First genome sequences of buffalo coronavirus from water buffaloes in Bangladesh

Lau, S.K.P.; Tsang, A.K.L.; Shakeel Ahmed, S.; Mahbub Alam, M.; Ahmed, Z.; Wong, P.-C.; Yuen, K.-Y.; Woo, P.C.Y.

We report the complete genome sequences of a buffalo coronavirus (BufCoV HKU26) detected from the faecal samples of two domestic adult water buffaloes (Bubalus bubalis) in Bangladesh. RT-PCR for coronavirus detection, and complete genome sequencing and analysis were performed as described previously [11, 12] . The genomes of BufCoV HKU26 strains B1-24F and B1-28F were 31 021 and 30 975 in length, with G+C content of 40%. They possessed 98-99% nucleotide identities to the genomes of BCoVs, supporting the classification of BufCoV HKU26 as a member of the species Betacoronavirus 1 (Fig. 1) . The genome organization is also characteristic of lineage A Betacoronavirus, with the putative transcription regulatory sequence motif 5 0 -C(U/C)AAAC-3 0 (Fig. 1) . The two BufCoV HKU26 genomes encode five putative accessory proteins conserved among most members of Betacoronavirus 1, including a 32 kDa protein between ORF1ab and haemagglutininesterase, three proteins between spike (S) and envelope (E) and one internal protein overlapping with N. In BCoV, the three proteins between S and E were of typical size: 4.9, 4.8 and 12.8 kDa respectively. In BufCoV, the 4.9 kDa protein is replaced by a 2.9 kDa protein (25 aa) due to a premature stop codon. The 4.8 kDa protein of BufCoV HKU26 was also different from that of BCoVs, with a smaller protein of 29 aa in strain B1-24F and a protein of 44 aa in strain B1-28F due to a frameshift mutation caused by a single nucleotide deletion after the original start codon. Compared to other BCoV-like viruses, BufCoV HKU26 possessed a unique serine/asparagine substitution at position 354 of N protein. In contrast to murine coronavirus, which utilizes carcinoembryonic antigen-related cell adhesion molecule 1 as a receptor, BCoV and HCoV OC43 bind to N-acetyl-9-O acetyl neuraminic acid for cell entry [13, 14] . All the known critical and noncritical sugar-binding residues in the N-terminal domain of S protein in BCoV are conserved in BufCoV HKU26 [15] . The genome sequences of BufCoV HKU26 have been lodged at GenBank under accession numbers KU558922 and KU558923.