Genetic characterization of 2008 reassortant influenza A virus (H5N1), Thailand

Abstract

In January and November 2008, outbreaks of avian influenza have been reported in 4 provinces of Thailand. Eight Influenza A H5N1 viruses were recovered from these 2008 AI outbreaks and comprehensively characterized and analyzed for nucleotide identity, genetic relatedness, virulence determinants, and possible sites of reassortment. The results show that the 2008 H5N1 viruses displayed genetic drift characteristics (less than 3% genetic differences), as commonly found in influenza A viruses. Based on phylogenetic analysis, clade 1 viruses in Thailand were divided into 3 distinct branches (subclades 1, 1.1 and 1.2). Six out of 8 H5N1 isolates have been identified as reassorted H5N1 viruses, while other isolates belong to an original H5N1 clade. These viruses have undergone inter-lineage reassortment between subclades 1.1 and 1.2 and thus represent new reassorted 2008 H5N1 viruses. The reassorted viruses have acquired gene segments from H5N1, subclade 1.1 (PA, HA, NP and M) and subclade 1.2 (PB2, PB1, NA and NS) in Thailand. Bootscan analysis of concatenated whole genome sequences of the 2008 H5N1 viruses supported the reassortment sites between subclade 1.1 and 1.2 viruses. Based on estimating of the time of the most recent common ancestors of the 2008 H5N1 viruses, the potential point of genetic reassortment of the viruses could be traced back to 2006. Genetic analysis of the 2008 H5N1 viruses has shown that most virulence determinants in all 8 genes of the viruses have remained unchanged. In summary, two predominant H5N1 lineages were circulating in 2008. The original CUK2-like lineage mainly circulated in central Thailand and the reassorted lineage (subclades 1.1 and 1.2) predominantly circulated in lower-north Thailand. To prevent new reassortment, emphasis should be put on prevention of H5N1 viruses circulating in high risk areas. In addition, surveillance and whole genome sequencing of H5N1 viruses should be routinely performed for monitoring the genetic drift of the virus and new reassorted strains, especially in light of potential reassortment between avian and mammalian H5N1 viruses.

Evolutionary and Ecological Dynamics of Transboundary Disease Caused by H5N1 Virus in Southeast Asia

“…In 2007, clade 2.3.4 strains replaced clade 1 viruses and thrived in northern Vietnam, which were susceptible to amantadine but showed reduced susceptibility to oseltamivir (Le et al., ). The clade 2.3.4 viruses (Fujian‐like) isolated from Thailand contain CK/THA/NP‐172/06, Ck/Mukdahan/NIAH403901/07, Dk/Nong‐Khai/THA/KU‐56/07 and Ck/Nongkhai/NIAH400802/07, which were detected in 2006 and 2007 in the north‐eastern region of Thailand, and the locations where viruses were detected, Nakhon Panom, Mukdahan and NongKhai, form the border with Laos (Amonsin et al., ). Furthermore, the Laos H5N1 strains in 2007 clustered with 2007 isolates from Vietnam and Thailand, belonging to clade 2.3.4.…”

“…In 2008, PC168‐like and PC170‐like viruses were replaced by the reassorted viruses from these two lineages. CUK2‐like and reassorted viruses represent the predominant lineages and have been circulating in Thailand (Amonsin et al., ). The timing of H5N1 clade isolation in Vietnam indicated the evolution of lineages.…”

Risk Factors for Exposure to Influenza A Viruses, Including Subtype H5 Viruses, in Thai Free-Grazing Ducks

“…Experimental studies report low influenza HI titres in ducks after experimental infection (Saito et al, 2009). Regardless of aetiology, low titres could allow persistence of virus in ducks during the hot summer months as suggested elsewhere Amonsin et al, 2010;Magor, 2011). Additionally, minimal duck seroconversion may help limit virus evolution in Central Thailand, particularly in an unvaccinated population, as host immunity plays a role in influenza virus evolution (Webster et al, 1992).…”

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.…”