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.

Evolutionary Dynamics of Multiple Sublineages of H5N1 Influenza Viruses in Nigeria from 2006 to 2008

“…Notably, all of the Nigerian reassortant viruses possess an NS gene of sublineage I origin and PB2, PA, MP, and NA genes belonging to sublineage II, perhaps suggesting that these segments confer a selective advantage. Cocirculation of multiple genetically distinct sublineages has also been reported in others countries, such as China (31), Vietnam (24), Indonesia (16), and Thailand (29). To explain the observed patterns of genetic reassortment of H5N1 in China, Vijaykrishna et al suggested that viruses undergo regular reassortment with endemic H5N1 viruses in domestic ducks and subsequently are transmitted to poultry (31).…”

Introduction of Virulence Markers in PB2 of Pandemic Swine-Origin Influenza Virus Does Not Result in Enhanced Virulence or Transmission

“…20090508.1722). It has previously been suggested that the E667G substitution in PB2 of HPAI H5N1 virus was under positive selection and possibly played a role in sustainable transmission in humans (14).…”

Increased substitution rate in H5N1 avian influenza viruses during mass vaccination of poultry

“…However, such work was hindered either by inadequate sequences available in GenBank, or by the frequent gene re-assortment between H5N1 HPAI viruses and other avian influenza viruses [10,12,[47][48][49][50][51]. Some re-assortment activities involving similar sequences cannot be easily identified through phylogenetic analysis, and the substitution rate may be overestimated if some re-assortment activities are ignored in the estimation.…”

“…Circulation of H5N1 HPAI virus in Indonesia was firstly identified in 2003, and was confirmed in each of the subsequent years [12]. Gene sequences of some H5N1 HPAI vi-ruses circulating in Indonesia in [2003][2004][2005][2006][2007][2008][2009] have been available in GenBank.…”