Whole-genome characterization of Newcastle disease virus isolates of sub-genotype VII.1.1 from chickens in Ethiopia

Newcastle disease (ND) is a serious poultry disease in Ethiopia. F gene sequences have shown that the velogenic Newcastle disease virus (NDV) sub-genotype VII.1.1 is prevalent in Ethiopia and other East African countries. However, the F gene sequence alone is not enough to fully understand the pathogenicity, antigenicity, and epidemiological characteristics of NDVs. Whole-genome characterizations of currently circulating virus strains are needed to understand the molecular basis of the pathogenicity and antigenicity differences between vaccine and field strains. In this study, we obtained the complete genome sequences of seven NDV sub-genotype VII.1.1 isolated from chicken farms in Ethiopia and compared them with closely related NDVs and vaccine strains. Whole-genome sequencing revealed that all isolates have genome length of 15,192 nucleotides and are composed of six genes in the order 3'-NP-P-M-F-HN-L-5'. Phylogenetic analysis of the whole genomes showed that sub-genotype VII.1.1 can be classified into three distinct lineages and that the Ethiopian isolates in this study clustered within lineage 1. Unique amino acid substitutions were identified in all six genes of the Ethiopian isolates when compared to closely related NDV strains and commonly used vaccine strains. Some of these substitutions have been linked to antigenic variation. Although sub-genotype VII.1.1 is widespread in Ethiopia and other horn of African countries, to the best of our knowledge, this is the first report describing its whole-genome characteristics in this region. The findings in this study are expected to support effective ND control strategies in the region.