title: Genetic diversity of Newcastle disease virus in Pakistan: a countrywide perspective.
abstract: BACKGROUND
  Newcastle disease (ND) is one of the most deadly diseases of poultry around the globe. The disease is endemic in Pakistan and recurrent outbreaks are being reported regularly in wild captive, rural and commercial poultry flocks. Though, efforts have been made to characterize the causative agent in some of parts of the country, the genetic nature of strains circulating throughout Pakistan is currently lacking.
  
  
  METHODS
  To ascertain the genetics of NDV, 452 blood samples were collected from 113 flocks, originating from all the provinces of Pakistan, showing high mortality (30-80%). The samples represented domesticated poultry (broiler, layer and rural) as well as wild captive birds (pigeons, turkeys, pheasants and peacock). Samples were screened with real-time PCR for both matrix and fusion genes (1792 bp), positive samples were subjected to amplification of full fusion gene and subsequent sequencing and phylogenetic analysis.
  
  
  RESULTS
  The deduced amino acid sequence of the fusion protein cleavage site indicated the presence of motif (112RK/RQRR↓F117) typical for velogenic strains of NDV. Phylogenetic analysis of hypervariable region of the fusion gene indicated that all the isolates belong to lineage 5 of NDV except isolates collected from Khyber Pakhtunkhwa (KPK) province. A higher resolution of the phylogenetic analysis of lineage 5 showed the distribution of Pakistani NDV strains to 5b. However, the isolates from KPK belonged to lineage 4c; the first report of such lineage from this province.
  
  
  CONCLUSIONS
  Taken together, data indicated the prevalence of multiple lineages of NDV in different poultry population including wild captive birds. Such understanding is crucial to underpin the nature of circulating strains of NDV, their potential for interspecies transmission and disease diagnosis and control strategies.
authors.affiliation: Quality Operations Laboratory, University of Veterinary and Animal Sciences, Lahore, Pakistan. vetvains@uvas.edu.pk
authors.forename: Muhammad Zubair
authors.initials: MZ
authors.lastname: Shabbir
authors.forename: Siamak
authors.initials: S
authors.lastname: Zohari
authors.forename: Tahir
authors.initials: T
authors.lastname: Yaqub
authors.forename: Jawad
authors.initials: J
authors.lastname: Nazir
authors.forename: Muhammad Abu Bakr
authors.initials: MA
authors.lastname: Shabbir
authors.forename: Nadia
authors.initials: N
authors.lastname: Mukhtar
authors.forename: Muhammad
authors.initials: M
authors.lastname: Shafee
authors.forename: Muhammad
authors.initials: M
authors.lastname: Sajid
authors.forename: Muhammad
authors.initials: M
authors.lastname: Anees
authors.forename: Muhammad
authors.initials: M
authors.lastname: Abbas
authors.forename: Muhammad Tanveer
authors.initials: MT
authors.lastname: Khan
authors.forename: Asad Amanat
authors.initials: AA
authors.lastname: Ali
authors.forename: Aamir
authors.initials: A
authors.lastname: Ghafoor
authors.forename: Abdul
authors.initials: A
authors.lastname: Ahad
authors.forename: Aijaz Ali
authors.initials: AA
authors.lastname: Channa
authors.forename: Aftab Ahmad
authors.initials: AA
authors.lastname: Anjum
authors.forename: Nazeer
authors.initials: N
authors.lastname: Hussain
authors.forename: Arfan
authors.initials: A
authors.lastname: Ahmad
authors.forename: Mohsan Ullah
authors.initials: MU
authors.lastname: Goraya
authors.forename: Zahid
authors.initials: Z
authors.lastname: Iqbal
authors.forename: Sohail Ahmad
authors.initials: SA
authors.lastname: Khan
authors.forename: Hassan Bin
authors.initials: HB
authors.lastname: Aslam
authors.forename: Kiran
authors.initials: K
authors.lastname: Zehra
authors.forename: Muhammad Umer
authors.initials: MU
authors.lastname: Sohail
authors.forename: Waseem
authors.initials: W
authors.lastname: Yaqub
authors.forename: Nisar
authors.initials: N
authors.lastname: Ahmad
authors.forename: Mikael
authors.initials: M
authors.lastname: Berg
authors.forename: Muhammad
authors.initials: M
authors.lastname: Munir
mesh_terms: D000818:Animals; D001717:Birds; D016000:Cluster Analysis; D014644:Genetic Variation; D005838:Genotype; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D009521:Newcastle Disease / Q000453:epidemiology* / Q000821:virology*; D009522:Newcastle disease virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D010154:Pakistan / Q000453:epidemiology; D010802:Phylogeny; D011200:Poultry; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D014760:Viral Fusion Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D014760:Viral Fusion Proteins