"Sequence identities for RmYN02 compared with the SARS-CoV GZ02 (accession number AY390556); the bat SARS-like coronaviruses RaTG13 (EPI_ISL_402131), ZC45 (MG772933), and ZXC21 (MG772934); and the pangolin SARS-like coronaviruses"

University of Michigan - Ann Arbor

- RmYN02 is found to be another potential relative of SARS-CoV-2 with a 93.3% identical sequence identity. However, this percentage is still less than the comparison of nucleotide sequence between SARS-CoV-2 and RaTG13 of 96.1% sequence identity. 
- Other genomic regions were found to have a >96% identical sequence identity between SARS-CoV-2 and RmYN02, but there was only a 71.8% and 72.9% nucleotide and amino acid identity, respectively, in the S gene. SARS-CoV-2 and RaTG13 S gene were found to have 97.4% amino acid identity in the S gene. 
- The receptor-binding domain of SARS-CoV-2 and RmYN02 also has significantly less amino acid identity compared to SARS-CoV-2 and RaTG13, with a 62.4% amino acid identity compared to 97.4%. 

Sequence identity of RmYN02 and SARS-CoV-2

Zhou, H., Chen, X., Hu, T., Li, J., Song, H., Liu, Y., Wang, P., Liu, D., Yang, J., Holmes, E. C., Hughes, A. C., Bi, Y., & Shi, W. (2020). A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein. Current biology : CB, 30(11), 2196–2203.e3. https://doi.org/10.1016/j.cub.2020.05.023

A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein

Table 1. Sequence Identity for SARS-CoV-2 Compared with RmYN02 and Representative Beta-CoV Genomes

"(A) Whole-genome similarity plot between SARS-CoV-2 and representative viruses listed in Table 1. The analysis was performed using Simplot, with a window size of 1,000 bp and a step size of 100 bp.

(B) Similarity plot in the spike gene (positions 1–1,658) between SARS-CoV-2 and representative viruses listed in Table 1. The analysis was performed using Simplot, with a window size of 150 bp and a step size of 5 bp."

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