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BackgroundAvian influenza virus (AIV) infections have caused heavy economic losses to the poultry industry in Pakistan as well as numerous other regions worldwide. The first introduction of H7N3 AIV to Pakistan occurred during 1995, since then H7N3, H9N2 and H5N1 AIVs have each been sporadically isolated. This report evaluates the genetic origin of the H7N3 viruses from Pakistan collected 1995-2004 and how they disseminated within the country. To accomplish this we produced whole genome sequences for 6 H7N3 viruses and data for the HA and NA genes of an additional 7 isolates. All available sequence from H7N3 AIV from Pakistan was included in the analysis.ResultsPhylogenetic analysis revealed that there were two introductions of H7 into Pakistan and one N3 introduction. Only one of the H7 introductions appears to have become established in poultry in Pakistan, while the other was isolated from two separate outbreaks 6 years apart. The data also shows that reassortment has occurred between H7N3 and H9N2 viruses in the field, likely during co-infection of poultry. Also, with the exception of these few reassortant isolates, all 8 genes in the predominant H7N3 virus lineage have evolved to be phylogenetically distinct.ConclusionsAlthough rigorous control measures have been implemented in commercial poultry in Pakistan, AIV is sporadically transmitted to poultry and among the different poultry industry compartments (broilers, broiler breeders, table egg layers). Since there is one primary H7 lineage which persists and that has reassorted with the H9N2 AIV in poultry, it suggests that there is a reservoir with some link commercial poultry. On a general level, this offers insight into the molecular ecology of AIV in poultry where the virus has persisted despite vaccination and biosecurity. This data also illustrates the importance of sustained surveillance for AIVs in poultry.

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From November 2003 to June 2004 an epidemic of high pathogenicity avian influenza (HPAI) virus of subtype H7N3 affected the major layer and broiler-breeder raising areas of the country. This was accompanied by an outbreak of low pathogenicity avian influenza (LPAI) virus of type H9N2 in broilers and layers, which continued during 2005. Subsequently, in February 2006 avian influenza virus (AIV) subtype H5N1 was for the first time found in two isolated commercial flocks in this country. The HPAI outbreak of 2003-2004 was eventually overcome by enforcing biosecurity measures, controlling poultry movements, using inactivated vaccines, and introducing a comprehensive AI surveillance network throughout the country. However, similar measures undertaken to control H9N2 outbreaks have not been successful in the affected areas, with continuing increased mortality and heavy production losses in broilers and layers, respectively. A similar strategy has been devised to combat the spread of newly introduced H5N1 HPAIV. The description of these outbreaks and the results of the control strategy are reported here.

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