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

Muhammad Zubair Shabbir1*, Siamak Zohari2, Tahir Yaqub1, Jawad Nazir3, Muhammad Abu Bakr Shabbir1, Nadia Mukhtar1, Muhammad Shafee4, Muhammad Sajid5, Muhammad Anees6, Muhammad Abbas7, Muhammad Tanveer Khan8, Asad Amanat Ali9, Aamir Ghafoor10, Abdul Ahad11, Aijaz Ali Channa12, Aftab Ahmad Anjum3, Nazeer Hussain13, Arfan Ahmad10, Mohsan Ullah Goraya14, Zahid Iqbal6, Sohail Ahmad Khan6, Hassan bin Aslam3, Kiran Zehra15, Muhammad Umer Sohail16, Waseem Yaqub1, Nisar Ahmad17, Mikael Berg14 and Muhammad Munir18*

Author Affiliations

1 Quality Operations Laboratory, University of Veterinary and Animal Sciences, Lahore, Pakistan

2 National Veterinary Institute, Uppsala, Sweden

3 Department of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan

4 University of Baluchistan, Quetta, Pakistan

5 Veterinary Research and Disease Investigation Center, Abbottabad, Pakistan

6 Livestock and Dairy Development Department, Punjab, Pakistan

7 Veterinary Research Institute, Lahore, Pakistan

8 Department of Biology, University of Bergen, Bergen, Norway

9 Poultry Research Institute, Rawalpindi, Pakistan

10 University Diagnostic Laboratory, University of Veterinary and Animal Sciences, Lahore, Pakistan

11 Department of Microbiology, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladesh

12 Department of Theriogenology, University of Veterinary and Animal Sciences, Lahore, Pakistan

13 Sindh Poultry Vaccine Center, Karachi, Pakistan

14 Swedish University of Agricultural Sciences, Uppsala, Sweden

15 Department of Geography, Government College University, Lahore, Pakistan

16 Government Collage University Faisalabad, Faisalabad, Pakistan

17 Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan

18 The Pirbright Institute, Compton Laboratory, Compton, Berkshire RG20 7NN, United Kingdom

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Virology Journal 2013, 10:170  doi:10.1186/1743-422X-10-170

Published: 30 May 2013

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.

Material and 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.

Keywords:
Lineages; Newcastle disease virus; Pakistan; Phylogenetic analysis; Poultry