Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA 30605, USA.
Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, Nairobi 00200, Kenya.
Genes (Basel). 2023 Sep 23;14(10):1852. doi: 10.3390/genes14101852.
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) 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 ( 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) protein]-[ORFs 4a/4c]-[ORFs 5a/5b]-[nucleocapsid (N) protein]-[ORF6b]-3'UTR. 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.
使用靶向下一代测序（NGS）对坦桑尼亚阿鲁沙一个活禽市场后院鸡的咽拭子进行检测，确定了一株禽冠状病毒（AvCoV；27663bp，不包括 3'端 poly(A)尾）的完整基因组序列。坦桑尼亚株 TZ/CA127/19 的开放阅读框（ORFs）组织方式与典型的γCoV（科）相同：5'UTR-[ORFs 1a/1b 编码复制酶复合物（Rep1ab）非结构肽 nsp2-16]-[刺突（S）蛋白]-[ORFs 3a/3b]-[小包膜（E）蛋白]-[膜（M）蛋白]-[ORFs 4a/4c]-[ORFs 5a/5b]-[核衣壳（N）蛋白]-[ORF6b]-3'UTR。TZ/CA127/19 的结构（S、E、M 和 N）和 Rep1ab 蛋白包含禽冠状病毒中通常保守的特征，包括 Rep1ab 和 S 中的切割位点和功能基序。其基因组骨架（非刺突区）与亚洲 GI-7 和 GI-19 传染性支气管炎病毒（IBV）最接近，核苷酸（nt）同一性为 87.2-89.7%，但 S 基因与重组株 ck/CN/ahysx-1/16 最为接近（nt 同一性为 98.9%）。其 3a、3b E 和 4c 序列与鸭 CoV 株 DK/GD/27/14 的 nt 同一性分别为 99.43%、100%、99.65%和 99.38%。其 S 基因系统发育聚类与北美 TCoV 和法国鹧鸪 CoV 相关，而其他病毒基因则与欧亚 GI-7/GI-19 IBV 和中国重组禽冠状病毒一起形成单系群。检测到一个长 4445nt 的重组片段，其断点位于 19961 位和 24405 位（分别为 nsp16 和 E 的 C-和 N-末端），强烈表明 TZ/CA127/19 通过与未知禽冠状病毒的重组从 LX4 型（GI-19）田间株获得了其基因组骨架。这是坦桑尼亚首例禽冠状病毒的报告，但其出现和生物学意义仍有待解答。
