Characterization and Phylogenetic Analysis of Avian Influenza Virus Subtype H9N2 in Pakistan
Characterization and Phylogenetic Analysis of Avian Influenza Virus Subtype H9N2 in Pakistan
Muhammad Abid1*, Tahir Yaqub2, Arslan Mehboob3 and Muhammad Zubair Shabbir4
ABSTRACT
H9N2 avian influenza viruses are currently endemic in Pakistan and outbreaks are continuously being reported with high morbidity, drop in egg production and reduced weight gain. Besides economic losses to the poultry industry, these viruses pose a significant threat to public health. Owing to significant involvements of neuraminidase (NA) gene in virus pathobiology by mediating virus entry and release, the present study was conducted to determine the phylogenetic relationship of currently prevailing H9N2 isolates in Pakistan. A sum of ten H9N2 AIVs were isolated from 400 suspected samples and were confirmed through serological and molecular assays. The sequence analysis of NA genes shown 99% homology with the H9N2 AIV recently isolated from Pakistan and their phylogenetic analysis revealed that all the isolates belonged to the G- lineage. Amino acid analysis of NA stalk regions of these isolates illustrated no insertion, deletion and substitutions compared to A/DK/HK/Y280/97 lineage and human isolates (A/HK/1073/99 and A/HK/1074/99). Several amino acid substitutions at various regions of the NA protein were determined with unknown functions and consequences. These findings warrant future studies for analysis of whole genome sequencing of prevailing H9N2 viruses in Pakistan which may further contribute towards the better understanding of the genetic nature and evolutionary behavior of these viruses in the country.
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