Evolutionary dynamics of influenza a viruses in US exhibition swine

Journal of Infectious Diseases

Volumn 213, Issue 2, 2016, Pages 173-182

  Nelson, Martha I ^a   Wentworth, David E ^b,f   Das, Suman R ^b   Sreevatsan, Srinand ^c   Killian, Mary L ^d   Nolting, Jacqueline M ^e   Slemons, Richard D ^e   Bowman, Andrew S ^e  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

^d National Veterinary Services Laboratories   (United States)

^e OHIO STATE UNIVERSITY   (United States)

^f CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

Author keywords

evolution; exhibition animals; gene flow; genomics; human animal interface; influenza Avirus; swine; United States

Indexed keywords

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; EXHIBITION SWINE; GENETIC VARIABILITY; GENOME ANALYSIS; INFLUENZA A VIRUS (H3N2); NONHUMAN; PHYLOGENY; PIG; PRIORITY JOURNAL; UNITED STATES; VIRUS DETECTION; VIRUS GENOME; VIRUS ISOLATION; VIRUS STRAIN; VIRUS TRANSMISSION; ANIMAL; EVOLUTION; GENETIC REASSORTMENT; GENETIC VARIATION; GENETICS; GENOTYPE; HUMAN; INFLUENZA A VIRUS; INFLUENZA, HUMAN; ORTHOMYXOVIRIDAE INFECTIONS; SWINE DISEASES; TIME FACTOR; TRANSMISSION; VETERINARY; VIROLOGY; ZOONOSIS;

ANIMALS; BIOLOGICAL EVOLUTION; GENETIC VARIATION; GENOME, VIRAL; GENOTYPE; HUMANS; INFLUENZA A VIRUS; INFLUENZA, HUMAN; ORTHOMYXOVIRIDAE INFECTIONS; PHYLOGENY; REASSORTANT VIRUSES; SWINE; SWINE DISEASES; TIME FACTORS; UNITED STATES; ZOONOSES;

EID: 84959879143     PISSN: 00221899     EISSN: 15376613     Source Type: Journal    
DOI: 10.1093/infdis/jiv399     Document Type: Article

References (30)

1. Standardization of terminology for the variant A(H3N2) virus recently infecting humans. Joint announcement of FAO, OIW, WHO. 23 December 2011. http://www.who.int/influenza/gisrs-laboratory/terminology-Ah3n2v/en/. Accessed 10 August 2015.
2. Blanton L, Brammer L, Smith S, et al. Update: influenza activity-United States and worldwide, May 18-September 20, 2014. MMWR Morb Mortal Wkly Rep 2014; 63:861-4.
3. Jhung MA, Epperson S, Biggerstaff M, et al. Outbreak of variant influenza A(H3N2) virus in the United States. Clin Infect Dis 2013; 57:1703-12.
4. Garten RJ, Davis CT, Russell CA, et al. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 2009; 325:197-201.
5. Smith GJD, Vijaykrishna D, Bahl J, et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 2009; 459:1122-5.
6. Vijaykrishna D, Poon LLM, Zhu HC, et al. Reassortment of pandemic H1N1/2009 influenza A virus in swine. Science 2010; 328:1529.
7. Harder TC, Grosse Beilage E, Lange E, et al. Expanded cocirculation of stable subtypes, emerging lineages, and new sporadic reassortants of porcine influenza viruses in swine populations in Northwest Germany. J Virol 2013; 87:10460-76.
8. Ducatez MF, Hause B, Stigger-Rosser E, et al. Multiple reassortment between pandemic (H1N1) 2009 and endemic influenza viruses in pigs, United States. Emerg Infect Dis 2011; 17:1624-9.
9. Nelson MI, Vincent AL, Kitikoon P, Holmes EC, Gramer MR. Evolution of novel reassortant A/H3N2 influenza viruses in North American swine and humans, 2009-2011. J Virol 2012; 86:8872-8.
10. Kitikoon P, Nelson MI, Killian ML, et al. Genotype patterns of contemporary reassorted H3N2 virus in US swine. J Gen Virol 2013; 94(Pt 6):1236-41.
11. Marsh B, Scheftel J, Bender J, et al. Measures to minimize influenza transmission at Swine exhibitions, 2014. 2014.
12. Anderson TK, Nelson MI, Kitikoon P, Swenson SL, Korslund JA, Vincent AL. Population dynamics of cocirculating swine influenza A viruses in the United States from 2009 to 2012. Influenza Other Respi Viruses 2013; 7(suppl 4):42-51.
13. Bowman AS, Nelson SW, Page SL, et al. Swine-To-human transmission of influenza A(H3N2) virus at agricultural fairs, Ohio, USA, 2012. Emerg Infect Dis 2014; 20:1472-80.
14. Bowman AS, Nolting JM, Nelson SW, Slemons RD. Subclinical influenza virus A infections in pigs exhibited at agricultural fairs, Ohio, USA, 2009-2011. Emerg Infect Dis 2012; 18:1945-50.
15. Zhou B, Donnelly ME, Scholes DT, et al. Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses. J Virol 2009; 83:10309-13.
16. Djikeng A, Halpin R, Kuzmickas R, et al. Viral genome sequencing by random priming methods. BMC Genomics 2008; 9:5.
17. Squires RB, Noronha J, Hunt V, et al. Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza Other Respi Viruses 2012; 6:404-16.
18. Bao Y, Bolotov P, Dernovoy D, et al. The influenza virus resource at the National Center for Biotechnology Information. J Virol 2008; 82:596-601.
19. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792-7.
20. Swofford DL. Phylogenetic analysis using parsimony ( and other methods). Sunderland, MA: Sinauer Associates, 2003.
21. Nelson MI, Stratton J, Killian ML, Janas-Martindale A, Vincent AL. Continual reintroduction of human pandemic H1N1 influenza A viruses into Swine in the United States, 2009 to 2014. J Virol 2015; 89:6218-26.
22. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688-90.
23. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28: 2731-9.
24. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 2012; 29:1969-73.
25. Suchard MA, Rambaut A. Many-core algorithms for statistical phylogenetics. Bioinformatics 2009; 25:1370-6.
26. Minin VN, Suchard MA. Counting labeled transitions in continuous-Time Markov models of evolution. J Math Biol 2008; 56:391-412.
27. Bielejec F, Rambaut A, Suchard MA, Lemey P. SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics 2011; 27:2910-2.
28. Feng Z, Gomez J, Bowman AS, et al. Antigenic characterization of H3N2 influenza A viruses from Ohio agricultural fairs. J Virol 2013; 87:7655-67.
29. Bowman AS, Sreevatsan S, Killian ML, et al. Molecular evidence for interspecies transmission of H3N2pM/H3N2v influenza A viruses at an Ohio agricultural fair, July 2012. Emerg Microbes Infect 2012; 1:e33.
30. Nelson MI, Lemey P, Tan Y, et al. Spatial dynamics of human-origin H1 influenza A virus in North American swine. PLoS Path 2011; 7:e1002077.