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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Exotic & Emerging Avian Viral Diseases Research » Research » Publications at this Location » Publication #407922

Research Project: Intervention Strategies to Predict, Prevent, and Control Emerging Strains of Virulent Newcastle Disease Viruses

Location: Exotic & Emerging Avian Viral Diseases Research

Title: Molecular characterization of complete genome sequence of an avian coronavirus identified in a backyard chicken from Tanzania

item KARIITHI, HENRY - Orise Fellow
item VOLKENING, JEREMY - Base2bio
item CHIWANGA, GASPAR - Tanzania Veterinary Laboratory Agency
item GORAICHUK, IRYNA - Orise Fellow
item MSOFFE, PETER - Sokoine University Of Agriculture
item Suarez, David

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/21/2023
Publication Date: 9/23/2023
Citation: Kariithi, H.M., Volkening, J.D., Chiwanga, G.H., Goraichuk, I.V., Msoffe, P.L., Suarez, D.L. 2023. Molecular characterization of complete genome sequence of an avian coronavirus identified in a backyard chicken from Tanzania. Genes. 14(10):1852.

Interpretive Summary: The use of Next Generation Sequencing (NGS) techniques continue to identify pathogens in clinical samples continues to improve. Often full-length viral genomes can be identified in samples and this sequence information can be used to not only identify what pathogens are in samples, but also determine the genotype, pathotype, or lineage of a virus. In a surveillance study of chickens in live bird markets in Tanzania a unique infectious bronchitis virus was identified and sequenced through NGS testing. It is unclear from this study if the virus caused disease in poultry because the study only provided the sequence information of the virus. The use of NGS for diagnostic testing and full sequence analysis provides a useful tool for characterizing new or unique viruses.

Technical Abstract: A complete genome sequence of an avian coronavirus (AvCoV; 27,663 bp excluding 30 poly(A) tail) was determined using nontargeted next-generation sequencing (NGS) of an oropharyngeal swab from a backyard chicken in a live bird market in Arusha, Tanzania. The open reading frames (ORFs) of the Tanzanian strain TZ/CA127/19 are organized as typical of gammaCoVs (Coronaviridae family): 50UTR-[ORFs 1a/1b encoding replicase complex (Rep1ab) non-structural peptides nsp2-16]-[spike (S) protein]-[ORFs 3a/3b]-[small envelop (E) protein]-[membrane (M) protein]-[ORFs 4a/4c]-[ORFs 5a/5b]-[nucleocapsid (N) protein]-[ORF6b]-30UTR. The structural (S, E, M and N) and Rep1ab proteins of TZ/CA127/19 contain features typically conserved in AvCoVs, including the cleavage sites and functional motifs in Rep1ab and S. Its genome backbone (non-spike region) is closest to Asian GI-7 and GI-19 infectious bronchitis viruses (IBVs) with 87.2–89.7% nucleotide (nt) identities, but it has a S gene closest (98.9% nt identity) to the recombinant strain ck/CN/ahysx-1/16. Its 3a, 3b E and 4c sequences are closest to the duck CoV strain DK/GD/27/14 at 99.43%, 100%, 99.65% and 99.38% nt identities, respectively. Whereas its S gene phylogenetically cluster with North American TCoVs and French guineafowl COVs, all other viral genes group monophyletically with Eurasian GI-7/GI-19 IBVs and Chinese recombinant AvCoVs. Detection of a 4445 nt-long recombinant fragment with breakpoints at positions 19,961 and 24,405 (C- and N terminus of nsp16 and E, respectively) strongly suggested that TZ/CA127/19 acquired its genome backbone from an LX4-type GI-19)field strain via recombination with an unknown AvCoV. This is the first report of AvCoV in Tanzania and leaves unanswered the questions of its emergence and the biological significance.