Virulent Newcastle disease virus in Nigeria: identification of a new clade of sub-lineage 5f from livebird markets.

Newcastle disease (ND), caused by Avian Paramyxovirus Type 1, is a highly contagious and devastating viral disease of poultry of worldwide distribution with an enormous economic impact. Although ND 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 (LBMs). Recent studies reported the identification of three unique sub-lineages. namely; 5f, 5g and 5h in West Africa, and sub-lineages 5f and 5g in particular in non-commercial farms in Nigeria. In this study, 33 NDV isolates, which included NDVs recovered from LBMs in Nigeria, during active surveillance from 2007 to 2008 and viruses recovered from outbreaks in backyard and commercial chicken farms within the same period were analysed. Based on determination of the F(0) cleavage site amino acid sequence and phylogenetic analysis, the isolates were classified as virulent; 16 strains were identified as sub-lineage 5g and 17 as sub-lineage 5f. Interestingly, 13 strains from the 5f group formed a distinct cluster that was not identified by other groups in similar studies. The close genetic similarities identified, provided evidence for the first time of the epidemiological link between the viruses circulating in the LBMs and those recovered from outbreaks in backyard and commercial chicken farms in Nigeria between 2007 and 2008. The emergence and identification of new sub-lineages provide an insight into the high rate of genetic drift occurring in NDV strains in Nigeria, and raises a lot of concerns about the efficacy of current ND control measures in the country.