Circulation, genomic characteristics, and evolutionary dynamics of class I Newcastle disease virus in China

References

• Bucko M, and Gieger S. Newcastle Disease (wild birds) (Infection with). OIE. 2019. https://www.oie.int/en/document/newcastle-disease-virus-wild-birds-infection-with/.
   Google Scholar
• OIE. 2018. Newcastle Disease (Infection with Newcastle Disease Virus). OIE TErrestrial Manual Chapter, 3.14.
   Google Scholar
• Ganar K, Das M, Sinha S, et al. Newcastle disease virus: current status and our understanding. Virus Res. 2014;184:71–81.
   PubMed Web of Science ®Google Scholar
• Alexander DJ, Aldous EW, Fuller CM. The long view: a selective review of 40 years of Newcastle disease research. Avian Pathol. 2012;41(4):329–335.
   PubMed Web of Science ®Google Scholar
• Rima B, Balkema-Buschmann A, Dundon WG, et al. ICTV Virus Taxonomy Profile: paramyxoviridae. J Gen Virol. 2019;100(12):1593–1594.
   PubMed Web of Science ®Google Scholar
• Kattenbelt JA, Stevens MP, Gould AR. Sequence variation in the Newcastle disease virus genome. Virus Res. 2006;116(1–2):435–446.
   Web of Science ®Google Scholar
• Dortmans JCFM, Koch G, Rottier P, et al. Virulence of Newcastle disease virus: what is known so far? Vet Res. 2011;42(1):122.
   PubMed Web of Science ®Google Scholar
• Absalon AE, Cortes-Espinosa DV, Lucio E, et al. Epidemiology, control, and prevention of Newcastle disease in endemic regions: latin America. Trop Anim Health Prod. 2019;51(5):1033–1048.
   PubMed Web of Science ®Google Scholar
• Pordany AB, Wehmann E, Herczeg J, et al. Identification and grouping of Newcastle disease virus strains by restriction site analysis of a region from the F gene. Arch Virol. 1996;141(2):243–261.
   PubMed Web of Science ®Google Scholar
• Dimitrov KM, Abolnik C, Afonso CL, et al. Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus. Infect Genet Evol. 2019;74:103917.
   PubMed Web of Science ®Google Scholar
• Diel DG, da Silva Lh, Liu H, et al. Genetic diversity of avian paramyxovirus type 1: proposal for a unified nomenclature and classification system of Newcastle disease virus genotypes. Infect Genet Evol. 2012;12(8):1770–1779.
   PubMed Web of Science ®Google Scholar
• Schirrmacher V. Fifty Years of Clinical Application of Newcastle Disease Virus: time to Celebrate! Biomedicines. 2016;4(3):16.
   PubMedGoogle Scholar
• Wang J, Lv Y, Zhang Y, et al. Genomic Characterizations of a Newcastle Disease Virus Isolated from Ducks in Live Bird Markets in China. PLoS One. 2016;11(7):e0158771.
   PubMed Web of Science ®Google Scholar
• Zhu J, Xu H, Liu J, et al. Surveillance of avirulent Newcastle disease viruses at live bird markets in Eastern China during 2008–2012 reveals a new sub-genotype of class I virus. Virol J. 2014;11(1). DOI:10.1186/s12985-014-0211-2
   Google Scholar
• Meng C, Qiu X, Yu S, et al. Evolution of Newcastle Disease Virus Quasispecies Diversity and Enhanced Virulence after Passage through Chicken Air Sacs. J Virol. 2016;90(4):2052–2063.
   PubMed Web of Science ®Google Scholar
• Venkatesh D, Poen MJ, Bestebroer TM, et al. Avian Influenza Viruses in Wild Birds: virus Evolution in a Multihost Ecosystem. J Virol. 2018;92(15). DOI:10.1128/JVI.00433-18
   PubMed Web of Science ®Google Scholar
• Hoque MA, Burgess GW, Karo-Karo D, et al. Monitoring of wild birds for Newcastle disease virus in north Queensland, Australia. Prev Vet Med. 2012;103(1):49–62.
   PubMed Web of Science ®Google Scholar
• Cardenas Garcia S, Navarro Lopez R, Morales R, et al. Molecular epidemiology of Newcastle disease in Mexico and the potential spillover of viruses from poultry into wild bird species. Appl Environ Microbiol. 2013;79(16):4985–4992.
   PubMed Web of Science ®Google Scholar
• Liu H, Xiong C, Chen J, et al. Two genetically diverse H7N7 avian influenza viruses isolated from migratory birds in central China. Emerg Microbes Infect. 2018;7(1):62.
   PubMedGoogle Scholar
• Chen H, Smith GJD, Li KS, et al. Establishment of multiple sublineages of H5N1 influenza virus in Asia: implications for pandemic control. Proc Natl Acad Sci U S A. 2006;103(8):2845–2850.
   PubMed Web of Science ®Google Scholar
• Ni M, Chen C, Qian J, et al. Intra-host dynamics of Ebola virus during 2014. Nat Microbiol. 2016;1(11):16151.
   PubMed Web of Science ®Google Scholar
• Chen S, Zhou Y, Chen Y, et al. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–i890.
   PubMed Web of Science ®Google Scholar
• Li D, Luo R, Liu CM, et al. MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods. 2016;102:3–11.
   PubMed Web of Science ®Google Scholar
• Martin DP, Lemey P, Lott M, et al. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics. 2010;26(19):2462–2463.
   PubMed Web of Science ®Google Scholar
• Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–1797.
   PubMed Web of Science ®Google Scholar
• Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–1313.
   PubMed Web of Science ®Google Scholar
• Bouckaert R, Heled J, Kuhnert D, et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2014;10(4):e1003537.
   PubMed Web of Science ®Google Scholar
• Rambaut A, Drummond AJ, Xie D, et al. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Syst Biol. 2018;67(5):901–904.
   PubMed Web of Science ®Google Scholar
• Bielejec F, Baele G, Vrancken B, et al. SpreaD3: interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes. Mol Biol Evol. 2016;33(8):2167–2169.
   PubMed Web of Science ®Google Scholar
• Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359.
   PubMed Web of Science ®Google Scholar
• Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. BIOINFORMATICS. 2009;25(16):2078–2079.
   PubMed Web of Science ®Google Scholar
• Crooks GE, Hon G, Chandonia JM, et al. WebLogo: a sequence logo generator. Genome Res. 2004;14(6):49–62.
   Web of Science ®Google Scholar
• Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 1997;13(5):555–556.
   PubMedGoogle Scholar
• Kumar CS, Kumar S. Species based synonymous codon usage in fusion protein gene of Newcastle disease virus. PLoS One. 2014;9(12):e114754.
   PubMed Web of Science ®Google Scholar
• Boere G, Galbraith CA, Stroud DA 2006. Scottish natural heritage (agency): waterbirds around the world: a global overview of the conservation, management and research of the world’s waterbird flyways. The Stationery Office: Edinburgh.
   Google Scholar
• Yuan P, Paterson RG, Leser GP, et al. Structure of the ulster strain Newcastle disease virus hemagglutinin-neuraminidase reveals auto-inhibitory interactions associated with low virulence. PLoS Pathog. 2012;8(8):e1002855.
   PubMed Web of Science ®Google Scholar
• Rehman ZU, Meng C, Sun Y, et al. Pathobiology of Avian avulavirus 1: special focus on waterfowl. Vet Res. 2018;49(1):94.
   PubMedGoogle Scholar
• Miller PJ, Decanini EL, Afonso CL. Newcastle disease: evolution of genotypes and the related diagnostic challenges. Infect Genet Evol. 2010;10(1):26–35.
   PubMed Web of Science ®Google Scholar
• Ramey AM, Reeves AB, Ogawa H, et al. Genetic diversity and mutation of avian paramyxovirus serotype 1 (Newcastle disease virus) in wild birds and evidence for intercontinental spread. Arch Virol. 2013;158(12):2495–2503.
   PubMed Web of Science ®Google Scholar
• Lu X, Wang X, Zhan T, et al. Surveillance of Class I Newcastle Disease Virus at Live Bird Markets and Commercial Poultry Farms in Eastern China Reveals the Epidemic Characteristics. Virol Sin. 2021. DOI:10.1007/s12250-021-00357-z
   Web of Science ®Google Scholar
• Chen L, Song J, Liu H, et al. Phylodynamic analyses of class I Newcastle disease virus isolated in China. Transbound Emerg Dis. 2020. DOI:10.1111/tbed.13785
   Web of Science ®Google Scholar
• Domingo E, Sheldon J, Perales C. Viral quasispecies evolution. Microbiol Mol Biol Rev. 2012;76(2):159–216.
   PubMed Web of Science ®Google Scholar
• Granoff A. Studies on mixed infection with Newcastle disease virus. III. Activation of nonplaque-forming virus by plaque-forming virus. Virology. 1961;14(1):143–144.
   PubMed Web of Science ®Google Scholar
• Kattenbelt JA, Stevens MP, Selleck PW, et al. Analysis of Newcastle disease virus quasispecies and factors affecting the emergence of virulent virus. Arch Virol. 2010;155(10):1607–1615.
   PubMed Web of Science ®Google Scholar
• McGinnes L, Sergel T, Morrison TG. Mutations in the Transmembrane Domain of the HN Protein of Newcastle Disease Disease Virus Affect the Structure and Activity of the Protein. VIROLOGY. 1993;196(1):101–110.
   PubMed Web of Science ®Google Scholar
• Dortmans JC, Rottier PJ, Koch G, et al. The viral replication complex is associated with the virulence of Newcastle disease virus. J Virol. 2010;84(19):10113–10120.
   PubMed Web of Science ®Google Scholar
• Madansky CH, Bratt MA. Noncytopathic mutants of Newcastle disease virus are defective in virus-specific RNA synthesis. J Virol. 1981;37(1):317–327.
   PubMed Web of Science ®Google Scholar
• Dolan PT, Whitfield ZJ, Andino R. Mapping the Evolutionary Potential of RNA Viruses. Cell Host Microbe. 2018;23(4):435–446.
   PubMed Web of Science ®Google Scholar