Genetic relatedness of the novel human group C betacoronavirus to Tylonycteris bat coronavirus HKU4 and Pipistrellus bat coronavirus HKU5

Woo, Patrick CY; Lau, Susanna KP; Li, Kenneth SM; Tsang, Alan KL; Yuen, Kwok-Yung

The genome characteristics and organization of HCoV-EMC are similar to those of Ty-BatCoV HKU4 and Pi-BatCoV HKU5. Ty-BatCoV HKU4 was discovered from lesser bamboo bats (Tylonycteris pachypus) and Pi-BatCoV HKU5 was discovered from Japanese pipistrelles (Pipistrellus abramus) in Hong Kong. 9 Both lesser bamboo bats and Japanese pipistrelles are insectivorous microbats found in China and some other parts of Asia. The size of the genome of HCoV-EMC is 30 106 bases, slightly smaller than those of Ty-BatCoV HKU4 (30 286 to 30 316 bases) and Pi-BatCoV HKU5 (30 482 to 30 488 bases); and the G1C content is 41%, in between those of Ty-BatCoV HKU4 (38%) and Pi-BatCoV HKU5 (43%). The replicase ORF1ab occupies 21.5 kb of the genome. This ORF encodes 16 putative non-structural proteins, including nsp3 (which contains the putative papain-like protease (PL pro )), nsp5 (putative chymotrypsin-like protease (3CL pro )), nsp12 (putative RdRp), nsp13 (putative helicase (Hel)) and other proteins of unknown functions. These proteins are produced by proteolytic cleavage of the large replicase polyprotein by PL pro and 3CL pro at specific sites which are conserved with those in Ty-BatCoV HKU4 and/or Pi-BatCoV HKU5 (Table 1) .