Amjad Khan
University of Veterinary and Animal Sciences, Pakistan
Title: Molecular Epidemiology of a novel re-assorted epidemic strain of equine influenza virus in Pakistan in 2015-16
Biography
Biography: Amjad Khan
Abstract
A widespread epidemic of equine influenza (EI) occurred in nonvaccinated equine population across multiple districts in Khyber
Pakhtunkhwa Province of Pakistan during 2015-2016. An epidemiological surveillance study was conducted from Oct 2015 to
April 2016 to investigate the outbreak. EI virus strains were isolated in embryonated eggs from suspected equines swab samples and
were subjected to genome sequencing using M13 tagged segment specific primers. Phylogenetic analyses of the nucleotide sequences
were concluded using Geneious. Haemagglutinin (HA), Neuraminidase (NA), Matrix (M) and Nucleoprotein (NP) genes nucleotide
and amino acid sequences of the isolated viruses were aligned with those of OIE recommended, FC-1, FC-2, and contemporary isolates
of influenza A viruses from other species. HA and NA gene amino acid sequences were very similar to Tennessee/14 and Malaysia/15
of FC-1 and clustered with the contemporary isolates recently reported in the USA. Phylogenetic analysis showed that these viruses
were mostly identical (with 99.6% and 97.4% nucleotide homology) to, and were reassortants containing chicken/Pakistan/14
(H7N3) and Canine/Beijing/10 (H3N2) like M and NP genes. Genetic analysis indicated that A/equine/Pakistan/16 viruses were
most probably the result of several re-assortments between the co-circulating avian and equine viruses, and were genetically unlike
the other equine viruses due to the presence of H7N3 or H3N2 like M and NP genes. Epidemiological data analysis indicated the
potential chance of mixed and management such as mixed farming system by keeping equine, canine and backyard poultry together
in confined premises as the greater risk factors responsible for the re-assortments. Other factors might have contributed to the spread
of the epidemic, including low awareness level, poor control of equine movements, and absence of border control disease strategies.