The contrasting phylodynamics of human influenza B viruses

eLife

Volumn 2015, Issue 4, 2015, Pages

  Vijaykrishna, Dhanasekaran ^a,b,c   Holmes, Edward C ^d   Joseph, Udayan ^a   Fourment, Mathieu ^d   Su, Yvonne C F ^a   Halpin, Rebecca ^e   Lee, Raphael T C ^f   Deng, Yi Mo ^c   Gunalan, Vithiagaran ^f   Lin, Xudong ^e   Stockwell, Timothy B ^e   Fedorova, Nadia B ^e   Zhou, Bin ^e   Spirason, Natalie ^c   Küuhnert, Denise ^g   Bošková, Veronika ^g   Stadler, Tanja ^g   Costa, Anna Maria ^h   Dwyer, Dominic E ⁱ   Huang, Q Sue ^j   Jennings, Lance C ^k   Rawlinson, William ^l   Sullivan, Sheena G ^c   Hurt, Aeron C ^c,m   Maurer Stroh, Sebastian ^f,n,o   Wentworth, David E ^e   Smith, Gavin J D ^a,c,p   Barr, Ian G ^c,q   more..

^a DUKE NUS MEDICAL SCHOOL   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c PETER DOHERTY INSTITUTE FOR INFECTION AND IMMUNITY   (Australia)

^d University of Sydney   (Australia)

^e J CRAIG VENTER INSTITUTE   (United States)

^f BIOINFORMATICS INSTITUTE   (Singapore)

^g ETH ZURICH   (Switzerland)

^h ROYAL CHILDREN'S HOSPITAL   (Australia)

ⁱ UNIVERSITY OF SYDNEY   (Australia)

^j INSTITUTE OF ENVIRONMENTAL SCIENCE AND RESEARCH   (New Zealand)

^k CANTERBURY HEALTH LABORATORIES   (New Zealand)

^l PRINCE OF WALES HOSPITAL   (Australia)

^m UNIVERSITY OF MELBOURNE   (Australia)

ⁿ NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^o MINISTRY OF HEALTH   (Singapore)

^p DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^q UNIVERSITY OF BALLARAT   (Australia)

more..

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS RNA; ASPARAGINE; INFLUENZA VIRUS HEMAGGLUTININ; VIRUS ANTIGEN;

ANTIGENICITY; ARTICLE; DISEASE SURVEILLANCE; ECOLOGICAL GENETICS; GENETIC ASSOCIATION; GENETIC VARIABILITY; INFLUENZA VIRUS B; MICROBIAL POPULATION DYNAMICS; NONHUMAN; PHYLOGENY; PHYLOGEOGRAPHY; VIRAL GENETICS; VIRAL PHYLODYNAMICS; VIROLOGY; VIRUS INFECTION; VIRUS ISOLATION; VIRUS TRANSMISSION; AGE DISTRIBUTION; ANIMAL; AUSTRALIA; CHEMICAL STRUCTURE; DOG; GENETIC REASSORTMENT; GENETIC SELECTION; GENETICS; GLYCOSYLATION; HUMAN; IMMUNOLOGY; INFLUENZA A VIRUS; INFLUENZA B VIRUS; INFLUENZA, HUMAN; MDCK CELL LINE; METABOLISM; MOLECULAR EVOLUTION; NEW ZEALAND; TIME; TRANSMISSION; VIRUS GENOME;

CERCOPITHECINE HERPESVIRUS 1;

AGE DISTRIBUTION; ANIMALS; ANTIGENS, VIRAL; ASPARAGINE; DOGS; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, VIRAL; GLYCOSYLATION; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HUMANS; INFLUENZA A VIRUS; INFLUENZA B VIRUS; INFLUENZA, HUMAN; MADIN DARBY CANINE KIDNEY CELLS; MODELS, MOLECULAR; NEW ZEALAND; PHYLOGENY; REASSORTANT VIRUSES; SELECTION, GENETIC; TIME FACTORS; VICTORIA;

EID: 84922021071     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.05055     Document Type: Article

References (65)

1. Klimov AI, Garten R, Russell C, Barr IG, Besselaar TG, et al. (2012) WHO recommendations for the viruses to be used in the 2012 southern hemisphere inuenza vaccine: epidemiology, antigenic and genetic characteristics of inuenza A(H1N1)pdm09, A(H3N2) and B inuenza viruses collected from February to September 2011. Vaccine 30: 6461-71.
2. Burnham AJ, Baranovich T, Govorkova EA (2013) Neuraminidase inhibitors for inuenza B virus infection: e_cacy and resistance. Antiviral Res 100: 520-34.
3. Paul Glezen W, Schmier JK, Kuehn CM, Ryan KJ, Oxford J (2013) The burden of inuenza B: a structured literature review. Am J Public Health 103: e43-51.
4. McCauley JW, Hongo S, Kaverin NV, Kochs G, Lamb RA, et al. (2012) Family-Orthomyxoviridae. In: King AMQ, Lefkowitz E, Adams MJ, Carstens EB, editors, Virus taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses, San Diego: Elsevier. pp. 749-761.
5. Chen R, Holmes EC (2008) The evolutionary dynamics of human inuenza B virus. J Mol Evol 66: 655-63.
6. Tan Y, Guan W, Lam TTY, Pan S, Wu S, et al. (2013) Difiering epidemiological dynamics of inuenza B virus lineages in Guangzhou, southern China, 2009-2010. J Virol 87: 12447-56.
7. Neumann G, Noda T, Kawaoka Y (2009) Emergence and pandemic potential of swine-origin H1N1 inuenza virus. Nature 459: 931-9.
8. Smith GJD, Bahl J, Vijaykrishna D, Zhang J, Poon LLM, et al. (2009) Dating the emergence of pandemic inuenza viruses. Proc Natl Acad Sci U S A 106: 11709-12.
9. Francis Jr T, et al. (1940) A new type of virus from epidemic inuenza. American Association for the Advancement of Science Science 92: 405-8.
10. Osterhaus AD, Rimmelzwaan GF, Martina BE, Bestebroer TM, Fouchier RA (2000) Inuenza B virus in seals. Science 288: 1051-3.
11. Bodewes R, Morick D, de Mutsert G, Osinga N, Bestebroer T, et al. (2013) Recurring inuenza B virus infections in seals. Emerg Infect Dis 19: 511-2.
12. Russell CA, Jones TC, Barr IG, Cox NJ, Garten RJ, et al. (2008) The global circulation of seasonal inuenza A (H3N2) viruses. Science 320: 340-6.
13. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, et al. (2008) The genomic and epidemiological dynamics of human inuenza A virus. Nature 453: 615-9.
14. Bedford T, Cobey S, Beerli P, Pascual M (2010) Global migration dynamics underlie evolution and persistence of human inuenza A (H3N2). PLoS Pathog 6: e1000918.
15. Bahl J, Nelson MI, Chan KH, Chen R, Vijaykrishna D, et al. (2011) Temporally structured metapopulation dynamics and persistence of inuenza A H3N2 virus in humans. Proc Natl Acad Sci U S A 108: 19359-64.
16. Fitch WM, Bush RM, Bender CA, Cox NJ (1997) Long term trends in the evolution of H(3) HA1 human inuenza type A. Proc Natl Acad Sci U S A 94: 7712-8.
17. Nelson MI, Viboud C, Simonsen L, Bennett RT, Griesemer SB, et al. (2008) Multiple reassortment events in the evolutionary history of H1N1 inuenza A virus since 1918. PLoS Pathog 4: e1000012.
18. Kanegae Y, Sugita S, Endo A, Ishida M, Senya S, et al. (1990) Evolutionary pattern of the hemagglutinin gene of inuenza B viruses isolated in Japan: Cocirculating lineages in the same epidemic season. J Virol 64: 2860-5.
19. Rota PA, Wallis TR, Harmon MW, Rota JS, Kendal AP, et al. (1990) Cocirculation of two distinct evolutionary lineages of inuenza type B virus since 1983. Virology 175: 59-68.
20. Ferguson NM, Galvani AP, Bush RM (2003) Ecological and immunological determinants of inuenza evolution. Nature 422: 428-33.
21. Bedford T, Suchard MA, Lemey P, Dudas G, Gregory V, et al. (2014) Integrating inuenza antigenic dynamics with molecular evolution. Elife 3: e01914.
22. Nelson MI, Edelman L, Spiro DJ, Boyne AR, Bera J, et al. (2008) Molecular epidemiology of A/H3N2 and A/H1N1 inuenza virus during a single epidemic season in the United States. PLoS Pathog 4: e1000133.
23. Goldstein E, Cobey S, Takahashi S, Miller JC, Lipsitch M (2011) Predicting the epidemic sizes of inuenza A/H1N1, A/H3N2, and B: A statistical method. PLoS Med 8: e1001051.
24. Minin VN, Bloomquist EW, Suchard MA (2008) Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol 25: 1459-71.
25. Bedford T, Cobey S, Pascual M (2011) Strength and tempo of selection revealed in viral gene genealogies. BMC Evol Biol 11: 220.
26. Zinder D, Bedford T, Gupta S, Pascual M (2013) The roles of competition and mutation in shaping antigenic and genetic diversity in inuenza. PLoS Pathog 9: e1003104.
27. Grenfell BT, Pybus OG, Gog JR, Wood JLN, Daly JM, et al. (2004) Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303: 327-32.
28. Kühnert D, Stadler T, Vaughan TG, Drummond AJ (2014) Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model. J R Soc Interface 11: 20131106.
29. Minin VN, Suchard MA (2008) Counting labeled transitions in continuous-time Markov models of evolution. J Math Biol 56: 391-412.
30. Dudas G, Bedford T, Lycett S, Rambaut A (2015) Reassortment between inuenza B lineages and the emergence of a coadapted PB1-PB2-HA gene complex. Mol Biol Evol 32: 162-72.
31. Smith DJ, Lapedes AS, de Jong JC, Bestebroer TM, Rimmelzwaan GF, et al. (2004) Mapping the antigenic and genetic evolution of inuenza virus. Science 305: 371-6.
32. Koel BF, Burke DF, Bestebroer TM, van der Vliet S, Zondag GCM, et al. (2013) Substitutions near the receptor binding site determine major antigenic change during inuenza virus evolution. Science 342: 976-9.
33. Sočan M, Prosenc K, Učakar V, Berginc N (2014) A comparison of the demographic and clinical characteristics of laboratory-con_rmed inuenza B Yamagata and Victoria lineage infection. J Clin Virol 61: 156-60.
34. Anderson R, May R (1992) Infectious Diseases of Humans: Dynamics and Control. Oxford science publications. OUP Oxford.
35. Velkov T (2013) The specificity of the inuenza B virus hemagglutinin receptor binding pocket: what does it bind to? J Mol Recognit 26: 439-49.
36. Wang YF, Chang CF, Chi CY, Wang HC, Wang JR, et al. (2012) Characterization of glycan binding specificities of inuenza B viruses with correlation with hemagglutinin genotypes and clinical features. J Med Virol 84: 679-85.
37. Gambaryan AS, Robertson JS, Matrosovich MN (1999) Effects of egg-adaptation on the receptor-binding properties of human inuenza A and B viruses. Virology 258: 232-9.
38. Nicholls JM, Bourne AJ, Chen H, Guan Y, Peiris JSM (2007) Sialic acid receptor detection in the human respiratory tract: evidence for widespread distribution of potential binding sites for human and avian inuenza viruses. Respir Res 8: 73.
39. Walther T, Karamanska R, Chan RWY, Chan MCW, Jia N, et al. (2013) Glycomic analysis of human respiratory tract tissues and correlation with inuenza virus infection. PLoS Pathog 9: e1003223.
40. Skowronski DM, Hottes TS, Chong M, De Serres G, Scheifele DW, et al. (2011) Randomized controlled trial of dose response to inuenza vaccine in children aged 6 to 23 months. Pediatrics 128: e276-89.
41. Skowronski DM, Hamelin ME, Janjua NZ, De Serres G, Gardy JL, et al. (2012) Cross-lineage inuenza B and heterologous inuenza A antibody responses in vaccinated mice: immunologic interactions and B/Yamagata dominance. PLoS One 7: e38929.
42. Vijaykrishna D, Holmes E, Joseph U, Fourment M, Su Y, et al. Data from: The contrasting phylodynamics of human inuenza viruses.
43. Deng YM, Iannello P, Caldwell N, Jelley L, Komadina N, et al. (2013) The use of pyrosequencer-generated sequence-signatures to identify the inuenza B-lineage and the subclade of the B/Yamataga-lineage viruses from currently circulating human inuenza B viruses. J Clin Virol 58: 94-9.
44. Zhou B, Lin X, Wang W, Halpin RA, Bera J, et al. (2014) Universal inuenza B virus genomic amplification facilitates sequencing, diagnostics, and reverse genetics. J Clin Microbiol 52: 1330-7.
45. Minh BQ, Nguyen MAT, von Haeseler A (2013) Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 30: 1188-95.
46. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29: 1969-73.
47. Rambaut A (2014) Figtree. URL http://tree.bio.ed.ac.uk/software/figtree/.
48. Lemey P, Rambaut A, Drummond AJ, Suchard MA (2009) Bayesian phylogeography nds its roots. PLoS Comput Biol 5: e1000520.
49. Bahl J, Krauss S, Kuhnert D, Fourment M, Raven G, et al. (2013) Inuenza a virus migration and persistence in North American wild birds. PLoS Pathog 9: e1003570.
50. Nunes MRT, Faria NR, Vasconcelos HB, Medeiros DBdA, Silva de Lima CP, et al. (2012) Phylogeography of dengue virus serotype 4, Brazil, 2010-2011. Emerg Infect Dis 18: 1858-64.
51. Kosakovsky Pond SL, Frost SDW (2005) Not so different after all: A comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22: 1208-22.
52. Murrell B, Moola S, Mabona A, Weighill T, Sheward D, et al. (2013) FUBAR: A fast, unconstrained bayesian approximation for inferring selection. Mol Biol Evol 30: 1196-205.
53. Delport W, Poon AFY, Frost SDW, Kosakovsky Pond SL (2010) Datamonkey 2010: A suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26: 2455-7.
54. Yang Z (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-91.
55. Cai Z, Zhang T, Wan XF (2010) A computational framework for inuenza antigenic cartography. PLoS Comput Biol 6: e1000949.
56. WHO Global Inuenza Surveillance Network (2011) Manual for the laboratory diagnosis and virological surveillance of inuenza. URL http://www.who.int/influenza/en/.
57. Wan XF (2010) Antigenic Map. URL http://sysbio.cvm.msstate.edu/AntigenMap/.
58. Krieger E, Joo K, Lee J, Lee J, Raman S, et al. (2009) Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins 77 Suppl 9: 114-22.
59. Webb B, Sali A (2014) Comparative protein structure modeling using MODELLER. Curr Protoc Bioinformatics 47: 561-5632.
60. Dreyfus C, Laursen NS, Kwaks T, Zuijdgeest D, Khayat R, et al. (2012) Highly conserved protective epitopes on inuenza B viruses. Science 337: 1343-8.
61. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-9.
62. Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM (2006) MUSTANG: A multiple structural alignment algorithm. Proteins 64: 559-74.
63. Xu R, McBride R, Nycholat CM, Paulson JC, Wilson IA (2012) Structural characterization of the hemagglutinin receptor specificity from the 2009 H1N1 inuenza pandemic. J Virol 86: 982-90.
64. Lin YP, Xiong X, Wharton SA, Martin SR, Coombs PJ, et al. (2012) Evolution of the receptor binding properties of the inuenza A(H3N2) hemagglutinin. Proc Natl Acad Sci U S A 109: 21474-9.
65. Wang Q, Tian X, Chen X, Ma J (2007) Structural basis for receptor specificity of inuenza B virus hemagglutinin. Proc Natl Acad Sci U S A 104: 16874-9.