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:
naila.nrlpd@gmail.com
Abstract
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