Genetic Diversity of Newcastle Disease Virus Involved in the 2021 Outbreaks in Backyard Poultry Farms in Tanzania

SIMPLE SUMMARY: The genetic nature of currently circulating Newcastle disease virus (NDV) genotypes in backyard poultry flocks in East Africa is poorly understood. Genetic characterization of the NDV fusion gene of field isolates collected from six regions (Arusha, Dar es Salaam, Dodoma, Iringa, Morogoro and Rukwa) of Tanzania during 2021 highlighted the spread of NDV genotype VII in Tanzanian backyard poultry. The class II subgenotype VII.2 of the virus has been identified as the currently dominant strain in all studied regions, followed by class II subgenotype XIII.1.1. Our findings provide foundational information on the genetic diversity of NDV in several regions of Tanzania, which is important for better design of vaccines and subsequent control of the disease in the country and the region. ABSTRACT: Newcastle disease virus is a significant avian pathogen with the potential to decimate poultry populations all over the world and cause enormous economic losses. Distinct NDV genotypes are currently causing outbreaks worldwide. Due to the high genetic diversity of NDV, virulent strains that may result in a lack of vaccine protection are more likely to emerge and ultimately cause larger epidemics with massive economic losses. Thus, a more comprehensive understanding of the circulating NDV genotypes is critical to reduce Newcastle disease (ND) burden. In this study, NDV strains were isolated and characterized from backyard poultry farms from Tanzania, East Africa in 2021. Reverse-transcription polymerase chain reaction (RT-PCR) based on fusion (F) gene amplification was conducted on 79 cloacal or tracheal swabs collected from chickens during a suspected ND outbreak. Our results revealed that 50 samples out 79 (50/79; 63.3%) were NDV-positive. Sequencing and phylogenetic analyses of the selected NDV isolates showed that 39 isolates belonged to subgenotype VII.2 and only one isolate belonged to subgenotype XIII.1.1. Nucleotide sequences of the NDV F genes from Tanzania were closely related to recent NDV isolates circulating in southern Africa, suggesting that subgenotype VII.2 is the predominant subgenotype throughout Tanzania and southern Africa. Our data confirm the circulation of two NDV subgenotypes in Tanzania, providing important information to design genotype-matched vaccines and to aid ND surveillance. Furthermore, these results highlight the possibility of the spread and emergence of new NDV subgenotypes with the potential of causing future ND epizootics.