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Isolation and Sequence Analysis of Reassortant Low Pathogenic Avian Influenza Virus H4N6 from Duck and Chicken in Live Bird Markets from Pakistan
Naila Siddique1*, Khalid Naeem1, Zaheer Ahmed1, Muhammad Athar Abbas1, Akbar Ali1, Saba Rafique1, Farooq Rashid1, Imrana Begum1 and Rashid Farooq2
1National Reference Laboratory for Poultry Diseases, Animal Sciences Institute, National Agricultural Research Center, Park Road, Islamabad, Pakistan; 2Poultry Research Institute, Karachi, Pakistan
*Corresponding author:


The Live bird Markets (LBM) can serve as a paramount source of AIV infections. During routine Avian Influenza surveillance in Pakistan, low-pathogenic avian influenza virus subtype H4N6 was isolated first time from Khaki Campbell duck (Anas platyrhynchos) during 2010 and from broiler chicken during 2011 in the live bird markets (LBMs) from the port city of Karachi in Sindh province. Whole genome sequencing revealed introduction of a new reassortant Eurasian avian virus strain. Phylogenetically HA, NA, M, NP and PB2 genes clustered mostly with Russian strains of influenza viruses and PA gene with AI isolates from Netherlands, whereas NS and PB1 genes clustered with a Pakistani isolate of H3N1. Sequence analysis revealed a LP amino acid motif (PEKASR), avian-like receptors, conservation of amino acids at the receptor binding sites and the amino acids known to be associated with sensitivities to antiviral drugs, loss of glycosylation site in NA gene and attainment of unique PDZ domain motif (ESEI) at the C terminal of NS gene. The seroconversion against H4N6 subtype was observed mostly in the bird populations of Sindh and Khyber Pakhtoon Khawa provinces. The isolation divulged the role of LBM where mingling of different bird species provides an excellent environment for dissemination and potential reassortment of AIV. Moreover, various point mutations in these H4N6 isolates and close relationship with Pakistani H3N1 and other Eurasian strains also reflect prevailing diversity among AIVs circulating in the local LBMs.

Key words: Avian influenza virus, H4N6, Live bird market, Pakistan, Poultry


ISSN 0253-8318 (Print)
ISSN 2074-7764 (Online)