicine, wearing a face mask, increased use of hand sanitizer, increased hand washing, increased social distancing, and reduced use of public transportation. bar charts show median values and 95%ci as errors. weighted sample. as shown in figure 4c , behaviors related to covid-19 are sex-specific, with female respondents showing the highest adoption rates for specific behaviors 8 . the development of behaviors over time shows different temporal patterns between countries, as can be seen in figure 4d . in particular, the use of a face mask substantially increased over time (all p < 0.001, except belgium, and the netherlands), as well as hand hygiene in germany, italy, the united kingdom, and the united states (p < 0.04), and the reduced use of transportation in the united kingdom (p < 0.001), and the united states (p < 0.001). social distancing has increased sharply in the united kingdom (p < 0.001), and in the united states (p < 0.001), whereas it has decreased in germany (p = 0.001), reflecting different stages of the epidemic and different policies. . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 15, 2020 understanding how different demographic groups perceive the risk of covid-19, and thus adopt specific behaviors in response to it, is key to enable public health agencies to develop optimal intervention strategies to contain the spread of the disease. in this paper, we have presented insights from survey data collected through a cross-national online survey, the covid-19 health behavior survey (chbs). the survey is ongoing, and here we presented results based on data collected during the period march 13-april 19, 2020 in belgium, france, germany, italy, the netherlands, spain, the united kingdom, and the united states. in this closing section, we summarize the main findings and provide our interpretation in light of the current evidence on the covid-19 pandemic. first, we found that the perception of the threat that covid-19 poses was on average highest in italy, followed by the united kingdom, spain, belgium, france, the united states, the netherlands, and germany. conversely, respondents' confidence in the preparedness of local and national organizations to deal with covid-19 was on average highest in the netherlands, followed by italy, germany, spain, the united kingdom, the united states, belgium, and france. in particular, italy was the first most affected country in europe in terms of numbers of cases and deaths, as well as the first country in europe to implement a nationwide lockdown on march 11, 2020 . this may explain the high threat perceived by the population in this country, and, together with the high confidence in the different health systems and different levels of government, the willingness to adopt preventive behaviors and adhere to social distancing measures. after italy, nationwide lockdowns were implemented also in spain (march 14), france (march 17), belgium (march 18), the netherlands (march 24), and the united kingdom (march 24) to slow the progression of the virus and to prevent overloading the healthcare system [30] . in the united states, instead, restrictive measures were implemented at the state level, starting in california on march 19, 2020 . notably, regarding the united kingdom and the united states, our data collected before and after lockdown measures were implemented (considering the united states as a whole) allow to observe temporal variation in the self-reported behaviors and attitudes: the perceived threat has increased in the population, along with the adoption of social distancing measures. in the case of the united kingdom, after the lockdown was implemented, the level of confidence in the health systems and different levels of government sharply increased, possibly reflecting discontent in the population about previously announced strategies. by contrast, the results for germany are more difficult to interpret. in germany, somewhat less restrictive measures were implemented on march 22, including school closures, cancellations of public gatherings, and the encouragement of social distancing. however, in contrast to the united kingdom and the united states, for which we observe a change in the temporal trends only after the implementation of non-pharmaceutical interventions, we find for germany that the share of respondents who had adopted social distancing measures was already high before such measures were implemented, and did not change much after this point. furthermore, compared to other countries, the level of confidence in the health systems and different levels of government in germany was high from the beginning of our observation period, and has further increased since then, whereas the perceived threat of covid-19 has decreased over time. this might be interpreted as a case of spontaneous bottom-up behavioral changes emerging from the population, following high trust in decisions and preparedness of the government. also, of the european countries considered in this study, germany had the third highest number of cases (about 140,000), but placed only sixth in terms of deaths (about 4,000) as of april 19, 2020 [31] , which might explain the lower perceived risk perception in the 13 . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 15, 2020. . second, we observe a clear pattern in threat perceptions regarding different levels of society, sharply increasing from moderate threat for the personal sphere (threat to oneself and the family) to very high threat for more distal contexts (i.e. the local community, the country, and the world). yet, even though the perception of threat to oneself among our respondents was comparatively low, we found that a high share of them had increased their hand hygiene. this insight renders it uncertain as to what extent behavior can be straightforwardly linked to perceptions of personal threat. furthermore, we found that the perceived threat posed by covid-19 is significantly higher than the perceived threat posed by seasonal influenza. one likely explanation for this is that although seasonal influenza causes regular annual epidemics worldwide [32] , the novelty and uncertainty that surround covid-19 leads risk perception to be substantially higher. third, apart from variation at the country level, we also found sex-and age-specific differences. looking at the age component, our findings suggest that younger people perceive the threat to themselves lower than older people. this is in line with the evidence that older adults are at highest risk of severe complications following infection from covid-19 [33] . by contrast, the age structure in the perceived threat to the family is less pronounced, which suggests that respondents were concerned about their family members, regardless of their own age and the perceived threat to themselves. fourth, we also found sex-specific patterns in the data. specifically, female respondents perceived the threat that covid-19 poses substantially higher, reported a lower level of confidence in the health system, and were more willing to adopt protective behaviors. since the case fatality rate for covid-19 is substantially higher for men [34] , we might expect that men are more concerned about it. our results demonstrate that this is not necessarily true, and fact may have to be considered in the design of future communication campaigns. we gained these insights by using a novel approach to collecting health behavior data in times of a pandemic. we employed facebook advertising campaigns to continuously recruit a large number of participants for our survey over a long period of time. this approach allows us to target specific demographic groups in a comparative, cross-national approach, and to collect balanced samples to which post-stratification methods can be applied. these advantages notwithstanding, our approach also has some limitations. first, online surveys potentially suffer from bias due to self-selection and non-representativeness of the sample. in the case of facebook, there is increasing evidence that samples obtained from this social media network are not significantly different in central demographic and psychometric characteristics from samples obtained by more traditional recruitment and sampling techniques [12] . furthermore, by applying post-stratification weighting, which is a standard procedure in survey research, we can correct for non-representativeness in observable characteristics (but not necessarily for self-selection based on unobservable characteristics), at least at the level of the entire sample. ideally, in our cross-temporal comparisons, we would apply this approach at the level of the week, to warrant complete comparability of observations over time, but issues of data sparsity complicate this approach. we do not expect this to strongly affect our results, but it should be kept in mind that our weekly results might suffer from somewhat larger bias than our aggregate results. second, our data collection started at different time points across countries, and also pertains to different points in the trajectory of the pandemic across countries. this also encompasses differences in the implementation of non-pharmaceutical interventions ordered by local and national governments, and needs to be kept in mind when comparing and interpreting our results across countries. 14 . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may 15, 2020. . third, the data presented here have the form of repeated cross sections, which enables us to assess changes in the population samples over time, but does not allow us to assess changes within individuals. we are planning to address some of the limitations in the future in the following way. first, we aim to expand our post-stratification weighting scheme, by applying multilevel poststratification, which will enable us to achieve greater consistency among differently sized strata and greater precision in the estimates for population subsets, such as the weekly estimates presented here. second, we aim to carry out a follow-up survey among participants who agreed to provide their email address for this. this panel perspective offers a unique possibility to understand how the covid-19 pandemic affects the population in the long run and to assess the impact of loosening the lockdown measures on social contact patterns and health behaviors in a cross-national perspective. to conclude, our work reduces the gap in human behavioral data, by providing timely and accurate data on individual behaviors and attitudes across countries. our work also illustrates how social media networks, like facebook, together with appropriate survey designs and statistical methods, offer an innovative and powerful tool for rapid and continuous data collection to monitor trends in behaviors relevant for mitigation strategies of covid-19. taken together, the insights gained from our survey data are particularly relevant for policy makers and help design appropriate public health strategies and communication campaigns, and to design realistic epidemic models, which can account not only for the spatio-temporal spread of the infection, but also for accurate data on individual human behaviors. . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may 15, 2020. . https://doi.org/10.1101/2020.05.09.20096388 doi: medrxiv preprint . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may 15, 2020. . https://doi.org/10.1101/2020.05.09.20096388 doi: medrxiv preprint . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may 15, 2020. . https://doi.org/10.1101/2020.05.09.20096388 doi: medrxiv preprint world health organization world health organization estimating the number of infections and the impact of non-pharmaceutical interventions on covid-19 in european countries: technical description update how will country-based mitigation measures influence the course of the covid-19 epidemic? capturing human behaviour non-pharmaceutical interventions for pandemic influenza, national and community measures behavioural change models for infectious disease transmission: a systematic review towards a data-driven characterization of behavioral changes induced by the seasonal flu how behavioural science data helps mitigate the covid-19 crisis what's to like? facebook as a tool for survey data collection demographic research with non-representative internet data traditional versus facebook-based surveys: evaluation of biases in self-reported demographic and psychometric information are people excessively pessimistic about the risk of coronavirus infection? evaluating covid-19 public health messaging in italy: self-reported compliance and growing mental health concerns social psychological measurements of covid-19: coronavirus perceived threat, government response, impacts, and experiences questionnaires data for good: new tools to help health researchers track and combat covid-19 public opinion on the coronavirus outbreak: a multi-country poll from ipsos social contacts and mixing patterns relevant to the spread of infectious diseases facebook reports third quarter 2019 results social media use 2018: demographics and statistics measuring labour mobility and migration using big data: exploring the potential of social-media data for measuring eu mobility flows and stocks of eu movers online surveys and digital demography in the developing world: facebook users in kenya migrant sampling using facebook advertisements: a case study of polish migrants in four european countries broad reach and targeted recruitment using facebook for an online survey of young adult substance use quota sampling using facebook advertisements not by the book: facebook as a sampling frame eurostat regional yearbook annual estimates of the resident population by sex, age, race, and hispanic origin for the united states and states covid-19 pandemic in europe coronavirus source data world health organization people who are at higher risk: older adults covid-19 weekly surveillance report we would like to thank all the participants who took the time to voluntarily complete our survey, and the staff and colleagues of the max planck institute for demographic research who contributed to the realization of this project, in particular k. this study was funded through the support of the max planck institute for demographic research, which is part of the max planck society. this study was conducted in agreement with the data protection regulations valid in germany. informed consent was obtained from all participants, enabling the collection, storage, and processing of their answers. ethical approval for the study was obtained from the ethics council of the max planck society. all authors designed the questionnaire and collected the data. dp conceived the project idea, devised the idea for the manuscript, analyzed the data, and wrote the manuscript. ag developed the strategy and technical implementation for data collection and the recruitment of survey participants, and wrote the manuscript. fr supported the strategy development and the technical implementation of the data collection, and wrote the manuscript. jc and edf designed the post-stratification weighting scheme. dp, ag led the project and the implementation of the online survey. all authors provided input and edited and reviewed the manuscript. the authors declare that they have no competing interests. key: cord-011794-ejoufvvj authors: binder, florian; reiche, sven; roman-sosa, gleyder; saathoff, marion; ryll, rené; trimpert, jakob; kunec, dusan; höper, dirk; ulrich, rainer g. title: isolation and characterization of new puumala orthohantavirus strains from germany date: 2020-04-23 journal: virus genes doi: 10.1007/s11262-020-01755-3 sha: doc_id: 11794 cord_uid: ejoufvvj orthohantaviruses are re-emerging rodent-borne pathogens distributed all over the world. here, we report the isolation of a puumala orthohantavirus (puuv) strain from bank voles caught in a highly endemic region around the city osnabrück, north-west germany. coding and non-coding sequences of all three segments (s, m, and l) were determined from original lung tissue, after isolation and after additional passaging in veroe6 cells and a bank vole-derived kidney cell line. different single amino acid substitutions were observed in the rna-dependent rna polymerase (rdrp) of the two stable puuv isolates. the puuv strain from veroe6 cells showed a lower titer when propagated on bank vole cells compared to veroe6 cells. additionally, glycoprotein precursor (gpc)-derived virus-like particles of a german puuv sequence allowed the generation of monoclonal antibodies that allowed the reliable detection of the isolated puuv strain in the immunofluorescence assay. in conclusion, this is the first isolation of a puuv strain from central europe and the generation of glycoprotein-specific monoclonal antibodies for this puuv isolate. the obtained virus isolate and gpc-specific antibodies are instrumental tools for future reservoir host studies. electronic supplementary material: the online version of this article (10.1007/s11262-020-01755-3) contains supplementary material, which is available to authorized users. puumala orthohantavirus (puuv) is the most important hantavirus in europe [1] . it causes the majority of human hantavirus infections and hemorrhagic fever with renal syndrome (hfrs) cases [2] . in central and western europe hantavirus outbreaks occur in two to five year intervals and are driven by massive increase of the bank vole (myodes glareolus) population, the reservoir of this orthohantavirus species [3] . human hantavirus disease is notifiable in germany since 2001 and the majority of recorded cases is mainly due to puuv infections in southern and western parts of germany, whereas dobrava-belgrade orthohantavirus (dobv) with the striped edited by detlev h. kruger. the online version of this article (https ://doi.org/10.1007/s1126 2-020-01755 -3) contains supplementary material, which is available to authorized users. field mouse as reservoir causes infections in the northeastern part of germany [3] . the characterization of the pathogenicity and identification of virulence markers are highly dependent on adequate puuv isolates. currently, the number of puuv isolates is very limited and does not represent the real diversity of puuv strains in europe. in particular, no central european puuv isolate exists [4] . the majority of puuv isolates, and hantaviruses in general, was obtained based on passaging in reservoir animals or veroe6 cells and is highly adapted [5] [6] [7] . previous investigations indicated that veroe6 cell adaptation of puuv kazan strain results in the inability of the adapted strain to infect the bank vole reservoir [8] . the recent development of bank vole-derived primary or permanent cell lines may allow the isolation of reservoir-adapted puuv strains [9] [10] [11] [12] . hantavirus proteins are usually detected in infected cells by monoclonal antibodies. nucleocapsid (n) protein-specific monoclonal antibodies have been developed against a large range of hantaviruses [13] [14] [15] . in contrast, the number of glycoprotein precursor (gpc), as well as gc-and gn-specific monoclonal antibodies is rather low [16] [17] [18] . the majority of these antibodies were raised by infection of bank voles or immunization with recombinant n protein or heterologous virus-like particles (vlps). the generation of envelope protein-specific monoclonal antibodies with reactivity to virus proteins in infected cells is highly dependent on structural constraints [19] . autologous vlps represent a useful tool to generate highly efficient immune responses against a variety of viruses and for the generation of monoclonal antibodies in particular [20] . puuv strain astrup [21] gpc-derived vlps were generated in this study as previously described for maporal orthohantavirus [22] . lower saxony, north-west germany, and district osnabrück in particular, is a well-known endemic region for puuv infections [23, 24] . this endemic region was also again heavily affected by the hantavirus outbreak year 2019 [25] . here, we aimed to isolate a central european puuv strain from bank voles in the district of osnabrück using standard veroe6 cells and the recently established carpathian lineage bank volederived kidney cell line (mgn-2-r [10] ). complete genome determination by shot-gun and hybrid-capture-mediated highthroughput sequencing (hts) was used to follow the potential adaptation of the puuv isolates in veroe6 and reservoir cell lines. finally, the reactivity of the isolates was determined with novel monoclonal antibodies raised against puuv gpc vlps. bank voles were trapped in spring 2019 in the puuv endemic region around osnabrück following a standard snap trapping protocol [25, 26] . in the field, a small piece of lung was taken for virus isolation and rt-qpcr analysis. thereafter, carcasses were frozen, transported to the laboratory and completely dissected according to standard protocols. chest cavity lavage was collected by rinsing the chest cavity by 1 ml phosphate-buffered saline (pbs) and investigated for the presence of puuv-reactive antibodies. the presence of hantavirus rna was analyzed from lung tissue and were, in part, previously published in a surveillance study [25] . for virus isolation and further infection studies, veroe6 and bank vole kidney (mgn-2-r; [10] ) cells were used in parallel. virus titration was done on veroe6 cells only. mgn-2-r cells were grown in an equal mixture of hams' f12 and iscove's modified dulbecco's medium (imdm) + 10% fetal calf serum (fcs) and passaged two times per week at a 1:6 ratio. veroe6 cells were passaged twice a week in minimal essential medium (mem) + 10% fetal calf serum (fcs) and a split ratio of 1:4. for virus isolation, 1 × 10 5 mgn-2-r or veroe6 cells were seeded in 12.5 cm 2 flasks one day before rodent sampling in the field. the cells were carried to trapping sites in an isolation box with heat packs (around 33 °c constant for 2 days with outside temperature of 5-10 °c). after collecting voles from traps, a small incision in the chest area was made and a piece of lung (pea-sized) was taken and transferred into 1 ml dulbecco's modified eagle's medium (dmem) + 5% fcs + penicillin/streptomycin (ps) in a 5 ml safe lock tube. lung tissue material was homogenized in the field by grinding it through a fine metal grid against the tube wall. the homogenized tissue material was sterile filtered (0.45 µm) directly onto the cells resulting in approximately 500 µl tissue/medium suspension per 12.5 cm 2 flask. after 1-2 h incubation in the isolation box, 4 ml dmem + 5% fcs + ps was added. upon arrival in the laboratory flasks were incubated in a cell culture incubator at 37 °c and 5% co 2 for 10 days until first passage. in parallel, a pinhead-sized piece of lung was taken for rna isolation in 1 ml trizol (qia-gen, hilden, germany). after 10 days, trypsinized cells were resuspended in 2 ml dmem + 5% fcs + ps. for puuv rna screening, 325 µl of each cell suspension was taken for rna extraction and analyzed by rt-qpcr (see below). fresh veroe6 cells were resuspended in 2 ml dmem + 5% fcs + ps and 200 µl were mixed 1:1 with 200 µl of the inoculated cell suspension in a new 12.5 cm 2 flask. afterwards, 4 ml dmem + 5% fcs + ps were added and cells were incubated for 10 days until next passage. in parallel, one uninfected flask of veroe6 or mgn-2-r cells was passaged as a control. this procedure was continued until rt-qpcr-positive samples were detected. after first screening, only the flasks of the rt-qpcr-positive samples were further passaged. for detection of puuv nucleic acid, rna was extracted from homogenized lung tissue, or cell culture passages using qiazol lysis reagent (qiagen, hilden, germany) followed by a novel puuv s segment-specific rt-qpcr. for rt-qpcr, primers puuv-nss-s (5′-gwnata rcy cgy cat garc-3′) and puuv-nss-as (5′-art gct gac act gty tgt tg-3′) and the probe (5′-6-fam-crg tgg rrrt-gkacc crg atga-bhq-1-3′) were used. the pcr was done according to the quantitect probe one-step rt-qpcr mix (qiagen, hilden germany) protocol and contained 20 pmol/µl of each primer and 5 pmol/µl probe (eurofins, hamburg, germany). the following cycler protocol was used: 30 min of reverse transcription at 50 °c; 15 min initial denaturation at 95 °c; 45 cycles of 10 sec at 95 °c, 25 sec at 50 °c and 25 sec at 72 °c. for quantification of the number of rna copies/µl and sample, an in vitro transcribed rna was used. the in vitro transcription of a plasmid coding for nucleotides 83-355 of the s segment of a puuv strain from baden-wuerttemberg (binder et al., unpublished) was done according to the protocol of the manufacturer (riboprobe® in vitro transcription system t7, promega gmbh, mannheim, germany). the transcribed rna was serially diluted from 10 -2 to 10 -11 ng/ml with 700 rna copies/µl limit of detection (lod). initial tissue samples were screened for puuv rna and viral load as rna copies/µl was determined in triplicates for organs of isolated positive animals. rna from the cell culture adapted strains puuv sotkamo and tulv moravia were used as positive and negative control for the rt-qpcr, respectively. for metagenomics, we extracted rna from either a pinheadsized piece of lung tissue or 250 µl cell culture supernatant using 750 µl qiazol lysis reagent (qiagen, hilden, germany) in combination with rneasy mini kit (qiagen, hilden, germany). for generation of complete genomes of cell culture supernatants, a previously published workflow was used [27] . double-stranded, non-directional cdna libraries from lung tissue for sequencing on the illumina platform were prepared from total rna using the nebnext ultra ii rna library prep kit for illumina (new england biolabs, ipswich, ma, usa). per reaction, a total of 100 ng rna was used as an input. rna was fragmented for 8 min and final cdna libraries were amplified by 8 cycles of pcr to complete adapter ligation and to generate enough material for target sequence enrichment. a custom-made mybaits target capture array (arbor biosciences, ann arbor, mi, usa), containing biotinylated rna probes against all available puuv sequences deposited in ncbi genbank database (august, 2018), was employed to capture puuv-containing sequences from total cellular cdna sequencing libraries. the hybridization-based sequence enrichment (chemistry v3) was performed according to the manufacturer's instructions (arbor biosciences, ann arbor, mi, usa). the enriched cdna sequencing libraries were amplified with 14 pcr cycles to produce enough dna material for hts on the illumina platform. the enriched cdna libraries were quantified with the nebnext library quantification kit (new england biolabs, ipswich, ma, usa), pooled in equimolar amounts, and sequenced with a 600 cycle miseq reagent kit v3 (illumina, san diego, ca, usa) using paired-end sequencing (2 × 300 cycles) on a miseq sequencer (illumina, san diego, ca, usa). the resulting reads were trimmed and assembled against the known complete genome of strain astrup from the osnabrück region [21] with geneious r11.1.5 (https ://www.genei ous.com). for sequences lacking the 5′ and 3′ ends of the m segment, rna ligation was done using t4 rna ligase (thermo fisher scientific, waltham, ma, usa) and subsequent in vitro transcription with a first strand cdna synthesis kit (thermo fisher scientific, waltham, ma, usa). sequences were obtained by conventional dideoxy-chain termination sequencing after pcr with primers puuv os m2 fwd-5′ tga ggg caa tta tta tgt aa 3′ and puuv os m2 rev 5′ cca att gta tgt ggg cat tcc 3′. the obtained sequences were deposited at gen-bank, accession numbers mn639737-mn639763. phylogenetic trees were reconstructed with four novel and 18 published concatenated s, m, and l coding sequences or 202 partial s segment sequences of 365 nucleotides length. published sequences of other hantaviruses were obtained from genbank. analysis was performed by bayesian algorithms via mrbayes v.3.2.6 (https ://sourc eforg e.net/proje cts/ mrbay es/files /mrbay es/) on the cipres online portal [28] . a mixed nucleotide substitution matrix was specified in 4 independent runs of 10 7 generations. phylogenetic relations are shown as a maximum clade credibility phylogenetic tree with posterior probabilities for major nodes. for immunofluorescence assay (ifa), veroe6 and mgn-2-r cells were inoculated with 500 µl puuv osnabrück/v29 or puuv osnabrück/m43 supernatant in dmem + 5% fcs as described previously [10] . infected cells were fixed 10 days 1 3 post infection with a 1:1 mixture of acetone and methanol for 20 min at − 20 °c. after fixation cells were dried, re-hydrated with phosphate-buffered saline (pbs) and incubated with nucleocapsid (n) protein-specific antibody 5e11 [13] diluted 1:1000 in pbs for 1 h at room temperature (rt). a secondary anti-mouse alexa fluor 488 conjugated antibody (abcam, cambridge, uk) was used for detection of hantavirus proteins. nuclei were stained with 4′,6-diamidino-2-phenylindole (dapi, thermo fisher scientific). for titration studies of puuv, mgn-2-r and veroe6 cells were inoculated with 500 µl of the puuv osnabrück/v29 or puuv osnabrück/m43 virus isolate and passaged three times as described above. supernatants of both cell lines were collected after passage three and frozen at − 80 °c. subsequently, supernatants were serially diluted from 10 -1 to 10 -7 in dmem containing 5% fcs in a 96-well plate with three replicates each. a volume of 100 µl of each dilution was added to 24 h old cell monolayers of veroe6 cells in a 96-well plate. after incubation for 10 days, the virus titer was calculated using ifa for puuv n protein detection as described above. titers were calculated as 50% tissue culture infectious dose (tcid 50 )/ml by the spearman/kärber method [29] and mean titers of three experiments are given. titers after isolation (passage 3 of original lung tissue-derived sample) were used for comparison. for expression and generation of vlps in hek293 cells, a codon-optimized synthetic gene of the puuv gpc of the strain astrup [21] was purchased (geneart, regensburg, germany). the gene encoding the glycoproteins was pcr amplified using primer pair o grs 101/o grs 102 (aat-taaggt acc tcc aga ggc gac acc cgg aacc and aattattaag ctt tca ggg ctt gtg ttc ttt gg) and the pcr product and the acceptor vector phan-1 (roman-sosa, unpublished) were digested with the restriction endonucleases kpni and hindiii. the expression plasmid phan-2 was generated by standard molecular biology protocols. in this plasmid, the endogenous signal sequence of the puuv gn is substituted by the igg-light chain signal sequence and a double strep-tag with a glycine/serine-rich linker between the tags. then a permanently transfected hek293 cell line was generated upon transfection of the cells and selection in the presence of geneticin at 0.5 mg/ml. the vlps were affinity purified from the cell supernatants essentially as described [22] . recombinant vlps were used for five immunizations of four weeks apart of female balb/c mice. hybridoma cells producing monoclonal antibodies (mabs) were generated by standard fusion procedure [30, 31] and screened using a 2 µg/ml stock solution of vlps according to an in-house elisa protocol [32] and buffers without tween. resulting mabs were analyzed by ifa and western blot test for their reactivity to puuv osnabrück/v29, puuv sotkamo, puuv vranica and tulv moravia. veroe6 cells were infected with puuv osnabrück/v29, puuv sotkamo, puuv vranica or tulv moravia at moi 0.1 in dmem + 5% fcs. cells were harvested 10 (puuv osnabrück/v29, sotkamo) or 3 (puuv vranica, tulv moravia) days post infection in sds sample buffer (62.5 mm trishcl ph 6.8, 2% sds,10% glycerol, 6 m urea, 0.01% bromophenol blue, 0.01% phenol red) and proteins were separated by sds page, blotted onto polyvinylidenfluorid (pvdf) membranes. after blocking, the membranes were cut into strips and incubated over night with the antibodies 2e10 (1:1), 5f12 (1:1), 3b12 (1:200), 5b8 (1:1), 5h1 (1:1), 4g10 (1:100), 1b12 (1:2), 1g9 (1:100), 8g4 (1:50), 1h7 (1:1), 2h11 (1:5) or n protein-specific antibody 5e11 (1:1000, [13] , all diluted in pbs-tween 0.05%) at 4 °c. a horseradish peroxidase (hrp) labeled secondary goat anti-mouse igg antibody diluted 1:3000 in pbs-tween 0.05% (bio-rad, hercules, ca, usa) was used for detection of hantaviral proteins. a rabbit anti-β-tubulin antibody (abcam, cambridge, uk) was used as a loading control. investigation of chest cavity lavage samples from bank voles was done by igg elisa using recombinant puuv strain bawa n protein, as described earlier [32] . the monoclonal antibody 5e11 was used as a positive control [13] , chest cavity lavage of a igg elisa-and rt-pcr-negative bank vole was used as negative control. chest cavity lavage samples with an optical density (od) value below the lower cut-off value were considered as negative. positive and doubtful samples were retested a second time. when the od value of the elisa was in a range between the lower and upper cut-off value defined according to our standard protocol [32] , animals were considered doubtful. when the od value was above the upper cut-off value, the samples were considered as positive. rodent trapping at five sites from april 11th to 12th, 2019 in the osnabrück region resulted in the collection of 57 bank voles [25] . dissection on site and inoculation of veroe6 and bank vole mgn-2-r cells with homogenized lung samples resulted after three blind passages in four potential isolates that were detected by a novel puuv rt-qpcr (table s1 , fig. 1) . two of the potential candidates showed only low levels of puuv rna and were not able to consistently infect further passages (m52, m62). quantification by rt-qpcr analysis of different tissues from these four bank voles confirmed lung tissue for most of the samples as having the highest puuv rna load, although it was detected in almost all other tissues investigated (fig. s1 ). rt-qpcr investigation of lung tissues of all 57 bank voles resulted in the detection of hantavirus rna in 44 animals (tables 1, s1, [25] ). puuv rna-positive animals originated from all five trapping sites. serological analysis of chest cavity lavages detected puuv n protein reactive antibodies in 24 of 57 bank voles (tables 1, s1). five additional animals, positive for puuv rna, were found to be equivocal in our serological test. all 24 antibody-positive animals were also found to be puuv rna positive, indicating a high number of persistently infected voles. fifteen additional bank voles were only positive for puuv rna, but not for anti-puuv antibodies, indicating a high number of acutely infected animals in spring in this region (table 1) . interestingly three of the four potential isolates originated from seronegative bank voles (table s1 ). two isolates (osnabrück v29 and osnabrück m43) were obtained by passaging in veroe6 or mgn-2-r cells, which reached titers of almost 10 3 tcid 50 /ml ( fig. 2a and b , titer after isolation). shot-gun and hybrid-capture-mediated hts of both isolates resulted in the generation of complete genome sequences which are identical in sequence to the respective original strain in bank vole lung tissue except for one amino acid (aa) exchange each in the rna-dependent fig. 3 ). the genome organization of the novel puuv isolates indicated the typical sequence elements for puuv: the small (s) segment encodes an n protein of 433 aa residues and a putative nss protein of 90 aa in an + 1 overlapping reading frame, the medium (m) segment codes for the 1148 aa gpc and the large (l) segment for the rdrp of 2156 aa (see fig. 3 , genbank accession numbers: mn639737-mn639748). phylogenetic analysis of the concatenated s, m and l segment coding sequences grouped the novel isolates together with astrup prototype strain in sister relationship to puuv sequences from france (fig. 4a) . the phylogenetic analysis of a partial s segment sequence of the novel isolates and representative strains of all puuv clades and subclades from germany confirmed the close relationship of the new isolates to the osnabrück hills subclade (fig. 4b) . the puuv osnabrück m43 isolate was found to be contaminated by a bank vole reovirus; hts derived sequences of the passaged reovirus (genbank accession numbers: mn639755-mn639763) showed a strong similarity to a bank vole reovirus strain, but much lower similarity to a common vole reovirus [33] ). the non-reovirus contaminated isolate osnabrück v29 from veroe6 cells was found to have an insertion of 20 nucleotides in the 3′ non-coding region (ncr) when compared to the other isolate and the astrup reference sequence (fig. 3) . however, this insertion was also found in the original lung sample and therefore no cell culture-specific adaptations were observed in the ncrs of both virus isolates (fig. 3 ). figs. 1 and 2 ). this passaging resulted in no further mutations (genbank accession numbers: mn639749-mn639754). however, the virus isolate passaged in veroe6 cells is accompanied by an increase in the virus titer to 10 4 tcid 50 /ml (fig. 2) . in contrast, the passaging of the osnabrück v29 strain in mgn-2-r cells resulted in a decreased virus titer. as no cytopathic effect was observed, virus detection for titration in both cell lines was done by immunofluorescence assay using an n proteinspecific monoclonal antibody (fig. 2a) . eleven monoclonal antibodies were produced in this study by immunization of mice with puuv strain astrup gpcderived vlps. evaluation of the virus isolate osnabrück v29 using these monoclonal antibodies resulted in typical immunofluorescence patterns in the cytoplasm (fig. 5) . further analysis by western blot test using a lysate of isolate osnabrück v29 from veroe6 cells suggested that the majority of anti-gpc antibodies are directed against conformational epitopes; however, some recognize linear epitopes in gc or gn (table 2 ). subsequent evaluation of the reactivity of these monoclonal antibodies with other puuv strains and tulv strain moravia indicated some level of crossreactivity for some of them (table 2) . here, we describe the first isolation of a central european puuv strain. this strain of the central european lineage increases the available panel of puuv isolates: currently available isolates sotkamo, umea, vranica, and kazan, belong to the clades finnish, north scandinavian, most likely north scandinavian, and russian, respectively [34] . the puuv-like hokkaido virus strain kitahiyama128 originates from japan [12] . in our study, the isolation was based on an in-field dissection and inoculation of cells to prevent freeze/thaw cycles. the subsequent investigation of all 57 bank voles indicated that three of four isolates originated from anti-puuv-seronegative voles. this finding illustrates that a serological test in the field might be misleading in selection of samples for successful virus isolation. instead, an on-site molecular assay may enhance the chance for a successful virus isolation. nevertheless, the approach used here still indicates the challenges of hantavirus isolation; only four isolates were obtained from a total of 15 acutely infected bank voles. in addition, the determination of the complete genome sequences of two isolates including the ncrs expands our knowledge on the sequence diversity of puuv strains within the different regions of the genome. moreover, the hybrid-capture-based enrichment of puuv sequences allows a rapid determination of the complete genome and underlines the value of this workflow for hantavirus surveillance and molecular evolution studies [35] . a phylogenetic analysis of partial s segment nucleotide sequences confirmed the previously reported subclades of puuv in germany; the novel isolates belong to the subclade osnabrück hills within the central european clade. the position within the phylogenetic tree also confirms the local evolution pattern of puuv reported before [23, 36] . the observed high level of rt-qpcr-positive bank voles (44/57; 77%) confirms the district of osnabrück in spring 2019 as a hantavirus outbreak region [25] . the puuv rna detection rate was similarly high at all five trapping sites of bank voles. although 2019 was identified as a hantavirus outbreak year in germany, the distribution of notified human puuv cases was not as homogeneous as in previous outbreak years [25] . the passage of the puuv strains for isolation resulted in non-synonymous nucleotide exchanges in the l segment responsible for single amino acid exchanges in the rdrp (i3749m in m43 and d3963y in v29). the substituted amino acid residues are each very similar in their properties and, presumably, might not influence protein function. a more divergent adaptation at position s2053f has previously been observed for puuv strain kazan [8, 37] . although in this previous study nucleotide exchanges in the ncr of the s segment were observed [37] , here we did not find relevant mutations in this region after passaging in cell culture. the v29 strain showed an insertion in the 3′ ncr, but this insert was also found in the original lung material used for isolation. additionally, this sequence insert was found in another sequence from the same region (jn696358.1, [36] ). the isolate v29 was shown to replicate in veroe6 and a bank vole kidney cell line. the low titer in the bank vole mgn-2-r cell line might be due to the evolutionary lineage origin of this cell line (carpathian lineage); in central europe puuv is harbored by the western evolutionary lineage with spillover to the carpathian lineage in regions with sympatric occurrence of both [24] . in line with the assumption of an association of a puuv clade with an evolutionary bank vole lineage, the vranica puuv strain replicated in mgn-2-r cells, but not in bank vole kidney cells of another evolutionary lineage [9, 10] . interestingly, replication of puuv-like hokkaido virus in cells of its host, the gray red-backed vole, was comparable to puuv infection [12] . future investigations in cell lines and animals of different bank vole lineages are required to confirm this conclusion directly. the orthoreovirus contamination of one of the puuv isolates illustrates that bank voles may harbor additional reactivity of novel puuv gpc-specific monoclonal antibodies with hantavirus-infected veroe6 cells in immunofluorescence assay (ifa). antibodies were generated by immunization of balb/c mice with gpc-derived virus-like particles of puuv strain astrup. after screening and subcloning, monoclonal antibodies were tested in ifa. veroe6 cells were infected with puuv osnabrück v29 iso-late on coverslips and fixed for ifa after 10 days. the monoclonal antibodies were administered for 1 h at rt. detection of the specific antibody binding was done using an anti-mouse alexa fluor 488 conjugated antibody. after staining, coverslips were mounted on glass slides for imaging infectious agents that may influence the susceptibility to puuv infections or their outcome. of note, in bank voles several viruses have been detected, i.e., polyoma-, herpesand hepaciviruses [38] [39] [40] [41] , but also bacterial agents and endoparasites [42] [43] [44] . similarly, a hantavirus isolation approach was previously hampered by the coinfection by a striped field mouse adenovirus [45] . future investigations are needed to evaluate potential influences of coinfections in bank voles. it has been shown that hantavirus gn and gc form complex spike-shaped structures [46] that build conformational epitopes [17, 18] . therefore, we selected an immunization procedure using puuv-gpc-derived vlps, as the organization of the glycoproteins resembles the one of the virion. a panel of eleven monoclonal antibodies was produced here and all of them were reactive with the new puuv isolate in immunofluorescence assay. the staining pattern, which is reminiscent of the one of the secretory pathway organelles, i.e., the golgi apparatus and the endoplasmic reticulum, suggests that the epitopes recognized by these antibodies are already accessible during the maturation process of the proteins. interestingly, some of the monoclonal antibodies recognize linear epitopes as revealed by a western blot assay. although preliminary results suggest that the antibodies do not neutralize the virus when tested individually, synergistic effects with a protective effect cannot be ruled out yet as shown for anti-ebola virus monoclonal antibodies [47] . therefore, the novel antibodies represent a useful tool for further experimental, diagnostic, and therapeutic applications. in conclusion, the puuv isolate described here replicates in a bank vole cell line and its n and gpc proteins can be detected by specific monoclonal antibodies. therefore, this isolate will be useful for further studies on the virulence markers of central european puuv, its reservoir host association and the route of pathogenicity in the bank vole model. the novel gpc-specific monoclonal antibodies will enable future studies on virus entry and important domains for exposed immunogenic regions. funding florian binder acknowledges intramural funding by the friedrich-loeffler-institut. additional funding was provided by the bundesminsterium für bildung und forschung through the research network zoonotic infections (robopub consortium, fkz 01ki1721a, awarded to rgu; fkz 01ki1721h, awarded to laves) for trapping and rodent screening, the rapid project within the infect control veroe6 cells were inoculated with puumala virus (puuv) osnabrück/v29, puuv sotkamo, puuv vranica or tula virus (tulv) strain moravia. infected cells were fixed 10 (puuv osnabrück/v29, sotkamo) or 3 (puuv vranica, tulv moravia) days post infection for immunofluorescence assays or collected in sample buffer for western blot analysis. after fixation or western blot transfer, novel gpc-specific mabs 2e10, 5f12, 3b12, 5b8, 5h1, 4g10, 1b12, 1g9, 8g4, 1h7, and 2h11 were administered. gn-and gcreactive mabs were assigned where possible according to molecular weight of the immunoreactive bands in western blot analysis − negative; (+) weak reactivity; + positive; ++ strongly positive conflict of interest the authors declare that they have no competing interests. ethical approval all animals were handled according to the applicable institutional, national and international guidelines for the care and use of animals. bank vole trapping was conducted in line with the regular pest control of the laves veterinary task-force in lower saxony, germany (department of pest control, oldenburg) according to german federal law ( § 18, gesetz zur verhütung und bekämpfung von infektionskrankheiten beim menschen). the immunization of mice was done in line with the general immunization program of the friedrich-loeffler-institut (landesamt für landwirtschaft, lebensmittelsicherheit und fischerei, mecklenburg-vorpommern, permit: 28/17). open access this article is licensed under a creative commons attribution 4.0 international license, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the creative commons licence, and indicate if changes were made. the images or other third party material in this article are included in the article's creative commons licence, unless indicated otherwise in a credit line to the material. if material is not included in the article's creative commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. to view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/. hantavirus infections hantaviruses-globally emerging pathogens weiss s (2019) molecular and epidemiological characteristics of human puumala and dobrava-belgrade hantavirus infections coding strategy of the s and m genomic segments of a hantavirus representing a new subtype of the puumala serotype isolation of the causative agent of hantavirus pulmonary syndrome propagation of nephropathia epidemica virus in cell culture isolation and characterization of puumala hantavirus from norway: evidence for a distinct phylogenetic sublineage cell culture adaptation of puumala hantavirus changes the infectivity for its natural reservoir, clethrionomys glareolus, and leads to accumulation of mutants with altered genomic rna s segment a new permanent cell line derived from the bank vole (myodes glareolus) as cell culture model for zoonotic viruses common vole (microtus arvalis) and bank vole (myodes glareolus) derived permanent cell lines differ in their susceptibility and replication kinetics of animal and zoonotic viruses more novel hantaviruses and diversifying reservoir hosts-time for development of reservoirderived cell culture models? viruses isolation of hokkaido virus, genus hantavirus, using a newly established cell line derived from the kidney of the grey red-backed vole (myodes rufocanus bedfordiae) characterization of monoclonal antibodies against hantavirus nucleocapsid protein and their use for immunohistochemistry on rodent and human samples sensitive detection of hantaviruses by biotin-streptavidin enhanced immunoassays based on bank vole monoclonal antibodies novel serological tools for detection of thottapalayam virus, a soricomorpha-borne hantavirus bank vole monoclonal antibodies against puumala virus envelope glycoproteins: identification of epitopes involved in neutralization the use of chimeric virus-like particles harbouring a segment of hantavirus gc glycoprotein to generate a broadly-reactive hantavirusspecific monoclonal antibody human recombinant neutralizing antibodies against hantaan virus g2 protein hantavirus gn and gc envelope glycoproteins: key structural units for virus cell entry and virus assembly virus-like particles: a versatile tool for basic and applied research on emerging and reemerging viruses. viral nanotechnologies complete genome of a puumala virus strain from central europe protocadherin-1 is essential for cell entry by new world hantaviruses spatiotemporal dynamics of puumala hantavirus associated with its rodent host myodes glareolus host-associated absence of human puumala virus infections in northern and eastern germany heterogeneous puumala orthohantavirus situation in endemic regions in germany in summer aphaea/ewda species card: voles and mouses a versatile sample processing workflow for metagenomic pathogen detection a restful api for access to phylogenetic tools via the cipres science gateway beitrag zur kollektiven behandlung pharmakologischer reihenversuche antigenic and cellular localisation analysis of the severe acute respiratory syndrome coronavirus nucleocapsid protein using monoclonal antibodies indirect elisa based on hendra and nipah virus proteins for the detection of henipavirus specific antibodies in pigs phylogenetic analysis of puumala virus subtype bavaria, characterization and diagnostic use of its recombinant nucleocapsid protein isolation and complete genome characterization of novel reassortant orthoreovirus from common vole (microtus arvalis) phylogeography of puumala orthohantavirus in europe secondary contact between diverged host lineages entails ecological speciation in a european hantavirus multiple synchronous outbreaks of puumala virus adaptation of puumala hantavirus to cell culture is associated with point mutations in the coding region of the l segment and in the noncoding regions of the s segment evidence for novel hepaciviruses in rodents identification of two novel members of the tentative genus wukipolyomavirus in wild rodents identification of novel rodent herpesviruses, including the first gammaherpesvirus of mus musculus molecular detection and characterization of the first cowpox virus isolate derived from a bank vole leptospira genomospecies and sequence type prevalence in small mammal populations in germany high prevalence of rickettsia helvetica in wild small mammal populations in germany. ticks and tick-borne diseases occurrence of gastrointestinal parasites in small mammals from germany. vector borne zoonotic dis a novel cardiotropic murine adenovirus representing a distinct species of mastadenoviruses molecular organization and dynamics of the fusion protein gc at the hantavirus surface cooperativity enables non-neutralizing antibodies to neutralize ebolavirus acknowledgements open access funding provided byprojekt deal. the authors would like to thank sönke röhrs for help with rodent trapping, stephan drewes for help with phylogenetic analysis and sven sander and patrick zitzow for excellent technical support with generation of monoclonal antibodies and sequencing of puuv isolates. the authors thank martin beer, klaus osterrieder and nicole tischler for constant support and helpful discussions.author contributions rgu and fb designed the study and wrote the manuscript. fb did virus isolation, infection studies, sequence analysis, phylogenetic analysis, and testing of monoclonal antibodies. sr and fb generated and screened the monoclonal antibodies. grs produced the vlps for immunization. ms and fb performed rodent trapping. dh, jt, and dk did the complete genome sequencing of puuv isolates. rr developed the puuv-specific rt-qpcr assay. all authors gave significant ideas for the presented work and were involved in writing and proof reading of the manuscript. key: cord-289555-1z4vbldd authors: mühldorfer, kristin; speck, stephanie; kurth, andreas; lesnik, rené; freuling, conrad; müller, thomas; kramer-schadt, stephanie; wibbelt, gudrun title: diseases and causes of death in european bats: dynamics in disease susceptibility and infection rates date: 2011-12-28 journal: plos one doi: 10.1371/journal.pone.0029773 sha: doc_id: 289555 cord_uid: 1z4vbldd background: bats receive increasing attention in infectious disease studies, because of their well recognized status as reservoir species for various infectious agents. this is even more important, as bats with their capability of long distance dispersal and complex social structures are unique in the way microbes could be spread by these mammalian species. nevertheless, infection studies in bats are predominantly limited to the identification of specific pathogens presenting a potential health threat to humans. but the impact of infectious agents on the individual host and their importance on bat mortality is largely unknown and has been neglected in most studies published to date. methodology/principal findings: between 2002 and 2009, 486 deceased bats of 19 european species (family vespertilionidae) were collected in different geographic regions in germany. most animals represented individual cases that have been incidentally found close to roosting sites or near human habitation in urban and urban-like environments. the bat carcasses were subjected to a post-mortem examination and investigated histo-pathologically, bacteriologically and virologically. trauma and disease represented the most important causes of death in these bats. comparative analysis of pathological findings and microbiological results show that microbial agents indeed have an impact on bats succumbing to infectious diseases, with fatal bacterial, viral and parasitic infections found in at least 12% of the bats investigated. conclusions/significance: our data demonstrate the importance of diseases and infectious agents as cause of death in european bat species. the clear seasonal and individual variations in disease prevalence and infection rates indicate that maternity colonies are more susceptible to infectious agents, underlining the possible important role of host physiology, immunity and roosting behavior as risk factors for infection of bats. bats are among the most successful and diverse mammals on earth. approximately 1230 chiropteran species are found on every continent except antarctica and inhabit a multitude of diverse ecological niches [1] . bats play essential roles in maintaining healthy ecosystems, as they act as plant pollinators, seed dispersers, and predators of populations of insects including harmful forest and agricultural pests [2] . most bat species are listed in the iucn red list of endangered species and almost half of these are considered threatened or near-threatened [3] . to estimate and prevent further population declines, research has been primarily focused on bat biology, ecology and behavior, while disease aspects were largely neglected [4] . in the last two decades, the importance of chiropteran species as potential vectors of significant viral diseases especially in regard to zoonoses has received growing attention. besides bat rabies that has been studied for more than half a century, extensive research efforts identified a large number of microbial agents [5] including important emerging zoonotic viruses detected in bats across the world [6] [7] [8] [9] [10] [11] [12] . however, most studies are limited to the identification of microorganisms detected and investigations regarding infectious diseases and causes of death in bats are sparse [13] [14] [15] [16] . in europe, research is predominantly focused on european bat lyssaviruses [17, 18] and coronaviruses [19, 20] , but first indications of bat-pathogenic bacteria [13, 14, [21] [22] [23] and novel viruses [24, 25] isolated from deceased bats in germany and great britain were found. in this study, we provide new data on infectious diseases in european bat species, considering factors likely to affect the susceptibility of bats to infectious agents including effects of seasonality, individual and species-specific heterogeneities, and possible intra-and inter-species transmission dynamics. all bat species in europe are strictly protected under the flora-fauna-habitat guidelines of the european union (http://ec.europa. eu/environment/nature/legislation/habitatsdirective/index_en.htm) (92/43/eec) and the agreement on the conservation of populations of european bats (www.eurobats.org) that prohibit invasive sampling of bats for research purposes. for the animals investigated in this study, carcasses of deceased bats found in germany were kindly provided by bat researchers and bat rehabilitation centers of different federal states. between 2002 and 2009, a total of 486 deceased bats of 19 european vespertilionid species (i.e., family vespertilionidae) were investigated (fig. 1a , [26] ). the bat carcasses originated from 6 different geographic regions in germany, i.e. berlin greater metropolitan area (n = 223), bavaria (n = 165), brandenburg (n = 38), lower saxony (n = 36), thuringia (n = 21), and baden-wuerttemberg (n = 3), and were collected by bat researchers and bat rehabilitation centers. most animals represented individual cases that were found dead, injured or moribund near human habitation. thus, the species composition in this study predominately reflected the urban and suburban bat fauna, which is characterized by a disproportionate abundance of a few bat species (fig. 1a , [27, 28] ). two groups of 2 and 21 adult noctules (nyctalus noctula), respectively, were collected from tree hibernacula destroyed during wood logging. a further group of 25 deceased adult n. noctula originated from a colony that was trapped in a rain pipe in december. nine dead juvenile pipistrellus pipistrellus were collected from a nursery roost. if bats died in care or had to be euthanized for animal welfare reasons, the carcasses were immediately stored at 220uc and were shipped to the leibniz institute for zoo and wildlife research, berlin, germany, for diagnostic investigations. of all carcasses examined histo-pathologically, about 90% were suitable for bacteriological investigation. a lesser extend (43%) was also examined for selected viral agents at the robert koch institute, berlin, germany. in addition, a brain sample of each animal was submitted to the friedrich-loeffler-institute, wusterhausen, germany, for rabies diagnosis. a full necropsy was performed on each bat and all macroscopic findings including ectoparasite infestation were recorded. for histo-pathological examination, small slices of multiple organ tissues (i.e., lung, liver, heart, kidney, adrenal gland, spleen, intestine, pancreas, brain, tongue, larynx, salivary gland and pectoral muscle) and tissues conspicuous for pathological changes were fixed in buffered 4% formalin, processed using standard methods and embedded in liquid paraffin. sections were cut at 2-5 mm and routinely stained with hematoxylin-eosin (he). in addition, special histological staining methods were used depending on microscopic findings, i.e. for the detection of bacteria (gram or giemsa staining), fungi (periodic acid schiff or grocott's gomori methenamine silver nitrate staining), iron (prussian blue stain), mineralization (von kossa staining), connective and collagen tissue (trichrome staining). details on pathological results are published elsewhere [26] . the causes of mortality were rigorously standardized with the primary cause of death identified for each bat as the most serious injury, disease or event subsequently fatal to the animal. to ensure independence of primary and contributing causes of death, the categorization was based on the severity of pathological findings. samples of lung, liver, heart and kidney, and tissues conspicuous for pathological changes (e.g. enlarged spleen) of 430 bats were plated onto columbia (5% sheep blood), chocolate, gassner, and macconkey agar (oxoid, germany) and were incubated at 37uc (chocolate agar 5% co 2 ) for 24-48 h. specific culture media and conditions for the isolation of yersinia, salmonella and anaerobic bacteria were used if appropriate. primary identification of bacterial strains was based on colony morphology, hemolysis, gram-staining, indol production, catalase and oxidase reaction. bacterial species identification was carried out using the relevant commercial api test system (biomérieux, germany). additional conventional biochemical tests [29, 30] were applied to confirm api test results where necessary. in case of ambiguous biochemical test results, 16s rdna gene analysis was performed for final identification [23] . salmonella isolates were characterized at the national reference laboratory for the analysis and testing of zoonoses (salmonella) at the federal institute for risk assessment, berlin, germany. identification and characterization of yersinia and pasteurella species have been reported earlier [22, 23] . homogenized organ tissue of lung, liver, heart, kidney, spleen, brain and salivary gland of 210 bats were pooled for each individual and used for rna/dna extraction and further molecular analysis by generic pcr assays detecting flavi[31] , hanta[32] , corona[33] , and influenza a-viruses [34] . also, pcr assays specific for 8 previously described herpesviruses [24] from european vespertilionid bats were used. for this purpose, rna/ dna was isolated using the nucleospinh rna ii kit (macherey-nagel, germany) and the nucleospinh tissue kit (macherey-nagel), respectively, according to the manufacturer's instructions. because of limitations in sample volume, for 180 out of the 210 bats pcr assays could only be applied for 4 different bat herpesviruses. internal controls were used for all pcr assays to test for inhibition. for confirmation, all retrieved fragments of bat herpesvirus-specific pcr assays were checked for sequence identity to previously published isolates [24] . for detection of lyssavirus antigen in brain tissue the fluorescent antibody test (fat) using a polyclonal antirabies conjugate (sifin, germany) was used [35] . fat-positive brain tissues were subject of virus isolation in murine neuroblastoma cell culture (na 42/13) using the rabies tissue culture infection test (rtcit) as described elsewhere [36] . lyssaviruses isolated in cell culture were characterized using both a panel of 10 anti-nucleocapsid monoclonal antibodies (mab) [37] and partial sequencing of a fragment of the nucleoprotein gene after rna extraction using trizol (invitrogen, germany) essentially as described [18] . genomic dna was extracted from organ homogenates using the nucleospinh tissue kit (macherey-nagel) according to manufacturer's recommendations. genetic identification of the bat species was performed by amplification and sequencing of a 241 bp fragment of the cytochrome b (cytb) gene [38] using primers fm up (59-ccc chc chc aya tya arc cmg art gat a -39) and fm down (59-tcr acd ggn tgy cct ccd att cat gtt a -39). in addition, for differentiation of the 2 distinct pipistrellus species, p. pipistrellus and p. pygmaeus, a rapid multiplex pcr assay was performed as described by kaňuch et al. the bat data were categorized in regard to different explanatory numeric and factor variables, e.g. bat species, sex and age class. the variable 'age class' ranked between 1 and 4 with increasing age (i.e. neonates, juveniles, subadults, and adults) and was used as numeric variable. for endoparasitic analysis, we defined a 3 level variable 'bat size' according to the body size of a certain bat species to reduce the degrees of freedom of the full model, i.e. large species (n. noctula, eptesicus serotinus, and vespertilio murinus), medium-sized species (e. nilssonii, plecotus auritus, myotis daubentonii, m. nattereri, and p. nathusii) and small species (p. pipistrellus, and m. mystacinus). to detect effects of seasonality, 4 different activity periods were specified according to the date of sampling, i.e. hibernation period (november to march), post-hibernation period (april/may), maternity period (june to august), and swarming period (september/october). as dependent binary variable for the respective models we either classified the mortality cause being disease or not (i.e. trauma), or the presence-absence of bacterial, ecto-and endoparasitic infections. we formulated 4 different hypotheses to test for individual and species-specific differences in disease susceptibility and infection rates: (a) disease-related mortality in bats is influenced by sex, age and species-specific differences, and degree of endoparasitic infection. (b) bacterial infection in bats is influenced by sex, age and species-specific differences, occurrence of traumatic injuries and cat predation. (c) ecto-or (d) endoparasitic infection in bats is affected by age, sex and species-specific differences. seasonal effects were not analyzed because of too many missing data points. because the long-term dataset was highly biased towards sampling procedure, preservation of bat carcasses and following diagnostic investigations, we split and filtered the full data into several subsets reflecting the different analyses (table 1) . all statistical analyses were performed using the r software v. 2.13.1 (r development core team 2011, vienna, austria). we used the chi-square test for given probabilities to evaluate significant differences in the sex ratio among bats of different species. for hypotheses a and b, we used a generalized linear mixed modeling approach (binomial glmm using function lmer in library lme4) with bat species included as random effect. this variable had not been significant as fixed effect (results not shown), but from other studies we can assume that there are speciesspecific differences in susceptibility of bats to certain infectious agents and therefore included it as random effect. we further used generalized linear models (glm with logit link and binomial error structure; for datasets with bat species .10 individuals) to test for individual and species-specific differences in parasite infection rates (hypotheses c and d). we created a full model for each hypothesis (a-d) to examine multiple and interaction effects of the specified variables. to select the final model variables, we used a stepwise backward algorithm (function stepaic in library mass) based on akaike's information criterion (aic) [40] . the daic of the final model was calculated relative to a random intercept model to demonstrate the effect size of the selected variables. results of the diagnostic analyses follow the full data splitting into several subsets (see section 'statistical analysis' in material and methods; table 1 ). all sampled bats belonged to 7 different genera (i.e. pipistrellus, nyctalus, myotis, eptesicus, plecotus, vespertilio, and barbastella) and 19 european vespertilionid species (fig. 1a) . three bat species, the common pipistrelle (p. pipistrellus, n = 138), the noctule bat (n. noctula, n = 92), and the serotine bat (e. serotinus, n = 53) constituted about 60% of all bat carcasses investigated in this study, whereas p. pygmaeus, nyctalus leisleri, myotis brandtii, m. bechsteinii, m. dasycneme, plecotus austriacus and barbastella barbastellus were represented in small numbers of 1 to 4 animals. the overall sex ratio was 1.5 males to 1 female with significant species-specific differences (fig. 1b) . animals in their first year of life (neonates, juveniles, and subadults) represented one third (32.5%, n = 158) of bat samples (fig. 1c) . overall, we were able to assign a cause of death to 70% (n = 304) of bats investigated in this study. two thirds of mortality were due to trauma (n = 145) or disease (n = 144), while almost 4% of bats had died of other non-infectious causes like pulmonary edema, dehydration and hypoglycemia (table 2 ). in 30% (n = 129) no significant pathological findings could be found. among the 145 traumatized bats, additional mild (n = 42), moderate (n = 28) and severe (n = 4) inflammatory organ changes were noted in one half (50.9%) of individuals, and 23% of the bats revealed bacterial (n = 19) and/or parasitic infections (n = 15) ( table 3) . of the 144 bats considered as dying of disease, fatal bacterial (n = 54), viral (n = 5) and parasitic infections (n = 2) were observed in 42%. besides, amniotic fluid aspiration was noted in a neonate noctule bat (n. noctula), and a juvenile common pipistrelle (p. pipistrellus) was euthanized because of severe forearm bone deformation. the remaining 81 bats (56.3%) revealed moderate to severe pathological changes of unknown etiology or unconfirmed bacterial or viral cause ( table 2 ). based on the glmm analysis, significant age-and sexdependent differences (daic = 23.13) were detected between the general causes of mortality, disease and trauma ( table 4 ). the disease presence in bat samples decreased continuously with increasing age. neonates and juveniles of both sexes were significantly more affected by disease than older age classes (table 4 ; fig. 2a) . we also found a significant trend in diseaseassociated mortality between the sexes, with adult females displaying higher disease prevalence (52.5%) than males (36.4%) ( table 4 ). no significant association was observed between a certain cause of mortality (i.e. disease or trauma) and severity of endoparasitic infection (daic = 0.75, result not shown). the seasonal distribution of disease-related mortality cases (fig. 2b ) described a trimodal pattern, with peaks in spring (april), summer (june to august) and winter (december). the proportion of traumatized individuals also increased obviously during the summer months up to and including the swarming period, but was low during the rest of the year. about 90% (n = 430) of bat samples were examined bacteriologically. among these, 42 different bacterial genera with more than 53 bacterial species were identified (table s1 ). predominant bacteria isolated were enterococcus faecalis (14.7%, n = 63), hafnia alvei (11.2%, n = 48), serratia liquefaciens (10%, n = 43), and pasteurella multocida (7.7%, n = 29). in 37% (n = 157) of bats no bacterial growth was observed at all. comparative bacteriologic and histo-pathologic analysis identified 22 different bacterial species that were clearly associated with pathological lesions and/or systemic infection, found in 17% (n = 73) of bats investigated bacteriologically ( table 5) . members of the families pasteurellaceae (above all p. multocida) (41.1%, n = 30), enterobacteriaceae (various bacterial species) (28.8%, n = 21), and streptococcaceae (above all enterococcus spp.) (21.9%, n = 16) were predominant bacteria associated with disease. more than half (54.8%, n = 40) of bacterial infections were observed in bats with traumatic injuries. the glmm analysis revealed low sex-and age-dependent differences in bacterial infection (daic = 1.97, result not shown). female bats (21.9%) and adults (21.6%) showed marginally higher prevalence of bacterial disease compared to males (18.3%) and to other age classes (15.6%), respectively. however, we found a strong influence of cat predation (daic = 16) associated with bacterial infection in bats (table 4 ). testing for human-pathogenic zoonotic viruses, no examined bat sample (0/210) was positive for influenza a virus, corona-, hanta-and flaviviruses, respectively. no inhibition of the pcr assays was notified. out of 486 bats tested for rabies virus infection, 2 serotine bats (e. serotinus) were positive for lyssavirus by fat and rtcit. the viruses were identified as european bat lyssavirus type 1 (eblv-1) sublineage a, both using mabs and sequencing. applying bat herpesvirus-specific pcr assays, 63 out of 210 bats proved to be infected with 7 of the previously described 8 bat herpesviruses ( table 6 ). the highest prevalence of 65% (24/37) was observed for bat gammaherpesvirus 6 (batghv6) in common pipistrelle bats (p. pipistrellus), followed by bat gammaherpesvirus 5 (batghv5, 42.1%) in nathusius' pipistrelle bats (p. nathusii) and bat gammaherpesvirus 4 (batghv4, 33.8%) in noctule bats (n. noctula). co-infection with different bat herpesviruses were recognized in 4 n. noctula (7.4%) infected with batghv3 and batghv4, and in one n. noctula (1.5%) infected with batghv4 and batghv5. batghv5 was not only detected in its initially specific host p. nathusii, but also in 3 other bat species, i.e. n. noctula, myotis myotis and m. mystacinus. although the prevalence of batghv3 (13.0%) and batghv4 (33.8%) differed significantly within its migrating host n. noctula, no difference was observed between the sexes. two juvenile n. noctula were found to be infected with batghv4. interestingly, for the sedentary bat species p. pipistrellus being infected with batghv6, a considerably higher prevalence was observed in 22 juvenile bats (72.7%) resulting in an overall prevalence of 65% also without difference between adult male and female bats. ectoparasites (mites, fleas, and ticks) were noted in 14% (n = 62) of bats, but a potential bias in ectoparasite numbers collected from dead animals in comparison to ectoparasite abundance on live animals has to be taken in account. female bats (17.1%) were slightly more infested by ectoparasites than males (14.7%), whereas in different age classes ectoparasite prevalence was almost balanced. the glm analysis revealed significant species-specific differences in ectoparasite infestation (daic = 14.58, table 4 ). most bat species revealed low ectoparasite prevalence (range 5.3-11.8%), while almost 43% (n = 20) of n. noctula were infested with mites and/or fleas (fig. 3a) . microscopic examination of organ tissues revealed endoparasitic infection in 29% (n = 124) of investigated bats, involving different protozoan (families eimeriidae and sarcocystidae) and helminth parasites (trematodes, cestodes, and nematodes). helminthes were predominantly found in the gastro-intestinal tract of the bats, while in some animals, granulomatous organ lesions were associated with larval migration of nematode species. based on the glm analysis, clear age-and species-specific differences (daic = 24.95) were observed between infected and non-infected bats ( table 4 ). the prevalence of endoparasitic infection in bat samples increased significantly with increasing age, whereas the increase in prevalence was more rapid between juveniles and subadults (8.5%) compared to the older age classes (4.5%). marginal differences were also observed between the sexes, with female bats showing slightly higher (30.4%) endoparasite prevalence than males (24.4%). regarding species-specific differences, large bats like n. noctula, e. serotinus and v. murinus revealed higher endoparasite prevalence compared to individuals of medium-sized or small vespertilionid species (table 4 ; fig. 3b ). this study was based on a passive surveillance sampling strategy that inherently influences the composition of bats sampled for diagnostic investigations [27] and might also effect the data presented on causes of death by ecological and anthropogenic impacts of urban landscapes [41] . trauma and disease represented the most important causes of mortality in deceased bats from germany, which differ from results of previous studies [13] [14] [15] where disease-related mortality often played a subordinate role. young bats and adult females were significantly more affected by disease, indicating that sex-and age-related disease prevalence in table 3 . pathological findings and bacterial, viral and parasitic infections specified for the general causes of mortality, trauma and disease. bats are strongly correlated with the maternal season. this assumption is further supported by the distinct increase of diseaserelated mortality from june to august, which corresponds to the maternity period of central european bat species. similar seasonal prevalence patterns in bats have also been described for parasitic (e.g. [42] [43] [44] [45] ) and viral infections (e.g. [19, 46, 47] ). in contrast, the increase of trauma-associated mortality cases from july to october resembles 4 major behavioral activity patterns of european bat species (i.e. weaning, mating, pre-hibernal fat storage, and migration) [48] and could therefore predispose bats to trauma. however, both seasonal peaks also coincide with time and locations where sick, injured or dead bats are more likely to be discovered as well as with the seasonal roosting behavior of bats adapted on urban habitats [27] . the additional seasonal peaks of disease-associated mortality corresponded to the post-hibernal and the early hibernal period of temperate zone bats. currently, there is a lack of knowledge of bat immunology. it is known for other mammalian species that hibernation reduces the innate and adaptive immune response; likewise an increasing risk of infection could be assumed for hibernating bats [49] . with the start of the hibernation season, large aggregations of bats originating from various colonies might enhance the risk of spreading infectious agents similar to maternity colonies. equally, the post-hibernal increase of disease-related mortality is suggestive for reduced immunity in association with prolonged fasting during hibernation. bacterial diseases have rarely been documented in bats. pasteurella spp., here identified in 7% of bats, were the predominant bacterial pathogens reported in european bats and infection appears to be strongly correlated with cat predation [13, 14, 23, 26] . in our study, bacterial infections were confirmed in 17% of bats investigated bacteriologically. most of these bacterial isolates represented opportunistic pathogens that usually do not harm the host unless the immune system is weakened [50] or preceding injury to natural host barriers (e.g. skin abrasion). primary bacterial pathogens like samonella enterica serovar typhimurium, s. enteritidis and yersinia pseudotuberculosis [22] were identified in almost 12% of affected bats. some of the bacterial species (e.g. burkholderia sp., cedecea davisae and clostridium sordellii) are newly described in bats. nevertheless, bacteriologic analyses can markedly be influenced by post-mortem bacterial invaders, freezing and storage of bat carcasses and the inability to detect certain bacteria by routine culture methods, resulting in some bacterial species that might have escaped detection. we found a strong association between cat predation and bacterial infection in bats as almost one half of bats (44%) caught by cats were affected by bacterial disease. various bacteria can be transmitted via cat bites [51] ; hence bats attacked by cats are likely to succumb to bacterial infection even if non-fatal injuries were present. this relation has been proven for p. multocida infections in european bat species [13, 14, 23, 26] . on the other hand, bats already debilitated by disease might easier fall prey to predators like cats. consequently, bats may also act as vectors for zoonotic pathogens, as domestic cats could pass these infectious agents on to humans. such cross-species transmission events from bats to domestic animals are well documented [9, 52] . for all tested human-pathogenic zoonotic viruses no infected bat could be detected in this study except lyssaviruses. bat rabies is the only bat transmitted zoonosis in europe that is known to have resulted in human cases [53] . unlike in other mammals table 4 . result of the final model variables corresponding to 4 different analyses: (a) disease-vs. trauma-related mortality, and presence-absence of (b) bacterial, (c) ecto-and (d) endoparasitic infection. where lyssaviruses ultimately cause lethal rabies, in bats nonlethal lyssavirus infections may also lead to the development of immunity [47] . with the detection of eblv-1 we confirm that this lyssavirus circulates among e. serotinus as previous studies showed [18] . in germany, bat rabies is also caused by eblv-2 and bokeloh bat lyssavirus (bblv) [54, 55] , but while the latter was recently isolated from m. nattereri, eblv-2 is associated with m. daubentonii and m. dasycneme [56] . the apparent absence of eblv-2 and bblv in the sampled bats is likely due to the fact that lyssavirus infections have a very low incidence in bat populations [18] and that the sample size was too limited, especially concerning the relevant species. there is a high prevalence for herpesviruses in different insectivorous bat species in germany (this study, [24] ). most of the previously described bat herpesviruses have been detected in low numbers in more than one bat species [24] . here, we observed a high species-specific prevalence among herpesvirusinfected bats, indicating that a certain type of european bat herpesvirus is primarily associated with a single bat species. this is supported by batghv6 and batghv7 that were again only identified in their initial hosts p. pipistrellus and p. auritus (both sedentary), respectively, underlining the typical strong speciesspecificity of mammalian herpesviruses. however, species' range overlap and close inter-species contacts in bat roosts may result in cross-species transmission and could explain the observed overcoming of the species barrier (this study batghv5, [24] ). interspecies transmission have also been discussed for other mammalian herpesviruses, i.e. bovine and equine herpesviruses (e.g. [57, 58] ). furthermore, for rna viruses (i.e. rabies virus) phylogenetic distance between different host species and overlap in geographic range have recently been demonstrated as strong predictors of host shifts and cross-species transmission in bats [59] . some of the bat species (i.e. n. noctula, p. pipistrellus, and p. nathusii) in this study appear to be more susceptible to herpesvirus infection. in n. noctula, 3 different gammaherpesviruses (batghv3, 4, 5) with significant prevalence differences were recognized. such type-specific differences in prevalence between the phylogenetically distant viruses batghv3 (13.0%) and batghv4 (33.8%) within one bat species indicates co-evolutionary virus-regulated mechanisms. parasite infestation in wildlife often occurs without clinical effects, but severe infection can reduce host fitness either in terms of survival or reproductive success [60] . most data on infection dynamics in bats came from parasite studies focusing on individual and seasonal variations in ectoparasite prevalence (e.g. [43] [44] [45] 61] ). host density, roost preference and movement pattern seem to be important factors explaining individual and speciesspecific parasite infestation rates in bats [43] [44] [45] . in european vespertilionid species, female-biased parasite loads are most likely associated with host physiology and differences in roosting behavior [42, 44] . we also found species-specific seasonal variations in ectoparasitic infestation, with n. noctula and m. daubentonii showing higher ectoparasite prevalence in spring and autumn compared to the breeding season (data not shown), which is in accordance with zahn and rupp [43] . additional findings of our parasite analyses are distinct variations in ecto-and endoparasite prevalence in relation to bat species. bats primarily roosting in trees or nest boxes were more frequently infested with ectoparasites like n. noctula (43%) and m. daubentonii (25%) compared to other species (range 5-12%) investigated in this study. high ectoparasite loads have generally been described in bats preferring enclosed roosts like burrows and cavities [61, 62] , suggesting that structural characteristics and the microclimate of roosting habitats influence ectoparasite survival and re-infection of bat hosts. this assumption is in accordance with results of pearce and o'shea [63] who found differences in ectoparasite prevalence and intensity in eptesicus fuscus in relation to environmental factors (i.e. temperature and humidity) of different roost sites. in contrast to these results, the endoparasite prevalence in european vespertilionid bats seems to be correlated with the body size of the bat species [26] . species-specific variations in diet and prey selection could possibly effect endoparasite prevalence in insectivorous bats [64] , as larger bats feed on insects of a wider size range including hard-bodied prey [65, 66] . this assumption is supported by the clear prevalence increase in subadult and adult bats compared to low endoparasite infection rates in juveniles primarily feeding on milk. a multitude of publications is restricted to pathogen presence or absence in different chiropteran species; here we demonstrate the impact of diseases and infectious agents on bats themselves. alongside to trauma-associated mortality and undefined mortality cases, disease aspects represented one third of mortality causes in 486 investigated bats of 19 european vespertilionid species. by comparing pathology and bacteriology results, we were able to detect 22 different bacterial species that were clearly associated with disease in bats. at least 12% of all bats had died due to bacterial, viral and parasitic infections. finally, we found clear seasonal and individual variations in disease prevalence and infection rates, indicating an increased susceptibility to infectious agents in female bats and juveniles during the maternity season. our data emphasize and provide the basis for disease related studies in bat species on population level to elucidate the complexity of the ecology of infectious agents and host species likewise. table s1 bacteria isolated from bats found in germany. 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bacterial pathogenesis bacteriologic analysis of infected dog and cat bites european bat lyssavirus transmission among cats human rabies due to lyssavirus infection of bat origin first isolation of eblv-2 in germany novel lyssavirus in natterer's bat bat rabies serological survey of herpesvirus infections in wild ruminants of france and belgium new hosts for equine herpesvirus 9 host phylogeny constrains cross-species emergence of rabies virus in bats behavioral adaptations to parasites: an ethological approach relationships between roost preferences, ectoparasite density, and grooming behaviour of neotropical bats roosting habits of bats affect their parasitism by bat flies (diptera: streblidae) ectoparasites in an urban population of big brown bats (eptesicus fuscus) in colorado when parasites become prey : ecological and epidemiological significance of eating parasites the implications of food hardness for diet in bats prey consumed by eight species of insectivorous bats from southern illinois the authors would like to thank berliner artenschutz team-bat-e.v., f. key: cord-310775-6d5vi2c5 authors: brinks, verena; ibert, oliver title: from corona virus to corona crisis: the value of an analytical and geographical understanding of crisis date: 2020-06-09 journal: tijdschr econ soc geogr doi: 10.1111/tesg.12428 sha: doc_id: 310775 cord_uid: 6d5vi2c5 the term ‘crisis’ is omnipresent. the current corona virus pandemic is perceived as the most recent example. however, the notion of crisis is increasingly deployed as a signifier of relevance, rather than as an analytical concept. moreover, human geography has so far little contributed to the interdisciplinary crisis research field which is fixated on the temporal aspects of crisis but neglects its spatiality. against this background, the first aim of the paper is to demonstrate the value of thinking about crisis analytically. therefore, we introduce theoretical knowledge developed within a recently emerging literature on crisis management. second, we demonstrate the relevance of including geographical thinking into crisis research more systematically. based on the tpsn‐framework by jessop et al., we illustrate spatial dimensions of the ‘corona crisis’, its perception and handling in germany. the empirical references are based on media reports. the spread of the coronavirus has turned into a crisis. this finding is hardly surprising and the majority of readers will agree. but when and how did it turn into a crisis? this question is much more difficult to answer, mainly due to the fact that the term 'crisis' is anything but easy to grasp. it is omnipresent and frequently used in very different contexts. the term is, for instance, used to signify the enhanced relevance of the respective research. as a consequence, the notion of crisis is mainly deployed intuitively, rather than analytically. similar to other disciplines, most geographical contributions related to crisis dynamics are driven by an empirical phenomenon, which is framed as being in crisis. in economic geography, the 'financial crisis' has received particular attention and geographers have made significant contributions by exploring the manifold spatial references of this global phenomenon (e.g. aalbers 2009; martin 2011) . within the geographic discipline, diagnoses of 'crisis' are often associated with neoliberalism and capitalism apparently producing manifold social, economic and political stresses (jones & ward 2002; larner 2011) . particularly, geographers in marxist tradition (most prominently represented by david harvey) deploy crises as an inherent and recurring feature of capitalism; or to cite harvey (2011, p. 11) : 'capital never solves its crisis tendencies' (emphasis in orig.). in addition, climate change, rising religious fundamentalism and newly emerging economic powers outside the traditional industrial centres pose challenges of truly global scope that invoke crises in all parts of the world (larner 2011) . this literature emphasises that we live in times of crises and doubtlessly provide important insights on the social, economic and political configurations that contribute to crisis diagnosis. however, so far little attention has been paid to specify the nature of 'crisis' itself as an exceptional and stressful human experience. if we accept the diagnosis that we live in times of crises, it becomes more important than ever to develop a more profound understanding of crisis as a particular context for action and a possibility for intervention. in this paper, we therefore propose a conceptual shift from the structural conditions that cause crises to an actor-centric approach focused on the practical consequences of crisis for individual and collective agency. we introduce theoretical knowledge developed within a recently emerging, interdisciplinary literature on crisis management. moreover, we illustrate this analytical understanding with reference to the recent 'corona crisis' to connect abstract ideas on the general characteristics of crises with empirical observations. the term crisis is ripe with temporal implications. these temporal aspects predominate in the crisis management literature. what lacks so far, however, is a systematic conceptualisation of the spatial aspects of crisis. while the crisis management literature does use spatial categories, such as epicentres, distance, scaling or territories, it lacks a systematic approach to integrate spatial imaginations into theories and practices of crisis management. social and economic geographers could thus contribute to the inter-disciplinary discourse by integrating the spatial dimension into the conceptualisation of crisis. in this paper, we set out to suggest a conceptualisation of the 'geography of crisis' informed by social and economic geography. the empirical material presented in this paper stems from different media sources. it has to be mentioned that this paper does not draw on an already fully-elaborated or finalised media analysis but is inevitably provisional and selective due to the highly dynamic development at the time this paper has been written. the analytical and conceptual thoughts presented here are based on current research on crises (brinks & ibert 2020) . within different research contexts, we analysed literature on crisis (management) and also benefited from empirical insights collected in interviews with crisis experts and own participation in interdisciplinary workshops on crisis and crisis management. the paper is subdivided into two main parts. first, the subsequent chapter introduces our definition of crisis based on literature from the interdisciplinary practice of crisis management and social scientific crisis research. second, we outline a geographical perspective on crisis, by exploring different dimensions of the spatiality of crisis. we use the tpsn approach as suggested by jessop et al. (2008) to systematise our observations. the paper concludes by highlighting the added value of a geographical approach. a crisis is related to, yet distinct from other terms, such as 'problem'. a problem denotes a gap between an observed condition and a desired condition (rittel & webber 1973) . such a gap is present in every crisis as well, for example, the gap between the fastgrowing numbers of people who became infected with the corona virus and the general desire that the population should be healthy. yet, such a gap is not a sufficient condition for a crisis. in order to talk of a crisis, a few more ingredients are necessary: uncertainty, urgency and threat (boin & 't hart 2007) . uncertainty denotes 'that we cannot predict or foresee what will happen when acting or not acting' (aspers 2018, p. 133) . in the corona case, uncertainty is caused by a lack of knowledge (e.g. about the ways of infections, dark figures of a-symptomatic cases), ambiguous signals (e.g. unspecific symptoms), a lack of viable means to counter the epidemic (e.g. the absence of an effective medicine and vaccination) and undetermined timeframes (e.g. when will a vaccination be available), to mention only few. the second ingredient, urgency, refers to the necessity to act, despite high degrees of uncertainty. in crisis, inactivity and non-decision are no options as they will only exacerbate the serious situation. yet, as acting has to take place under conditions of uncertainty, routines are no longer available and action has a strongly improvisational or experimental character (boin & rhinard 2008; milstein 2015) . the last ingredient to crisis is an existential threat of highly valued societal assets. the corona pandemic does not only threaten the health and lives of wide parts of the population, but also imperils economic interests and core institutions of the political order. due to the underlying fundamental uncertainty, 'the emotional response to crisis is not fear (such as fear from fire) but existential angst, which has no identifiable object that could offer a grip for a learnt response' (kornberger et al. 2020, p. 242) . in addition to these fundamental characteristics of crisis it is important to unpack the term a bit further. it is important to understand how crisis becomes enacted in practice. a crisis as an empirical observation cannot be deduced directly from the underlying societal conditions. rather similar, objectively measurable conditions (like unemployment rates, levels of distrust in political institutions) sometimes entail crisis diagnosis, and sometimes do not. sometimes relatively unimportant issues are treated as a crisis (the 'brent spar' controversy is a widely cited example of an escalating risk communication; löfstedt & renn 1997) , while even the most alarming scientific reports about climate change are not sufficient to mobilise a collective sense of urgency. what all crises share in common, thus, is not only a severe problem, but a shared perception of uncertainty, threat and urgency around that problem. the key importance of perceptions can also be found in the corona case. in our observation of the public discourse in germany, at the beginning of 2020 the government as many others in the western hemisphere looked at the early epicentre of the pandemic, the wuhan region in china, 'with a combination of fascination and fear' but without any sense of urgency or immediate threat until new information about corona infections in europe emerged (boin et al. 2020) . not earlier than 26 february 2020, we noticed a shift from 'corona epidemic' to 'corona crisis' in the german speaking debate for the first time in an article published in the online portal of the german newspaper der spiegel. two days earlier, in many parts of germany, carnival was celebrated on the streets -a mass meeting with thousands of people standing close to each other. from 16 march onwards, all public events of major size were prohibited, schools were closed across all federal states in germany and a few days later restaurants, production plants and retail shops followed. it was a matter of days, during which the publicly shared framing of the situation has changed fundamentally. typically, at some stage in the public 'framing contest' that takes place in advance of a crisis, the public opinion transcends an invisible 'tipping point' beyond which a problematic situation turns into a crisis (boin et al. 2009 ). however, this tipping point can only be noticed ex post, while it is impossible to determine it in advance. for most participants, thus, crisis comes unexpected. crisis is not only a matter of perception; it also unfolds performative qualities. here, performative means that the crisis diagnosis is not a mere description of the state of reality rather, a crisis diagnosis changes reality and therefore contributes to the enactment of crisis: 'if individuals (and the media) define a situation as a crisis, it is a crisis in its consequences' (rosenthal & kouzmin 1997, p. 286) . for decision-makers, once in place, the crisis immediately ascends the first place of the agenda. due to the performative qualities, the crisis unfolds its dynamics irrespective of subjective interpretations or experiences. for individual decision-makers, it is for instance no longer possible to ignore the crisis, or, if one tries, like donald trump did until the first weeks of march, it happens at immense political and economic costs. for professional crisis managers, the declaration of a crisis has very practical and robust consequences. they perceive a crisis as an effective 'coping structure' (term used in crisis management practice jargon) societies and organisations have to prioritise a certain topic and to mobilise resources to address a problem. crisis diagnoses emerge in multi-stakeholder constellations. some stakeholders even support the escalation of a crisis or reframe the crisis diagnosis in ways that exert pressure on organisations or states. crisis diagnoses thus are contested and the framing is subject to controversy in the public debate (boin et al. 2009 ). in contrast to the term 'catastrophe', the term crisis highlights that despite existential threats, it is not yet too late to prevent the disaster (boin & 't hart 2007) . in medicine, crisis marks the decisive phase in the course of an illness in which a positive or negative outcome is still possible (ricoeur 1988) . crisis, in other words, is strongly associated with the idea of an open future (kornberger et al. 2020 ) that can be created through individual or collective agency. in the current crisis, the first discussions emerge about the potential long-term structural effects of the corona crisis. for instance, visionaries from silicon valley highlight the enhanced possibilities to establish new practices of remote digital learning and work (thrun 2020) . at the same time, warning voices (sennett 2020 ) point at potentially problematic long-term effects of lockdown policies and the increased use of surveillance technologies on the human rights situation and vulnerable democratic institutions in weak democracies. when we think of or undertake research on crisis, we should also be aware of one additional observation. as mentioned above, decisions in crisis have to be made while the present is uncertain and the future is open (kornberger et al. 2020) . under such conditions, action does not take place within a given frame of meaning. rather, in crisis participants are forced to learn by interpreting the situation tentatively while acting on it. therefore, crises are usually perceived twice. in a first loop, participants encounter a critical turn in the course of events surprisingly. they experience an open-ended phase of chaos and escalation during which they struggle to regain control while action and sensemaking remain incompletely connected. in contrast to the abrupt beginning, the end of the acute crisis comes much more gradually. as a first step toward a (new) normality, after having responded to the challenges, participants eventually perceive a slowing down in the dynamic of escalation and try out new interpretations of the situation. however, against the background of the previously experienced uncertainty, participants tend to distrust this new stability. they remain unsure, how far their explanations will hold and whether or not the absence of another surprising turn is just a pause in the course of escalation or already a (re)turn to (new) normality. the ultimate end of the crisis, however, has to be 'declared' by decision-makers, which is another performative act. in a second loop, the course of events that led to the acute crisis is reconstructed ex post in the light of the newly established sense and certainty. as an interpretative act of sensemaking, the starting point and the end of the second loop are not fixed and can never be defined in advance. according to weick (1988, p. 306) , sensemaking is enacted since 'parts of what the explorer discovers retrospectively are consequences of his own making'. by the very process of acting in crisis, a rising stream of new information and experiences have to be included in the sensemaking process. thus, the second loop always starts after the first loop but usually at an early stage in the crisis course. in this second loop, the crisis is deliberately embedded in the classical phase model encompassing the phases of pre-crisis, acute crisis and post-crisis (e.g. fink 2002) , while the boundaries between the phases are still in motion. during sensemaking the considered timeframe is expanded both, into the past and the future. when reflecting on the pre-crisis phase, the focus is on weak warning signals that have been neglected beforehand or wrong decisions that contributed to an escalation of events. the post-crisis phase, in contrast, provides the (oftentimes missed) opportunity to learn from the crisis (birkland et al. 2009 ). once the crisis is overcome, time is ripe to reiterate the acute crisis several times in order to get a detailed understanding of the sequential order of actions. of course, the acute crisis itself cannot be repeated. yet, the pre-and post-crisis phases cannot emerge without the experiences made during the acute crisis. the awareness of these two loops of crisis experience is helpful to keep in mind for the corona crisis. while writing this paper, we are still witnessing the escalation of events and the tentative form of sensemaking while acting on the situation. yet, we can already discover first signs of time expansion. presently the public debate has already turned towards the past by discovering early warning signs that have previously been ignored. for example, a paper published in march 2019, in which the authors warned against (at that time) future outbreaks of a corona virus caused by cross-species transmission (fan et al. 2019) has received broader attention in the last weeks, that is one year after publication. in china and in italy suspicious accumulations of pneumonia cases attract the attention of epidemiologists aiming at reconstructing the outbreak. at about the same time, governments around the world start to plan for the future. they design graduated schemes back to normality, envisioning the possible ends of the crisis and speculating about new post-corona normalities. finally, the severity of a crisis is widely associated with its perceived scope. the scope of the crisis describes the degree to which the perceived escalation of problematic events can be contained within separable units of society. critical events are much more likely perceived as severe crises, the more they 'spill over' (bundy et al. 2017 ) existing boundaries. on the territorial level, 'transboundary crises' (boin & rhinard 2008) have an inter-regional or even an inter-national character. transboundary also denotes the overstepping of institutionalised boundaries, for example, the vertical sectoral responsibilities of political or administrative bodies (boin & rhinard 2008) . a true sense of crisis tends to emerge if multiple boundaries are overstepped and causes and effects of a crisis spill over from one compartment into the other. the scope of a crisis is also dependent on the sources of uncertainty. sometimes, these sources are clearly external, for instance, an earthquake or a cyber-attack. such external events can unfold disruptive qualities, yet they are usually easier to manage, as no decision-maker can be directly blamed for them. it thus seems sufficient to manage their negative consequences before returning back to old normality. more difficult are crises that are driven by internal sources. for instance, the structural crisis of a whole industry to a wide degree is caused by the insufficient strategic capabilities of the core decision-makers. here, the crisis is interpreted as a 'brutal audit' (orton & o'grady 2016 ) that unveils the lack of foresight and understanding of decision-makers. crises caused by internal factors enact a much higher degree of uncertainty, as any framing of the problem goes hand in hand with blaming of responsible persons or organisational units (boin et al. 2009 ). of course, in practice, it is difficult to clearly separate internal from external sources of uncertainty, as often critical external events raise the awareness of internal deficiencies. in the case of the corona pandemic, the crisis fulfils the character of a 'transboundary crisis' (boin & rhinard 2008) in an almost ideal-typical sense. the spread of the virus is no longer restricted to any geographically confined territory, vertical segments of society or particular societal layers. rather, within a few months, the virus is present almost everywhere on the globe, justifying the whoclassification as a 'pandemic'. further, it affects several societal systems, most crucially the health services, but beyond that also has severe spill-over effects to almost every economic sector, a wide range of institutions of political order and all parts of society. the tendency to transgress boundaries also makes the corona crisis particularly threatening. while the origin of the crisis is external to society, the corona pandemic can be seen as a brutal stress test that unveils internal dysfunctionalities in national health systems, social security programmes or value chains. even though the geographical dimensions of crisis are recognised by some crisis scholars, a systematic and theoretically-guided analysis of the spatiality of crisis has not yet been advanced in this field. such a systematic exploration, we argue, is a possible contribution of economic and social geography to social scientific crisis research. the agenda we suggest here is thus a bit different from previous geographical studies that use the term crisis prominently to signify they are dealing with severe problems within specific empirical fields, like, for instance, the bursting of financial bubbles in mortgage and real estate markets (e.g. aalbers 2009) or emergency practices in humanitarian aid (e.g. fredriksen 2014 ). we suggest the use of the tpsn framework (territory, place, scale, network), as developed by jessop et al. (2008) to explore the geography of crisis. according to gailing et al. (2019, p. 15 ) it provides a useful heuristic that can be flexibly applied to diverse empirical fields 'to allow for a synoptic perspective on this field'. at the same time, the authors also warn that tpsn should not be mistaken as a 'complete answer to everything' (gailing et al. 2019, p. 15) , as it lacks the necessary, field-specific theoretical terminology. hence, they argue that tpsn needs to be complemented with the respective theoretical terminology to unfold its full explanatory potential. for our agenda, the absence of theoretical assumptions in the tpsn-heuristic is an advantage. crisis, as we understand it, is not an 'empirical field' in the sense of gailing et al. (2019) , but rather a conceptual endeavour to advance a general understanding of practices and dynamics prevailing in situations of uncertainty, threat and urgency. in the following paragraph, we thus use theoretical claims from social scientific crisis research and combine it with spatial dimensions as suggested in the tpsn heuristic in order to delve deeper into the so far underdeveloped spatial aspects of crisis theory. in the following, some starting points for such an investigation are indicated by referring to the corona crisis as one illustrative empirical field (table 1) . even though crises increasingly cross territorial boundaries, the territorial dimension remains particularly important. the corona crisis produces countless cartographic visualisations documenting the spread of the pandemic. the number of infections announced by the johns hopkins university (2020) has become an internationally much-cited data source for tracing the dynamic development of the spread as well as regional differences worldwide. the total number of confirmed cases worldwide is presented on the national level. recently, a further map demonstrating the intensity of the outbreak in us counties has been launched by the university (johns hopkins university 2020). the territorial representation of the corona crisis is largely caused by the report system of public agencies which are bound to territorial units. likewise, many institutional crisis responses, such as the official declaration of an emergency situation, are bound to territories. however, territory affects crisis even beyond administrative responsibilities. the crossing of a territorial boundary, for instance, frequently cause shifts in the perception of crises as being more threatening (since the perceived distance to crisis declines) and escalating (fear of losing control). 'patient 1' as the first documented case in a certain territory is well reported as well as the first case of covid-19 outside of china on 13 january. manifold media reports refer to 'first cases' or 'first deaths' inside or outside a specific territorial unit. some places are more affected by crisis than others (see aalbers 2009 for the financial crisis). some crises culminate in a single epicentre. a school shooting creates such a mono-centric geography and 'place renewal' can be an adequate way for crisis recovery (wombacher et al. 2018 ). more typically, however, crises unfold complex, multi-local geographies. in the case of the corona pandemic, we can already identify several symbolically charged places. above all, the huanan seafood market in wuhan has been reported as the point of origin of the outbreak. related to that, the use of the term 'wuhan virus' by the us government can be conceived as a framing and blaming strategy jessop et al. 2008) . portrayal of outbreak according to territorial entities activation of territoriallybound resources 'first case' inside or outside a territory place emergence of places of crisis such as supermarkets 'epicentre' and 'superspreader' locations scale assignment of responsibility inter-national organisations such as the who network expert communities '#flattenthecurve' (boin et al. 2009 ) through spatial dissociation and association (ibert et al. 2019) . further places, such as the notorious après ski bars in ischgl in austria, or the football stadium in milan have become spots of investigation as potential 'super spreader' locations from where the virus disseminated across europe (merlot 2020) . surprisingly, supermarkets have emerged as relevant places of the corona crisis. as places of food provision, in times of lockdown these facilities have transformed rapidly into critical infrastructures equipped with additional safety precautions. in contrast, hospitals represent classical institutions of crisis response. yet, when becoming activated for this crisis, their regular safety standards needed to be adapted to the particular challenges of the corona pandemic. the notion of scale is closely related to spatial hierarchies (jessop et al. 2008) . it is a particularly important dimension in crises when it comes to negotiation of responsibility and coordination of action (which scale is the right one to (re)act on crises?). the corona crisis provides a vivid example here. in germany, for instance, the corona crisis induced a discussion of the federal constitution. where in other states, the national governments decided about the closing of retail stores, etc., the national government in germany is not authorised to decide about such measures since infection protection is situated at the federal state-level (bundesländer) (leitlein & schuler 2020) . moreover, the health authorities, which report about confirmed corona infections and are authorised to impose measures such as quarantine, are based on the level of administrative districts (landkreis) or district-free cities in germany. located at an inter-national scale, the who receives particular attention in these days. though not authorised to impose measures, the who has an important function in terms of policy recommendation. the who's declaration of the covid-19 outbreak being a 'pandemic' on 11 march can be interpreted as a means justifying considerable state interference with fundamental rights. the network perspective on crisis focuses on the relations between nodes (of every kind). it can be enriched by deploying the concept of 'relational proximity' (gertler 2008 ) and the function of medical experts in the corona crisis. medical professionals such as epidemiologists and virologists currently receive particular attention as policy advisors. they are embedded in trans-local professional communities. they share knowledge about the corona virus internationally, for instance, through rapid publication practices in academic journals (see for instance the lancet). members of these professional communities are characterised by relational proximity, which means that based on a shared repertoire of practices and similar expertise they are able to collaborate closely even across physical distance. another example of the network dimension are social media having an enormous relevance in the corona crisis in terms of establishing a common understanding of the situation and sharing (similar) experiences across distance. calls such as 'flatten the curve' or 'stay at home' went viral online and contributed to a shared perception of the corona crisis even when the locations and individual concerns with the corona virus are different. as jessop et al. (2008) argue, the empirical reality cannot be separated into the categories territory, place, scale and network. rather, the dimensions are interwoven in 'sociospatial relations'. similarly, gailing et al. (2019) find typical nexuses between several dimensions when studying empirical cases from the german energiewende. the following sub-sections aim at providing some examples of such interactions between spatial dimensions in the corona crisis -importantly, without any claim of completeness and admittedly presented in a rather sketchy and unsystematic fashion. at the present state, it would be an impossible endeavour to outline all spatial relations, too dynamic is the escalation in the course of events. therefore, we focus on three nexuses that can be detected in prominent public discourses to demonstrate the principle of our approach. network-place: topologies of interconnected places -as mentioned earlier, supermarkets have turned into strategic places in the fight against the pandemic across the globe. during the past few weeks, we witness a gradual reshaping of their physical setup and practices of staff to accommodate these places to the new requirements of 'social distancing' while maintaining a high turn-over of people. items from hospital environments, like surgical masks and gloves have been transferred to supermarkets in order to protect staff and clients. planes of acrylic glass have been fixed at checkout counters to minimise the physical contact between cashiers and customers and tapes attached on the floor remind shoppers to hold minimum distance. at the same time, familiar items, such as customer divider bars, loyalty cards or cash money have been banned from some supermarkets as they are now reinterpreted as potential carriers of the virus. however, it would be inaccurate to primarily conceive supermarkets as singular places. most supermarkets are not single-owned stores but rather branch stores belonging to chains of multi-national retail chains. of course, supermarkets are places, though places that belong to wider networks operated and orchestrated by grand retailers. supermarkets, in other words, are part of networks of practices (brown & duguid 2001) . the concrete local practices and settings are thus not idiosyncratic, but depend strongly on the affiliation to a certain retail chain. moreover, these practices might vary slightly from chain to chain while they are made similar from place to place through standards orchestrated through the respective networks. a similar topological perspective on crisis has been elaborated by fredriksen (2014) . the author focuses on emergency infrastructure which is used in different humanitarian crises. according to the author, emergency tents as material objects, which have constantly been developed further after crisis experiences, represent 'lessons learned' from different crises. moreover, since they are highly mobile and used at different sites affected by crisis, the places resemble one another and thus become nodes in a 'network topology' of crises (fredriksen 2014) . in a longer timeframe, experiences gained in supermarkets will most probably turn out to be extremely important for all kinds of retail stores. as soon as legislation will step by step relax the regulations on social distancing, the network of practice will most likely expand from the realm of supermarket(s) (chains) to other retailers, for instance in fashion retail or book stores. negotiation of crisis governance -the connection of scale and territory is obvious in crisis settings since public crisis response strategies are usually immediately connected to territorial units. scaling in the sense of deciding which level is the most effective one for coping with crises is a key question in crisis management (e.g. boin et al. 2005) . the different levels usually present territorial units where the smallest level is always fully integrated in the next larger level (municipal level, national scale, european scale, etc.). this leads to the key issue of coordination in crises. a certain threatening situation has to be assigned to a specific scale, responsible for crisis response. these responsibilities are usually determined beforehand. in the corona crisis, the formal assignment of authority in epidemic events (as mentioned, the federal states (bundesländer) are responsible instead of the national government in germany) is now critically eyed and political efforts have been started to change the respective law in order to allow the upscaling of competencies to the national level in such crises (waschinsky 2020). at the same time, local hubs of the outbreak are intensively investigated such as the district of heinsberg in the federal state of north rhine-westphalia in germany. authorities aim at deriving strategies for larger territorial areas, arguing that 'the district of heinsberg portrays the nationwide occurrence of infections in a nutshell' (ärzteblatt 2020) . however, in the corona crisis some of the limitations of thinking of crisis in territorial units and instruments of territorial scaling also come to light. even though the corona virus crosses geographical and territorial boundaries, the virus does not spread homogeneously in space. as in many other countries, the shutdown of public life in germany is a nationwide strategy (with variances across different federal states). this also means that more and less affected areas are treated the same way. when discussing potential strategies for the time after the shutdown these questions of territorial on a more general level, the corona crisis demonstrates the interplay of territory and scale by pointing to strategies, limitations and challenges of upscaling and downscaling processes (see also boin et al. 2005, on upscaling) . also fundamental differences occur between centralistic and federal states. determining the right scale, activation of respective structures when necessary and flexible adjustments in territorial scaling are central issues of crisis management. yet, as observed in other cases, the transgressive forces driving the corona crisis requires complex settings of multi-level governance that includes several scales and political sectors (bundy et al. 2017) . another interesting question is whether or not the scale of the crisis and the scale of crisis response always have to be congruent for most effective crisis management. territory-place-network: 'social distancing' policies -the spreading of the corona virus takes place from human to human being. without changes in the social behaviour, every infected person in average spreads the virus to 2-3 other people. therefore, most national authorities have enforced so-called 'social distancing' policies. the aim is to reduce the ratio of infection, in the ideal case below 1 (which means in the long run the epidemic will run out because then, statistically, each infected person infects less than one other person). a chain of infections can be interpreted as a network (kuebart & stabler, 2020) , with every infected person representing a node and every infection from person to person representing a tie. in the terminology of structural network analysis, decreasing infection rates lead to decreasing network connectivity. from a geographically informed perspective on proximity and distance, the term 'social distancing' is a bit misleading, as it suggests that social contacts should be avoided. in fact, rather on the contrary, social distancing encompasses a set of behavioural regulations that seek to allow social contacts, yet in a way that minimises physical proximity and thus promises to disrupt the chain of infections. 'social proximity' thus enables physical distancing since through grown and trusted relationships, familiar face-to-face interaction in physical co-presence can partly be substituted by online media and the like (boschma 2005) . social distancing policies do not only address interaction between people, they also include the spatial setting in which interaction occurs. the discourse on super-spreaders, for instance, focuses not only particular persons who spread the virus at disproportionally high rates, but almost always also includes particular types of places, where the infective encounters took place. hence, social distancing policies almost always are place sensitive and frequently entail the closure of the respective venues (night clubs, pubs, sports stadiums, concert halls, even playgrounds). finally, social distancing policies are enforced on a territorial level, most typically by the national states. however, different territorial approaches co-existed. while today most countries pursue social distancing policies, not all did so or did not from the very beginning. for instance, sweden, the netherlands and the uk preferred another approach of isolating only the most vulnerable individuals while the rest of the population can face the risk of infection in order to reach 'herd immunity' sooner rather than later. other countries, especially in asia, concentrated on infected persons and followed the strategy of preemptive mass-testing to identify infections early on and of isolating infected persons from the rest of the population. territorial differences in terms of crisis response are also known from other crises. regarding the h1n1 pandemic 2009 (better known as swine flu), baekkeskov and öberg (2017) analysed different vaccination policies of denmark and sweden, each supported by the dominant national expert opinions. while sweden followed the approach of vaccinating large parts of its population, denmark decided to recommend vaccination for risk groups only. both policies were supported by the majority of expert opinions reported in the respective national mass media. their findings emphasise that territorial differences in policy strategies are reflected by public discourses on the crisis in the territories. even though the general direction of social distancing policies is similar everywhere, there is much variation in detail between territories. for instance, italy and spain sought to decrease the amount of social contacts by imposing a lockdown, hence people are no longer allowed to leave their private homes apart from buying food or for health services. in germany, in contrast, authorities declared a prohibition of social interaction. german citizens are thus still allowed to leave their homes, as long as they follow the commandments of keeping a minimum distance to other citizens of 1.5 metres and seeking only the company of members who live in the same household or at most one other person. as a federal state, however, germany resembles a fragmented patchwork of territories with slightly different rules and approaches (see above). another set of interesting territorial differences in social distancing policies occur in the attribution of surgical masks in public spaces. in japan, for instance, 'mask-wearing since the 2000s … became a civic duty of those who sneeze and cough not to be a source infection, while for the healthy general public, mask-wearing embodies neoliberal ethics of being self-caring and self-responsible to one's health' (horii 2014) . while japan is the internationally most well-known example, similar practices can be observed in other countries, especially in east asia, as well. in the european context, by contrast, the same practice has been widely dismissed by public opinion until very recently. here, the wearing of surgical equipment is seen as part of a professional practice that is little useful when used inappropriately by laypersons and outside of the professional setting. therefore, surgical masks played a major role in some national policies in the east-asian context while they have been ignored in most western contexts. however, the perception of masks has shifted quickly recently, as austria exemplifies, whose government decreed at the beginning of april 2020 the duty of wearing a mask when entering a supermarket. in germany, the national government recommended the use of masks in the public space in mid-april. one by one, the federal states governments did not only take up this recommendation but, similar to austria, even tighten the rule by declaring the obligation of wearing masks in retail stores or in public transport. in this paper we set out to suggest a conceptually grounded notion of crisis and to explore its geography. the present corona crisis served as an illustrative empirical background to substantiate the analytical spatial dimensions with concrete examples. the term crisis, we suggest with references to contributions from crisis management and organisation studies, encompasses the elements of uncertainty, urgency and threat. crises are related to societal problems, yet cannot directly be deduced from them. rather, a crisis becomes only a crisis, if the situation is collectively perceived and declared as a crisis. moreover, crisis has performative qualities. a crisis diagnosis thus is not primarily a proper description of reality, but a creator of a new reality in which uncertainty, urgency and threat predominate, no matter if decision-makers like it or not. right because of the performative nature of crisis diagnoses, the discursive framing of the crisis is a highly contested issue in public debates. it takes place in complex, multi-stakeholder settings and different interests and worldviews are mobilised. some stakeholders might even be driven by a strategic interest in further escalating the situation (löfstedt & renn 1997) . while crisis management has spent considerable effort to theorise on the temporal aspects of crisis, reference to its spatial aspects remained sparse. against this background, we suggest that human geography can contribute to inter-disciplinary research on crisis by unpacking the geographical aspects systematically. we used the tpsn heuristic as suggested by jessop et al. (2008) to delve into the different dimensions of the spatiality of crisis: we explored its territorial dimension, its scalarity, place-based accounts and the relational spaces of networks. furthermore, the corona crisis served as a vivid example to illustrate that the tpsn approach is not primarily valuable to disentangle empirical observations and rearrange them along separate dimensions. rather on the contrary, we used the examples of the recently observable restructuring of supermarket spaces, of flexible re-scaling of crisis response policies and of social distancing policies to demonstrate that it seems much more promising to scrutinise the multiple forms of interaction and overlap of several spatial dimensions in the same empirical observation. what is the particular contribution of a conceptually informed, geographical understanding of crisis? we see at least three distinct qualities of such an approach: first, an emerging topic related to the corona crisis is regionally specific response strategies. here a geographically informed understanding of crisis has much to contribute to the debate. it could support approaches that seek to adapt policies to different regional characteristics (e.g. social distancing policies for urban or rural regions) or to regionally unequally affected areas (e.g. hotspots of the crisis vs. little or no affected areas). second, and related to the first point, systematically thinking about the geography of crisis can contribute a lot to the question of scalarity in crisis. the corona crisis (as many other crises) demonstrates the challenge of defining the scale of the crisis and respective crisis response strategies (which scale is the right one to (re)act on crises? how to choose the right scale? does the chosen scale necessarily have to match with a territorial unit?). in fact, due to its transboundary character it evades any single scale and instead calls for complex strategies of multilevel governance adapted to the institutional idiosyncrasies of different nation states. third, the corona crisis forces the rapid implementation of several new practices such as avoiding hand contact in supermarkets. thus, specific places transformed into critical localities, rapidly equipped with special safety infrastructure. the transformation of specific places is observable in our daily lives; however, it cannot fully be understood without references to other similar places. geography established an analytical understanding of the relations between mobility of practices (supermarket a and supermarket b) and context dependency of practices, enabling a more profound understanding of currently emerging crisis topologies. the corona crisis will certainly occupy us for a long time. a variety of studies and research projects will surely start in the near future (some already started) in order to reflect on specific aspects of the crisis. our aim in this paper was to closer investigate the notion of crisis and how a crisis diagnosis changes the present, as well as the view of the past and the future. crises unfold in time and space. the exact geography of a crisis, of course, depends on the empirical case. however, just as thinking about the temporality of crisis, the spatiality of crisis is worth investigating. we made one proposal by drawing on the tpsn framework (jessop et al. 2008 ) but possible approaches are far from exhausted. we argue for a stronger engagement with 'crisis' within human geography since its spatiality is so far kind of an empty space in crisis research. geographies of the financial crisis heinsberg-studie zur klärung von ansteckungswegen beginnt forms of uncertainty reduction: decision, valuation, and contest freezing deliberation through public expert advice disasters, lessons learned, and fantasy documents the corona crisis: a creeping crisis managing transboundary crises: what role for the european union? 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