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.
Highlights
The H5N1 highly pathogenic avian influenza (HPAI) virus was originally isolated from a farmed goose in Guangdong province of China in 1996 [1], and soon spread to live-poultry markets in Hong Kong [2], resulting in 18 cases of human infection in 1997, 6 of which were fatal [3,4]
H5N1 highly pathogenic avian influenza (HPAI) virus emerged in China in 1996, and has spread beyond Asia since 2003
Following the first outbreak reported in Indonesian poultry farms in December 2003, the virus spilled over to 27 Indonesian provinces by June 2006, and became endemic in the country
Summary
The H5N1 highly pathogenic avian influenza (HPAI) virus was originally isolated from a farmed goose in Guangdong province of China in 1996 [1], and soon spread to live-poultry markets in Hong Kong [2], resulting in 18 cases of human infection in 1997, 6 of which were fatal [3,4]. H5N1 outbreaks recurred in 2003, persistently affecting poultry farms in many Southeast Asia countries, such as China, Thailand, Vietnam, Indonesia and Cambodia. Occasional zoonotic transmissions to humans occurred in most of the affected Asian countries and the virus continued to pose a serious threat to global public health [6]. The virus rapidly became endemic in Indonesia [9,10], and continued to cause sporadic zoonotic transmissions to humans beginning in July 2005 [9]. As of April 8, 2008, Indonesia had 132 confirmed human cases with 107 deaths [13], the largest number of deaths among all affected countries
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