Molecular characterization of Newcastle Disease Virus in domestic poultry in Uganda

Abstract

Newcastle disease caused by Newcastle disease virus continues to be a threat to the poultry industry worldwide. The disease has become more pronounced in resource constrained households that rely on backyard poultry system as a source of income and animal protein particularly in under developed countries including Uganda. Newcastle disease virus in different geographical locations has been found to differ in both virulence and epidemiology, and the recent discovery of unique Newcastle disease virus strains in Uganda in 2004 call for enhanced vigilance and research into Newcastle disease virus strains in Uganda so as to contribute to an efficient control strategy. This study was undertaken to determine the prevalence of Newcastle disease virus in apparently healthy birds, identify the Newcastle disease virus pathotypes and genotypes circulating in Uganda and to compare the regional distribution of these strains in live bird markets in Uganda. Six hundred fifty (each of cloacal and oropharyngeal swabs) samples were collected from live bird markets in all the regions of Uganda. In addition, five pooled tissue samples were collected from an outbreak in Iganga district. The samples were processed and inoculated in 10-day old embryonated chicken eggs and incubated for 72 hours. Allantoic fluid was harvested and tested for the presence of Newcastle disease virus using hemagglutination and hemagglutination inhibition tests. One hundred thirteen Newcastle disease virus isolates were obtained from 91 birds. The prevalence of Newcastle disease virus in live bird markets in Uganda was 14%. The highest prevalence was observed in Gulu and Arua districts at 46.7% (n=30) and 40% (n=30) respectively. The lowest prevalence was in Kisoro where no virus was isolated. From the 113 isloates, 90 representative samples were purposively selected to represent each region and RNA extracted. Nested PCR was done to amplify a 400 base pair fragment of the fusion protein gene flanking the fusion protein cleavage site. The resulting fragments were purified and sequenced using capillary Sanger method. The isolates had a sequence similarity of ~98%. Out of the 58 sequenced isolates, 3 had lentogenic F-protein cleavage motif (112GRQGRL117) and 55 had velogenic F-protein cleavage site motif (112RRQKRF117). Phylogenetic analysis revealed genotypes/lineages circulating in Uganda i.e. lineage 3c (genotype V) which formed the velogenic cluster and lineage 2 (genotype II) which formed the lentogenic cluster. There is therefore need for further investigation the epidemiology of Newcastle disease virus in Uganda so as to guide in the design and implementation of an effective control program.