All that glitters is not gold - Founder effects complicate associations of flu mutations to disease severity

Virology Journal

Volumn 7, Issue , 2010, Pages

  Lee, Raphael Tc ^a   Santos, Cecília Ls ^b   Maria De Paiva, Terezinha ^b   Cui, Lin ^c   Sirota, Fernanda L ^a   Eisenhaber, Frank ^a,d,e   Maurer Stroh, Sebastian ^a,f  

^a BIOINFORMATICS INSTITUTE   (Singapore)

^b INSTITUTO ADOLFO LUTZ   (Brazil)

^c MINISTRY OF HEALTH   (Singapore)

^d NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^e NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^f NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DISEASE ASSOCIATION; DISEASE SEVERITY; EPIDEMIOLOGICAL DATA; FATALITY; FOUNDER EFFECT; FUTUROLOGY; GENE; GENE MUTATION; GENOME; HA D239G GENE; HA D239N GENE; HA Q310 H GENE; INFLUENZA; NONHUMAN; NUCLEOTIDE SEQUENCE; PB2 K340N GENE; PHENOTYPE; PHYLOGENETIC TREE; SAMPLE; VIRUS GENOME; CHEMICAL STRUCTURE; GENETICS; HUMAN; INFLUENZA VIRUS A H1N1; MISSENSE MUTATION; PATHOGENICITY; PATHOLOGY; PHYLOGENY; PREVALENCE; PROTEIN TERTIARY STRUCTURE; VIROLOGY; VIRULENCE;

HEMAGGLUTININ FUSOGENIC PEPTIDE, INFLUENZA VIRUS; VIRULENCE FACTOR; VIRUS HEMAGGLUTININ; VIRUS RNA;

FOUNDER EFFECT; HEMAGGLUTININS, VIRAL; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA, HUMAN; MODELS, MOLECULAR; MUTATION, MISSENSE; PHYLOGENY; PREVALENCE; PROTEIN STRUCTURE, TERTIARY; RNA, VIRAL; VIRULENCE; VIRULENCE FACTORS;

EID: 77958537904     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-7-297     Document Type: Article

References (28)

1. Founder effects in the assessment of HIV polymorphisms and HLA allele associations. T Bhattacharya M Daniels D Heckerman B Foley N Frahm C Kadie J Carlson K Yusim B McMahon B Gaschen S Mallal JI Mullins DC Nickle J Herbeck C Rousseau GH Learn T Miura C Brander B Walker B Korber, Science 2007 315 1583 1586 10.1126/science.1131528 17363674
2. The early diversification of influenza A/H1N1pdm. M Nelson D Spiro D Wentworth E Beck J Fan E Ghedin R Halpin J Bera E Hine K Proudfoot T Stockwell X Lin S Griesemer S Kumar M Bose C Viboud E Holmes K Henrickson, PLoS Curr Influenza 2009 3 1 RN1126
3. A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. S Maurer-Stroh RTC Lee F Eisenhaber L Cui SP Phuah RT Lin, PLoS Curr Influenza 2010 RRN1162
4. Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites. S Maurer-Stroh J Ma RTC Lee FL Sirota F Eisenhaber, Biol Direct 2009 4 18 discussion 18 10.1186/1745-6150-4-18 19457254
5. Observed association between the HA1 mutation D222G in the 2009 pandemic influenza A(H1N1) virus and severe clinical outcome, Norway 2009-2010. A Kilander R Rykkvin SG Dudman O Hungnes, Euro Surveill 2010 15 http://www.ncbi.nlm.nih.gov/pubmed/20214869
6. WHO | Pandemic (H1N1) 2009 - update 76. http://www.who.int/csr/disease/ swineflu/laboratory27-11-2009/en/index.html
7. Occurrence of haemagglutinin mutation D222G in pandemic influenza A(H1N1) infected patients in the West of Scotland, United Kingdom, 2009-10. RR Miller AR MacLean RN Gunson WF Carman, Euro Surveill 2010 15 http://www.ncbi.nlm.nih. gov/pubmed/20429998 20429998
8. Association of D222G substitution in haemagglutinin of 2009 pandemic influenza A (H1N1) with severe disease. GC Mak KW Au LS Tai KC Chuang KC Cheng TC Shiu W Lim, Euro Surveill 2010 15 http://www.ncbi.nlm.nih.gov/pubmed/20394715 20394715
9. Preliminary review of D222G amino acid substitution in the haemagglutinin of pandemic influenza A (H1N1) 2009 viruses. Wkly Epidemiol Rec 2010 85 21 22 20095109
10. Genomic analysis of pandemic (H1N1) 2009 reveals association of increasing disease severity with emergence of novel hemagglutinin mutations. GV Glinsky, Cell Cycle 2010 9 958 970 20160492
11. The influenza virus resource at the National Center for Biotechnology Information. Y Bao P Bolotov D Dernovoy B Kiryutin L Zaslavsky T Tatusova J Ostell D Lipman, J Virol 2008 82 596 601 10.1128/JVI.02005-07 17942553
12. MAFFT version 5: improvement in accuracy of multiple sequence alignment. K Katoh K Kuma H Toh T Miyata, Nucleic Acids Res 2005 33 511 518 10.1093/nar/gki198 15661851
13. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. W Li A Godzik, Bioinformatics 2006 22 1658 1659 10.1093/bioinformatics/btl158 16731699
14. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 696 704 10.1080/10635150390235520 14530136
15. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738
16. Identification of shared populations of human immunodeficiency virus type 1 infecting microglia and tissue macrophages outside the central nervous system. TH Wang YK Donaldson RP Brettle JE Bell P Simmonds, J Virol 2001 75 11686 11699 10.1128/JVI.75.23.11686-11699.2001 11689650
17. A cladistic measure of gene flow inferred from the phylogenies of alleles. M Slatkin WP Maddison, Genetics 1989 123 603 613 2599370 (Pubitemid 19274683)
18. Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. J Parker A Rambaut OG Pybus, Infect Genet Evol 2008 8 239 246 10.1016/j.meegid.2007.08.001 17921073
19. BEAST: Bayesian evolutionary analysis by sampling trees. AJ Drummond A Rambaut, BMC Evol Biol 2007 7 214 10.1186/1471-2148-7-214 17996036
20. Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus. R Xu DC Ekiert JC Krause R Hai JE Crowe IA Wilson, Science 2010 328 357 360 10.1126/science.1186430 20339031
21. The structural basis for cap binding by influenza virus polymerase subunit PB2. D Guilligay F Tarendeau P Resa-Infante R Coloma T Crepin P Sehr J Lewis RWH Ruigrok J Ortin DJ Hart S Cusack, Nat Struct Mol Biol 2008 15 500 506 10.1038/nsmb.1421 18454157
22. Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field. E Krieger G Koraimann G Vriend, Proteins 2002 47 393 402 10.1002/prot.10104 11948792
23. Evolutionary pattern of pandemic influenza (H1N1) 2009 virus in the late phases of the 2009 pandemic. MB Valli S Meschi M Selleri P Zaccaro G Ippolito MR Capobianchi S Menzo, PLoS Curr 2010 RRN1149 20228856
24. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. GJD Smith D Vijaykrishna J Bahl SJ Lycett M Worobey OG Pybus SK Ma CL Cheung J Raghwani S Bhatt JSM Peiris Y Guan A Rambaut, Nature 2009 459 1122 1125 10.1038/nature08182 19516283
25. Replication, pathogenesis and transmission of pandemic (H1N1) 2009 virus in non-immune pigs. SM Brookes A Ñez B Choudhury M Matrosovich SC Essen D Clifford MJ Slomka G Kuntz-Simon F Garcon B Nash A Hanna PMH Heegaard S Quéguiner C Chiapponi M Bublot JM Garcia R Gardner E Foni W Loeffen L Larsen K Van Reeth J Banks RM Irvine IH Brown, PLoS ONE 2010 5 9068 10.1371/journal.pone.0009068 20140096
26. Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays. CWH Lee CW Koh YS Chan PPK Aw KH Loh BL Han PL Thien GYW Nai ML Hibberd CW Wong W Sung, Nucleic Acids Res 2010 38 111 10.1093/nar/gkq089 20185568
27. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. RJ Garten CT Davis CA Russell B Shu S Lindstrom A Balish WM Sessions X Xu E Skepner V Deyde M Okomo-Adhiambo L Gubareva J Barnes CB Smith SL Emery MJ Hillman P Rivailler J Smagala M de Graaf DF Burke RAM Fouchier C Pappas CM Alpuche-Aranda H Lápez-Gatell H Olivera I Lápez CA Myers D Faix PJ Blair C Yu KM Keene PD Dotson D Boxrud AR Sambol SH Abid K St George T Bannerman AL Moore DJ Stringer P Blevins GJ Demmler-Harrison M Ginsberg P Kriner S Waterman S Smole HF Guevara EA Belongia PA Clark ST Beatrice R Donis J Katz L Finelli CB Bridges M Shaw DB Jernigan TM Uyeki DJ Smith AI Klimov NJ Cox, Science 2009 325 197 201 10.1126/science. 1176225 19465683
28. Genomic signature and mutation trend analysis of pandemic (H1N1) 2009 influenza A virus. C Pan B Cheung S Tan C Li L Li S Liu S Jiang, PLoS ONE 2010 5 9549 10.1371/journal.pone.0009549 20221396