Surveillance and Genetic Characterization of Virulent Newcastle Disease Virus Subgenotype V.3 in Indigenous Chickens from Backyard Poultry Farms and Live Bird Markets in Kenya

Abstract

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.

Unique Variants of Avian Coronaviruses from Indigenous Chickens in Kenya

“…In addition to IBV, sample A374 contained RNAs of three other viral agents, i.e., virulent Newcastle disease virus (vNDV), avian rotavirus-G (AvRV-G), and pigeon picornavirus B (PiPV-B) and one avian pathogenic bacterium ( Ornithobacterium rhinotracheale ; ORT), whereas sample A376 contained NDV and two avian pathogenic bacteria (ORT and Riemerella anatipestifer ). We have recently published complete genome sequences of the vNDVs that co-infect with the IBVs [ 29 ].…”

“…Furthermore, the absence of overt signs of respiratory or other diseases in the chickens at the sampling time agrees with gastrointestinal tract IBV infections that are yet to be demonstrated to result in enteropathogenesis [ 60 ]. We have recently reported sequences of novel subgenotype V.3 vNDVs in A374 CL and A376 OP samples [ 29 ], and five low pathogenic influenza A subtype H9N2 viruses [ 61 ] from other samples from the same LBM as those in the current study (collected at the same time and originating from the same Machakos county). It is highly likely that these respiratory viruses have been disseminated to other Kenyan and East African regions, because the LBMs and associated trade routes form the backbone of the poultry industry in these regions [ 29 , 61 ].…”

“…Here, we report genome analysis of the first AvCoV sequenced from Kenya and the East African region, as inadvertently discovered by untargeted next-generation sequencing of clinical samples collected from indigenous chickens during a 2016–2018 surveillance for vNDVs in domestic and wild avian species in the country [ 29 ].…”

When Vibrios Take Flight: A Meta-analysis of Pathogenic Vibrios Species in Wild and Domestic Birds

“…In our meta-analysis, disease was most commonly associated with V. cholerae , followed by V. metschnikovi and V. parahaemolyticus – notably, 11 of 39 study records were associated with domestic ducks ( Anas platyrhynchos or Anser anser ) or domestic chickens [66, 67, 75, 77, 87, 96]. This may have implications for agriculturally associated species in areas of the world where backyard birds are the primary protein source for pastoral families [132–134].…”

Internet search data with spatiotemporal analysis in infectious disease surveillance: Challenges and perspectives

“…Google Flu Trends have made some great progress in the finer spatiotemporal resolution analysis, which offers city-level or finer spatial resolution internet search data in influenza surveillance (61). Although a finer spatiotemporal resolution in internet search data is limited by the capacity of data aggregation and internet search volume, the rapidly increasing use of internet search as a health knowledge tool could lead to the development of a better spatiotemporal analysis using a finer resolution internet search data in space and time (62).…”