Molecular Characterization of Complete Genome Sequence of an Avian Coronavirus Identified in a Backyard Chicken from Tanzania

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