Live bird markets as evolutionary epicentres of H9N2 low pathogenicity avian influenza viruses in Korea

References

• Webster RG, Bean WJ, Gorman OT, et al. Evolution and ecology of influenza A viruses. Microbiol Rev. 1992 Mar;56(1):152–179. doi: 10.1128/MMBR.56.1.152-179.1992
   PubMedGoogle Scholar
• Lee DH, Song CS. H9N2 avian influenza virus in Korea: evolution and vaccination. Clin Exp Vaccine Res. 2013 Jan;2(1):26–33. doi: 10.7774/cevr.2013.2.1.26
   PubMedGoogle Scholar
• Wei K, Li Y. Global genetic variation and transmission dynamics of H9N2 avian influenza virus. Transbound Emerg Dis. 2018 Apr;65(2):504–517. doi: 10.1111/tbed.12733
   PubMed Web of Science ®Google Scholar
• Guan Y, Shortridge KF, Krauss S, et al. H9N2 influenza viruses possessing H5N1-like internal genomes continue to circulate in poultry in southeastern China. J Virol. 2000 Oct;74(20):9372–9380. doi: 10.1128/JVI.74.20.9372-9380.2000
   PubMed Web of Science ®Google Scholar
• Lin YP, Shaw M, Gregory V, et al. Avian-to-human transmission of H9N2 subtype influenza A viruses: relationship between H9N2 and H5N1 human isolates. Proc Natl Acad Sci USA. 2000 Aug;97(17):9654–9658. doi: 10.1073/pnas.160270697
   PubMed Web of Science ®Google Scholar
• Lam TT-Y, Wang J, Shen Y, et al. The genesis and source of the H7N9 influenza viruses causing human infections in China. Nature. 2013 Oct 10;502(7470):241–244. doi: 10.1038/nature12515
   PubMed Web of Science ®Google Scholar
• Liu M, Li X, Yuan H, et al. Genetic diversity of avian influenza A (H10N8) virus in live poultry markets and its association with human infections in China. Sci Rep. 2015 Jan;5:7632. doi: 10.1038/srep07632
   PubMed Web of Science ®Google Scholar
• Pu J, Wang S, Yin Y, et al. Evolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus. Proc Natl Acad Sci USA. 2015 Jan;112(2):548–553. doi: 10.1073/pnas.1422456112
   PubMed Web of Science ®Google Scholar
• Iqbal M, Yaqub T, Reddy K, et al. Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. PLoS One. 2009 Jun;4(6):e5788. doi: 10.1371/journal.pone.0005788
   PubMed Web of Science ®Google Scholar
• Shanmuganatham K, Feeroz MM, Jones-Engel L, et al. Genesis of avian influenza H9N2 in Bangladesh. Emerg Microbes Infect. 2014 Dec;3(12):e88.
   PubMedGoogle Scholar
• Dong G, Xu C, Wang C, et al. Reassortant H9N2 influenza viruses containing H5N1-like PB1 genes isolated from black-billed magpies in Southern China. PLoS One. 2011;6(9):e25808. doi: 10.1371/journal.pone.0025808
   PubMed Web of Science ®Google Scholar
• Seiler P, Kercher L, Feeroz MM, et al. H9N2 influenza viruses from Bangladesh: transmission in chicken and New World quail. Influenza Other Respir Viruses. 2018 Nov;12(6):814–817. doi: 10.1111/irv.12589
   PubMed Web of Science ®Google Scholar
• Shanmuganatham KK, Jones JC, Marathe BM, et al. The replication of Bangladeshi H9N2 avian influenza viruses carrying genes from H7N3 in mammals. Emerg Microbes Infect. 2016 Apr 20;5:1–12. doi: 10.1038/emi.2016.29
   PubMed Web of Science ®Google Scholar
• Mo IP, Song CS, Kim KS, et al. An occurrence of non-highly pathogenic avian influenza in Korea Avian Dis. In: Proceedings of the 4th International Symposium on Avian Influenza; Vol. 47; 1998. p. 379–383.
   Google Scholar
• Lee C-W, Song C-S, Lee Y-J, et al. Sequence analysis of the hemagglutinin gene of H9N2 Korean avian influenza viruses and assessment of the pathogenic potential of isolate MS96. Avian Dis. 2000 Jul-Sep;44(3):527–535. doi: 10.2307/1593091
   PubMed Web of Science ®Google Scholar
• Choi YK, Seo SH, Kim JA, et al. Avian influenza viruses in Korean live poultry markets and their pathogenic potential. Virology. 2005 Feb;332(2):529–537. doi: 10.1016/j.virol.2004.12.002
   PubMed Web of Science ®Google Scholar
• Lee Y-J, Shin J-Y, Song M-S, et al. Continuing evolution of H9 influenza viruses in Korean poultry. Virology. 2007 Mar;359(2):313–323. doi: 10.1016/j.virol.2006.09.025
   PubMed Web of Science ®Google Scholar
• Lee HJ, Kwon JS, Lee DH, et al. Continuing evolution and interspecies transmission of influenza viruses in live bird markets in Korea. Avian Dis. 2010 Mar;54(1 Suppl):738–748. doi: 10.1637/8785-040109-ResNote.1
   PubMed Web of Science ®Google Scholar
• Moon HJ, Song MS, Cruz DJM, et al. Active reassortment of H9 influenza viruses between wild birds and live-poultry markets in Korea. Arch Virol. 2010 Feb;155(2):229–241. doi: 10.1007/s00705-009-0577-4
   PubMed Web of Science ®Google Scholar
• Lee D-H, Fusaro A, Song C-S, et al. Poultry vaccination directed evolution of H9N2 low pathogenicity avian influenza viruses in Korea. Virology. 2016 Jan;488:225–231. doi: 10.1016/j.virol.2015.11.023
   PubMed Web of Science ®Google Scholar
• Chrzastek K, Lee D-H, Smith D, et al. Use of sequence-independent, single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses. Virology. 2017 Sep;509:159–166. doi: 10.1016/j.virol.2017.06.019
   PubMed Web of Science ®Google Scholar
• Afgan E, Baker D, Batut B, et al. The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018 Jul;46(W1):W537–W544. doi: 10.1093/nar/gky379
   PubMed Web of Science ®Google Scholar
• Fu L, Niu B, Zhu Z, et al. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012 Dec;28(23):3150–3152. doi: 10.1093/bioinformatics/bts565
   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. doi: 10.1093/nar/gkh340
   PubMed Web of Science ®Google Scholar
• Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014 May;30(9):1312–1313. doi: 10.1093/bioinformatics/btu033
   PubMed Web of Science ®Google Scholar
• Rambaut A, Lam TT, Max Carvalho L, et al. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016 Jan;2(1):vew007. doi: 10.1093/ve/vew007
   PubMed Web of Science ®Google Scholar
• Posada D. Jmodeltest: phylogenetic model averaging. Mol Biol Evol. 2008 Jul;25(7):1253–1256. doi: 10.1093/molbev/msn083
   PubMed Web of Science ®Google Scholar
• Suchard MA, Lemey P, Baele G, et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 2018 Jan;4(1):vey016. doi: 10.1093/ve/vey016
   PubMed Web of Science ®Google Scholar
• Suchard MA, Weiss RE, Sinsheimer JS. Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol. 2001 Jun;18(6):1001–1013. doi: 10.1093/oxfordjournals.molbev.a003872
   PubMed Web of Science ®Google Scholar
• Bahl J, Pham TT, Hill NJ, et al. Ecosystem interactions underlie the spread of avian influenza A viruses with pandemic potential. PLoS Pathog. 2016 May;12(5):e1005620. doi: 10.1371/journal.ppat.1005620
   PubMed Web of Science ®Google Scholar
• Minin VN, Suchard MA. Counting labeled transitions in continuous-time Markov models of evolution. J Math Biol. 2007;56(3):391–412. doi: 10.1007/s00285-007-0120-8
   PubMed Web of Science ®Google Scholar
• Kwon YK, Lee YJ, Choi JG, et al. An outbreak of avian influenza subtype H9N8 among chickens in South Korea. Avian Pathol. 2006 Dec;35(6):443–447. doi: 10.1080/03079450601009571
   PubMed Web of Science ®Google Scholar
• Lu L, Lycett SJ, Leigh Brown AJ. Reassortment patterns of avian influenza virus internal segments among different subtypes. BMC Evol Biol. 2014 Jan;14:16. doi: 10.1186/1471-2148-14-16
   PubMed Web of Science ®Google Scholar
• Dugan VG, Chen R, Spiro DJ, et al. The evolutionary genetics and emergence of avian influenza viruses in wild birds. PLoS Pathog. 2008 May;4(5):e1000076. doi: 10.1371/journal.ppat.1000076
   PubMed Web of Science ®Google Scholar
• Zeldovich KB, Liu P, Renzette N, et al. Positive selection drives preferred segment combinations during influenza virus reassortment. Mol Biol Evol. 2015 Jun;32(6):1519–1532. doi: 10.1093/molbev/msv044
   PubMed Web of Science ®Google Scholar
• Yan L, Liu Q, Su X, et al. Pathogenicity of reassortant H9 influenza viruses with different NA genes in mice and chickens. Vet Res. 2016 Jun;47(1):67. doi: 10.1186/s13567-016-0352-y
   PubMed Web of Science ®Google Scholar
• Choi J-G, Kang H-M, Kim M-C, et al. Genetic relationship of H3 subtype avian influenza viruses isolated from domestic ducks and wild birds in Korea and their pathogenic potential in chickens and ducks. Vet Microbiol. 2012 Mar;155(2-4):147–157. doi: 10.1016/j.vetmic.2011.08.028
   PubMed Web of Science ®Google Scholar
• Kim H-R, Park C-K, Oem J-K, et al. Characterization of H5N2 influenza viruses isolated in South Korea and their influence on the emergence of a novel H9N2 influenza virus. J Gen Virol. 2010 Aug;91(Pt 8):1978–1983. doi: 10.1099/vir.0.021238-0
   PubMed Web of Science ®Google Scholar
• Deng G, Tan D, Shi J, et al. Complex reassortment of multiple subtypes of avian influenza viruses in domestic ducks at the Dongting Lake Region of China. J Virol. 2013 Sep;87(17):9452–9462. doi: 10.1128/JVI.00776-13
   PubMed Web of Science ®Google Scholar
• Gu M, Xu L, Wang X, et al. Current situation of H9N2 subtype avian influenza in China. Vet Res. 2017 Sep;48(1):49. doi: 10.1186/s13567-017-0453-2
   PubMed Web of Science ®Google Scholar
• Wang C, Wang Z, Ren X, et al. Infection of chicken H9N2 influenza viruses in different species of domestic ducks. Vet Microbiol. 2019 Jun;233:1–4. doi: 10.1016/j.vetmic.2019.04.018
   PubMed Web of Science ®Google Scholar
• Peacock THP, James J, Sealy JE, et al. A global perspective on H9N2 avian influenza virus. Viruses. 2019 Jul;11(7): 620. Another issue. doi: 10.3390/v11070620
   PubMed Web of Science ®Google Scholar
• Park KJ, Kwon H-I, Song M-S, et al. Rapid evolution of low-pathogenic H9N2 avian influenza viruses following poultry vaccination programmes. J Gen Virol. 2011 Jan;92(Pt 1):36–50. doi: 10.1099/vir.0.024992-0
   PubMed Web of Science ®Google Scholar
• Lee Y-N, Lee D-H, Park J-K, et al. Isolation and characterization of a novel H9N2 influenza virus in Korean native chicken farm. Avian Dis. 2011 Dec;55(4):724–727. doi: 10.1637/9774-050911-Case.1
   PubMed Web of Science ®Google Scholar
• Kang M, Jang HK. Genetics and biological property analysis of Korea lineage of influenza A H9N2 viruses. Vet Microbiol. 2017 May;204:96–103. doi: 10.1016/j.vetmic.2017.04.014
   PubMed Web of Science ®Google Scholar