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Newcastle disease (ND) is a major constraint to Kenya’s poultry production, which is comprised of approximately 80% indigenous chickens (ICs; caged and free-range system) and 20% exotic chickens (intensive system). This study analyzed cases reported as suspected ND in Kenya between 2005 and 2015. Of the suspected 332 ND reported cases from the three production systems in 27 locations within six Kenyan Agro-Ecological Zones (AEZs), 140 diagnosed as infected with avian orthoavulavirus 1 (AOaV-1; formerly Newcastle disease virus) were present in every year in all AEZs. The numbers of AOaV-1-positive cases differed significantly (p < 0.05) between the production systems across the years depending on the season, climate, and location. In the free-range system, both ambient temperatures and season associated significantly (p = 0.001 and 0.02, respectively) with the number of cases, while in the intensive and caged systems, the positive cases correlated significantly with season and relative humidity, respectively (p = 0.05). Regardless of the production systems, the numbers of clinically sick birds positively correlated with the ambient temperatures (r = 0.6; p < 0.05). Failure to detect AOaV-1 in 58% of the ND cases reported, and mortalities exceeding the observed numbers of clinically sick birds suggest deficiencies in the current ND reporting and diagnostic system. Intensive farmers were the slowest in reporting the cases and diagnostic deficiencies were most evident by failure to test the exposure of ICs to natural infection with AOaV-1 and for the AOaV-1-negative cases lack of testing for other pathogens and/or AOaV-1 variants. This study indicates a need for improved surveillance and diagnostics in Kenyan domestic poultry.

Kenyan poultry consists of ~80% free-range indigenous chickens kept in small flocks (~30 birds) on backyard poultry farms (BPFs) and they are traded via live bird markets (LBMs). Newcastle disease virus (NDV) was detected in samples collected from chickens, wild farm birds, and other domestic poultry species during a 2017–2018 survey conducted at 66 BPFs and 21 LBMs in nine Kenyan counties. NDV nucleic acids were detected by rRT-PCR L-test in 39.5% (641/1621) of 1621 analyzed samples, of which 9.67% (62/641) were NDV-positive by both the L-test and a fusion-test designed to identify the virulent virus, with a majority being at LBMs (64.5%; 40/62) compared to BPFs (25.5%; 22/62). Virus isolation and next-generation sequencing (NGS) on a subset of samples resulted in 32 complete NDV genome sequences with 95.8–100% nucleotide identities amongst themselves and 95.7-98.2% identity with other east African isolates from 2010-2016. These isolates were classified as a new sub-genotype, V.3, and shared 86.5–88.9% and 88.5–91.8% nucleotide identities with subgenotypes V.1 and V.2 viruses, respectively. The putative fusion protein cleavage site (113R-Q-K-R↓F 117) in all 32 isolates, and a 1.86 ICPI score of an isolate from a BPF chicken that had clinical signs consistent with Newcastle disease, confirmed the high virulence of the NDVs. Compared to genotypes V and VI viruses, the attachment (HN) protein of 18 of the 32 vNDVs had amino acid substitutions in the antigenic sites. A time-scaled phylogeographic analysis suggests a west-to-east dispersal of the NDVs via the live chicken trade, but the virus origins remain unconfirmed due to scarcity of continuous and systematic surveillance data. This study reveals the widespread prevalence of vNDVs in Kenyan backyard poultry, the central role of LBMs in the dispersal and possibly generation of new virus variants, and the need for robust molecular epidemiological surveillance in poultry and non-poultry avian species.

Indigenous chicken farming is an important source of livelihood for rural families in Kenya. However, the farmers experience challenges including infections from poultry diseases such as Newcastle disease. Vaccination has been used over the years to provide immunity in flocks against disease outbreaks. However, Newcastle diseases virus (NDV) outbreaks are still reported among vaccinated flocks. This study examined the presence of Newcastle disease virus among vaccinated indigenous chicken (IC), in relation to weather (temperature, rainfall, humidity, wind speed), production system, and interspecies interaction. Samples were collected from flocks of indigenous chicken vaccinated with NDV vaccine from 68 households in six counties in Kenya (Bomet, Baringo, Kilifi, Nakuru, Kakamega, and Machakos). Some of the households (n=5 (9%) reported previous ND outbreaks. All the households had other mixed species of birds (ducks, geese, turkey, wild birds). The total number of samples collected was n=1210, oropharyngeal swabs-650, cloacal swab-650. The total number of the pooled sample was 246 pools. The samples were analysed by RT-qPCR targeting the NDV matrix gene. NDV matrix gene was detected in the pooled samples n=177(72%). Out of the positive samples, n=56(32%) were from vaccinated flocks, 91(51%) were from the cloacal swab and 86(49%) from the oropharyngeal swab. The samples were collected during varying weather (temperature, rainfall, humidity and wind speed). There was a statistical significance on the relationship between the presence of NDV and the Vaccination history (p=0.034); production system, (p=0.004), and month of sample collection (p<0.0001). However, there was no significance on the relationship between the presence of NDV and the interaction of IC and other birds. Failure to vaccinate IC results in the presence of the NDV. The free-range production system can have many cases of NDV due to the lack of biosecurity measures. Therefore, farmers should be advised to vaccinate their IC.

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