Molecular characterization of Newcastle disease viruses from live bird markets in Nigeria

Abstract

Although Newcastle disease is reported to be endemic in Nigeria, little information exists on the molecular epidemiology and the lineage distribution of the Newcastle disease viruses (NDVs) in the country, especially in the live bird markets. Recent studies reported the identification of three distinct sub-lineages namely; 5f, 5g and 5h in West Africa, particularly sub-lineages 5f and 5g were identified in Nigeria. In this study a total of 41 NDV isolates were analysed. Thirty six NDVs were recovered from a variety of poultry species from live bird markets in the six geo-political zones of Nigeria during active surveillance from 2007 to 2008. Five NDVs recovered from outbreaks in backyard and commercial poultry farms within the same period were also genetically characterized. A commonly used region of the virus genome that spans nucleotide 61 to nucleotide 374 of the Fusion protein, including the cleavage site was targeted. Based on sequence analysis, 39 of the isolates were classified as virulent. Of these, 20 were classified as sub-lineage 5g and 17 were classified as sub-lineage 5f. One isolate differ markedly from all other strains included in the phylogeny. Interestingly, 13 strains from the 5f group formed a distinct cluster that was not identified by other groups in similar studies. Phylogenetic analysis, amino acid sequence determination of the F0 cleavage site sequence analysis, pair wise distance analysis of the partial fusion protein gene sequences and Geographic Information System (GIS) mapping was done. Results showed close genetic similarities and provided evidence for the first time of the epidemiological link between the viruses circulating in the LBMs and those identified in outbreaks in backyard and commercial farms in Nigeria between 2007 and 2008. The emergence and identification of new sub-lineages gives an insight in to the high rate of genetic drift occurring in NDV strains in Nigeria, and raises concerns about the efficacy of current NDV control measures in the country. Thus there is need for continuous surveillance and characterization of NDV from Nigeria to monitor the emergence of new lineages and sub-lineages in the Nigerian poultry industry. Copyright