key: cord-352322-tsjwnvkk
authors: Khamassi Khbou, Médiha; Daaloul Jedidi, Monia; Bouaicha Zaafouri, Faten; Benzarti, M’hammed
title: Coronaviruses in farm animals: Epidemiology and public health implications
date: 2020-09-25
journal: Vet Med Sci
DOI: 10.1002/vms3.359
sha: 
doc_id: 352322
cord_uid: tsjwnvkk

Coronaviruses (CoVs) are documented in a wide range of animal species, including terrestrial and aquatic, domestic and wild. The geographic distribution of animal CoVs is worldwide and prevalences were reported in several countries across the five continents. The viruses are known to cause mainly gastrointestinal and respiratory diseases with different severity levels. In certain cases, CoV infections are responsible of huge economic losses associated or not to highly public health impact. Despite being enveloped, CoVs are relatively resistant pathogens in the environment. Coronaviruses are characterized by a high mutation and recombination rate, which makes host jumping and cross‐species transmission easy. In fact, increasing contact between different animal species fosters cross‐species transmission, while agriculture intensification, animal trade and herd management are key drivers at the human‐animal interface. If contacts with wild animals are still limited, humans have much more contact with farm animals, during breeding, transport, slaughter and food process, making CoVs a persistent threat to both humans and animals. A global network should be established for the surveillance and monitoring of animal CoVs.

CoVs isolated from carnivores, herbivores and omnivores fosters the interspecies transmission and virus adaptation to new hosts (Song et al., 2005) . In fact, cross-species transmission and host jumping are the most important driver for virus emergence (Holmes, 2016) and

CoVs specifically are dotted with a high rate of mutation and recombination, making them a continuous threat for humanity. Mutations result from errors during viral genome replication by the RNA-dependent RNA polymerase, which reaches 5.7 × 10 -6 nucleotide substitutions per site per day for the SARS-CoV and the accumulated mutations at some sites could have important implication on virus properties (Vega et al., 2004) . Recombination appears to be more important in CoV genome than mutation; it consists of gaining genome fragment from another CoV, which implies the adaptation to new hosts (Worobey & Holmes, 1999) . As consequences of such genomic mutation and recombination the transmissible gastroenteritis virus (TGEV) of swine and the bovine CoV (BCoV) likely originated from the closely related canine coronavirus (CCoV) (Pratelli, 2011) . A deletion that occurred in the S protein of the TGEV resulted in the rising of the porcine respiratory CoV with a marked changing tropism from the gastrointestinal to the respiratory tract (Peiris, 2012) . There is evidence that the feline infectious peritonitis virus (FIPV) is originated from the feline enteric CoV (FECoV) by mutation in the region of the S1/S2 of the spike protein (Licitra et al., 2013) .

The best opportunity that would allow viruses to jump new species occurs at the moment of feeding, when a predator consumes prey and all the viruses infecting it (French & Holmes, 2020) .

Beside feeding, physical contact between different host species increase host range expansion probability (Wang, Vlasova, Kenney, & Saif, 2019) as it was the case for the swine influenza viruses (subtypes H1N1 and H1N2) and the Nipah virus that were transmitted from pigs to humans (Chua et al., 2002; Gray et al., 2007) . New porcine CoV emerged in China (Guangdong Province) in 2017, namely the swine acute diarrhoea syndrome CoV (SADS-CoV) with high sequence identity to bat-CoV HKU2 (Gong et al., 2017) . The high density of pig farms and slaughterhouses in Guangdong Province associated to the wide distribution of bat species explained the cross-species transmission. Indeed, as pork meat is considered as the most commonly consumed meat in non-Muslim countries, pigs may be an effective intermediate host for the emergence of novel CoVs of highly public health concerns (Wang, Su, Bi, Wong, & Gao, 2018 ).

Coronaviruses of farm animals including large and small ruminants, dromedaries, horses, pigs and chickens were reviewed; cetacean CoVs were also considered, as marine mammals are a food source in many countries around the world. The aim of this review is to summarize the epidemiological knowledge about CoVs of farm animals, to discuss the public health implications and to address the gap of knowledge useful for future research direction. & Stokstad, 2017). Furthermore, high animal density seems to be the main BCoV risk factors (Boileau & Kapil, 2010) .

The BCoV is one of the main causative agents of neonatal calf diarrhoea during the first month of life (Ammar et al., 2014; Brandão et al., 2006) and the most common deathly disease in calves (Gomez & Weese, 2017) . Other studies showed that BCoV may be involved in 10 to 30% of neonatal diarrhoea cases (Alfieri et al., 2018) .

In adult cattle, the WD occurs as epidemics during winter and is characterized by a contagious watery diarrhoea, fever, depression and reduced milk yield (Toftaker et al., 2017) . Singasa, Songserm, Lertwatcharasarakul, and Arunvipas (2017) reported that milk production might decrease up to 10% for 2 weeks during the BCoV infection.

Vaccines are available for the prevention of BCoV infections in neonatal calves and in adult. An inactivated virus vaccine was developed for pregnant cows to enhance passive maternal immunization of calves via colostrum and prevent neonatal diarrhoea (Decaro et al., 2009) . Another inactivated hemagglutinating antigens-enriched vaccine showed their efficacy to protect cattle against WD (Takamura, Matsumoto, & Shimizu, 2002) .

The BCoV was also associated, alone or with other pathogens, to respiratory infections such as enzootic pneumonia in calves and shipping fever in young cattle (Saif, 2010) . The prevention from respiratory CoV in cattle is based on multivalent killed or attenuated-live intra-nasally administrated vaccines (Hay et al., 2016; Richeson et al., 2019) . 

A bovine-like CoV in water buffalo (Bubalus bubalis) was first described in 1985 in Bulgaria, using serological methods (Muniiappa, Mitov, & Kharalambiev, 1985) . The sequencing of the isolated buffalo CoV from Italy, showed sequence homology with the BCoV, with some differences justifying its classification as a new variant of BCoV and was named as Bubaline CoV (BuCoV) (Decaro, Martella, et al., 2008) . In Italy, gastroenteritis disease among water buffalo calves is caused by both BuCoV and BCoV (Decaro et al., 2010) .

Closely related strains to the BCoV (displaying 98% sequence homology) were also detected among faecal samples of domestic buffaloes in Bangladesh (Lau et al., 2016) . Infection of water buffalo calves was also reported from three districts in Egypt, with an overall molecular prevalence of 26.8% (22/82) in faecal samples (El-

Sadek et al., 2019) ( Table 2) .

Although the BCoV is initially a cattle virus, it is occurring also in small ruminants, in which it was neglected for a long time due to its low prevalence and insignificant clinical manifestation (Amer et al., 2019) . In Australia, sheep were reported in 1978 to excrete

CoV-like particles that were visualized by electron microscopy examination during a diarrhoea episode (Tzipori, Smith, Makin, & McCaughan, 1978) . The infection of small ruminants by the BCoV is rather to occur through close contact with cattle in mixed flocks than as a natural infection (Tråvén, Carlsson, Lundén, & Larsson, 1999) .

The most recent study in Ghana reported anti-BCoV antibodies in F I G U R E 1 Phylogenetic tree of different representative CoVs based on the Spike (S) protein gene (the strain responsible for the pandemic SARS-CoV-2 in humans is shown with the bolded character among the Betacoronavirus genus). The shown animals are hosts from where the corresponding CoVs were isolated. The sequences of all animal CoVs were downloaded from the National Center for Biotechnology Information (NCBI) GenBank database (https://www.ncbi.nlm.nih.gov/genba nk/). The tree was constructed using the Neighbour-Joining method (bootstrap resampling = 1,000 replicates and bootstrap values are indicated as % at branch points) (Saitou & Nei, 1987) . The evolutionary distances were computed using the Maximum Composite Likelihood method (Tamura et al., 2004) and are in the units of the number of base substitutions per site. All positions containing either gaps or missing data were eliminated. There were a total of 2044 positions in the final dataset. Evolutionary analyses were made with MEGA7 (Kumar et al., 2016) BOX (Burimuah et al., 2020) (Table 2) .

Nowadays, it is well established that dromedaries are the natural host of the MERS-CoV and a source for human and other domestic animals infections (Kandeil et al., 2019) . Since the first case of human infected by the MERS-CoV was identified in September 2012 in Saudi Arabia (World Health Organization, 2019), interest to dromedaries as sources of the virus increased and the isolated strains were shown to be genetically very similar to those isolated from humans (Omrani, Al-Tawfiq, & Memish, 2015) .

The close contacts between infected dromedaries and humans enhance the continuing zoonotic transmission and may explain why the MERS-CoV continues to occur in humans (De Wit et al., 2016) . Moreover, the MERS-CoV was also detected in sheep, goats and donkeys reared close to camels (Kandeil et al., 2019) .

Transmission from dromedaries to humans occurs by direct contact with mucous and nasal discharge or by consumption of meat or raw milk (Gossner et al., 2016; Mirkena et al., 2018) . Indeed, MERS-CoV RNA was detected using qRT-PCR in whole and skimmed milk collected from milking animals that were kept with camels that have frequent contact with multiple origin camels participating at racing events .

The MERS-CoV detection in dromedaries is difficult as the infection is asymptomatic. However, experimental MERS-CoV infection of dromedaries caused mild to moderate rhinitis with nasal discharge, tracheitis and bronchitis in addition to the shedding of a large amount of virus from the respiratory tract (Haverkamp et al., 2018) .

Several studies showed that the wild strains of the MERS-CoV circulate in dromedaries in more than 24 countries across Africa and the Middle East ( Figure 2) , with high seroprevalences rates recorded from Egypt (71%) (Ali et al., 2017) , Nigeria (94%) (Reusken, Messadi, et al., 2014) 

dromedaries increases with age, reaching 80%-100% in adults (Harrath & Abu Duhier, 2018) .

In experimentally challenged dromedaries, a modified orthopox-based vaccine expressing the MERS-CoV spike protein conferred mucosal immunity. This vaccine induced a significant reduction of virus shedding, and the conferred protection was associated with neutralizing antibodies production (Haagmans et al., 2016) .

As a strategy to prevent human contaminations, mass vaccination of camels is discussed (Dighe et al., 2019) .

Following a severe diarrhoea outbreak that induced high morbidity and 

The equine coronavirus (ECoV) was isolated for the first time from a foal in North Carolina (USA) (Guy, Breslin, Breuhaus, Vivrette, & Smith, 2000) , since then, multiple outbreaks were documented in different countries but epidemiological information on ECoV still scanty (Pusterla, Vin, Leutenegger, Mittel, & Divers, 2016) . The ECoV was reported from Japan, Saudi Arabia, France, the United Kingdom and the United States (Table 2 ). Phylogenetic analyses showed that ECoV isolated from Japan and the United States, were genetically close (Nemoto et al., 2015) . 

The morbidity rates of ECoV infection ranged from 10% to 83% and the lethality rate is classified from rare to 27% (Fielding et al., 2015; Oue et al., 2011; Oue, Morita, Kondo, & Nemoto, 2013; Pusterla et al., 2013) . Up to 83% of infected horses remain asymptomatic, while their faeces contain the ECoV (Pusterla et al., 2013) .

The transmission route of the ECoV occurs through a faecal-oral route (Pusterla et al., 2013) and the disease occurs mainly in winter (Nemoto et al., 2014) . The ECoV could be detected from diarrheic horses 2 to 5 weeks after the beginning of the infection (Pusterla et al., 2016) but also from healthy horses (Hemida, Elmoslemany, et al., 2017) . The peak of faecal shedding occurs 3 to 4 days after the onset of the disease (Bryan et al., 2019) and nasal secretions could be positive to the ECoV at this moment, but the epidemiological role of these secretions in transmitting the virus is not known (Nemoto et al., 2014) . According to the observations of Pusterla, Vin, Leutenegger, Mittel, and Divers (2018), draft horses showed higher infection rate than other breeds, this could be explained by the stress induced by working conditions. Some attempts of vaccination using the BCoV gave promising results but need further investigations (Nemoto et al., 2017) .

Six coronaviruses were isolated from pigs belonging to three genera: (Table 1) , beside a re-emerging highly virulent strains of the PEDV that were described since 2010 (Sun et al., 2012) .

The TGE is the sole mammalian disease caused by a CoV in the World (Piñeyro et al., 2018) .

Domestic animals such as cats and dogs may play a role as host for the TGEV (Sestak & Saif, 2002) .

As for most of mammalian CoVs, the TGE occurs during winter after an incubation period varying between 18 hr and 3 days (Pensaert, 1976) . The course of the disease is characterized by vomiting and profuse diarrhoea and is marked by high morbidity and mortality rates mainly among piglets (Animal Health Australia, 2016). Although pigs of all ages are susceptible to the TGEV infection, animals older than 5 weeks display milder clinical symptoms than piglets (Piñeyro et al., 2018) .

As the TGEV shares common epitopes for neutralizing antibodies with PRCV, a significant decrease of the TGE incidence occurred as a consequence of the cross protection conferred by the PRCV (Wesley & Woods, 1996) . 

The emergence of the PHE was traced back to 1957 in Canada, with the occurrence of high several episodes of vomiting, wasting and anorexia followed by neurological signs in pig nurseries (Roe & Alexander, 1958) . In 1962, the virus was isolated from baby pigs suffering from encephalomyelitis (Greig et al., 1962) , then several outbreaks with similar clinical signs were reported in Canada and Europe and the disease was named vomiting and wasting disease (VWD) (Cartwright et al., 1969) . In 1971, the PHEV was classified as a CoV (Greig et al., 1971 ) and subsequently the disease was reported the colostral immunity transferred to newborn piglets, which is considered as the best way to prevent from the infection (Rho et al., 2011) .

The porcine epidemic diarrhoea (PED) was reported for the first time in England in 1971, but the viral aetiology was only proved in 1978 (Pensaert & de Bouck, 1978) . The PEDV spread to other European countries (Belgium, France, Hungary and Czech Republic…) (Pensaert & Martelli, 2016) and to Asia where it became enzootic particularly in most prosper pork industry countries like China, South Korea and Philippines (Song & Park, 2012) . The economic losses induced by the occurrence of the PED are dramatic since, high mortality rate is associated to the infection, mainly among < 10 days old piglets (Antas & Woźniakowski, 2019) . Mortality reached 100% in newborn and suckling piglets in Japan during 1993 and 1994 (Sueyoshi et al., 1995) and in Thailand during 2007 and 2008 (Puranaveja et al., 2009 ). In the United States, the PEDV emerged in 2013, where almost 10% of the pig population died in less than 1 year after several outbreaks Stevenson et al., 2013) and spread to Mexico and Canada in 2014 (Kochhar, 2014) . sow's sera and piglets sera after suckling (Paudel et al., 2014) . In Japan, live attenuated virus is used since 1997 (Usami, Yamaguchi, & Kumanomido, 1998) and oral vaccination started in South Korea and Philippines, since 2004 and 2011 respectively (Garcia et al., 2018; Park et al., 2018) . As new virulent strains are circulating, trials for more effective vaccine are undergoing using swine-poxvirus-based vaccines designed to express the A epitope of the spike protein (Yuan, Lin, Li, He, & Fan, 2017) .

The porcine respiratory coronavirus (PRCV) is a mutant of the TGEV, due to a deletion in spike gene (Laude et al., 1993) . It was identified first in Belgium in 1984 (Pensaert, Callebaut, & Vergote, 1986) and spread to almost all European countries including France (Madec et al., 2004) , Denmark (Have, 1990 ) and the United Kingdom (Brown & Cartwright, 1986) . The PRCV was soon reported from the United States (Halbur et al., 2003) and Japan (Usami et al., 1998) .

Most of the PRCV infections are subclinical or inducing mild symptoms (Caswell & Williams, 2016) , this could be due to the low proinflammatory cytokines synthesis activation (Van Reeth, Labarque, Nauwynck, & Pensaert, 1999) . The PRCV is still detected upto the 21st day in the lungs of experimentally infected pigs and high titres reached 10 8.3 median tissue culture infectious doses (TCDI50) per gram of lung tissue (Jung et al., 2007) . Faecal shedding of PRCV was also reported from 37% (21/57) of sentinel pigs introduced in PRCV-infected herds (Costantini et al., 2004) .

Because of the insignificant clinical course of the PRCV infection, neither treatment nor vaccination, is applied. However, countries exporting live pigs need negative status to PRCV, which could be obtained only if piglets are pre-weaned early at the 7th day, together with strict all-in, all-out managed barns, rigorous disinfection and cleaning of pig barns and regular seronegative tests in sows (Burlatschenko & Arsenault, 2015) .

The porcine deltacoronavirus ( Moreover, in orally PDCoV-inoculated calves, a persisting faecal viral RNA shedding associated to PDCoV-specific serum IgG antibody responses were observed (Jung et al., 2017) . There is no commercial available vaccine for the prevention from the PDCoV infection (Zhang, Liu, et al., 2019) . Active surveillance programme effectively led to the decrease of the PDCoV herd-level prevalence below 0.5% in two years in Canada (Ajayi et al., 2018) .

The swine acute diarrhoea syndrome virus (SADS-CoV) has emerged in pigs in China since August 2016 (Zhou, Sun, et al., 2019) . This virus, also qualified as Porcine entreric alphacoronavirus (PEAV) or Swine enteric coronavirus (SeCoV) (Pan et al., 2017) was associated with the occurrence of severe diarrhoea of suckling piglets in Guangdong province in 2017 (Gong et al., 2017; Pan et al., 2017) and 2019 (Zhou, Li, et al., 2019) , and in Fujian province in 2018 . The economic loss induced by the SADS-CoV was dramatically high, as 24,693 piglets in four farms, died from the infection in Guangdong province, where the first human SARS epidemic started in 2003 .

This virus is antigenically distinct from the PEDV, the TGEV and the PDCoV (Yang, Yu, & Huang, 2020) . Nevertheless, the complete genome sequencing of the N and the S genes showed a high nucleotides homology (96%-98%) with those of four bat-CoV HKU2 (Gong et al., 2017) . During the first outbreak in China, the SADS-CoV infection was controlled by immunizing pregnant sows using inactivated filtrated virus obtained from infected piglets intestines (Zhou, Sun, et al., 2019b) . As there is an urgent need to develop efficient vaccines to control the SADS-CoV in pigs, trials on attenuation of a virulent strain via cell culture passage are now on-going .

decaA new chimeric virus containing the S protein of the PEDV on a TGEV backbone was discovered in Italy in 2016 and might circulate there from mid-2009 to 2012 according to Boniotti et al. (2016) . This recombinant virus was also detected in Germany, Central Eastern Europe and Slovakia precluding for an old circulation in Europe (Akimkin et al., 2016; Belsham et al., 2016; Mandelik et al., 2018) .

In 2012, a novel Beta-CoV was isolated from domestic rabbit and characterized as rabbit coronavirus HKU14 (RbCoV HKU14), causing no clinical manifestation. The virus was detected in 8.1% (11/136) rabbit faecal samples using RT-PCR and phylogenetic analysis showed that the novel RbCoV HKU14 is most closely related to betacoronavirus 1 species (BCoV, ECoV, CCoV, HCoV-OC43) . The authors hypothesized that the virus may have emerged as a result of interspecies transmission between different animal species in Chinese markets.

Three species of sea mammals were shown to be susceptible to CoVs: harbor seals, white beluga whale and bottlenose dolphins.

In 1987, three captive seals (Phoca vitulina) at the Miami Seaquarium expressed acute enteritis associated with dehydration and leucocytosis. The pathological examination showed bronchoalveolar oedema and haemorrhage. Fluorescent antibody staining yielded positive results to TGEV, FIPV and CCoV antisera, which precluded to an Alpha-CoV, but the virus was not yet assigned to the genus (Bossart & Schwartz, 1990 ).

Ten years later, a captive beluga whale (Delphinapterus leucas), in the United States suffering from a generalized pulmonary disease, died from acute liver failure caused by a CoV (Mihindukulasuriya, Wu, St. Leger, Nordhausen, & Wang, 2008) . Phylogenetic analyses revealed that the causative agent was closely related to the infectious bronchitis virus (IBV) of chickens, and the pathogen, named

BWCoV SW1 was assigned to the Gamma-CoV genus (de Groot et al., 2012) .

In bottlenose dolphins (Tursiops aduncus), the first report of a 

Avian CoVs are the main representative of the Gamma-CoV genus, including the IBV in chickens as the most studied CoV, and unique among all other animal CoVs. Similar CoVs to the IBV were detected and isolated from domestic galliformes: turkey (TCoV), guinea fowl (GfCoV) and pheasants (PhCoV) (Cavanagh, 2005) , but also from non-galliformes namely: Columbiformes, Psittaciformes and Anseriformes (Domanska-Blicharz et al., 2014; Jonassen et al., 2005) . Seven other avian CoVs are included in the Delta-CoV genus . Only the IBV will be treated in this section.

The first isolation of the IBV was made in 1930s in the United States (Massachusetts) and it was thought that only one serotype exists, until 1956 exists, until , when Jungherr et al. (1957 In 2016, Valastro et al. (2016) suggested a method to harmonize the nomenclature of the IBV using a phylogeny-based classification and complete genome sequencing of the S1 gene. Today, the IBV is divided to seven genotypes including 35 distinct viral lineages based on the complete S1 gene sequencing Xu et al., 2019) .

The geographic distribution of the IBV is worldwide (Figure 2) and some genotypes are present more in certain regions than in others. Indeed, two different lineages GI-21 and GII-1 were considered as specific to Europe (Fan et al., 2019) , while GI-9, GI-27 and GIV-1

were considered specific to North America (Lin & Chen, 2017 ) and the GI-11 is an exclusively South American lineage, very prevalent in Brazil and Uruguay (Marandino et al., 2019) .

The IBV is a highly contagious virus of the upper respiratory tract of chickens, leading to 100% morbidity and a mortality rate ranging from 0% to 82% depending upon several factors such as the age of the birds, their immune status, and the involvement of secondary pathogens (Ramakrishnan & Kappala, 2019) . The IBV infects chickens of all ages, although young are most susceptible, and may die directly from the IBV infection or from mixed infections mainly caused by Escherichia coli, leading to heavy losses to the breeding industry (Jackwood, 2012) . In Brazil, which is considered as the biggest broiler meat exporter (Nääs, Mollo Neto, Canuto, Waker, Oliveira, & Vendrametto, 2015) , the total loss (in US$) induced by the IBV infection were estimated per 1,000 birds to 4,210.8 and to 266.3, in breeders and broiler respectively (Colvero et al., 2015) . 

Except the SARS-CoV, the MERS-CoV and the most recent SARS-CoV-2, the other documented human CoVs are specific to human beings (Corman et al., 2018) . It is well established that domestic or wild animals were involved in the three epidemics either as reservoir or as intermediate hosts.

The & Xu, 2003) . Several wild animals, including palm civets (Paguma larvata), raccoon dogs (Nyctereutes procyonoides) and horseshoe bats (Rhinolophus hipposideros) were involved in the SARS-CoV epidemic during 2003 and were tested positive using virological and or serological tests (Guan et al., 2003) . While phylogenetic analyses showed that bats are reservoir for the SARS-CoV and allowing genetic recombination, civets seem to be an intermediate host, as they were tested negative in their wild free lands (Su et al., 2016) .

The showed that the MERS-CoV evolve exclusively in camels while humans act as terminal host (Dudas et al., 2018) . The epidemiology of MERS remains to date not well understood, as heavily exposed persons to infected camels lead only to seropositivity and any of persons confirmed with the MERS-CoV reported previous exposure to infected animals (Hemida, Elmoslemany, et al., 2017) . The main factor that could play a role in the transmission of MERS-CoV from infected dromedaries to humans, is the consumption of raw camel milk . Neither the consumption of meat and organs nor the consumption of urine for medicinal use might cause the infection of humans (Adney et al., 2014) and

further investigations on experimentally inoculated animals are needed to confirm such definite conclusions.

For the current COVID-19 epidemic, the bat involvement as advanced by is not excluded, as the SARS-CoV-2 displayed 96% identity to the whole genome of bat-CoV. Moreover the SARS-CoV-2 was closely related to five wild animal CoVs, including civets and pangolin . Experimental studies showed that ferrets and cats are highly susceptible to the SARS-CoV-2. After an intra-nasal inoculation of 10 5 plaque-forming units (PFU) to multiple animal species including dogs, cats and ferrets, the infectious virus was detected in nasal turbinate, soft palate and tonsils of all inoculated ferrets. The SARS-CoV-2 RNA was also detected in rectal swabs and efficacious droplet transmission was confirmed among exposed cats .

The phylogenetic studies associated to amino acid sequence comparison of the ACE2 receptor has predicted cow, buffalo, goat, sheep and swine, as well as other wild species as the potential intermediate hosts for the SARS-CoV-2 (Qiu et al., 2020) . These findings highlighted the threat from the interspecies transmission of the SARS-CoV-2 between multiple animal species, and from animals to human and vice versa.

Multiple factors are playing an important role in increasing the exposure of humans to CoVs of infected animals.

Intensification of livestock production implies increasing animal density in farms and increasing movement of human and vehicles on and off farms, which promotes pathogen transmission and spreading (Cutler, Fooks, & van der Poel, 2010) . The intensively development of swine industry the last decade is considered of high risk for the trigger of severe pandemic viruses for humans (Borkenhagen, Salman, Ma, & Gray, 2019) . This was shown particularly with swine influenza viruses, and Nipah virus. Indeed, swine exposed workers displayed significantly higher titers (in hemagglutination inhibition assay) against swine influenza subtypes H1N1 and H1N2 than nonexposed workers (Odds Ratio = 54.9 and 95% confidence interval:

[13.0-232.6] (Gray et al., 2007) . In late 1998 and 1999, several fatal encephalitis cases (n = 105) caused by a Paramyxovirus were recorded in Malaysia (Chua, 2000) and quickly spread to Singapore (Paton et al., 1999) . Respiratory disease and encephalitis were recorded few weeks ago in pigs in the same district and the isolated virus, named Nipah virus, was shown to be transmitted from bats to pigs, then to humans (Chua et al., 2002) .

The consequences of anthropogenic activities leading to deforestation, habitat fragmentation and replacement of natural vegetation by crops definitely modify wildlife biology. These anthropogenic activities foster wildlife migration and create new environments that increase host, vector and pathogen contacts (Jones et al., 2013) .

Indeed, the deforestation was incriminated in the occurrence of the Nipah virus outbreak by pushing fruitbats (the natural reservoir of the Nipah virus) to pig farms high-density areas and fostered the contact between both species (Chua et al., 2002) .

It is well established that animals and animal product trade foster pathogens spreading (Travis, Watson, & Tauer, 2011) . A study on livestock trade network assessment in Europe, showed that pigs (for fattening and slaughter) and cattle (for fattening) were ranked second as the most heavily moved animal species within Europe in 2011, which foster the risk for exotic diseases introduction (Hardstaff, Häsler, & Rushton, 2015) .

Thousands of wild animals are traded in Asian markets every day, such as raccoon dogs, pangolin, masked palm civets, ferret badgers and hedgehogs (www.anima lasia.org). As several domestic and wild animals were shown to harbour CoVs, handling, touching or eating these animals, could increase the risk for humans to be in contact with CoVs.

Rodents have a worldwide distribution and were shown to harbour more than 60 known pathogens infecting both animals and humans (Meerburg, Singleton, & Kijlstra, 2009) , including CoVs . Bats also are considered to be the most abundant and diverse vertebrate after rodents (Rodhain, 2015) , with more than 1,300 known species and worldwide geographic distribution (Teeling, Jones, & Rossiter, 2016) . Bats are considered as an important reservoir of highly lethal zoonotic viruses and were shown to harbour more CoVs than any other animal species (Hu et al., 2015) .

Indeed, beside the SARS-CoV, the SARS-CoV-2 and the MERS-CoV, two porcine CoVs, have a bat-CoV origin: the SADS-CoV and the PEDV (Banerjee, Kulcsar, Misra, Frieman, & Mossman, 2019) . The geographical range of some bat species was estimated to expand by near to 400% in the last four decades as a response to climate change (Ancillotto, Santini, Ranc, Maiorano, & Russo, 2016) . One could imagine, that this expansion would be favourable to a higher contact likelihood with wild and domestic animals.

Mixing different animal species would increase CoVs host jumping probability. The BCoV contaminates sheep and goats, when they share the same barns or graze with infected cattle (Tråvén et al., 1999) . The MERS-CoV was also detected from sheep, goats and donkeys kept in close contact with infected dromedaries (Reusken et al., 2013) .

The ability of CoVs to mutate and to adapt to a new environment makes them a continuous threat to human lives and to domestic animals, mainly of farm industries. Pig CoVs are well described and documented in part because pork meat is the most widely consumed in several countries around the world. Nevertheless, data on several animal CoVs are scarce from multiple countries, mainly from Africa.

There is an urgent need to characterize the extent of CoVs infections among domesticated animals in the world using serological investigations for screening, virological studies as confirmatory and phylogenetic studies as comprehensive of the mutation and recombination phenomena. Continuous surveillance programme for CoVs genetic evolution should be implemented and would serve for at risk areas prediction. To date, only one mammal animal CoV is registered in the OIE list, namely the TGEV and one avian, the IBV. More attention should be given to the other animal CoVs and a specific surveillance system must be implemented in all the OIE member countries to monitor the introduction and the emergence of novel CoV strains in new areas. Strict regulation is to be implemented for farm animal trade. Thus, it is urgent to assess if meat, milk, semen and other animal by-products are at risk for humans, either through manipulation, process or consumption.

The accumulated knowledge needs to be compiled, broaden and extensive to predict and prevent further fatal pandemic like the COVID-19.

No ethical approval was required as this is a review article with no original research data.

The authors acknowledge the valuable contribution of Professor Mohamed Hussni Omar from Cornell University for the English revision of the manuscript.

The authors declare that they have no conflict of interest. 

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Investigating the introduction of porcine epidemic diarrhea virus into an Ohio swine operation

Molecular analysis of Brazilian strains of bovine coronavirus (BCoV) reveals a deletion within the hypervariable region of the S1 subunit of the spike glycoprotein also found in human coronavirus OC43

New porcine coronavirus? Veterinary Record

Detection of equine coronavirus in horses in the United Kingdom

Sero-prevalence, cross-species infection and serological determinants of prevalence of bovine coronavirus in cattle, sheep and goats in Ghana

Weaning and segregation

Vomiting and wasting disease of piglets

Respiratory system

Coronaviruses in poultry and other birds

Potential pathogens in feces from unweaned llamas and alpacas with diarrhea

Seroprevalence of porcine respiratory coronavirus in selected Korean pigs

Decline of transmissible gastroenteritis virus and its complex evolutionary relationship with porcine respiratory coronavirus in the United States

Development of an immunochromatographic strip for serological diagnosis of porcine hemagglutinating encephalomyelitis virus

Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States

Nipah virus: A recently emergent deadly paramyxovirus

Anthropogenic deforestation, El Niño and the emergence of Nipah virus in Malaysia

Assessing the economic burden of avian infectious bronchitis on poultry farms in Brazil

Hosts and sources of endemic human coronaviruses

Advances in virus research

Respiratory and fecal shedding of porcine respiratory coronavirus (PRCV) in sentinel weaned pigs and sequence of the partial S-gene of the PRCV isolates

Identification of a novel coronavirus possibly associated with acute respiratory syndrome in alpacas (Vicugna pacos) in California

Public health threat of new, reemerging, and neglected zoonoses in the industrialized world

Coronaviridae. In Virus taxonomy: Ninth report of the international committee on taxonomy of viruses

SARS and MERS: Recent insights into emerging coronaviruses

Spotlight on avian pathology: Infectious bronchitis virus

Respiratory disease associated with bovine coronavirus infection in cattle herds in Southern Italy

A candidate modified-live bovine coronavirus vaccine: Safety and immunogenicity evaluation

Characterisation of bubaline coronavirus strains associated with gastroenteritis in water buffalo (Bubalus bubalis) calves

Biological and genetic analysis of a bovine-like coronavirus isolated from water buffalo (Bubalus bubalis) calves

A systematic review of MERS-CoV seroprevalence and RNA prevalence in dromedary camels: Implications for animal vaccination

Development of a multiplex RT-PCR for the detection of major diarrhoeal viruses in pig herds in China

Detection and molecular characterization of infectious bronchitis-like viruses in wild bird populations

Development of multi-specific humanized llama antibodies blocking SARS-CoV-2/ACE2 interaction with high affinity and avidity. Emerging Microbes and Infections

Porcine deltacoronavirus in mainland China

A transmissible gastroenteritis in pigs

MERS-CoV spillover at the camel-human interface

Investigation of Rota and Corona viruses as causative agents for diarrhea in Egyptian calves

Genetic analysis of avian coronavirus infectious bronchitis virus in Yellow chickens in Southern China over the past decade: Revealing the changes of genetic diversity, dominant genotypes, and selection pressure

Coronaviruses: An overview of their replication and pathogenesis

Disease associated with equine coronavirus infection and high case fatality rate

An ecosystems perspective on virus evolution and emergence

Characterisation of porcine epidemic diarrhea virus isolates during the 2014-2015 outbreak in the Philippines

Vaccines for porcine epidemic diarrhea virus and other swine coronaviruses

Viral enteritis in calves. The Canadian Veterinary Journal = La Revue Veterinaire Canadienne

A New bat-HKU2-like coronavirus in swine

Novel findings from a beta coronavirus outbreak on an American Miniature Horse breeding farm in upstate New York. Equine Veterinary Education

Human-dromedary camel interactions and the risk of acquiring zoonotic Middle East respiratory syndrome coronavirus infection

Swine workers and swine influenza virus infections

Encephalomyelitis of swine caused by a haemagglutinating virus VI. Morphology of the virus

A hemagglutinating virus producing encephalomyelitis in baby pigs

Isolation and characterization of viruses related to the SARS coronavirus from animals in Southern China

Characterization of a coronavirus isolated from a diarrheic foal

An orthopoxvirus-based vaccine reduces virus excretion after MERS-CoV infection in dromedary camels

Pathogenicity of three isolates of porcine respiratory coronavirus in the USA

Livestock trade networks for guiding animal health surveillance

Sero-prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) specific antibodies in dromedary camels in Tabuk, Saudi Arabia

Infection with a new porcine respiratory coronavirus in Denmark: Serologic differentiation from transmissible gastroenteritis virus using monoclonal antibodies

Experimental infection of dromedaries with Middle East respiratory syndrome-coronavirus is accompanied by massive ciliary loss and depletion of the cell surface receptor dipeptidyl peptidase

Associations between exposure to viruses and bovine respiratory disease in Australian feedlot cattle

First detection of bovine coronavirus in yak (Bos grunniens) and a bovine coronavirus genome with a recombinant HE gene

Coronavirus infections in horses in Saudi Arabia and Oman

MERS coronavirus in dromedary camel herd, Saudi Arabia

Dromedary camels and the transmission of Middle East respiratory syndrome coronavirus (MERS-CoV)

Evolution of RNA Viruses

Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan

Bat origin of human coronaviruses: Emerging and re-emerging pathogens in humans and animals

Review of infectious bronchitis virus around the world

Porcine Deltacoronavirus

Prevalence, complete genome sequencing and phylogenetic analysis of porcine deltacoronavirus in South Korea

Analysis of the genome sequence of an alpaca coronavirus

Molecular identification and characterization of novel coronaviruses infecting graylag geese (Anser anser), feral pigeons (Columbia livia) and mallards (Anas platyrhynchos)

Zoonosis emergence linked to agricultural intensification and environmental change

Altered pathogenesis of porcine respiratory coronavirus in pigs due to immunosuppressive effects of dexamethasone: Implications for corticosteroid use in treatment of severe acute respiratory syndrome coronavirus

Calves are susceptible to infection with the newly emerged porcine deltacoronavirus, but not with the swine enteric alphacoronavirus, porcine epidemic diarrhea virus

Immunologic differences in strains of infectious bronchitis virus

Middle East respiratory syndrome coronavirus infection in non-camelid domestic mammals. Emerging Microbes and Infections

Excretion and persistence of bovine coronavirus in neonatal calves

Prevalence of a novel bovine coronavirus strain with a recombinant hemagglutinin/ esterase gene in dairy calves in China

Canada porcine epidemic diarrhea in Canada: An emerging disease case study

Seroprevalence and risk factors for infection with equine coronavirus in healthy horses in the USA

MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets

Coronavirus: How a large RNA viral genome is replicated and transcribed

First genome sequences of buffalo coronavirus from water buffaloes in Bangladesh

Isolation and characterization of a novel Betacoronavirus subgroup A coronavirus, rabbit coronavirus HKU14, from domestic rabbits

Porcine respiratory coronavirus: Molecular features and virus-host interactions

Detection and phylogenetic analysis of porcine deltacoronavirus in Korean swine farms

Causative agents and epidemiology of diarrhea in Korean native calves

Structure, function, and evolution of coronavirus spike proteins

Full-length genome sequence of porcine deltacoronavirus strain USA/IA/2014/8734

Complete genome sequence of a novel swine acute diarrhea syndrome coronavirus

Susceptibility of chickens to porcine deltacoronavirus infection

Mutation in spike protein cleavage site and pathogenesis of feline coronavirus

Infectious bronchitis virus variants: Molecular analysis and pathogenicity investigation

Bovine coronavirus in neonatal calf diarrhoea in Iran

Role of transportation in spread of porcine epidemic diarrhea virus infection. United States

Novel genotype of infectious bronchitis virus isolated in China

Coronaviridae

Une étude épidémiologique à propos des manifestations d'allure grippale chez le porc en croissance

The detection and phylogenetic analysis of porcine deltacoronavirus from Guangdong Province in Southern China

First outbreak with chimeric swine enteric coronavirus (SeCoV) on pig farms in Slovakia -Lessons to learn

Genetic and antigenic heterogeneity of infectious bronchitis virus in South America: Implications for control programmes

Porcine deltacoronavirus from the United States

Neonatal calf diarrhea: Propagation, attenuation, and characteristics of a coronavirus-like agent

Rodent-borne diseases and their risks for public health rodent-borne diseases and their risks for public health

Vers une identification de nouveaux virus respiratoires bovins

Identification of a novel coronavirus from a beluga whale by using a panviral microarray

Camel production systems in Ethiopia: a review of literature with notes on MERS-CoV risk factors

First detection of equine coronavirus (ECoV) in Europe

Detecting and monitoring porcine hemagglutinating encephalomyelitis virus

Porcine hemagglutinating encephalomyelitis virus: A review

First detection and characterisation of porcine hemagglutinating encephalomyelitis virus in the Czech Republic

Demonstration of coronavirus infection in buffaloes

Brazilian chicken meat production chain: A 10-year overview

Antibody response to equine coronavirus in horses inoculated with a bovine coronavirus vaccine

Experimental inoculation of equine coronavirus into Japanese draft horses

Complete genome analysis of equine coronavirus isolated in Japan

Genetic evidence of Middle East respiratory syndrome coronavirus (MERS-Cov) and widespread seroprevalence among camels in Kenya

Middle East respiratory syndrome coronavirus (Mers-CoV): Animal to human interaction. Pathogens and Global Health

SARS-CoV-2 infection in farmed minks, the Netherlands

Isolation of an equine coronavirus from adult horses with pyrogenic and enteric disease and its antigenic and genomic characterization in comparison with the NC99 strain

Epidemic of equine coronavirus at Obihiro racecourse, Hokkaido, Japan in 2012

Discovery of a novel swine enteric alphacoronavirus (SeACoV) in Southern China

Prevalence of respiratory pathogens in diseased, non-vaccinated, routinely medicated veal calves

Porcine epidemic diarrhea vaccine evaluation using a newly isolated strain from Korea

Dual enteric and respiratory tropisms of winter dysentery bovine coronavirus in calves

Outbreak of Nipah-virus infection among abattoir workers in Singapore

Evaluation of antibody response of killed and live vaccines against porcine epidemic diarrhea virus in a field study

Coronaviruses

Transmissible gastroenteritis in swine

Isolation of a porcine respiratory, non-enteric coronavirus related to transmissible gastroenteritis

A new coronavirus-like particle associated with diarrhea in swine

Porcine epidemic diarrhea: A retrospect from Europe and matters of debate

Experimental inoculation of neonatal piglets with feed naturally contaminated with porcine epidemic diarrhea virus

First retrospective studies with etiological confirmation of porcine transmissible gastroenteritis virus infection in Argentina

The evolutionary processes of canine coronaviruses

Chinese-like strain of porcine epidemic diarrhea virus

Prevalence of equine coronavirus in nasal secretions from horses with fever and upper respiratory tract infection

Emerging outbreaks associated with equine coronavirus in adult horses

Equine coronavirus: An emerging enteric virus of adult horses. Equine Veterinary Education

Enteric coronavirus infection in adult horses

Geographic Information System

Emergence of porcine epidemic diarrhea viruses with the novel S genes in Tibetan pigs in the Qinghai-Tibetan plateau in China

Predicting the angiotensin converting enzyme 2 (ACE2) utilizing capability as the receptor of SARS-CoV-2

Hemagglutinating encephalomyelitis coronavirus infection in pigs

Isolation of MERS coronavirus from dromedary camel

Avian infectious bronchitis virus. Recent Advances in Animal Virology

Middle East respiratory syndrome coronavirus (MERS-CoV) RNA and neutralising antibodies in milk collected according to local customs from dromedary camels

Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: A comparative serological study. The Lancet Infectious Diseases

Geographic distribution of MERS coronavirus among dromedary camels

MERS-CoV infection of Alpaca in a region where MERS-CoV is endemic

Emerging strains of porcine epidemic diarrhoea virus (PEDv) in Mexico

Detection and genetic analysis of porcine hemagglutinating encephalomyelitis virus in South Korea

Vaccination management of beef cattle: delayed vaccination and endotoxin stacking. Veterinary Clinics of North America -Food Animal Practice

Molecular epidemiology of coronavirus in faeces of brazilian calves and peruvian camelid herds

Chauves-souris et virus : des relations complexes

A disease of nursing pigs previously unreported in Ontario

Outbreak of diarrhea among preweaning alpacas (Vicugna pacos) in the southern peruvian highland

Retrospective study, full-length genome characterization and evaluation of viral infectivity and pathogenicity of chimeric porcine deltacoronavirus detected in Vietnam

Different lineage of porcine deltacoronavirus in Thailand, Vietnam and Lao PDR in 2015

Bovine respiratory coronavirus. Veterinary Clinics of North America: Food Animal Practice

Winter dysentery in adult dairy cattle: Detection of coronavirus in the faeces. The Veterinary Record

Diseases of Swine

The neighbor-joining method: A new method for reconstructing phylogenetic trees

Coronaviruses: A paradigm of new emerging zoonotic diseases. Pathogens and Disease

Detection of bovine coronavirus in calf diarrheic samples by indirect antigen capture ELISA and RT-PCR

Evaluation of equine coronavirus fecal shedding among hospitalized horses

Coronavirus envelope protein: current knowledge

Trends in emerging viral infections of swine

Susceptibility of ferrets, cats, dogs, and different domestic animals to SARS-coronavirus-2. BioRxiv

Genetic characterization of bovine coronavirus in Vietnam

Molecular and phylogenetic characterization of bovine coronavirus virus isolated from dairy cattle in Central Region

Infectious agents associated with diarrhoea in neonatal foals in central Kentucky: A comprehensive molecular study

Porcine epidemic diarrhoea virus: A comprehensive review of molecular epidemiology, diagnosis, and vaccines

Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human

Emergence of porcine epidemic diarrhea virus in the United States: Clinical signs, lesions, and viral genomic sequences

Isolation of respiratory bovine coronavirus, other cytocidal viruses, and Pasteurella spp from cattle involved in two natural outbreaks of shipping fever

Epidemiology, genetic recombination, and pathogenesis of coronaviruses

An immunohistochemical investigation of porcine epidemic diarrhoea

Outbreak of porcine epidemic diarrhea in suckling piglets

Genetic characterization and phylogenetic analysis of porcine deltacoronavirus (PDCoV) in Shandong Province

Attenuation of a virulent swine acute diarrhea syndrome coronavirus strain via cell culture passage

Field study of bovine coronavirus vaccine enriched with hemagglutinating antigen for winter dysentery in dairy cows

Prospects for inferring very large phylogenies by using the neighbor-joining method

Epidemic and genetic characterization of porcine epidemic diarrhea virus strains circulating in the regions around Hunan

Phylogeny, genes, and hearing: Implications for the evolution of echolocation in bats

Evaluation of serological assays available in a biosafety level 2 laboratory and their application for survey of Middle East respiratory syndrome coronavirus among livestock in Ethiopia

A cohort study of the effect of winter dysentery on herd-level milk production

Bovine respiratory syncytial virus and bovine coronavirus antibodies in bulk tank milk -risk factors and spatial analysis

Serum antibodies to bovine coronavirus in Swedish sheep

The spread of pathogens through trade in wildlife. Revue Scientifique Et Technique De l'OIE

Confirmed cases of SARS-CoV-2 in animals in the United States

Antibody response of pregnant sows to porcine epidemic diarrhea virus live vaccine and maternally-derived antibodies of the piglets

S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification. Infection

High prevalence of Middle East respiratory coronavirus in young dromedary camels in Jordan. Vector-Borne and Zoonotic Diseases

Differential production of proinflammatory cytokines in the pig lung during different respiratory virus infections: Correlations with pathogenicity

Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003

Prevalence of enteric pathogens in diarrheic and non-diarrheic samples from pig farms with neonatal diarrhea in the North East of Spain

Genetic variability of the S1 subunit of enteric and respiratory bovine coronavirus isolates

Detection and genetic characterization of deltacoronavirus in pigs

Porcine coronavirus HKU15 detected in 9 US States

Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China

Detection and characterization of new coronavirus in bottlenose dolphin

Bat-origin coronaviruses expand their host range to pigs

Emerging and re-emerging coronaviruses in pigs. Current Opinion in Virology

Coronavirus pathogenesis

Induction of protective immunity against transmissible gastroenteritis virus after exposure of neonatal pigs to porcine respiratory coronavirus

Prevalence of coronavirus antibodies in Iowa swine

Discovery of seven novel mammalian and avian coronaviruses in the genus Deltacoronavirus supports bat coronaviruses as the gene source of Alphacoronavirus and Betacoronavirus and avian coronaviruses as the gene source of Gammacoronavirus and Deltacoronavi

Discovery of a novel bottlenose dolphin coronavirus reveals a distinct species of marine mammal coronavirus in gammacoronavirus

Coronavirus Disease 2019, weekly situation report. WHO/COVID19

Middle East respiratory syndrome coronavirus (MERS-CoV) global summary and assessment risk

World Organisation of Animal Health (2020)

Evolutionary aspects of recombination in RNA viruses

Isolation and characterization of a highly pathogenic strain of porcine enteric Alphacoronavirus causing watery diarrhoea and high mortality in newborn piglets

The structure and functions of coronavirus genomic 3' and 5' ends

Swine enteric alphacoronavirus (swine acute diarrhea syndrome coronavirus): An update three years after its discovery

Bovine coronavirus (BoCV) infection in calves with diarrhoea and their dams

Efficacy and immunogenicity of recombinant swinepox virus expressing the truncated S protein of a novel isolate of porcine epidemic diarrhea virus

Prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels in Abu Dhabi Emirate

Porcine deltacoronavirus: Overview of infection dynamics, diagnostic methods, prevalence and genetic evolution

Genomic characterization and pathogenicity of porcine Deltacoronavirus strain CHN-HG-2017 from China

Prevalence and phylogenetic analysis of porcine diarrhea associated viruses in southern China from

The re-emerging of SADS-CoV infection in pig herds in Southern China

Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China

Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin

A pneumonia outbreak associated with a new coronavirus of probable bat origin

Countrywide survey for MERS-coronavirus antibodies in dromedaries and humans in Pakistan