Mixture model analysis reflecting dynamics of the population diversity of 2009 pandemic H1N1 influenza virus

In Silico Biology

Volumn 11, Issue 5, 2012, Pages 225-236

  Long, Li Ping ^a   Yuan, Changhe ^b   Cai, Zhipeng ^a   Xu, Huiping ^c   Wan, Xiu Feng ^a  

^a MISSISSIPPI STATE UNIVERSITY   (United States)

^b City University of New York   (United States)

^c INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Expectation Maximization; Hemagglutinin; Influenza A virus; Influenza pandemic; Mixture model analysis; Population structure

Indexed keywords

INFLUENZA VIRUS HEMAGGLUTININ; VIRUS HEMAGGLUTININ;

ALGORITHM; ARTICLE; CLASSIFICATION; GENETIC VARIABILITY; GENETICS; HUMAN; INFLUENZA; INFLUENZA VIRUS A H1N1; MOLECULAR EVOLUTION; THEORETICAL MODEL; VIROLOGY;

ALGORITHMS; EVOLUTION, MOLECULAR; GENETIC VARIATION; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HEMAGGLUTININS, VIRAL; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA, HUMAN; MODELS, THEORETICAL;

EID: 84872479216     PISSN: 14343207     EISSN: None     Source Type: Journal    
DOI: 10.3233/ISB-2012-0457     Document Type: Article

References (28)

1. M. Ginsberg, et al., "Swine influenza A (H1N1) infection in two children-Southern California, March-April 2009," MMWR Morb Mortal Wkly Rep, vol. 58, pp. 400-402, Apr 24 2009.
2. F. S. Dawood, et al., "Emergence of a novel swine-origin influenza A (H1N1) virus in humans," N Engl J Med, vol. 360, pp. 2605-2615, Jun 18 2009.
3. H. Yang, et al., "Structure and Receptor binding properties of a pandemic H1N1 virus hemagglutinin," PLoS Curr Influenza, vol 2, p. RRN1152, 2010.
4. C. Pan, et al., "Genomic signature and mutation trend analysis of pandemic (H1N1) 2009 influenza A virus," PLoS One, vol. 5, p. e9549, 2010.
5. Y. L. Shu, et al., "Dual seasonal patterns for influenza, China," Emerg Infect Dis, vol. 16, pp. 725-726, Apr 2010.
6. X. F. Wan, et al., "A quantitative genotype algorithm reflecting H5N1 Avian influenza niches," Bioinformatics, vol. 23, pp. 2368-2375, Sep 15 2007.
7. H. Yang, et al., "Structure and Receptor binding properties of a pandemic H1N1 virus hemagglutinin," PLoS Curr Influenza, vol 2, p. RRN1152, 2010.
8. P. K. Chan, et al., "Clinical and virological course of infection with haemagglutinin D222G mutant strain of 2009 pandemic influenza A (H1N1) virus," J Clin Virol, vol. 50, pp. 320- 324, Apr 2011.
9. S. Chutinimitkul, et al., "Virulence-associated substitution D222G in the hemagglutinin of 2009 pandemic influenza A (H1N1) virus affects receptor binding," J Virol, vol. 84, pp. 11802-11813, Nov 2010.
10. K. H. Chan, et al., "Wild type and mutant 2009 pandemic influenza A (H1N1) viruses cause more severe disease and higher mortality in pregnant BALB/c mice," PLoS One, vol. 5, p. e13757, 2010.
11. Y. Liu, et al., "Altered receptor specificity and cell tropism of D222G hemagglutinin mutants isolated from fatal cases of pandemic A(H1N1) 2009 influenza virus," J Virol, vol. 84, pp. 12069-12074, Nov 2010.
12. S. Puzelli, et al., "Transmission of hemagglutinin D222G mutant strain of pandemic (H1N1) 2009 virus," Emerg Infect Dis, vol. 16, pp. 863-865, May 2010.
13. V. M. Deyde, et al., "Reply to Saito et al.," The Journal of Infectious Diseases vol. 197, pp. 632-633, 2008.
14. CDC, "Update: Influenza activity-United States and worldwide, 2006-07 season, and composition of the 2007-08 influenza vaccine," MMWR Morb Mortal Wkly Rep, vol. 56, pp. 789-794, Aug 10 2007.
15. R. Saito, et al., "Increased incidence of adamantane-resistant influenza A(H1N1) and A(H3N2) viruses during the 2006-2007 influenza season in Japan," J Infect Dis, vol. 197, pp. 630-632; author reply 632-3, Feb 15 2008. (Pubitemid 351321543)
16. N. J. Dharan, et al., "Infections with oseltamivir-resistant influenza A(H1N1) virus in the United States," Jama, vol. 301, pp. 1034-1041, Mar 11 2009.
17. R. M. Bush, et al., "Predicting the evolution of human influenza A," Science, vol. 286, pp. 1921-1925, Dec 3 1999. (Pubitemid 129515893)
18. Y. I. Wolf, et al., "Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus," Biol Direct, vol. 1, p. 34, 2006.
19. X. F. Wan, et al., "Computational identification of reassortments in avian influenza viruses," Avian Dis, vol. 51, pp. 434-439, Mar 2007.
20. X. F. Wan, et al., "Ubiquitous reassortments in influenza A viruses," J BioinformComput Biol, vol. 6, pp. 981-999,Oct 2008.
21. X. F. Wan, et al., "Evolution of highly pathogenic H5N1 avian influenza viruses in Vietnam between 2001 and 2007," PLoS One, vol. 3, p. e3462, 2008.
22. A. P. Dempster, et al., "Maximum likelihood from incomplete data via the EM algorithm," Journal of the Royal Statistical Society, Series B, vol. 34, pp. 1-38, 1977.
23. G. Schwartz, "Estimating the dimensions of a model," Ann. Stat., vol. 6, pp. 461-464, 1979.
24. Z. M. Zhao, et al., "Genotypic diversity of H5N1 highly pathogenic avian influenza viruses," J Gen Virol, vol. 89, pp. 2182- 2193, Sep 2008.
25. J. Felsenstein, "PHYLIP - Phylogeny Inference Package (Version 3.2)." Cladistics, vol. 5, pp. 164-166, 1989.
26. Z. Yang, "PAML: a program package for phylogenetic analysis by maximum likelihood," Comput Appl Biosci, vol. 13, pp. 555-556, Oct 1997. (Pubitemid 27480216)
27. Y. Bao, et al., "The influenza virus resource at the National Center for Biotechnology Information," J Virol, vol. 82, pp. 596-601, Jan 2008.
28. D. Posada and K. A. Crandall, "MODELTEST: testing the model of DNA substitution," Bioinformatics, vol. 14, pp. 817-818, 1998. (Pubitemid 28552116)