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Genetic diversity of Newcastle disease virus in Pakistan: a countrywide perspective.

ABSTRACT: 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.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.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.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.

SUBMITTER: Shabbir MZ

PROVIDER: S-EPMC3681574 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

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Genetic diversity of Newcastle disease virus in Pakistan: a countrywide perspective.

Shabbir Muhammad Zubair MZ Zohari Siamak S Yaqub Tahir T Nazir Jawad J Shabbir Muhammad Abu Bakr MA Mukhtar Nadia N Shafee Muhammad M Sajid Muhammad M Anees Muhammad M Abbas Muhammad M Khan Muhammad Tanveer MT Ali Asad Amanat AA Ghafoor Aamir A Ahad Abdul A Channa Aijaz Ali AA Anjum Aftab Ahmad AA Hussain Nazeer N Ahmad Arfan A Goraya Mohsan Ullah MU Iqbal Zahid Z Khan Sohail Ahmad SA Aslam Hassan Bin HB Zehra Kiran K Sohail Muhammad Umer MU Yaqub Waseem W Ahmad Nisar N Berg Mikael M Munir Muhammad M Munir Muhammad M

Virology journal 20130530

<h4>Background</h4>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.<h4>Material and methods</h4>To ascertain the genetics of NDV, 452 bl ...[more]

PMID: 23721461

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Project description:Banana Bunchy top virus (BBTV) is a multipartite circular single strand DNA virus that belongs to genus Babuvirus and family Nanoviridae. It causes significant crop losses worldwide and also in Pakistan. BBTV is present in Pakistan since 1988 however, till now only few (about twenty only) sequence of genomic components have been reported from the country. To have insights into current genetic diversity in Pakistan fifty-seven genomic components including five complete genomes (comprises of DNA-R, -U3, -S, -M, -C and -N components) were sequenced in this study. The genetic diversity analysis of populations from Pakistan showed that DNA-R is highly conserved followed by DNA-N, whereas DNA-U3 is highly diverse with the most diverse Common Region Stem-loop (CR-SL) in BBTV genome, a functional region, which previously been reported to have undergone recombination in Pakistani population. A Maximum Likelihood (ML) phylogenetic analysis of entire genomes of isolates by using sequence of all the components concatenated together with the reported genomes around the world revealed deeper insights about the origin of the disease in Pakistan. A comparison of the genetic diversity of Pakistani and entire BBTV populations around the world indicates that there exists a correlation between genetic diversity and recombination. Population genetics analysis indicated that the degree of selection pressure differs depending on the area and genomic component. A detailed analysis of recombination across various components and functional regions suggested that recombination is closely associated with the functional parts of BBTV genome showing high genetic diversity. Both genetic diversity and recombination analyses suggest that the CR-SL is a recombination hotspot in all BBTV genomes and among the six components DNA-U3 is the only recombined component that has extensively undergone inter and intragenomic recombination. Diversity analysis of recombinant regions results on average one and half fold increase and, in some cases up to four-fold increase due to recombination. These results suggest that recombination is significantly contributing to the genetic diversity of BBTV populations around the world.

Dataset Information

Genetic diversity of Newcastle disease virus in Pakistan: a countrywide perspective.

Publications

Genetic diversity of Newcastle disease virus in Pakistan: a countrywide perspective.

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