Influenza A(H5N1) virus surveillance at live poultry markets, Cambodia, 2011

Abstract

In Cambodia, influenza A(H5N1) virus surveillance at live poultry markets (LPMs) relies on virus isolation from poultry specimens; however, virus is rarely detected by this method. We tested 502 environmental LPM samples: 90 were positive by PCR, 10 by virus isolation. Virus circulation could be better monitored by environmental sampling of LPMs.

Figure 1

Prevalence of influenza A(H5N1) virus–positive environmental samples from live poultry markets, by collection week, during the Khmer New Year festival, Cambodia, 2011. The New Year festival occurred during week 4 of the study. M1, Orussey market (Phnom Penh); M2, Chamkar Doung market (Phnom Penh); M3, Takeo market (Takeo Province); M4, Kampong Cham market (Kampong Cham Province). Samples positive for the matrix, hemagglutinin 5, and neuraminidase 1 genes by quantitative real-time reverse transcription PCR were considered positive for subtype H5N1 virus. In rare instances, neuraminidase 1–negative samples that were positive for the matrix and hemagglutinin genes were considered positive for subtype H5N1 virus.

Figure 2

Phylogenetic relationship of the hemagglutinin (HA) gene among various influenza A(H5N1) strains; HA sequences for 48 strains (36 from Cambodia, 11 from Vietnam and one from China) were included in the analysis. Black triangles indicate viruses detected during this study of environmental samples from live poultry markets in Cambodia. Phylogenetic trees were generated by using the distance method and applying the neighbor-joining algorithm with bootstrap analysis (1,000 replicates). Analysis was based on nt 1–1,661 of the HA gene. The trees were rooted to A/goose/China/Guangdong/1/96 (H5N1). Numbers above and below branch nodes indicate bootstrap value of >70%. Scale bar represents the number of nucleotide changes per site. Lineage numbers 1–6, clades, and subclades indicate strains that are grouped in closely related phylogenetic lineages, as described (14). All sequences included in the analysis are available in GenBank.