title: Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia.
abstract: H5N1 highly pathogenic avian influenza (HPAI) viruses have seriously affected the Asian poultry industry since their recurrence in 2003. The viruses pose a threat of emergence of a global pandemic influenza through point mutation or reassortment leading to a strain that can effectively transmit among humans. In this study, we present phylogenetic evidences for the interlineage reassortment among H5N1 HPAI viruses isolated from humans, cats, and birds in Indonesia, and identify the potential genetic parents of the reassorted genome segments. Parsimony analyses of viral phylogeography suggest that the reassortant viruses may have originated from greater Jakarta and surroundings, and subsequently spread to other regions in the West Java province. In addition, Bayesian methods were used to elucidate the genetic diversity dynamics of the reassortant strain and one of its genetic parents, which revealed a more rapid initial growth of genetic diversity in the reassortant viruses relative to their genetic parent. These results demonstrate that interlineage exchange of genetic information may play a pivotal role in determining viral genetic diversity in a focal population. Moreover, our study also revealed significantly stronger diversifying selection on the M1 and PB2 genes in the lineages preceding and subsequent to the emergence of the reassortant viruses, respectively. We discuss how the corresponding mutations might drive the adaptation and onward transmission of the newly formed reassortant viruses.
authors: School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China.
authors: Tommy Tsan-Yuk
authors: TT
authors: Lam
authors: Chung-Chau
authors: CC
authors: Hon
authors: Oliver G
authors: OG
authors: Pybus
authors: Sergei L
authors: SL
authors: Kosakovsky Pond
authors: Raymond Tze-Yeung
authors: RT
authors: Wong
authors: Chi-Wai
authors: CW
authors: Yip
authors: Fanya
authors: F
authors: Zeng
authors: Frederick Chi-Ching
authors: FC
authors: Leung
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D005814:Genes, Viral; D006801:Humans; D007214:Indonesia / Q000453:epidemiology; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics* / Q000472:pathogenicity; D005585:Influenza in Birds / Q000453:epidemiology / Q000235:genetics* / Q000635:transmission*; D011200:Poultry; D011201:Poultry Diseases / Q000453:epidemiology / Q000235:genetics* / Q000635:transmission*