Indigenous chicken farming is a source of livelihood for rural and urban families in Kenya. However, the farmers experience challenges such as infections from Newcastle disease. Vaccination of flocks against Newcastle disease virus (NDV) outbreaks is an approach for controlling the spread of Newcastle disease (ND). Nevertheless, vaccinated chickens’ contract NDV. The study objective was to determine NDV in indigenous chickens (ICs) and the association of the disease with the weather (temperature, humidity, and wind speed) at the time of sample collection, production system, and the interaction of ICs with other species and make inference on the genetic diversity of the NDV matrix and fusion genes. A total of 1,585 samples were collected between 2017 and 2019 from NDV-vaccinated and unvaccinated ICs. The samples collected were from ICs in eight live bird markets in Nairobi (N=372) and ICs from 68 households (N=1210) within the Bomet, Baringo, Kilifi, Nakuru, Kakamega, and Machakos counties in Kenya and clinical samples (N=3). The collected samples were oropharyngeal and cloaca swabs from ICs in markets and households and samples (long bone and internal organs (liver, intestine, caecal tonsils, kidney and heart tissues)) from clinically sick ICs. NDV matrix genes were detected using quantitative reverse transcription-polymerase chain reaction (RT-qPCR), and amplicons of matrix and fusion genes were sequenced using a capillary sequencer. Chi-square and correlation tests were used to test the association between the prevalence of Newcastle disease in IC and the associated factors. The genetic diversity was analysed by haplotype analysis (TCS network) and phylogeny. The NDV prevalence in the Nairobi live bird markets was 65.3% and 72.4% in ICs from the household. Among the vaccinated ICs, the prevalence of NDV was 77%. There were significant relationships between the prevalence of NDV and vaccination history (p = 0.039), of the ICs, the type of production system for ICs (p <0.010) and the interaction between ICs and other birds (p = 0.037). There was no correlation between the prevalence of NDV and the prevailing weather condition. Haplotype analysis revealed non-synonymous mutation of sequences with low nucleotide densities and high haplotype density of the matrix gene and high nucleotide diversity and haplotype diversity of the fusion gene. The phylogeny revealed similarity for the matrix gene with previous isolates and heterogeneity of the fusion gene. The study also revealed the non-relatedness of the circulating NDV strains with the NDV La Sota strain used in NDV vaccine development. 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 occurrence of NDV among ICs and suggest the type of production system, viral shedding post-vaccination and interspecies transmission as the drivers of Newcastle disease outbreaks. Therefore, associated factors to the prevalence of NDV and the circulating strains should be considered during the development of vaccines for effective control of ND outbreaks in Kenya.

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