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 phylogenetic trees constructed using the amino acid sequences of the 3CL pro , RdRp, Hel, S and N of HCoV-EMC and other CoVs are shown in Figure 2 . For all the five genes, HCoV-EMC is clustered with Ty-BatCoV HKU4 and Pi-BatCoV HKU5, with high bootstrap supports in all cases, indicating that HCoV-EMC is a group C betaCoV (Figure 2 ). Although it seems that HCoV-EMC is clustered with Pi-BatCoV HKU5 in the phylogenetic trees constructed using RdRp and Hel, the bootstrap supports were only 652 and 588, respectively, suggesting that there is no obvious difference between the relatedness of HCoV-EMC to Ty-BatCoV HKU4 and Pi-BatCoV HKU5. Comparison of the amino acid identities of the seven conserved replicase domains for species demarcation (ADRP, nsp5 (3CL pro ), nsp12 (RdRp), nsp13 (Hel), nsp14 (ExoN), nsp15 (NendoU) and nsp16 (2'-O-MT)) between HCoV-EMC, Ty-BatCoV HKU4 and Pi-BatCoV HKU5 showed that there is less than 90% identity in four of the seven domains (ADRP 68%-69% identity, nsp5 81%-83% identity, nsp15 76%-80% identity and nsp16 84%-85% identity), indicating that HCoV-EMC is a novel CoV species. For nsp12, nsp13 and nsp14, there are 90%-92%, 92%-94% and 86%-92% amino acid identities between HCoV-EMC and Ty-BatCoV HKU4/Pi-BatCoV HKU5.