Genetic Study of H5N1 Yields Clues to Control

THAILAND - After working on the genetic characterisation of the 2008 bird flu virus, researchers at Chulalongkorn University recommend focussing on the prevention of the viruses circulating in high-risk areas, as well as continuous surveillance and whole genome sequencing of H5N1 viruses.
calendar icon 20 September 2010
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Alongkorn Amonsin and colleagues at Chulalongkorn University in Bangkok have published the genetic characterization of 2008 reassortant influenza A virus (H5N1) found in Thailand in Virology Journal.

In January and November 2008, outbreaks of avian influenza (AI) were reported in four provinces of Thailand, explain Amonsin and colleagues. Eight influenza A H5N1 viruses were recovered from these 2008 AI outbreaks and comprehensively characterised and analysed 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 three per cent genetic differences) as commonly found in influenza A viruses.

Based on phylogenetic analysis, clade 1 viruses in Thailand were divided into three distinct branches (subclades 1, 1.1 and 1.2). Six out of eight H5N1 isolates were 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 estimates 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 eight genes of the viruses have remained unchanged.

The Chulalongkorn group says that 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.

They recommend that 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.


Amonsin A., J. Lapkuntod, K. Suwannakarn, P. Kitikoon, S. Suradhat, R. Tantilertcharoen, S. Boonyapisitsopa, N. Bunpapong, M. Wongphatcharachai, T. Wisedchanwet, A. Theamboonlers, Y. Poovorawan, J. Sasipreeyajan and R. Thanawongnuwech. 2010. Genetic characterization of 2008 reassortant influenza A virus (H5N1), Thailand. Virology Journal. 7:233. doi:10.1186/1743-422X-7-233

Further Reading

- You can view the full report (as a provisional PDF) by clicking here.

Further Reading

- You can visit the Avian Flu page by clicking here.
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