Abstract
Identification of pathotype of Avian Influenza Virus (AIV) subtype H5N1 isolates is very important. This research aimed to identify the pathotype of AIV subtype H5N1 isolated from household waterfowls in West Java based on molecular markers of amino acid sequences of the Hemagglutinin (HA) cleavage site. Fragments of HA genes of 21 isolates were amplified using RT-PCR with a primer pair that flanking the cleavage site region, and sequenced with dideoxy-termination method with ABI automatic sequencer (Applied Biosystems). Multiple alignment of nucleotide and their deduced amino acid sequence were analyzed using ClustalW from MEGA 3.1 program. The result shows that all H5N1 isolates (21 isolates) possess polybasic cleavage sites with 2 patterns of amino acid sequence, i.e QRERRRKKR (20 isolates) and QRESRRKKR (1 isolate). This finding indicates that all of the viruses isolated in this research were of highly pathogenic avian influenza (HPAI) strains. Keywords: cleavage site, waterfowls, HPAI
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