Surveillance of Class I Newcastle Disease Virus at Live Bird Markets and Commercial Poultry Farms in Eastern China Reveals the Epidemic Characteristics

Abstract Background: Live bird markets (LBMs) serve as a natural reservoir for class I Newcastle disease virus (NDV) and play an important role in viral evolution and spread. LBMs and commercial farms are the main sources of daily poultry products. However, limited studies are available for the class I NDV circulating at LBMs and commercial farms. In this study, significant progress has been made in sample detection and genetic analysis at LBMs and commercial farms in Eastern China.Methods: A long-term epidemiological investigation at LBMs and commercial farms in Eastern China was conducted. We sequentially conducted the collection of samples, virus isolation, RNA extraction, RT-PCR, and phylogenetic analysis. We also analyzed class I NDVs deposited in NCBI during 2002–2018 from China in terms of the host, genotype, time, and functional domains.Results: Here we report that class I NDVs continue to circulate in LBMs. Class I NDVs were detected at a high prevalence in chickens (23/26) but were seldom detected in waterfowl (3/26) at LBMs. In contrast, class I NDVs were rarely detected in commercial chickens but were present in commercial waterfowl at a certain frequency before they were brought to the LBMs. This observation suggests that the mixture of poultry and the conventional housing at LBMs cause the spread of class I NDVs. Sequence analysis of Class I NDV genomes deposited in NCBI during 2002–2018 from China revealed a high prevalence of class I NDVs in terrestrial birds (82.7%), which was much higher than in water birds (17.3%). In addition, we found that the class I NDVs predominantly belonged to the sub-genotype 3c and rarely evolved into a new sub-genotype such as the 3d. Furthermore, the epidemic sub-genotype 3c seems to be under ongoing evolution.Conclusions: Our study provides evidence that the traditional feeding mode at LBMs causes the spread of class I NDVs and poses a great risk of NDV epidemics in the poultry industry in Eastern China. The sub-genotype 3c is circulating at LBMs and currently the terrestrial bird is the predominant host of class I NDVs.

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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

Viruses ◽

10.3390/v13010103 ◽

2021 ◽

Vol 13 (1) ◽

pp. 103

Author(s):

Henry M. Kariithi ◽

Helena L. Ferreira ◽

Catharine N. Welch ◽

Leonard O. Ateya ◽

Auleria A. Apopo ◽

...

Keyword(s):

Newcastle Disease Virus ◽

Disease Virus ◽

Newcastle Disease ◽

Clinical Signs ◽

Backyard Poultry ◽

Live Bird Markets ◽

Indigenous Chickens ◽

Virulent Newcastle Disease Virus ◽

Poultry Farms ◽

Live Bird

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.

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