Objective: To enrich the epidemiologic data of the waterfowl origin avian influenza virus (AIV).
Methods: The full genome of A/Muscovy Duck/Fujian/FZ01/2008 (H6N6), which was first isolated from domestic Muscovy duck in Fujian Province in southern China at 2008, was cloned and sequenced by reverse transcription polymerase chain reaction (RT-PCR).
Results: The motif of hemagglutinin (HA) cleavage site was PSMKVIV GL, which is a molecular characteristic of low pathogenic AIV, and the intravenoys pathogenicity index (IVPI) was 0.15. The HA gene, NP gene, gene and PB2 gene nucleotide sequences had similarity highest with A/duck/Kingmen/E322/04 (H6N2) at 94.2%, 95.7%, 97.2% and 95.6%, shared the same phylogenetic lineage. The neuraminidase (NA) gene had similarity highest with A/duck/Eastern China/01/2007 (H4N6) at 97.1 per cent, and also had 11 continuous amino acids (TNSTTTIINNN) deletion in the NA gene stalk region, which was first reported had deletion 11 amino acids in N6 subtype AIV NA genes' ORF. The NA gene had familiar phylogenetic relationship with H4N6 subtype AIV. The NS gene, PB1 gene and the PA gene had genetically close relationships with the H5N1 high pathogenic AIV strains isolated in Hong Kong at 1997. The eight genes also showed any immediate ancestor with other H6N6 subtype avian influenza viruses isolated in North America.
Conclusion: These data showed that A/Muscovy Duck/Fujian/FZ01/2008 (H6N6) was possibly a reassortant virus derived from H6N2 subtype, H4N6 subtype and H5N1 subtype AIV.