title: 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.
authors.affiliation: Emerging and Re-emerging Infectious Diseases in Animals, Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand. alongkorn.a@chula.ac.th
authors.forename: Alongkorn
authors.initials: A
authors.lastname: Amonsin
authors.forename: Jiradej
authors.initials: J
authors.lastname: Lapkuntod
authors.forename: Kamol
authors.initials: K
authors.lastname: Suwannakarn
authors.forename: Pravina
authors.initials: P
authors.lastname: Kitikoon
authors.forename: Sanipa
authors.initials: S
authors.lastname: Suradhat
authors.forename: Rachod
authors.initials: R
authors.lastname: Tantilertcharoen
authors.forename: Supanat
authors.initials: S
authors.lastname: Boonyapisitsopa
authors.forename: Napawan
authors.initials: N
authors.lastname: Bunpapong
authors.forename: Manoosak
authors.initials: M
authors.lastname: Wongphatcharachai
authors.forename: Trong
authors.initials: T
authors.lastname: Wisedchanwet
authors.forename: Apiradee
authors.initials: A
authors.lastname: Theamboonlers
authors.forename: Yong
authors.initials: Y
authors.lastname: Poovorawan
authors.forename: Jiroj
authors.initials: J
authors.lastname: Sasipreeyajan
authors.forename: Roongroje
authors.initials: R
authors.lastname: Thanawongnuwech
mesh_terms: D000818:Animals; D001717:Birds; D016000:Cluster Analysis; D004196:Disease Outbreaks; D005838:Genotype; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics* / Q000302:isolation & purification; D005585:Influenza in Birds / Q000453:epidemiology* / Q000821:virology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011200:Poultry; D012367:RNA, Viral / Q000235:genetics; D016865:Reassortant Viruses / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013785:Thailand / Q000453:epidemiology
chemical_list: D012367:RNA, Viral