Genome

Virology 328 (2004) 169 – 176 www.elsevier.com/locate/yviro

Rapid Communication

The genome sequence analysis of H5N1 avian influenza A virus isolated from the outbreak among poultry populations in Thailand
Nareerat Viseshakula, Roongroje Thanawongnuwecha, Alongkorn Amonsina, Sanipa Suradhat a, Sunchai Payungpornb, Juthatip Keawchareona, Kanisak Oraveerakula, Piya Wongyanina, SukanyaPlitkula, Apiradee Theamboonlersb, Yong Poovorawanb,*
a

Faculty of Veterinary Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand b Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand Received 6 May 2004; returned to author for revision 4 June 2004; accepted 24 June 2004 Available online 25 August 2004

Abstract In this report, the genome of the Thaiavian influenza virus A (H5N1); A/Chicken/Nakorn-Pathom/Thailand/CU-K2/04, isolated from the Thai avian influenza A (AI) epidemic during the early of 2004 was sequenced. Phylogenetic analyses were performed in comparison to AI viruses from Hong Kong 1997 outbreaks and other AI (H5N1) isolates reported during 2001–2004. Molecular characterization of the Thai AI (H5N1) HA gene revealed a commoncharacteristic of a highly pathogenic AI (HPAI), a 20-codon deletion in the neuraminidase gene, a 5codon deletion in the NS gene and polymorphisms of the M2 and PB2 genes. Moreover, the HA and NA genes of the Thai AI displayed high similarity to those of the AI viruses isolated from human cases during the same epidemic. Finally, our results demonstrated that the Thai AI emerged as a member of 2000’sAI lineage with most of the genetic sequences closely related to the Influenza A/Duck/China/E319.2/03 (H5N1). D 2004 Elsevier Inc. All rights reserved.
Keywords: Avian Influenza A; H5N1; Thailand

Introduction During the past few years, several subtypes of avian influenza A (AI) including H5N1, H7N7, H9N2, and possibly H7N3 have been reported to be capable of infecting humans (Trampuz et al.,2004). In 1997, the highly pathogenic AI, H5N1 subtype originating from avian species was isolated from an infected human in Hong Kong, demonstrating direct transmission of the AI virus to humans (Bender et al., 1999; Suarez et al., 1998). This has caused significant concern as a potential source of another influenza pandemic. Although a massive poultry depopulation policy by the Hong KongGovernment in 1997 had
* Corresponding author. Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV Road, Patumwan, Bangkok 10330, Thailand. Fax: +66 2256 4911. E-mail address: Yong.P@Chula.ac.th (Y. Poovorawan). 0042-6822/$ - see front matter D 2004 Elsevier Inc. All rights reserved. doi:10.1016/j.virol.2004.06.045

successfully terminated the potential pandemiccrisis, in a series of avian epidemics, a significant re-emergence, highly pathogenic avian influenza (HPAI) H5N1 has been reported in several Asian countries including Korea, Japan, Taipei, Cambodia, Laos, Pakistan, China, Indonesia, and Thailand, with additionally confirmed cases of human death in Vietnam (Hien et al., 2004). Early in 2004, the AI (H5N1) virus has emerged in Vietnam and Thailandcausing severe epidemics in the poultry industry that resulted in a major economic loss of over 250 million USD. In Vietnam, AI had killed 16 of 22 human patients, and poultry culling policy had to be granted to stop the epidemic. In Thailand, the AI epidemic has killed 8 of 12 infected humans and resulted in a massive slaughter of over 26 millions poultry (CDC, 2004). It should be noted that Thailandwas reportedly free from AI outbreak. All cases reported in humans during the 2004 epidemics could be directly traced back to infected poultry (CDC, 2004).

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Rapid Communication

Shortly after the start of the epidemic, the Thai AI virus; A/Chicken/Nakorn-Pathom/Thailand/CU-K2/04 was isolated from the infected laying hen and confirmed to be an H5N1 subtype. The 8 genome fragments of...