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Title: Sequence and phylogenetic analysis of H7N3 avian influenza viruses isolated from poultry in Pakistan 1995-2004

Author
item ABBAS, MUHAMMAD - National Agricultural Research Center - Pakistan
item Spackman, Erica
item Swayne, David
item AHMED, ZAHEER - National Agricultural Research Center - Pakistan
item Sarmento, Luciana
item SIDDIQUE, NAILA - National Agricultural Research Center - Pakistan
item NAEEM, KHALID - National Agricultural Research Center - Pakistan
item HAMEED, ABDUL - Quaid-I-university Islamabad
item REHMANI, SHAFQAT - Sindh Agricultural University

Submitted to: Virology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/18/2010
Publication Date: 7/1/2010
Citation: Abbas, M.A., Spackman, E., Swayne, D.E., Ahmed, Z., Sarmento, L., Siddique, N., Naeem, K., Hameed, A., Rehmani, S. 2010. Sequence and phylogenetic analysis of H7N3 avian influenza viruses isolated from poultry in Pakistan 1995-2004. Virology Journal. 7:137.

Interpretive Summary: Avian influenza virus has been sporadically isolated from poultry in Pakistan since 1995. The H7N3 subtype has been the most common subtype identified. In order to elucidate the origin and the spread of these viruses in Pakistan the genetic sequence of key genes was determined for numerous isolates. Our analysis combined this new data with all previously available data to show that there were probably two introductions of H7 subtype avian influenza virus into Pakistan and only one became established in poultry and spread throughout the country. The initial introductions probably came from wild birds, but later spread was probably through poultry, suggesting that there are epidemiological links among different poultry populations in different regions of the country. In addition, since vaccine has been used for control, this new data shows how related field strains are to the vaccine strains; the more closely related they are the better the vaccine works. This work also reinforces how important surveillance programs for avian influenza virus are for poultry.

Technical Abstract: Avian Influenza Viruses (AIV) are among the most prominent emerging viruses affecting animal and public health. This report was designed to explore the genetic variation, which has occurred among AIVs of the H7N3 subtype in the Northeast, Central and Southern Regions of Pakistan during the last decade. AIV infections have caused heavy economic losses to the poultry industry in Pakistan as well as other regions worldwide. The first introduction of H7N3 high pathogenicity (HP) AIV to Pakistan occurred during 1995 and is believed to have originated as a result of reassortment between low pathogenicity (LP) and HP AIVs of different subtypes and genetic lineages. Since then AIV isolates of the H7N3, H9N2 and H5N1 subtypes have each been sporadically isolated. To evaluate the genetic origin of the viruses we produced whole genome sequences for 6 H7N3 viruses and produced sequence data for the hemagglutinin and neuraminidase genes of an additional 7 isolates. Phylogenetic analysis was conducted and the data presented indicates reassortment events are occurring among the AIVs of serotypes H7N3 and H9N2 in the field. Due to the introduction of H5N1 into poultry populations in Pakistan, as well as the continued circulation of the H9N2 lineage viruses, the likelihood of additional re-assortment among the circulating viruses in poultry requires a sustained surveillance of AIVs in this country.