Virulent Newcastle disease virus genotypes V.3, VII.2 and XIII.1.1 and their coinfections with infectious bronchitis viruses and other avian pathogens in backyard chickens in Tanzania

Authors: KARIITHI, HENRY - Orise Fellow; VOLKENING, JEREMY - Base2bio; CHIWANGA, GASPER - Tanzania Veterinary Laboratory Agency; GORAICHUK, IRYNA - Orise Fellow; Olivier, Timothy; MSOFFE, PETER L - Sokoine University Of Agriculture; Suarez, David

Submitted to: Frontiers in Veterinary Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/4/2023
Publication Date: 10/19/2023
Citation: Kariithi, H.M., Volkening, J.D., Chiwanga, G.H., Goraichuk, I.V., Olivier, T.L., Msoffe, P.M., Suarez, D.L. 2023. Virulent Newcastle disease virus genotypes V.3, VII.2 and XIII.1.1 and their coinfections with infectious bronchitis viruses and other avian pathogens in backyard chickens in Tanzania. Frontiers in Veterinary Science. 10:1272402. https://doi.org/10.3389/fvets.2023.1272402.
DOI: https://doi.org/10.3389/fvets.2023.1272402

Interpretive Summary: As part of a collaborative project on Newcastle disease virus(NDV) in Tanzania, samples from chickens were collected at live bird markets from throughout the country. Newcastle disease virus is an important disease of poultry that remains a major impediment to poultry production in Africa. Although vaccines are available, both cost and availability remains an impediment. Samples were screened using PCR, and a high percentage of sample were positive. Samples with the highest levels of virus were directly sequenced to determine more about the viruses infecting the birds. Three distinct genotypes of NDV were found in the samples, which supports that NDV is widely disseminated in the country. This information helps inform the need for use of widespread vaccination in Tanzania to protect poultry from this deadly pathogen.

Technical Abstract: Oropharyngeal (OP) and cloacal (CL) swabs from 2049 adult backyard chickens collected at 12 live bird markets, two each in Arusha, Dar es Salaam, Iringa, Mbeya, Morogoro and Tanga regions of Tanzania were screened for Newcastle disease virus (NDV) using reverse transcription real-time PCR (rRT-PCR). The virus was confirmed in 25.23% of the birds (n'='517; rRT-PCR CT'='30), with the highest positivity rates observed in birds from Dar es Salaam region with higher prevalence during the dry season (September–November 2018) compared to the rainy season (January and April–May 2019). Next-generation sequencing of OP/CL samples of 20 out of 32 birds that had high amounts of viral RNAs (CT'='25) resulted in the assembly of 18 complete and two partial genome sequences (15,192'bp and 15,045–15,190'bp in length, respectively) of NDV sub-genotypes V.3, VII.2 and XIII.1.1 (n'='1, 13 and 4 strains, respectively). Two birds had mixed NDV infections (V.3/VII.2 and VII.2/XIII.1.1), and nine were coinfected with viruses of families Astroviridae,Coronaviridae, Orthomyxoviridae, Picornaviridae, Pneumoviridae, and Reoviridae. Of the coinfecting viruses, complete genome sequences of two avastroviruses (a recombinant chicken astrovirus antigenic group-Aii and avian nephritis virus genogroup-5) and two infectious bronchitis viruses (a turkey coronavirus-like recombinant and a GI-19 virus) were determined. The fusion (F)protein F1/F2 cleavage sites of the Tanzanian NDVs have the consensus motifs 112 RRRKR'F 117 (VII.2 strains) and 112 RRQKR'F 117 (V.3 and XIII.1.1 strains) consistent with virulent virus; virulence was confirmed by intracerebral pathogenicity index scores of 1.66–1.88 in 1-day-old chicks using nine of the 20 isolates. Phylogenetically, the complete F-gene and full genome sequences regionally cluster the Tanzanian NDVs with, but distinctly from, other strains previously reported in eastern and southern African countries. These data contribute to the understanding of NDV epidemiology in Tanzania and the region.