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.

Henry M Kariithi,Tim L Olivier,David L Suarez,Sonia M Hernandez,Auleria A Apopo,Catharine N Welch,Claudio L Afonso,Dana Goldenberg,Leonard O Ateya,Jeremy D Volkening,Helena L Ferreira,Richard Zoller,Dawn Williams-Coplin,Darren J Parris,Yatinder S Binepal

doi:10.3390/v13010103

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.

Highlights

Village chicken production is important in household and national economies of most African countries [1]
Most of the samples were swabbed from chickens at the backyard poultry farm (BPF) (n = 914) and live bird market (LBM) (n = 431)
All the LBM birds were chickens; there were no LBM birds sampled from Tana-River and Nakuru counties, and all birds from Nairobi county were swabbed at LBMs (n = 8)

Summary

Introduction

Village chicken production is important in household and national economies of most African countries [1]. Live poultry trade between the BPFs and live bird markets (LBMs) is highly unregulated, and biosecurity measures in the BPFs and along the trade routes are non-existent [3,4]. BPFs and transportation to urban/peri-urban LBMs potentially facilitates the spread of viral diseases to naïve poultry [5]. Poor poultry management favors the existence and spread of diseases due to gregarious interactions of different poultry species within BPFs and frequent introductions of birds sourced from LBMs [6]. Recent data suggest that wild birds at BPFs contribute to the circulation of NDV and spill-over of NDV vaccine into wild avian species [7,8]

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Conclusion