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

Muhammad A Abbas,Zaheer Ahmed,David E Swayne,Khalid Naeem,Luciana Sarmento,Abdul Hameed,Naila Siddique,Erica Spackman,Shafqat Rehmani

doi:10.1186/1743-422x-7-137

Muhammad A Abbas, Zaheer Ahmed + Show 7 more

Open Access

https://doi.org/10.1186/1743-422x-7-137

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Abstract

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.

Highlights

Avian influenza virus (AIV) infections have caused heavy economic losses to the poultry industry in Pakistan as well as numerous other regions worldwide
In November 1998 an outbreak that was later identified as H9N2 low pathogenicity (LP) AIV occurred in North West Frontier Province in otherwise healthy flocks that had not been vaccinated for AIV [1,3]
In 2000-2001, another outbreak was observed in Central Pakistan (Punjab), caused by H7N3 LP AIV which was controlled by ring vaccination with an aqueous-based vaccine produced with a local AIV strain followed by administration of an oil-based vaccine

Summary

Introduction

Avian influenza virus (AIV) infections have caused heavy economic losses to the poultry industry in Pakistan as well as numerous other regions worldwide. During early 2003, another outbreak of H7N3 LPAIV occurred in the Southern coastal region of the country, where more than 70% of the total commercial layer flocks in Pakistan are reared. Within months this LP AIV strain mutated to the HP form, producing a sudden increase in mortality and in November 2003 the H7N3 virus had an intravenous pathogenicity index of 2.8. The outbreak was controlled by adopting strict biosecurity measures, voluntary depopulation, strategic vaccination, and the implementation of a surveillance program in poultry populated areas throughout the country [4]

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