Genetic analysis of avian influenza A viruses isolated from domestic waterfowl in live-bird markets of Hanoi, Vietnam, preceding fatal H5N1 human infections in 2004

Abstract

The first known cases of human infection with highly pathogenic avian influenza (HPAI) H5N1 viruses in Vietnam occurred in late 2003. However, HPAI H5N1 and low-pathogenic avian influenza (LPAI) H5N2 and H9N3 viruses were isolated from domestic waterfowl during live-bird market (LBM) surveillance in Vietnam in 2001 and 2003. To understand the possible role of these early viruses in the genesis of H5N1 strains infecting people, we performed sequencing and molecular characterization. Phylogenetic analysis revealed that the hemagglutinin (HA) genes of two geese HPAI H5N1 strains belonged to clade 3, and their surface glycoprotein and replication complex genes were most closely related (98.5-99.7% homologous) to A/duck/Guangxi/22/01 (H5N1) virus, detected contemporarily in southern China, whilst the M and NS genes were derived from an A/duck/Hong Kong/2986.1/00 (H5N1)-like virus. The H5 HA gene of the duck HPAI H5N1 strain belonged to clade 5 and acquired a gene constellation from A/quail/Shantou/3846/02 (H5N1), A/teal/China/2978.1/02 (H5N1) and A/partridge/Shantou/2286/03 (H5N1)-like viruses. The phylogenetic analysis further indicated that all eight gene segments of goose and duck HPAI H5N1 and LPAI H5N2 viruses were distinct from those of H5N1 clade-1 viruses known to have caused fatal human infections in Vietnam since late 2003. The duck H9N3 isolates derived genes from aquatic-bird influenza viruses, and their H9 HA belonged to the Korean lineage. The PB2 gene of A/duck/Vietnam/340/01 (H9N3) virus had lysine at position 627. Based on the molecular characterization of specific amino acid residues in the surface and relevant internal protein-coding genes, the Vietnamese H5N1 and H9N3 virus isolates indicated specificity to avian cell surface receptor and susceptibility for currently licensed anti-influenza A virus chemotherapeutics. Our findings suggest that the H5N1 and H5N2 viruses that circulated among geese and ducks in LBMs in Hanoi, Vietnam, during 2001 and 2003 were not the immediate ancestors of the clade-1 viruses associated with fatal human infections in Vietnam. The clade-1 HPAI H5N1 viruses were independently introduced into Vietnam.

Complex Reassortment of Multiple Subtypes of Avian Influenza Viruses in Domestic Ducks at the Dongting Lake Region of China

“…Of the four human pandemic influenza viruses, at least half, the 1957 H2N2 "Asian flu" and the 1968 "Hong Kong flu," emerged in southern China (58). It is generally accepted that live poultry markets play an important role in the ecology of AIV (17,18,(59)(60)(61)(62)(63)(64)(65). In 1996, the first avian H5N1 influenza virus was isolated in Guangdong Province, in southern China (22,66).…”

Anticipating the Prevalence of Avian Influenza Subtypes H9 and H5 in Live-Bird Markets

“…H5 and H9 continue to be isolated from live-bird markets in multiple countries [3], [4], [5] and thus pose an ongoing public health threat as potential pandemic strains. Quantitative tools for anticipating prevalence patterns of these subtypes in markets are needed to improve prevention and response plans in a cost-effective manner.…”

Indications that Live Poultry Markets Are a Major Source of Human H5N1 Influenza Virus Infection in China

“…However, there has been a lack of direct evidence showing an association between human isolates and those from live poultry markets. On the other hand, various subtypes, including H5N1 HPAIV, have been isolated from poultry or the environment in Asian markets (8,9,13,18 In this study, we sequenced the genomes of 31 H5N1…”