        item: #1 of 48
          id: cord-252441-190jmgcq
      author: Liu, Yong-sheng
       title: The characteristics of the synonymous codon usage in enterovirus 71 virus and the effects of host on the virus in codon usage pattern
        date: 2011-03-05
       words: 4663
      flesch: 48
     summary: To investigate the characteristics of synonymous codon usage without the confounding influence of amino acid composition among different sequences, the relative synonymous codon usage (RSCU) values among different codons in the EV71 ORF was calculated according to the published equation (Sharp et al., 1986 ). By comparing between the patterns of synonymous codon usage of human cell and that of EV71 virus, we found that the pattern of synonymous codon usage of EV71 strains is partially antagonistic to that of human cells.
    keywords: codon; codon usage; ev71; strains; usage
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        item: #2 of 48
          id: cord-253090-kllrqoxi
      author: dos Passos Cunha, Marielton
       title: Codon adaptation biases among sylvatic and urban genotypes of Dengue virus type 2
        date: 2018-05-21
       words: 3284
      flesch: 35
     summary: How did zika virus emerge in the Pacific Islands and Latin America Pathways to zoonotic spillover FastTree 2 -approximately maximum-likelihood trees for large alignments CAIcal: a combined set of tools to assess codon usage adaptation E-CAI: a novel server to estimate an expected value of codon adaptation index (eCAI) Complete genome sequence of a highly divergent dengue virus type 2 strain, imported into Australia from Sabah American and American/Asian genotypes of dengue virus differ in mosquito infection efficiency: candidate molecular determinants of productive vector infection Dengue diversity across spatial and temporal scales: local structure and the effect of host population size The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference Phylogenetic relationships and differential selection pressures among genotypes of Dengue-2 virus Human adaptation of Ebola virus during the west African outbreak Evolutionary processes among sylvatic dengue type 2 viruses Potential of ancestral sylvatic dengue-2 viruses to re-emerge Fever from the forest: prospects for the continued emergence of sylvatic dengue virus and its impact on public health Evolutionary relationships of endemic/epidemic and sylvatic dengue viruses Global evolutionary history and spatio-temporal dynamics of dengue virus type 2 This work was supported by the Brazilian National Council of Scientific and Technological Development (CNPq) process The increase in mosquito populations has also been identified as a potential determinant of the emergence and increased transmission of arbovirus, particularly in immunologically naïve human populations (Dudas et al., 2018; Pettersson et al., 2016) .
    keywords: cai; codon; et al; genotypes; urban; usage; virus
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        item: #3 of 48
          id: cord-253245-433mg0ke
      author: Gao, Zhiru
       title: A systematic review of re-detectable positive virus nucleic acid among COVID-19 patients in recovery phase
        date: 2020-08-05
       words: 1855
      flesch: 46
     summary: However, there is currently insufficient knowledge about the characteristics of RP patients. In the manuscript, we reviewed characteristics, potential reasons, infectivity, treatment, and outcome of RP patients in order to explain this phenomenon.
    keywords: cov-2; patients
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        item: #4 of 48
          id: cord-255141-55ho9av4
      author: Abolnik, Celia
       title: Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus
        date: 2015-04-03
       words: 6285
      flesch: 43
     summary: For example, M together with the accessory proteins 4a, 4b and 5 were all found to prevent the synthesis of IFN-b through the inhibition of interferon promotor activation and IRF-3 function, thus influencing disease outcome (Yang et al., 2013) . functional role in the pathogenesis of IBV, the homolog in MERs-CoV is a potent interferon antagonist (Yang et al., 2013) .
    keywords: bronchitis; coronavirus; et al; gene; genome; ibv; orf; protein; rna; strain; subunit; virus
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        item: #5 of 48
          id: cord-257584-v38tjof3
      author: Fahmi, Muhamad
       title: Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV
        date: 2020-03-03
       words: 2992
      flesch: 43
     summary: We then determined the presence and absence of homolog proteins of one representative set of annotated 2019-nCoV proteins against other genome sequences in a database using tblastn with a threshold of > 50 and > 25 bits score for protein sequences > The phylogenetic profiling cluster of homolog proteins of one annotated 2019-nCoV protein against other genome sequences revealed two clades of ten 2019-nCoV proteins.
    keywords: bat; coronavirus; ncov; proteins; sars; tree
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        item: #6 of 48
          id: cord-259925-g28sx9qu
      author: Saleemi, Mansab Ali
       title: Emergence and molecular mechanisms of SARS-CoV-2 and HIV to target host cells and potential therapeutics
        date: 2020-10-06
       words: 6884
      flesch: 36
     summary: The dramatic reduction in the peripheral CD4+ and CD8+ T cells is one of the symptoms in COVID-19 cases related to HIV infection Diao et al., 2020) . Therefore, this review reflects the latest repurpose of existing antiviral therapeutic drug choices available to combat SARS-CoV-2. Coronaviruses (CoVs) are a group of enveloped and positive single-stranded RNA genome viruses that infect both animals and humans (Smith and Denison, 2013; Xu et al., 2020) .
    keywords: cd4; cells; coronavirus; cov-2; covid-19; et al; hiv; human; infected; novel; patients; sars; syndrome; transmission; virus
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        item: #7 of 48
          id: cord-260644-5moccf8c
      author: Hashemi, Seyed Ahmad
       title: Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2
        date: 2020-11-07
       words: 2178
      flesch: 60
     summary: Using bioinformatics databases and software, we designed the PCR-RFLP method for D614G mutation detection. key: cord-260644-5moccf8c authors: Hashemi, Seyed Ahmad; Khoshi, Amirhosein; Ghasemzadeh-moghaddam, Hamed; Ghafouri, Majid; Taghavi, Mohammadreza; Namdar-Ahmadabad, Hasan; Azimian, Amir title: Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2 date: 2020-11-07 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2020.104625 sha: doc_id: 260644 cord_uid: 5moccf8c In late 2019, an outbreak of respiratory disease named COVID-19 started in the world.
    keywords: samples; sars
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        item: #8 of 48
          id: cord-261547-8tfbhmzo
      author: Góes, Luiz Gustavo Bentim
       title: Genetic diversity of bats coronaviruses in the Atlantic Forest hotspot biome, Brazil
        date: 2016-07-26
       words: 1973
      flesch: 45
     summary: Similar results were previously reported for a variety of bat CoVs and are taken as evidence of co-evolution of CoV genotypes and specific host genera (Drexler et al., 2014; Corman et al., 2013; Anthony et al., 2013) . Although it is not possible to calculate the risk of spill over events of Brazilian bats CoVs to humans, our results reinforce the need for expanded and continuing surveillance of CoVs in bat fauna, including those in the AFB regions of Brazil.
    keywords: bats; cov; covs; et al; species
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        item: #9 of 48
          id: cord-261914-qfim8nu5
      author: Oem, Jae-Ku
       title: Genetic characteristics and analysis of a novel rotavirus G3P[22] identified in diarrheic feces of Korean rabbit
        date: 2019-06-04
       words: 3276
      flesch: 50
     summary: Oem, et al. Infection, Genetics and Evolution 73 (2019) 368-377 RVA/Cat-tc/AUS/Cat97/1984/G3P RVA/Rabbit-tc/ITA/30-96/1996/G3P[14] RVA/Rabbit-tc/ITA/30-96/1996/G3P[14] RVA/Cat-tc/AUS/Cat97/1984/G3P[3] RVA/Rabbit-tc/ITA/30-96/1996/G3P[14] RVA/Rabbit-tc/ITA/30-96/1996/G3P[14] RVA/Cat-tc/AUS/Cat97/1984/G3P[3] RVA/Rabbit-tc/ITA/30-96/1996/G3P[14] RVA/Rabbit-tc/30-96/1996/G3P[14] Whole genome characterization of new bovine rotavirus G21P[29] and G24P[33] strains provides evidence for interspecies transmission Identification of the novel lapine rotavirus genotype P [22] from an outbreak of enteritis in a Hungarian rabbitry Genetic diversity and zoonotic potential of human rotavirus strains Genetic heterogeneity in human G6P[14] rotavirus strains detected in Hungary suggests independent zoonotic origin Complete genome analysis of a rabbit rotavirus causing gastroenteritis in a human infant Update on rotavirus vaccines Comparative amino acid sequence analysis of the outer capsid protein VP4 from four lapine rotavirus strains reveals identity with genotype P[14] human rotaviruses Detection and characterisation of group A rotavirus in asymptomatic piglets in southern Ireland Human infection with a P[14], G3 lapine rotavirus Genetic characterization of a novel G3P[14] rotavirus strain causing gastroenteritis in 12 year old Australian child Rotavirus gene structure and function Full genomic analysis and possible origin of a porcine G12 rotavirus strain RU172 Full genomic analysis of rabbit rotavirus G3P[14] strain N5 in China: identification of a novel VP6 genotype Characterization of neutralization specificities of outer capsid spike protein VP4 of selected murine, lapine, and human rotavirus strains A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences MEGA7: molecular evolutionary genetics analysis Version 7.0 for bigger datasets RVA/Rabbit-tc/ITA/30-96/G3P[14] Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans Molecular characterization of the VP4, VP6, VP7, and NSP4 genes of lapine rotaviruses identified in Italy: emergence of a novel VP4 genotype Lapine rotaviruses of the genotype P[22] are widespread in Italian rabbitries Full genomic analysis of human rotavirus strain B4106 and lapine rotavirus strain 30/96 provides evidence for interspecies transmission Are human P[14] rotavirus strains the result of interspecies transmissions from sheep or other ungulates that belong to the mammalian order Artiodactyla? Simian rotaviruses possess divergent gene constellations that originated from interspecies transmission and reassortment Equine G3P[3] rotavirus strain [11] rotavirus strain Whole genome sequence analysis of bovine G6P[11] rotavirus strain found in a child with gastroenteritis Phylogenetic analyses of the VP4 and VP7 genes of porcine group A rotaviruses in Sao Paulo State, Brazil: first identification of G5P[23] in piglets Whole genome sequence and phylogenetic analyses reveal human rotavirus G3P[3] strains Ro1845 and HCR3A are examples of direct virion transmission of canine/feline rotaviruses to humans Full genome characterization of a porcine-like human G9P[6] rotavirus strain isolated from an infant in Belgium
    keywords: et al; lapine; rab1404; rabbit; rotavirus; strain
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        item: #10 of 48
          id: cord-262592-0rdiosxd
      author: Cuevas, José M.
       title: Human norovirus hyper-mutation revealed by ultra-deep sequencing
        date: 2016-04-17
       words: 5847
      flesch: 44
     summary: To more directly test for hyper-mutation, we performed transfection assays in which the production of mutations was restricted to a single cell infection cycle. Two of the samples showing hyper-mutation belonged to newborns, whereas the other two belonged to adults, with no significant association between age and hyper-mutation at this low sample size (Fisher's exact test, P = 0.547).
    keywords: base; et al; hyper; mutation; pcr; reads; region; rna; virus
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        item: #11 of 48
          id: cord-263476-ju7xqwa7
      author: Xia, Jing
       title: Phylogenetic and antigenic analysis of avian infectious bronchitis virus in southwestern China, 2012–2016
        date: 2016-08-13
       words: 5711
      flesch: 43
     summary: infectious bronchitis virus isolates in southern China Sequence analysis of infectious bronchitis virus isolates from the 1960s in the United States Dissecting RNA recombination in vitro: role of RNA sequences and the viral replicase Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran Isolation and molecular characterization of nephropathic infectious bronchitis virus isolates of Gujarat state Analysis of the S1 gene of the avian infectious bronchitis virus (IBV) reveals changes in the IBV genetic groups circulating in southern Thailand Genotypes and serotypes of avian infectious bronchitis viruses isolated during A simple method of estimating fifty percent endpoints Phylogenetic characterization of Newcastle disease virus isolated in the mainland of China during Genotyping of infectious bronchitis viruses from broiler farms in Iraq during The AU-rich RNA recombination hot spot sequence of Brome mosaic virus is functional in Tombusviruses: implications for the mechanism of RNA recombination Co-infection with multiple respiratory pathogens contributes to increased mortality rates in Algerian poultry flocks Infectious bronchitis virus variants: a review of the history, current situation and control measures The experimental infection of chickens with mixtures of infectious bronchitis virus and Escherichia coli Recombination in avian gamma-coronavirus infectious bronchitis virus Comparative analysis of oncogenic genes revealed unique evolutionary features of field Marek's disease virus prevalent in recent years in China Incorporation of spike and membrane glycoproteins into coronavirus virions Relationship between serotypes and genotypes based on the hypervariable region of the S1 gene of infectious bronchitis virus Evolutionary implications of genetic variations in the S1 gene of infectious bronchitis virus Some characteristics of isolates of infectious bronchitis virus from commercial vaccines Characterization and analysis of an infectious bronchitis virus strain isolated from southern China in 2013 Emergence of novel nephropathogenic infectious bronchitis viruses currently circulating in Chinese chicken flocks Serotype shift of a 793/B genotype infectious bronchitis coronavirus by natural recombination Molecular detection and smoothing spline clustering of the IBV strains detected in China during Safety and efficacy of an attenuated Chinese QX-like infectious bronchitis virus strain as a candidate vaccine Genetic analysis revealed LX4 genotype strains of avian infectious bronchitis virus became predominant in recent years in Sichuan area Two novel neutralizing antigenic epitopes of the s1 subunit protein of a QX-like avian infectious bronchitis virus strain Sczy3 as revealed using a phage display peptide library This work was financially supported by the Program for Chang-jiang Scholars and Innovative Research Team in University PCSIRT (Grant No. IRT0848). Isolation, propagation, identification and comparative pathogenicity of five Egyptian field strains of Eimeria tenella from broiler chickens in five different provinces in Egypt Persistent antigenic variation of influenza A viruses after incomplete neutralization in ovo with heterologous immune serum An in vitro system for the leader-primed transcription of coronavirus mRNAs Infectious bronchitis virus in different avian physiological systems-a field study in Brazilian poultry flocks Coronaviruses in poultry and other birds Phylogenetic analysis of hemagglutinin genes of 40 H9N2 subtype avian influenza viruses isolated from poultry in China from Molecular and antigenic characteristics of Massachusetts genotype infectious bronchitis coronavirus in China Assessing the economic burden of avian infectious bronchitis on poultry farms in Brazil Serotyping of avian infectious bronchitis viruses by the virus-neutralization test Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity Progression of lesions in the respiratory tract of broilers after single infection with Escherichia coli compared to superinfection with E. coli after infection with infectious bronchitis virus Prevalence and molecular characterization of avian infectious bronchitis virus in poultry flocks in Morocco from 2010 to 2014 and first detection of Italy 02 in Africa Phylogenetic analysis of avian infectious bronchitis virus S1 glycoprotein regions reveals emergence of a new genotype in Moroccan broiler chicken flocks Isolation and identification of a Taiwan genotype I avian infectious bronchitis virus and the pathogenicity identification Genotypes of infectious bronchitis viruses circulating in the Middle East between Prevalence of avian respiratory viruses in broiler flocks in Egypt Epidemiology of avian infectious bronchitis virus genotypes in Iran Attenuation mechanism of virulent infectious bronchitis virus strain with QX genotype by continuous passage in chicken embryos Identification of previously unknown antigenic epitopes on the S and N proteins of avian infectious bronchitis virus Survey indicates circulation of 4/91 and QX-type infectious bronchitis viruses in Hungary in 2014 -short communication Two genotypes of infectious bronchitis virus are responsible for serological variation in KwaZulu-Natal poultry flocks prior to 2012 Antigenic domains on the peplomer protein of avian infectious bronchitis virus: correlation with biological functions Circulation of infectious bronchitis virus strains from Italy 02 and QX genotypes in Slovenia between RNA recombination in animal and plant viruses Cloning and identification of ipaJ gene in Salmonella pullorum Serotype and genotype diversity of infectious bronchitis viruses isolated during 1985-2008 in Guangxi Genetic diversity of avian infectious bronchitis coronavirus in recent years in China Molecular characterization of major structural protein genes of avian coronavirus
    keywords: bronchitis; china; gene; ibvs; strains; type; vaccine; virus
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        item: #12 of 48
          id: cord-263481-w5ytp1q7
      author: Lokman, Syed Mohammad
       title: Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach
        date: 2020-06-02
       words: 3021
      flesch: 42
     summary: The spatial distribution of S protein sequences having different variation over time reveals that most of the variants (17 out of 240 S glycoprotein sequences) were reported from the US J o u r n a l P r e -p r o o f Journal Pre-proof followed by 3 out of 2 sequences (including Y145 deletion) and 2 out of 50 sequences from India and China, respectively (Fig. 5) . Based on the phylogenetic studies, the SARS-CoV-2 is categorized as a member of the genus Betacoronavirus, the same lineage that includes SARS coronavirus (SARS-CoV)
    keywords: coronavirus; cov-2; domain; glycoprotein; protein; receptor; sars; sequences; spike
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        item: #13 of 48
          id: cord-265329-bsypo08l
      author: van Dorp, Lucy
       title: Emergence of genomic diversity and recurrent mutations in SARS-CoV-2
        date: 2020-05-05
       words: 4923
      flesch: 40
     summary: However, this lineage shares 96% identity with SARS-CoV-2, which is not sufficiently high to implicate it as the immediate ancestor of SARS-CoV-2 (2) . Betacoronaviridae comprise a large number of lineages that are found in a wide range of mammals and birds (2) , including the other human zoonotic pathogens SARS-CoV-1 and MERS-COV.
    keywords: cov-2; data; diversity; figure; genome; genomic; homoplasies; human; mutations; pandemic; sars; sites
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        item: #14 of 48
          id: cord-266660-0wq77k6y
      author: Choi, Jong-Chul
       title: Comparative genome analysis and molecular epidemiology of the reemerging porcine epidemic diarrhea virus strains isolated in Korea
        date: 2014-06-19
       words: 1998
      flesch: 51
     summary: Korean PEDV strains are denoted using bold characters. Nucleotide sequence alignment and phylogenetic tree analysis for complete genomes of PEDV strains.
    keywords: complete; gene; genome; pedv; strains
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        item: #15 of 48
          id: cord-266914-3eatplc2
      author: Wang, Yongjin
       title: Nsp1 proteins of group I and SARS coronaviruses share structural and functional similarities
        date: 2010-06-02
       words: 4023
      flesch: 42
     summary: key: cord-266914-3eatplc2 authors: Wang, Yongjin; Shi, Huiling; Rigolet, Pascal; Wu, Nannan; Zhu, Lichen; Xi, Xu-Guang; Vabret, Astrid; Wang, Xiaoming; Wang, Tianhou title: Nsp1 proteins of group I and SARS coronaviruses share structural and functional similarities date: 2010-06-02 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2010.05.014 sha: doc_id: 266914 cord_uid: 3eatplc2 The nsp1 protein of the highly pathogenic SARS coronavirus suppresses host protein synthesis, including genes involved in the innate immune system. Nsp1 proteins of group I coronaviruses interacted with host ribosomal 40S subunit and did not inhibit IRF-3 activation.
    keywords: cells; coronavirus; cov; group; host; nsp1; proteins; sars
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        item: #16 of 48
          id: cord-267136-1abp6oom
      author: Lan, Yu-Ching
       title: Phylogenetic analysis and sequence comparisons of structural and non-structural SARS coronavirus proteins in Taiwan
        date: 2004-12-07
       words: 3111
      flesch: 54
     summary: A BLAST search was performed to locate SARS CoV sequences in the GenBank database. If we assume that the RBD is (a) conserved among different SCoVs, including civet SCoVs (Bonavia et al., 2002) , and (b) more than 30-50 amino acids in length (Lasky et al., 1987) , then it is possible that the RBD can be mapped onto amino acid residues 360-442. Identification of a receptor-binding domain of the spike glycoprotein of human coronavirus HCoV-229E Memoir of Severe Acute Respiratory Syndrome Control in Taiwan Severe acute respiratory syndrome Analysis of the whole-length sequences of ten strains of SARS coronavirus in Taiwan and its epidemiological implications Amino acid comparisons of S proteins from 44 human and civet SCoVs.
    keywords: amino; civet; epidemic; human; sars; scovs; sequences
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        item: #17 of 48
          id: cord-267168-qjktnnn6
      author: Wille, Michelle
       title: Evolutionary genetics of canine respiratory coronavirus and recent introduction into Swedish dogs
        date: 2020-03-20
       words: 6280
      flesch: 45
     summary: A small number of isolates have also been sequenced and characterized (An et al., 2010a; Erles et al., 2003 Erles et al., , 2007 Jeoung et al., 2014; Yachi and Mochizuki, 2006 infections in a number of avian and mammalian species. For the first approach, PCR reactions targeting the S, Membrane (M) and Hemagglutinin-esterase (HE) genes were carried out using previously published primers (An et al., 2010a; Erles et al., 2007) (Table A2 ) using KAPA2G Robust HotStart ReadyMix PCR Kit (KAPA Biosystems, Roche Sequencing, Pleasanton, CA, USA).
    keywords: bcov; canine; coronavirus; crcov; dogs; et al; fig; gene; recombination; respiratory; sequencing; sweden; swedish; usa; viruses
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        item: #18 of 48
          id: cord-268480-fd5xi4q1
      author: Rojas, Miguel A.
       title: Identification of two novel Rotavirus A genotypes, G35 and P[50], from Peruvian alpaca faeces
        date: 2017-09-01
       words: 1613
      flesch: 51
     summary: Sequences of Alp11B strain were aligned and compared to that of each corresponding gene of RVA strains obtained from GenBank, by using MegAlign, which are available in the Lasergene software package (DNASTAR, Madison, WI). Discovery and molecular characterization of a group A rotavirus strain detected in an Argentinean vicuña (Vicugna vicugna) Candidate new rotavirus species in Schreiber's bats, Serbia Rotaviruses Molecular characterization of rotavirus isolated from alpaca (Vicugna pacos) crias with diarrhea in the Andean Region of Cusco MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets RotaC: a web-based tool for the complete genome classification of group A rotaviruses Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments Are human P[14] rotavirus strains the result of interspecies transmissions from sheep or other ungulates that belong to the mammalian order
    keywords: alpaca; rotavirus; rva; strain
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        item: #19 of 48
          id: cord-268968-0s6e6y8s
      author: Kim, You-Jin
       title: Rapid replacement of human respiratory syncytial virus A with the ON1 genotype having 72 nucleotide duplication in G gene
        date: 2014-05-10
       words: 5814
      flesch: 44
     summary: Intrapatient variation of the respiratory syncytial virus attachment protein gene Molecular characterization of human respiratory syncytial virus, 2010-2011: identification of genotype ON1 and a new subgroup B genotype in Thailand Prevalence and genetic characterization of respiratory syncytial virus (RSV) in hospitalized children in Korea Molecular epidemiology of human respiratory syncytial virus over three consecutive seasons in Latvia Viral and atypical bacterial detection in acute respiratory infection in children under five years Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus Current progress on development of respiratory syncytial virus vaccine Respiratory viruses in neonates hospitalized with acute lower respiratory tract infections Genetic diversity and molecular epidemiology of the G protein of subgroup A and B of respiratory syncytial viruses isolated over 9 consecutive epidemics in Korea Viral and host factors in human respiratory syncytial virus pathogenesis Genetic variation in attachment glycoprotein genes of human respiratory syncytial virus subgroups A and B in children in recent five consecutive years Bayesian phylogenetics with BEAUti and the BEAST 1.7 Predicting linear B-cell epitopes using string kernels Genetic variability of human respiratory syncytial virus A strains circulating in Ontario: a novel genotype with a 72 nucleotide G gene duplication Biological challenges and technological opportunities for respiratory syncytial virus vaccine development Respiratory syncytial virus-associated hospitalizations among children less than 24 months of age CD-HIT Suite: a web server for clustering and comparing biological sequences The G glycoprotein of human respiratory syncytial viruses of subgroups A and B: extensive sequence divergence between antigenically related proteins Advances in and the potential of vaccines for respiratory syncytial virus Displacement of predominant respiratory syncytial virus genotypes in Malaysia between Molecular evolution of attachment glycoprotein (G) gene in human respiratory syncytial virus detected in Japan Improved method for predicting linear Bcell epitopes Complete genome sequence of human respiratory syncytial virus genotype A with a 72-nucleotide duplication in the attachment protein G gene Antigenic structure, evolution and immunobiology of human respiratory syncytial virus attachment (G) protein Severe lower respiratory tract infection in early infancy and pneumonia hospitalizations among children Antibody response to the central unglycosylated region of the respiratory syncytial virus attachment protein in mice Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: a systematic review and meta-analysis Genetic diversity among respiratory syncytial viruses that have caused repeated infections in children from rural India JModelTest: phylogenetic model averaging Novel respiratory syncytial virus A Genotype EMBOSS: The European Molecular Biology Open Software Suite Epitopia: a web-server for predicting B-cell epitopes Respiratory syncytial virus: current progress in vaccine development Kinetics of the neutralizing antibody response to respiratory syncytial virus infections in a birth cohort The path to an RSV vaccine Emerging genotypes of human respiratory syncytial virus subgroup A among patients in Japan Improved method for linear B-cell epitope prediction using antigen's primary sequence Respiratory syncytial virus genetic and antigenic diversity Genetic diversity of the attachment protein of subgroup B respiratory syncytial viruses MEGA5: molecular evolutionary distance, and maximum parsimony methods The comparative genomics of human respiratory syncytial virus subgroups A and B: genetic variability and molecular evolutionary dynamics Ten years of global evolution of the human respiratory syncytial virus BA genotype with a 60-nucleotide duplication in the G protein gene Natural history of human respiratory syncytial virus inferred from phylogenetic analysis of the attachment (G) glycoprotein with a 60-nucleotide duplication Genetic analysis of attachment glycoprotein (G) gene in new genotype ON1 of human respiratory syncytial virus detected in Japan Replacement of previously circulating respiratory syncytial virus subtype B strains with the BA genotype in South Africa Palivizumab for immunoprophylaxis of respiratory syncytial virus (RSV) bronchiolitis in high-risk infants and young children: a systematic review and additional economic modelling of subgroup analyses Prediction of B-cell linear epitopes with a combination of support vector machine classification and amino acid propensity identification PAML 4: phylogenetic analysis by maximum likelihood Prophylactic and therapeutic testing of nicotiana-derived RSVneutralizing human monoclonal antibodies in the cotton rat model Genetic variability of respiratory syncytial viruses (RSV) prevalent in southwestern China from 2006 to 2009: Human respiratory syncytial virus (HRSV) is recognized by pediatricians as the most common cause of acute respiratory tract infections and is a leading cause of hospital admissions and death among children aged <5 years worldwide (Hall et al., 2013; Cho et al., 2013; Munywoki et al., 2013; Bezerra et al., 2011; Nair et al., 2010) .
    keywords: analysis; et al; gene; genotype; hrsv; on1; protein; sequences; syncytial; virus
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        item: #20 of 48
          id: cord-269187-lt0uo7q3
      author: Saha, Indrajit
       title: Genome-wide analysis of Indian SARS-CoV-2 genomes for the identification of genetic mutation and SNP
        date: 2020-07-11
       words: 2306
      flesch: 51
     summary: Further, it has been classified into three groups (a) cluster of mutation points if the mutation appears more than two times in consecutive genomic positions (b) point mutations as substitution, deletion and insertion that are not present in clusters (c) Single Nucleotide Polymorphism (SNP) that appeared more than 1% of the population of SARS-CoV-2 used in our study. In this section, we have discussed the source of data or genomic sequence of virus and methods used in systemic way to accomplish this task of finding mutation points as substitution, deletion, insertion as well as SNPs.
    keywords: cov-2; mutation; sars; sequence; substitution; virus
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        item: #21 of 48
          id: cord-269283-jm18lj5t
      author: Uddin, Md Bashir
       title: Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective
        date: 2020-07-01
       words: 2746
      flesch: 43
     summary: Immunogenicity and epitope conservancy analyses of coronavirus proteins were performed to determine the potential B-cell epitopes that would interact efficiently with B lymphocytes to initiate the immune response against specific viral pathogens The cross-checked conservancy analysis of SARS-CoV-2 antigenic epitopes showed significant conservancy with antigenic epitopes derived from SARS-CoV.
    keywords: coronavirus; cov-2; covid-19; novel; proteins; sars
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        item: #22 of 48
          id: cord-269353-wgeuh1i2
      author: Tian, Lin
       title: The adaptation of codon usage of +ssRNA viruses to their hosts
        date: 2018-06-02
       words: 2574
      flesch: 51
     summary: Codon usage biases of influenza virus The 'effective number of codons' used in a gene Comparative characterization analysis of synonymous codon usage bias in classical swine fever virus Analysis of the codon usage of the ORF2 gene of feline calicivirus Analysis of codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus (NPV) and its relation to evolution The distribution of synonymous codon choice in the translation initiation region of dengue virus Codon usage is an important determinant of gene expression levels largely through its effects on transcription This work was supported by Guangdong Natural Science Funds for Distinguished Young Scholar (2014A030306046). Because the virus relies on the host's cellular machinery for its replication, codon usage bias was suggested to play a role in the adaptation of a virus to its host.
    keywords: bstvs; codon; hosts; usage; viruses
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        item: #23 of 48
          id: cord-271818-bedfwdyt
      author: Afelt, Aneta
       title: Distribution of bat-borne viruses and environment patterns
        date: 2017-12-23
       words: 5723
      flesch: 48
     summary: In order to investigate if bat viruses can be found in any kind of environment or are associated with specific landscapes, we conducted a multivariate analysis of isolated bat viruses, bats and environments previously described (Lacroix et al., 2017a (Lacroix et al., , 2017b . The distribution pattern of bat population has been found to also impact the viral richness of the host (Henle et al., 2004; Meyer et al., 2008; Gay et al., 2014) .
    keywords: areas; bats; cambodia; cluster; cover; et al; fig; forest; fragmentation; index; lacroix; species
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        item: #24 of 48
          id: cord-271897-9oqzsd70
      author: Domanska-Blicharz, Katarzyna
       title: Molecular epidemiology of infectious bronchitis virus in Poland from 1980 to 2017
        date: 2020-01-07
       words: 6560
      flesch: 46
     summary: The recombination analysis showed that Polish strains are a mosaic of different parental viruses most likely resulting from recombination events involving different IBV lineages, most frequently GI-13 and GI-19. Irrespective of year of isolation and S1-dependent genotype, the genome sequences of Polish IBV strains showed the presence of six genes and 13 ORFs: 5′UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR, however their individual genes and putative proteins had different lengths.
    keywords: analysis; bronchitis; et al; genome; ibv; ibv strains; lineage; poland; polish; region; strains; virus
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        item: #25 of 48
          id: cord-276052-gk6n8slx
      author: Yadav, Pragya
       title: Isolation of Tioman virus from Pteropus giganteus bat in North-East region of India
        date: 2016-09-09
       words: 3010
      flesch: 44
     summary: During the survey for Nipah virus among bats at North-East region of India; Tioman virus (TioV), a new member of the Paramyxoviridae family was isolated from tissues of Pteropus giganteus bats for the first time in India. Emerging paramyxoviruses: molecular mechanisms and antiviral strategies Completion of the full-length genome sequence of Menangle virus: characterization of the polymerase gene and genomic 5-trailer region A negative staining method for high resolution electron microscopy of viruses Bats: important reservoir hosts of emerging viruses Nipah virus-associated encephalitis outbreak Tioman virus, a novel paramyxovirus isolated from fruit bats in Malaysia Isolation of Nipah virus from Malaysian island flying-foxes.
    keywords: bats; cells; human; india; pteropus; tiov; virus; viruses
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        item: #26 of 48
          id: cord-278465-tjjkz16y
      author: Wille, Michelle
       title: Urbanization and the dynamics of RNA viruses in Mallards (Anas platyrhynchos)
        date: 2017-03-18
       words: 5894
      flesch: 41
     summary: All viruses were identified as gammacoronaviruses, and fell into the clade dominated by wild bird viruses and those recovered from domestic ducks. In context of IAV, and to a lesser degree CoV and APMV-1, an assessment of virus prevalence and diversity in an urban population will further allow us to assess if dynamics in wild birds are reflected in an urban setting.
    keywords: avian; birds; cov; ducks; et al; fig; iav; influenza; mallards; prevalence; rna; viruses; wild
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        item: #27 of 48
          id: cord-278973-82n0d1dh
      author: Li, Zhijie
       title: Characterization and pathogenicity of a novel mammalian orthoreovirus from wild short-nosed fruit bats
        date: 2016-05-31
       words: 3743
      flesch: 48
     summary: Considering the diversity and wide distribution of bats and the potential for transmission of bat viruses to humans and other animals, continued surveillance of MRVs in all host species is urgently needed. Reovirus infection in rat lungs as a model to study the pathogenesis of viral pneumonia Pathogenesis of reovirus gastrointestinal and hepatobiliary disease Bat flight and zoonotic viruses Novel human reovirus isolated from children with acute necrotizing encephalopathy Pulau virus; a new member of the Nelson Bay orthoreovirus species isolated from fruit bats in Malaysia High similarity of novel orthoreovirus detected in a child hospitalized with acute gastroenteritisto mammalian orthoreoviruses found in bats in Europe Broome virus, a new fusogenic orthoreovirus species isolated from an Australian fruit bat Isolation and molecular characterization of a novel type 3 reovirus from a child with meningitis Isolation and identification of a natural reassortant mammalian orthoreovirus from least horseshoe bat in China Bats as a continuing source of emerging infections in humans Isolation and identification of bat viruses closely related to human, porcine, and mink orthoreoviruses This work was supported by funds from the National Natural Science Foundation of China (31402204), the State Key Laboratory of Veterinary Biotechnology (SKLVBP201421), and the Basic Scientific Research Operation Cost of State-leveled Public Welfare Scientific Research Courtyard (0302014011).
    keywords: b/03; bats; infection; mice; mrv; orthoreovirus; pfu; strain; virus
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        item: #28 of 48
          id: cord-279202-iyteg4h9
      author: Shesheer Kumar, Munpally
       title: Expression of alternate reading frame protein (F1) of hepatitis C virus in Escherichia coli and detection of antibodies for F1 in Indian patients
        date: 2008-01-05
       words: 2092
      flesch: 42
     summary: Recovery, persistence, and sequelae in hepatitis C virus infection: a perspective on long-term outcome Programmed ribosomal frameshifting in decoding the SARS-CoV genome Non-A, non-B hepatitis and the anti-HCV assay Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a +1 reading frame relative to the polyprotein Functional properties of a 16 kDa protein translated from an alternative open reading frame of the core encoding genomic region of hepatitis C virus Unusual multiple recoding events leading to alternative forms of hepatitis C virus core protein from genotype 1b Triple decoding of hepatitis C virus RNA by programmed translational frameshifting Expression and identification of hepatitis C virus polyprotein cleavage products Transmission of hepatitis C by intrahepatic inoculation with transcribed RNA Comparative studies of the core gene products of two different hepatitis C virus isolates: two alternative forms determined by a single amino acid substitution Differential subcellular localization of hepatitis C virus core gene products Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line Internal ribosome entry site-mediated translation in hepatitis C virus replication Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization Characterization of the expression of the hepatitis C virus F protein Viral heterogeneity of hepatitis C virus Processing and functions of hepatitis C virus proteins Molecular biology of hepatitis C virus Alternate translation occurs within the core coding region of the hepatitis C viral genome Evidence for a new hepatitis C virus antigen encoded in an overlapping reading frame Synthesis of a novel hepatitis C virus protein by ribosomal frame shift Hepatitis C virus f protein is a short lived protein associated with the endoplasmic reticulum Hepatitis C virus: an infectious molecular clone of a second major genotype (2a) and lack of viability of intertypic 1a and 2a chimeras MSK is highly grateful to the CSIR, Govt. of India, New Delhi, for the award of fellowship. This subcellular localization of HCV F1 protein is similar to that of the HCV core and NS5A proteins, raising the hypothesis that the F1 protein may participate in HCV morphogenesis or replication .
    keywords: hcv; hepatitis; protein
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        item: #29 of 48
          id: cord-279495-zxerb7de
      author: Liu, Xiaoli
       title: Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome
        date: 2012-11-21
       words: 5252
      flesch: 42
     summary: A filterable virus, distinct from that of laryngotracheitis, the cause of a respiratory disease of chicks Development and use of the H strain of avian infectious bronchitis virus from the Netherlands as a vaccine: a review An efficient ribosomal frame-shifting signal in the polymeraseencoding region of the coronavirus IBV Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism Commentary: a nomenclature for avian coronavirus isolates and the question of species status Severe acute respiratory syndrome vaccine development: experiences of vaccination against avian infectious bronchitis coronavirus Coronaviruses in poultry and other birds Coronavirus avian infectious bronchitis virus Location of the amino acid differences in the S1 spike glycoprotein subunit of closely related serotypes of infectious bronchitis virus Amino acids within hypervariable region 1 of avian coronavirus IBV (Massachusetts serotype) spike glycoprotein are associated with neutralization epitopes Infectious bronchitis Variations in the spike protein of the 793/B type of infectious bronchitis virus in the field and during alternate passage in chickens and embryonated eggs A cis-acting function for the coronavirus leader in defective interfering RNA replication Virus Taxonomy, Classification and Nomenclature of Viruses, Ninth Report of the International Committee on Taxonomy of Viruses, International Union of Microbiological Societies, Virology Division Molecular epidemiology and evolution of avian infectious bronchitis virus in Spain over a fourteen-year period The early history of infectious bronchitis Evidence for variable rates of recombination in the MHV genome Map locations of mouse hepatitis virus temperature sensitive mutants: confirmation of variable rates of recombination A hypervariable region within the 3 0 cis-acting element of the murine coronavirus genome is nonessential for RNA synthesis but affects pathogenesis A 15-year analysis of molecular epidemiology of avian infectious bronchitis coronavirus in China Biologic, antigenic, and full-length genomic characterization of a bovine-like coronavirus isolated from a giraffe Feline coronavirus type II strains 79-1683 and 79-1146 originate from a double recombination between feline coronavirus type I and canine coronavirus The present of viral subpopulations in an infectious bronchitis virus vaccine with differing pathogenicity -a preliminary study Recombinational histories of avian infectious bronchitis virus and turkey coronavirus Multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase A novel variant of infectious bronchitis virus resulting from recombination among three different strains The neutralizing characteristics of strains of infectious bronchitis virus as measured by the constant virus variable serum methods in chicken tracheal cultures Experimental evidence of recombination in coronavirus infectious bronchitis virus Molecular analysis of infectious bronchitis viruses isolated in Slovenia between 1990 and 2005: a retrospective study Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Origin and evolution of Georgia 98 (GA98), a new serotype of avian infectious bronchitis virus The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase RNA recombination in a coronavirus: recombination between viral genomic RNA and transfected RNA fragments Molecular characterization and pathogenicity of infectious bronchitis coronaviruses: complicated evolution and epidemiology in China caused by cocirculation of multiple types of infectious bronchitis coronaviruses Genetic diversity of avian infectious bronchitis coronavirus in recent years in China High-frequency RNA recombination of murine coronaviruses The molecular biology of coronaviruses Isolation and characterization of a novel antigenic subtype of infectious bronchitis virus serotype DE072 Stem-loop III in the 5 0 untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication Stem-loop IV in the 5 0 untranslated region is a cisacting element in bovine coronavirus defective interfering RNA replication Molecular characterization of avian infectious bronchitis virus strains from outbreaks in Argentina Infectious bronchitis virus in Jordanian chickens: seroprevalence and detection An apparently new respiratory disease of chicks Evolutionary implications of avian infectious bronchitis virus (AIBV) analysis Unique and conserved features of genome and proteonome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage Phylogenetic analysis of infectious bronchitis coronaviruses newly isolated in China, and pathogenicity and evaluation of protection induced by Mass serotype H120 vaccine against strains of the LX4-type (QX) Differential stepwise evolution of SARS coronavirus functional proteins in different host species Evidence of natural recombination within the S1 gene of infectious bronchitis virus Evolutionary aspects of recombination in RNA viruses Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups Virus-encoded proteinases and proteolytic processing in the Nidovirales The autocatalytic release of a putative RNA virus transcription factor from its polyprotein precursor involves two paralogous papain-like proteases that cleave the same peptide bond Genetic interactions between an essential 3 0 cis-acting RNA pseudoknot, replicase gene products, and the extreme 3 0 end of the mouse coronavirus genome Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.meegid.2012. The etiology of IB, which was first demonstrated by Beach and Schalm (1936) , is infectious bronchitis virus (IBV).
    keywords: bronchitis; coronavirus; gene; ibv; mass; strains; type; virus
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        item: #30 of 48
          id: cord-279836-lyvvtwvg
      author: Li, Huiping
       title: Molecular detection and genomic characteristics of bovine kobuvirus from dairy calves in China
        date: 2019-06-24
       words: 2286
      flesch: 51
     summary: Interestingly, three potential novel VP1 lineages were identified from 15 complete VP1 sequences, and a unique triple nucleotide insertion which can result in an aa insertion, was first observed in the 11/12 VP0 fragments with 660 bp long in this study, compared with known BKoV VP0 sequences. A pair of primers was designed based on known BKoV VP0 sequences, located at positions 1012-1671 in CHZ/China genome sequence.
    keywords: bkov; china; sequences; vp0; vp1
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        item: #31 of 48
          id: cord-288687-2dz8bu73
      author: Zhai, Bintao
       title: First detection and molecular identification of Borrelia species in Bactrian camel (Camelus bactrianus) from Northwest China
        date: 2018-06-26
       words: 3774
      flesch: 51
     summary: key: cord-288687-2dz8bu73 authors: Zhai, Bintao; Niu, Qingli; Liu, Zhijie; Yang, Jifei; Pan, Yuping; Li, Youquan; Zhao, Hongxi; Luo, Jianxun; Yin, Hong title: First detection and molecular identification of Borrelia species in Bactrian camel (Camelus bactrianus) from Northwest China date: 2018-06-26 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2018.06.028 sha: doc_id: 288687 cord_uid: 2dz8bu73 Comprehensive epidemiological surveys for Lyme disease have not been conducted for the Bactrian camel in China. Borrelia species are distributed throughout the world and are maintained in nature within various arthropod vectors and mammalian, avian or reptilian hosts (Brisson et al., 2012; Vollmer et al., 2011) .
    keywords: 16s; borrelia; burgdorferi; china; rrna; sequences; spp
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        item: #32 of 48
          id: cord-293588-7pflfznh
      author: Zang, Minghui
       title: Analysis of the codon usage of the ORF2 gene of feline calicivirus
        date: 2017-06-16
       words: 3066
      flesch: 51
     summary: This phenomenon which called 'codon usage bias', can be found in numerous species such as prokaryotes, eukaryotes and viruses (Liu et al., 2011) . In contrast to the RSCU value, the smaller the ENC value, the greater the extent of codon usage bias.
    keywords: bias; codon; codon usage; fcv; orf2; usage
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        item: #33 of 48
          id: cord-297530-7zbvgvk8
      author: Kühnert, Denise
       title: Phylogenetic and epidemic modeling of rapidly evolving infectious diseases
        date: 2011-08-31
       words: 12828
      flesch: 33
     summary: Recent population genetic models account for population dynamics e.g., in order to enhance the understanding of allele fixation processes and the importance of demographic stochasticity (Parsons and Quince, 2007; Champagnat and Lambert, 2007; Non-parametric coalescent methods provide greater flexibility by estimating the population size as a function of time directly from the sequence data and can be used for data exploration to guide the choice of parametric population models for further analysis.
    keywords: analysis; bayesian; coalescent; data; dynamics; epidemic; et al; evolution; history; host; inference; influenza; methods; model; population; rate; sampling; size; time; transmission; tree; virus
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        item: #34 of 48
          id: cord-297679-swmb19ty
      author: Wang, Yong
       title: Genetic and phylogenetic analysis of canine bufavirus from Anhui Province, Eastern China
        date: 2020-10-20
       words: 2005
      flesch: 49
     summary: Subsequently, BuV was found in wild shrews, megabats, wild rats, pigs, dogs, and cats (Diakoudi et al., 2019; Huang et al., 2020; Martella et al., 2018; Sasaki et al., 2016; Sasaki et al., 2015) . Phylogenetic analysis was performed using PhyloSuite software (Zhang et al., 2020) .
    keywords: bufavirus; cbuv
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        item: #35 of 48
          id: cord-299827-lxyo3z3u
      author: Di Martino, Barbara
       title: A novel feline norovirus in diarrheic cats
        date: 2015-12-29
       words: 3265
      flesch: 47
     summary: Based on the full-length VP1 amino acid sequence, NoVs have been divided into six genogroups (GI to GVI) and several genotypes (Zheng et al., 2006; Martella et al., 2009; Green, 2013) . Following strictly the outlines of Zheng's classification (Zheng et al., 2006) , we classified the novel feline NoV, together with the canine strains Viseu and FD53, as a genotype 2 (N 85% pairwise aa identity intergenotypes), within the genogroup GVI (N 55% pairwise aa identity intergenogroups).
    keywords: canine; cats; et al; feline; ita; norovirus; novs; samples; strain
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        item: #36 of 48
          id: cord-299989-p59u6qa0
      author: Zhang, Lei
       title: Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues
        date: 2020-06-18
       words: 1283
      flesch: 36
     summary: We defined a tumor sample with RPHM  100 for a given virus as virus-positive and examined ACE2 expression across seven tumor types with frequent viral presence according to the previous study (Cao et al., 2016) (Supplementary Table) . (Fig. 3) , suggesting potential viral roles of ACE2 expression in HNSC.
    keywords: ace2; expression
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        item: #37 of 48
          id: cord-302679-wytog9cv
      author: Panda, Somnath
       title: Bioinformatics analysis reveals four major hexon variants of human adenovirus type-3 (HAdV-3) as the potential strains for development of vaccine and siRNA-based therapeutics against HAdV-3 respiratory infections
        date: 2020-06-23
       words: 2180
      flesch: 44
     summary: This study was designed to evaluate HAdV-3 hexon variants for the selection of potential vaccine candidates and the use of hexon gene as a target for designing siRNA that can be used as a therapy. Hexon variants were selected based on their duration of circulation, co-circulation and worldwide distribution.
    keywords: 3hv-1; hexon; sirnas; vaccine; variants
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        item: #38 of 48
          id: cord-311144-tumtzad8
      author: Franco-Muñoz, Carlos
       title: Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America
        date: 2020-09-17
       words: 2829
      flesch: 40
     summary: Recombinant proteins or synthetic peptides of SARS-CoV-2 are widely explored as alternatives to be used in serological tests and therapeutics against SARS-CoV-2 and related Betacoronavirus (Du et al., 2009; Jacofsky et al., 2020) , considering that S and N proteins are the major immunogenic proteins of SARS and MERS coronavirus and the first choice for producing recombinant antigens (Yan et al., 2020) . J o u r n a l P r e -p r o o f Journal Pre-proof Furthermore, non-synonymous mutations in the S and N proteins have been reported, their implications in the potential emergence of antigenically distinct and/or more virulent strains remain to be studied, although it was reported that mutations in the receptor-binding domain (RBD) at the S protein of SARS-CoV related viruses disrupt the antigenic structure and binding activity of RBD to ACE2 (Du et al., 2009 )
    keywords: colombia; proteins; sars; sequences; substitutions
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        item: #39 of 48
          id: cord-318577-04jsj9sb
      author: Bodnar, Livia
       title: Identification of a novel canine norovirus
        date: 2017-04-24
       words: 3743
      flesch: 44
     summary: NoVs have also been identified in several mammalian species, including cows, pigs, lion, cats, dogs, bats, sea lions and harbor porpoises (DeGraaf et al., 2017; Li et al., 2011; Martella et al., 2007 Martella et al., , 2008 Pinto et al., 2012; Scipioni et al., 2008; Sugieda et al., 1998; Wu et al., 2016) . The canine NoV strain Bari/91/2007/ITA, resembles GIV.2 NoVs in its pol gene (pol b) whilst it possesses a GVI.1 capsid (Martella et al., 2009 ).
    keywords: canine; dogs; et al; ita; norovirus; nov; novs; samples; strains
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        item: #40 of 48
          id: cord-318625-hf7fgtnp
      author: Vashi, Yoya
       title: Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens
        date: 2020-05-27
       words: 2926
      flesch: 46
     summary: The amino acid sequences (n=98) of S protein available at the time of study on targeted SARS-CoV-2 were downloaded from the National Centre for Biotechnological Information (NCBI) database. In the present study, peptide segments were identified on S proteins for the development of diagnostics and vaccines against SARS-CoV-2.
    keywords: binding; cell; cov-2; epitopes; protein; sars
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        item: #41 of 48
          id: cord-319399-r5hgfsxz
      author: Chakraborty, Supriyo
       title: Japanese encephalitis virus: A multi-epitope loaded peptide vaccine formulation using reverse vaccinology approach
        date: 2019-11-06
       words: 5157
      flesch: 43
     summary: Ten epitopes, i.e. NARDRS of E protein; KRSRRS, SKRSRR, DPEDVD and GNDPED of prM protein; KHNRRE and KECPDE of NS1 protein; GDRQEE of NS3 protein; and REKRPR and RRARRE of NS5 protein contained a single aliphatic amino acid. Seven epitopes, i.e. EPPFGDSY of E protein, NDPEDVDC of prM protein, TKEC-PDEH and ECPDEHRA of NS1 protein, DTPSPKPC of NS3 protein, and HKDPEHPY and FYKPSEPS of NS5 protein contained a single aliphatic amino acid.
    keywords: amino; cell; encephalitis; epitopes; jev; peptide; protein; vaccine; virus
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        item: #42 of 48
          id: cord-325679-4lfpy84d
      author: Niu, Ting-Jiang
       title: Detection and genetic characterization of kobuvirus in cats: The first molecular evidence from Northeast China
        date: 2018-12-06
       words: 4835
      flesch: 45
     summary: Then, we analyzed the amino acid mutation sites in the VP1 gene between the eight sequences and other FeKoV sequences previously described, and discovered that three identical amino acid substitutions at amino acid positions 182 (T → A), 235 (P → S) and 241(S → T) were exhibited in all sequences identified in this study (Table 3) . Bold text indicates the identical amino acid substitutions for FeKoV sequences that identified in the present study.
    keywords: acid; amino; cats; et al; fekov; kobuvirus; sequences; strains
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        item: #43 of 48
          id: cord-331237-t3z1hbox
      author: Ogawa, Hirohito
       title: Molecular epidemiology of pathogenic Leptospira spp. in the straw-colored fruit bat (Eidolon helvum) migrating to Zambia from the Democratic Republic of Congo
        date: 2015-03-16
       words: 2818
      flesch: 49
     summary: key: cord-331237-t3z1hbox authors: Ogawa, Hirohito; Koizumi, Nobuo; Ohnuma, Aiko; Mutemwa, Alisheke; Hang’ombe, Bernard M.; Mweene, Aaron S.; Takada, Ayato; Sugimoto, Chihiro; Suzuki, Yasuhiko; Kida, Hiroshi; Sawa, Hirofumi title: Molecular epidemiology of pathogenic Leptospira spp. Here, we investigated the prevalence and diversity of pathogenic Leptospira spp.
    keywords: bats; flab; helvum; leptospira; spp; zambia
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        item: #44 of 48
          id: cord-331503-whw2pq1f
      author: Torres, Orlando A.
       title: Role of the IFNG +874T/A polymorphism in Chagas disease in a Colombian population
        date: 2010-03-30
       words: 3097
      flesch: 33
     summary: None. Transforming growth factor beta 1 (TGFbeta1) gene polymorphisms and Chagas disease susceptibility in Peruvian and Colombian patients Chemokine receptor CCR5 polymorphisms and Chagas' disease cardiomyopathy Regulation of Trypanosoma cruzi infection in mice by gamma interferon and interleukin 10: role of NK cells The interferon gamma gene polymorphism +874 A/T is associated with severe acute respiratory syndrome Immunological imbalance between IFN-gamma and IL-10 levels in the sera of patients with the cardiac form of Chagas disease Arlequin (version 3.0): an integrated software package for population genetics data analysis Interleukin-1 gene cluster polymorphism in chagas disease in a Colombian case-control study Evidence that development of severe cardiomyopathy in human Chagas' disease is due to a Th1-specific immune response Comparison of four serological tests for the diagnosis of Chagas disease in a Colombian endemic area Association between the tumor necrosis factor locus and the clinical outcome of Leishmania chagasi infection Chagas' disease and the autoimmunity hypothesis The relative contribution of antibody production and CD8+ T cell function to immune control of Trypanosoma cruzi Interferon-gamma and interleukin-10 gene polymorphisms in pulmonary tuberculosis TGF-beta regulates pathology but not tissue CD8+ T cell dysfunction during experimental Trypanosoma cruzi infection Assessment of aryl hydrocarbon receptor complex interactions using pBEVY plasmids: expressionvectors with bi-directional promoters for use in Saccharomyces cerevisiae HLA haplotypes are associated with differential susceptibility to Trypanosoma cruzi infection IFNG +874T/A, IL10-1082G/A and TNF À308G/A polymorphisms in association with tuberculosis susceptibility: a meta-analysis study Clinical and epidemiological aspects of Chagas disease In vitro production of IFN-gamma correlates with CA repeat polymorphism in the human IFN-gamma gene A single nucleotide polymorphism in the first intron of the human IFN-gamma gene: absolute correlation with a polymorphic CA microsatellite marker of high IFN-gamma production The monocyte chemoattractant protein-1 gene polymorphism is associated with cardiomyopathy in human chagas disease Association of cytokine genetic polymorphism with hepatitis B infection evolution in adult patients Clinical management of chronic Chagas cardiomyopathy Tumor necrosis factor-alpha promoter polymorphism in Mexican patients with Chagas' disease Interleukin 10 and interferon gamma regulation of experimental Trypanosoma cruzi infection Tumor necrosis factor alpha mediates resistance to Trypanosoma cruzi infection in mice by inducing nitric oxide production in infected gamma interferon-activated macrophages Association of the macrophage migration inhibitory factor À173G/C polymorphism with Chagas disease Endogenous IFN-gamma is required for resistance to acute Trypanosoma cruzi infection in mice Control of Chagas disease Control of Chagas disease. Contrary to expectations, no significant differences were observed in the distribution of alleles or genotypes of the IFNG +874T/A polymorphism between cardiomyopathic and asymptomatic patients with Chagas disease, indicating no influence of this polymorphism on Chagas disease progression.
    keywords: chagas; disease; ifng; patients; polymorphism; susceptibility
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        item: #45 of 48
          id: cord-333712-sdtxi8xw
      author: Yu, Ping
       title: Geographical structure of bat SARS-related coronaviruses
        date: 2019-02-06
       words: 3666
      flesch: 35
     summary: Moreover, compared with other bat SARSr-CoVs, some viruses such as WIV1 and WIV16 had an additional ORF (named ORFx) in their gene organization, involved in modulation of the host immune response (Hu et al., 2017; Yang et al., 2015; Zeng et al., 2016) . In order to identify the relationships between bat CoVs and their hosts, a tanglegram was made connecting the RdRp phylogeny of the SARSr-CoVs and the cytochrome b (CytB) phylogeny of their hosts ( Fig. 2; Table S2 ).
    keywords: bat; bats; coronavirus; covs; et al; human; sars
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        item: #46 of 48
          id: cord-338723-3vm23fgy
      author: Lee, In-Hee
       title: A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations
        date: 2020-08-26
       words: 2788
      flesch: 45
     summary: key: cord-338723-3vm23fgy authors: Lee, In-Hee; Lee, Ji-Won; Kong, Sek Won title: A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations date: 2020-08-26 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2020.104507 sha: doc_id: 338723 cord_uid: 3vm23fgy The COVID-19 pandemic highlighted healthcare disparities in multiple countries. For ACE2, we investigated genetic variants in the residues on the interface to SARS-CoV-2 RBD from recent structural analyses (Hussain et al., 2020; Lan et al., 2020; Shang et al., 2020; Wrapp et al., 2020; Yan et al., 2020) .
    keywords: ace2; populations; sars; variants
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        item: #47 of 48
          id: cord-339120-38rsfs0d
      author: Yan, Nan
       title: Genome analysis of a G9P[23] group A rotavirus isolated from a dog with diarrhea in China
        date: 2019-02-20
       words: 2373
      flesch: 49
     summary: All genome segments except the VP1 gene were closely related to the genes from porcine RVA strains or porcine-like human RVA strains. MH910063-MH910073. Identification of enteric viruses circulating in a dog population with low vaccine coverage Structure of rotavirus outer-layer protein vp7 bound with a neutralizing fab Quantitation of canine coronavirus RNA in the faeces of dogs by TaqMan RT-PCR A realtime PCR assay for rapid detection and quantitation of canine parvovirus type 2 in the feces of dogs Completely genomic and evolutionary characteristics of human-dominant G9P group a rotavirus strains in Yunnan Molecular epidemiology of Rotavirus A, causing acute gastroenteritis hospitalizations among children in Nha Trang Detection of canine distemper virus in dogs by real-time RT-PCR genetic relationships with other G9 strains and detection of a new G9 subtype Infectious diseases of the dog and cat Identification and characterization of a human G9P[23] rotavirus strain from a child with diarrhoea in Thailand: evidence for porcine-to-human interspecies transmission Molecular characterization of unusual human g5p[6] rotaviruses identified in China Molecular epidemiology of G9 rotavirus strains in children with diarrhoea hospitalized in mainland China from Rare g3p[3] rotavirus strain detected in Brazil: possible human-canine interspecies transmission RotaC: a web-based tool for the complete genome classification of group a rotaviruses Full genome-based classification of rotaviruses reveals a common origin between human Wa-Like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains Identification of co-infection by rotavirus and parvovirus in dogs with gastroenteritis in Mexico Detection of rotavirus species a, b and c in domestic mammalian animals with diarrhoea and genotyping of bovine species a rotavirus strains Full-genome sequencing of a hungarian canine G3P[3] rotavirus a strain reveals high genetic relatedness with a historic italian human strain Genetic heterogeneity, evolution and recombination in emerging G9 rotaviruses Molecular characterization of a rare G9P[23] porcine rotavirus isolate from China A bovine G8P[1] group a rotavirus isolated from an asymptomatically infected dog Porcine rotaviruses: epidemiology, immune responses and control strategies Full genomic analysis of a porcine-bovine reassortant G4P[6] rotavirus strain R479 isolated from an infant in China
    keywords: g9p[23; rotavirus; rva; sccd; strain
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        item: #48 of 48
          id: cord-339259-4oi7slk9
      author: Naguib, Mahmoud M.
       title: Full genome sequence analysis of a newly emerged QX-like infectious bronchitis virus from Sudan reveals distinct spots of recombination
        date: 2016-10-26
       words: 4021
      flesch: 41
     summary: The Veterinary record Complete genomic sequence analysis of infectious bronchitis virus ark dpi strain and its evolution by recombination Isolation and characterization of infectious bronchitis virus strain 4/91 from commercial layer chickens in the sudan Serosurveillance study on avian infectious bronchitis virus in Sudan Mechanisms of coronavirus cell entry mediated by the viral spike protein Development and evaluation of a real-time taqman rt-pcr assay for the detection of infectious bronchitis virus from infected chickens Severe acute respiratory syndrome vaccine development: Experiences of vaccination against avian infectious bronchitis coronavirus Coronaviruses in poultry and other birds Coronavirus avian infectious bronchitis virus Infectious bronchitis virus: Avian pathology: journal of the W Avian infectious bronchitis virus Review of infectious bronchitis virus around the world A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains An infectious bat-derived chimeric influenza virus harbouring the entry machinery of an influenza a virus Mafft multiple sequence alignment software version 7: improvements in performance and usability Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data Evolution of infectious bronchitis virus in Taiwan: characterisation of rna recombination in the nucleocapsid gene Recombination in large rna viruses A new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and non-vaccinated flocks in China.
    keywords: bronchitis; genome; ibv; like; recombination; sudan; virus
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