Presence of Newcastle Disease Virus in Vaccinated Indigenous Chicken in Selected Regions in Kenya —A Cross-Sectional Study

Vaccination of flocks against Newcastle disease virus (NDV) outbreaks is the main approach for controlling the spread of Newcastle disease (ND). Nevertheless, NDV outbreaks have been reported in vaccinated chickens. In this study, we determined the prevalence of NDV among vaccinated indigenous chickens (ICs) and examined the relationship of the disease with the weather (temperature, rainfall, humidity, and wind speed) at the time of sample collection, production system, and the presence of other species. The genetic diversity of the NDV matrix and fusion genes was also inferred. A total of 1,210 swabs were collected between 2017 and 2018 from ICs that were vaccinated or unvaccinated against NDV in free-range and semi-free-range production systems. We collected 650 swabs each from the oropharynx and cloaca of ICs in 68 households within the Bomet, Baringo, Kilifi, Nakuru, Kakamega, and Machakos counties in Kenya. NDV matrix genes were detected using reverse transcription-polymerase chain reaction, and amplicons of matrix and fusion genes were sequenced using a capillary sequencer from the pooled samples. Among the vaccinated ICs, the prevalence of NDV was 78.5% (p=0.045). There were significant relationships between the presence of NDV and vaccination history of the ICs (p=0.034), the type of production system for ICs (p=0.004) and the months of sample collection (p < 0.0001). However, no significant relationship was found between the presence of NDV and the interaction between ICs and other birds. The presence of matrix and fusion genes in samples from vaccinated flocks indicated the presence of both virulent and low-virulence strains of NDV. These findings highlight the significant presence of NDV among vaccinated ICs and suggest the possibility of inadequate vaccination and viral shedding post-vaccination as the drivers of infections.