Phylodynamics of H5N1 avian influenza virus in Indonesia

Molecular Ecology

Volumn 21, Issue 12, 2012, Pages 3062-3077

  Lam, Tommy Tsan Yuk ^a,c   Hon, Chung Chau ^a   Lemey, Philippe ^b   Pybus, Oliver G ^c   Shi, Mang ^a   Tun, Hein Min ^a   Li, Jun ^a   Jiang, Jingwei ^a   Holmes, Edward C ^d,e   Leung, Frederick Chi Ching ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d PENNSYLVANIA STATE UNIVERSITY   (United States)

^e NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

agriculture; ecology; evolution; influenza; phylodynamics; phylogeography

Indexed keywords

INFLUENZA VIRUS HEMAGGLUTININ;

ANIMAL; ARTICLE; AVIAN INFLUENZA; BIRD DISEASE; EPIDEMIC; EVOLUTION; GENETIC VARIABILITY; GENETICS; HUMAN; INDONESIA; INFLUENZA; INFLUENZA VIRUS A H5N1; PHYLOGENY; PHYLOGEOGRAPHY; POULTRY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; VIROLOGY; ZOONOSIS;

ANIMALS; BIOLOGICAL EVOLUTION; DISEASE OUTBREAKS; GENETIC VARIATION; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HUMANS; INDONESIA; INFLUENZA A VIRUS, H5N1 SUBTYPE; INFLUENZA IN BIRDS; INFLUENZA, HUMAN; PHYLOGENY; PHYLOGEOGRAPHY; POULTRY; POULTRY DISEASES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; ZOONOSES;

ANIMALIA; AVIAN INFLUENZA VIRUS; ORTHOMYXOVIRIDAE;

EID: 84861998642     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05577.x     Document Type: Article

References (69)

1. Azhar M, Lubis AS, Siregar ES, et al. (2010) Participatory disease surveillance and response in Indonesia: strengthening veterinary services and empowering communities to prevent and control highly pathogenic avian influenza. Avian Diseases, 54, 749-753.
2. Baigent SJ, McCauley JW, (2001) Glycosylation of haemagglutinin and stalk-length of neuraminidase combine to regulate the growth of avian influenza viruses in tissue culture. Virus Research, 79, 177-185.
3. Bao Y, Bolotov P, Dernovoy D, et al. (2008) The influenza virus resource at the National Center for Biotechnology Information. Journal of Virology, 82, 596-601.
4. Biek R, Henderson JC, Waller LA, Rupprecht CE, Real LA, (2007) A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus. Proceedings of the National Academy of Sciences of the United States of America, 104, 7993-7998.
5. Boon AC, Sandbulte MR, Seiler P, et al. (2007) Role of terrestrial wild birds in ecology of influenza A virus (H5N1). Emerging Infectious Diseases, 13, 1720-1724.
6. Carrington CV, Foster JE, Pybus OG, Bennett SN, Holmes EC, (2005) Invasion and maintenance of dengue virus type 2 and type 4 in the Americas. Journal of Virology, 79, 14680-14687.
7. Chutinimitkul S, Songserm T, Amonsin A, et al. (2007) New strain of influenza A virus (H5N1), Thailand. Emerging Infectious Diseases, 13, 506-507.
8. Department of Agriculture (2004) Highly Pathogenic Avian Influenza in Indonesia. OIE, Jakarta, Indonesia.
9. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
10. Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W, (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics, 161, 1307-1320.
11. Drummond AJ, Rambaut A, Shapiro B, Pybus OG, (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution, 22, 1185-1192.
12. Drummond AJ, Ho SY, Phillips MJ, Rambaut A, (2006) Relaxed phylogenetics and dating with confidence. PLoS Biology, 4, e88.
13. Duffy S, Shackelton LA, Holmes EC, (2008) Rates of evolutionary change in viruses: patterns and determinants. Nature reviews. Genetics, 9, 267-276.
14. Dung Nguyen T, Vinh Nguyen T, Vijaykrishna D, et al. (2008) Multiple sublineages of influenza A virus (H5N1), Vietnam, 2005-2007. Emerging Infectious Diseases, 14, 632-636.
15. Edgar RC, (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
16. Edmonds CA, Lillie AS, Cavalli-Sforza LL, (2004) Mutations arising in the wave front of an expanding population. Proceedings of the National Academy of Sciences of the United States of America, 101, 975-979.
17. Grenfell BT, Pybus OG, Gog JR, et al. (2004) Unifying the epidemiological and evolutionary dynamics of pathogens. Science, 303, 327-332.
18. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696-704.
19. Holmes EC, (2008) Evolutionary history and phylogeography of human viruses. Annual review of microbiology, 62, 307-328.
20. Hon CC, Lam TY, Drummond A, et al. (2006) Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B. Journal of Virology, 80, 8503-8509.
21. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP, (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294, 2310-2314.
22. ILRI (2008) Operational Research in Indonesia for More Effective Control of Highly Pathogenic Avian Influenza. ILRI, Nairobi.
23. Kandun IN, Wibisono H, Sedyaningsih ER, et al. (2006) Three Indonesian clusters of H5N1 virus infection in 2005. New England Journal of Medicine, 355, 2186-2194.
24. Kaverin NV, Rudneva IA, Ilyushina NA, et al. (2002) Structure of antigenic sites on the haemagglutinin molecule of H5 avian influenza virus and phenotypic variation of escape mutants. Journal of General Virology, 83, 2497-2505.
25. Klopfstein S, Currat M, Excoffier L, (2006) The fate of mutations surfing on the wave of a range expansion. Molecular biology and evolution, 23, 482-490.
26. Lam TT, Hon CC, Pybus OG, et al. (2008a) Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia. PLoS Pathogens, 4, e1000130.
27. Lam TY, Hon CC, Wang Z, et al. (2008b) Evolutionary analyses of European H1N2 swine influenza A virus by placing timestamps on the multiple reassortment events. Virus research, 131, 271-278.
28. Lam TT, Hon CC, Tang JW, (2010) Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections. Critical reviews in clinical laboratory sciences, 47, 5-49.
29. Lam TT, Ip HS, Ghedin E, et al. (2012) Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds. Ecology letters, 15, 24-33.
30. Lemey P, Kosakovsky Pond SL, Drummond AJ, et al. (2007) Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Computational Biology, 3, e29.
31. Lemey P, Rambaut A, Drummond AJ, Suchard MA, (2009) Bayesian phylogeography finds its roots. PLoS Computational Biology, 5, e1000520.
32. Lemey P, Rambaut A, Welch JJ, Suchard MA, (2010) Phylogeography takes a relaxed random walk in continuous space and time. Molecular Biology and Evolution, 27, 1877-1885.
33. Long NT, Thanh TT, van Doorn HR, et al. (2011) Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. Transboundary and Emerging Diseases, 58, 537-543.
34. Munkemuller T, Travis MJ, Burton OJ, Schiffers K, Johst K, (2011) Density-regulated population dynamics and conditional dispersal alter the fate of mutations occurring at the front of an expanding population. Heredity, 106, 678-689.
35. Muse SV, Gaut BS, (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Molecular Biology and Evolution, 11, 715-724.
36. Normile D, (2006) Avian influenza. Human transmission but no pandemic in Indonesia. Science, 312, 1855.
37. Perdue ML, Suarez DL, (2000) Structural features of the avian influenza virus hemagglutinin that influence virulence. Veterinary Microbiology, 74, 77-86.
38. Perkins LE, Swayne DE, (2002) Pathogenicity of a Hong Kong-origin H5N1 highly pathogenic avian influenza virus for emus, geese, ducks, and pigeons. Avian Diseases, 46, 53-63.
39. Poetranto ED, Yamaoka M, Nastri AM, et al. (2011) An H5N1 highly pathogenic avian influenza virus isolated from a local tree sparrow in Indonesia. Microbiology and immunology, 55, 666-672.
40. Pond SL, Frost SD, Muse SV, (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics, 21, 676-679.
41. Pupko T, Pe'er I, Shamir R, Graur D, (2000) A fast algorithm for joint reconstruction of ancestral amino acid sequences. Molecular Biology and Evolution, 17, 890-896.
42. Pybus OG, Rambaut A, (2002) GENIE: estimating demographic history from molecular phylogenies. Bioinformatics, 18, 1404-1405.
43. Pybus OG, Rambaut A, (2009) Evolutionary analysis of the dynamics of viral infectious disease. Nature reviews. Genetics, 10, 540-550.
44. Pybus OG, Rambaut A, Harvey PH, (2000) An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics, 155, 1429-1437.
45. Pybus OG, Charleston MA, Gupta S, et al. (2001) The epidemic behavior of the hepatitis C virus. Science, 292, 2323-2325.
46. Real LA, Henderson JC, Biek R, et al. (2005) Unifying the spatial population dynamics and molecular evolution of epidemic rabies virus. Proceedings of the National Academy of Sciences USA, 102, 12107-12111.
47. Sedyaningsih ER, Isfandari S, Setiawaty V, et al. (2007) Epidemiology of cases of H5N1 virus infection in Indonesia, July 2005-June 2006. Journal of Infectious Diseases, 196, 522-527.
48. Shackelton LA, Parrish CR, Truyen U, Holmes EC, (2005) High rate of viral evolution associated with the emergence of carnivore parvovirus. Proceedings of the National Academy of Sciences USA, 102, 379-384.
49. Shigesada N, Kawasaki K, (1997) Biological Invasions: Theory and Practice. Oxford Univ. Press, Oxford.
50. Shortridge KF, Zhou NN, Guan Y, et al. (1998) Characterization of avian H5N1 influenza viruses from poultry in Hong Kong. Virology, 252, 331-342.
51. Slatkin M, Maddison WP, (1989) A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics, 123, 603-613.
52. Smith GJ, Vijaykrishna D, Bahl J, et al. (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature, 459, 1122-1125.
53. Soebandrio A, (2005) Avian influenza: the Indonesian experience. In International Conference on Biosafety and Biorisks. Lyon, France. 2-3 March, Lyon, France.
54. Stoops AC, Barbara KA, Indrawan M, et al. (2009) H5N1 surveillance in migratory birds in Java, Indonesia. Vector Borne and Zoonotic Diseases, 9, 695-702.
55. Suchard MA, Weiss RE, Sinsheimer JS, (2001) Bayesian selection of continuous-time Markov chain evolutionary models. Molecular Biology and Evolution, 18, 1001-1013.
56. Sumiarto B, Arifin B, (2008) Overview on Poultry Sector and HPAI Situation for Indonesia with Special Emphasis on the Island of Java-Background Paper. In: Africa/Indonesia Team Working Paper No. 3. International Food Policy Research Institute (IFPRI) with the International Livestock Research Institute (ILRI) and Royal Veterinary College (RVC).
57. Suwannakarn K, Amonsin A, Sasipreeyajan J, et al. (2009) Molecular evolution of H5N1 in Thailand between 2004 and 2008. Infection, Genetics and Evolution, 9, 896-902.
58. Swofford DL, (2003) PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates, Sunderland, Massachusetts.
59. Takano R, Nidom CA, Kiso M, et al. (2009) Phylogenetic characterization of H5N1 avian influenza viruses isolated in Indonesia from 2003-2007. Virology, 390, 13-21.
60. Talbi C, Lemey P, Suchard MA, et al. (2010) Phylodynamics and human-mediated dispersal of a zoonotic virus. PLoS pathogens, 6, e1001166.
61. Tang Y, Wu P, Peng D, et al. (2009) Characterization of duck H5N1 influenza viruses with differing pathogenicity in mallard (Anas platyrhynchos) ducks. Avian Pathology, 38, 457-467.
62. Travis JM, Munkemuller T, Burton OJ, et al. (2007) Deleterious mutations can surf to high densities on the wave front of an expanding population. Molecular biology and evolution, 24, 2334-2343.
63. Twiddy SS, Pybus OG, Holmes EC, (2003) Comparative population dynamics of mosquito-borne flaviviruses. Infection, Genetics and Evolution, 3, 87-95.
64. Wallace RG, Hodac H, Lathrop RH, Fitch WM, (2007) A statistical phylogeography of influenza A H5N1. Proceedings of the National Academy of Sciences USA, 104, 4473-4478.
65. Walsh PD, Biek R, Real LA, (2005) Wave-like spread of Ebola Zaire. PLoS Biology, 3, e371.
66. Webster RG, Guan Y, Peiris M, et al. (2002) Characterization of H5N1 influenza viruses that continue to circulate in geese in southeastern China. Journal of Virology, 76, 118-126.
67. WHO (2005) Evolution of H5N1 avian influenza viruses in Asia. Emerging Infectious Diseases, 11, 1515-1521.
68. WHO (2011) Cumulative Number of Confirmed Human Cases of Avian Influenza A/(H5N1) Reported to WHO. WHO, Geneva, Switzerland.
69. Xu X, Subbarao K, Cox NJ, Guo Y, (1999) Genetic characterization of the pathogenic influenza A/Goose/Guangdong/1/96 (H5N1) virus: similarity of its hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks in Hong Kong. Virology, 261, 15-19.