Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses

Virology Journal

Volumn 8, Issue , 2011, Pages

  Li, Wenfu ^a,b   Shi, Weifeng ^c   Qiao, Huijie ^a   Ho, Simon Y W ^d   Luo, Arong ^a,b   Zhang, Yanzhou ^a   Zhu, Chaodong ^a  

^a INSTITUTE OF ZOOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c UNIVERSITY COLLEGE DUBLIN   (Ireland)

^d UNIVERSITY OF SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

HEMAGGLUTININ; SIALIDASE; INFLUENZA VIRUS HEMAGGLUTININ; NA PROTEIN, INFLUENZA A VIRUS; VIRUS PROTEIN;

ARTICLE; FOWL; GENE SEQUENCE; INFLUENZA VIRUS A H1N1; NONHUMAN; PHYLOGENY; SWINE; VIRUS GENE; VIRUS IDENTIFICATION; VIRUS ISOLATION; VIRUS STRAIN; ANIMAL; AVIAN INFLUENZA; BIRD; CLASSIFICATION; ENZYMOLOGY; GENETIC SELECTION; GENETICS; HUMAN; INFLUENZA; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; ORTHOMYXOVIRUS INFECTION; SWINE DISEASE; VIROLOGY;

AVES; INFLUENZA A VIRUS; ORTHOMYXOVIRIDAE; SUIDAE;

ANIMALS; BIRDS; EVOLUTION, MOLECULAR; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA IN BIRDS; INFLUENZA, HUMAN; MOLECULAR SEQUENCE DATA; NEURAMINIDASE; ORTHOMYXOVIRIDAE INFECTIONS; PHYLOGENY; SELECTION, GENETIC; SWINE; SWINE DISEASES; VIRAL PROTEINS;

EID: 79954598776     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-8-183     Document Type: Article

References (28)

1. Pandemic (H1N1) 2009 weekly update. World Health Organizaiton, 2010 http://www.who.int/csr/don/2010-08-06/en/index.html
2. The 2009 H1N1 influenza outbreak in its historical context. D Gatherer, J Clin Virol 2009 45 174 178 10.1016/j.jcv.2009.06.004 19540156
3. Evolution and ecology of influenza A viruses. RG Webster WJ Bean OT Gorman TM Chambers Y Kawaoka, Microbiol Rev 1992 56 152 179 1579108
4. An overview of the epidemiology of avian influenza. DJ Alexander, Vaccine 2007 25 5637 5644 10.1016/j.vaccine.2006.10.051 17126960 (Pubitemid 47031360)
5. Influenza virus hemagglutinin cleavage into HA1, HA2: No laughing matter. JK Taubenberger, Proceedings of the National Academy of Sciences of the United States of America 1998 95 9713 9715 10.1073/pnas.95.17.9713 9707539 (Pubitemid 28415233)
6. The variable codons of H3 influenza A virus haemagglutinin genes. MJ Gibbs P Wayper ML Fourment JT Wood K Ohshima JS Armstrong AJ Gibbs, Arch Virol 2007 152 11 24 10.1007/s00705-006-0834-8 16957828 (Pubitemid 44974612)
7. Impact of neuraminidase mutations conferring influenza resistance to neuraminidase inhibitors in the N1 and N2 genetic backgrounds. Y Abed M Baz G Boivin, Antivir Ther 2006 11 971 976 17302366 (Pubitemid 44955172)
8. Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. T Miyata T Yasunaga, J Mol Evol 1980 16 23 36 10.1007/BF01732067 6449605 (Pubitemid 11202184)
9. Codon-Substitution Models to Detect Adaptive Evolution that Account for Heterogeneous Selective Pressures Among Site Classes. Z Yang WJ Swanson, Molecular Biology and Evolution 2002 19 49 57 11752189 (Pubitemid 34008046)
10. Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. YI Wolf C Viboud EC Holmes EV Koonin DJ Lipman, Biol Direct 2006 1 34 10.1186/1745-6150-1-34 17067369
11. Evolutionary Trends of A(H1N1) Influenza Virus Hemagglutinin Since 1918. J Shen J Ma Q Wang, PLoS ONE 2009 4 7789 10.1371/journal.pone.0007789 19924230
12. Early alterations of the receptor-binding properties of H1, H2, and H3 avian influenza virus hemagglutinins after their introduction into mammals. M Matrosovich A Tuzikov N Bovin A Gambaryan A Klimov MR Castrucci I Donatelli Y Kawaoka, J Virol 2000 74 8502 8512 10.1128/JVI.74.18.8502-8512.2000 10954551 (Pubitemid 30666701)
13. Comparison of selection pressures on the HA gene of pandemic (2009) and seasonal human and swine influenza A H1 subtype viruses. Y Furuse K Shimabukuro T Odagiri R Sawayama T Okada I Khandaker A Suzuki H Oshitani, Virology 2010 405 314 321 10.1016/j.virol.2010.06.018 20598336
14. Selection for resistance to oseltamivir in seasonal and pandemic H1N1 influenza and widespread co-circulation of the lineages. DA Janies IO Voronkin J Studer J Hardman BB Alexandrov TW Treseder C Valson, Int J Health Geogr 2010 9 13 10.1186/1476-072X-9-13 20181276
15. Evaluation of hemagglutinin subtype 1 swine influenza viruses from the United States. AL Vincent KM Lager W Ma P Lekcharoensuk MR Gramer C Loiacono JA Richt, Vet Microbiol 2006 118 212 222 10.1016/j.vetmic.2006.07.017 16962262 (Pubitemid 44781158)
16. Evidence of the concurrent circulation of H1N2, H1N1 and H3N2 influenza A viruses in densely populated pig areas in Spain. J Maldonado K Van Reeth P Riera M Sitja N Saubi E Espuna C Artigas, Vet J 2006 172 377 381 10.1016/j.tvjl.2005.04.014 15914047 (Pubitemid 44159267)
17. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. GJ Smith D Vijaykrishna J Bahl SJ Lycett M Worobey OG Pybus SK Ma CL Cheung J Raghwani S Bhatt, et al. Nature 2009 459 1122 1125 10.1038/nature08182 19516283
18. The epitope regions of H1-subtype influenza A, with application to vaccine efficacy. MW Deem K Pan, Protein Eng Des Sel 2009 22 543 546 10.1093/protein/gzp027 19578121
19. Genome-wide screening of human T-cell epitopes in influenza A virus reveals a broad spectrum of CD4(+) T-cell responses to internal proteins, hemagglutinins, and neuraminidases. JA Babon J Cruz L Orphin P Pazoles MD Co FA Ennis M Terajima, Hum Immunol 2009 70 711 721 10.1016/j.humimm.2009.06.004 19524006
20. Identifying Changes in Selective Constraints: Host Shifts in Influenza. AU Tamuri M dos Reis AJ Hay RA Goldstein, PLoS Comput Biol 2009 5 1000564 10.1371/journal.pcbi.1000564 19911053
21. Influenza A virus neuraminidase: regions of the protein potentially involved in virus-host interactions. TG Fanning AH Reid JK Taubenberger, Virology 2000 276 417 423 10.1006/viro.2000.0578 11040132
22. Virus glycosylation: role in virulence and immune interactions. DJ Vigerust VL Shepherd, Trends Microbiol 2007 15 211 218 10.1016/j.tim.2007.03.003 17398101 (Pubitemid 46660602)
23. Sequence analysis of the haemagglutinin (HA) of influenza A (H1N1) viruses present in clinical material and comparison with the HA of laboratory-derived virus. JS Robertson C Nicolson JS Bootman D Major EW Robertson JM Wood, J Gen Virol 1991 72 Pt 11 2671 2677 1940864
24. Studies on the molecular basis for loss of the ability of recent influenza A (H1N1) virus strains to agglutinate chicken erythrocytes. T Morishita E Nobusawa K Nakajima S Nakajima, J Gen Virol 1996 77 Pt 10 2499 2506 8887483 (Pubitemid 26348372)
25. Influenza Virus Resource. National Center for Biotechnology Information, 2010 http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/nph-select.cgi?go=database
26. HyPhy: hypothesis testing using phylogenies. SLK Pond SDW Frost SV Muse, Bioinformatics 2005 21 676 679 15509596 (Pubitemid 40424796)
27. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. A Stamatakis, Bioinformatics 2006 22 2688 2690 10.1093/bioinformatics/btl446 16928733 (Pubitemid 44642609)
28. Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection. SL Kosakovsky Pond SDW Frost, Molecular Biology and Evolution 2005 22 1208 1222 10.1093/molbev/msi105 15703242 (Pubitemid 40577758)