Dataset Information

Genomic and Pathogenic Characteristics of Virulent Newcastle Disease Virus Isolated from Chicken in Live Bird Markets and Backyard Flocks in Kenya.

ABSTRACT: Newcastle disease (ND) causes significant economic losses in the poultry industry in developing countries. In Kenya, despite rampant annual ND outbreaks, implementation of control strategies is hampered by a lack of adequate knowledge on the circulating and outbreak causing-NDV strains. This study reports the first complete genome sequences of NDV from backyard chicken in Kenya. The results showed that all three isolates are virulent, as assessed by the mean death time (MDT) and intracerebral pathogenicity index (ICPI) in specific antibody negative (SAN) embryonated eggs and 10-day-old chickens, respectively. Also, the polybasic amino acid sequence at the fusion-protein cleavage site had the motif 112RRQKRFV118. Histopathological findings in four-week-old SPF chicken challenged with the NDV isolates KE001, KE0811, and KE0698 showed multiple organ involvement at five days after infection with severe effects seen in lymphoid tissues and blood vessels. Analysis of genome sequences obtained from the three isolates showed that they were 15192 base pair (bp) in length and had genomic features consistent with other NDV strains, the functional sites within the coding sequence being highly conserved in the sequence of the three isolates. Amino acid residues and substitutions in the structural proteins of the three isolates were similar to the newly isolated Tanzanian NDV strain (Mbeya/MT15). A similarity matrix showed a high similarity of the isolates to NDV strains of class II genotype V (89-90%) and subgenotype Vd (95-97%). Phylogenetic analysis confirmed that the three isolates are closely related to NDV genotype V strains but form a distinct cluster together with NDV strains from the East African countries of Uganda and Tanzania to form the newly characterized subgenotype Vd. Our study provides the first description of the genomic and pathological characteristics of NDV of subgenotype Vd and lays a baseline in understanding the evolutionary dynamics of NDV and, in particular, Genotype V. This information will be useful in the development of specific markers for detection of viruses of genotype V and generation of genotype matched vaccines.

SUBMITTER: Ogali IN

PROVIDER: S-EPMC7450340 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Genomic and Pathogenic Characteristics of Virulent Newcastle Disease Virus Isolated from Chicken in Live Bird Markets and Backyard Flocks in Kenya.

Ogali Irene N IN Okumu Paul O PO Mungube Erick O EO Lichoti Jacqueline K JK Ogada Stephen S Moraa Grace K GK Agwanda Bernard R BR Ommeh Sheila C SC

International journal of microbiology 20200818

Newcastle disease (ND) causes significant economic losses in the poultry industry in developing countries. In Kenya, despite rampant annual ND outbreaks, implementation of control strategies is hampered by a lack of adequate knowledge on the circulating and outbreak causing-NDV strains. This study reports the first complete genome sequences of NDV from backyard chicken in Kenya. The results showed that all three isolates are virulent, as assessed by the mean death time (MDT) and intracerebral pa ...[more]

PMID: 32908524

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Project description: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.

Project description:Live bird markets (LBMs) provide integral hubs for 95% of poultry produced for food. Surveillance systems in LBMs serving smallholder farmers in sub-saharan Africa are often non-functional, and data about public health risks and emerging pathogens are lacking. Studies in Kenya have reported 29-44% Campylobacter prevalence in poultry. We analysed such LBMs in Kenya for likely transmission of Campylobacter from poultry to humans. We conducted a cross-sectional survey among 186 live poultry traders (LPTs) in 14 LBMs in a region with widespread backyard poultry systems. A pretested structured questionnaire was administered to all LPTs having regular contacts with poultry to gather market data and risk information on campylobacteriosis. Campylobacter was detected in individual cloacal cultures and identified through PCR. The median score obtained from the outcome of risk assessment dichotomized respondents into high and low risk categories. We performed logistic regression at 95% confidence interval (CI) to compare market characteristics and Campylobacter positivity to risk categories to identify LBM-associated public health risks. Markets had a median of 13 traders, and mean age of 46.3 ± 13.7 years. Majority 162/186 (87.1%) were males. Market behavioural processes by LPTs varied: Only 58.6% LPTs held bird species separate; onsite slaughter (38.7%); encountered sick-bird (93%) and dead-bird (83%) amidst limited health inspection (31.2%). Campylobacter positivity in live birds was 43/112 (38.4%, 95% CI: 29.4-48.1). Risk information on campylobacteriosis was low 41/114 (36%, 95% CI: 27.2-45.5). Sanitary risks were related to accumulation of litter (adjusted prevalence odds ratio [aPOR]: 19.67, 95% CI: 3.01-128.52). Accessing hand-wash facilities (aPOR: .32, 95% CI: .13-.78) and access to information (aPOR: .24, 95% CI: .09-.61) were protective. Sanitary risks were related to poor hygiene. LBMs could be central surveillance sites for Campylobacter. Public health authorities/actors should consider appropriate targeting to improve sanitary measures and Campylobacter control strategies.

Dataset Information

Genomic and Pathogenic Characteristics of Virulent Newcastle Disease Virus Isolated from Chicken in Live Bird Markets and Backyard Flocks in Kenya.

Publications

Genomic and Pathogenic Characteristics of Virulent Newcastle Disease Virus Isolated from Chicken in Live Bird Markets and Backyard Flocks in Kenya.

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