The phylogenetic analysis shows that SARS-CoV-2 and RmYN02 are the most closely related in most of the genome, although a long branch length still separates the two viruses from each other. 

Phylogenetic analysis of RmYN02 and SARS-CoV-2 full-length genome

SARS-CoV-2 and RmYN02 are relatively distant from each other in the spike gene tree, with SARS-CoV-2 being more clustered with RaTG13.

Phylogenetic analysis of RmYN02 and SARS-CoV-2 S gene

In the receptor-binding domain (RBD) phylogeny, SARS-CoV-2 is more closely related to pangolin-CoV/GD than RmYN02.

Phylogenetic analysis of RmYN02 and SARS-CoV-2 receptor-binding domain

A RNA-dependent RNA polymerase (RdRp) phylogeny indicates that RmYN02, RaTG13, and SARS-CoV-2 form a cluster separate from pangolin viruses. 

Phylogenetic analysis of RmYN02 and SARS-CoV-2 RNA-dependent RNA polymerase

- Full-length genome
- S protein genome
- Receptor-binding domain 
- RNA-dependent RNA polymerase

University of Michigan - Ann Arbor

- Sequence identity
- Receptor-binding domain
- S glycoprotein
- Phylogenetic analysis

Comparison of RmYN02 and SARS-CoV-2

- 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

- The two loops in the receptor-binding domain (RBD) of the RmYN02 are shorter than those of SARS-CoV-2 due to amino acid deletions. Additionally, the RmYN02 does not have a conserved disulfide bond present in SARS-CoV-2 and RaTG13. These variations can prevent binding between RmYN02 RBD and ACE2 receptor due to conformation differences. 
- There are six amino acid residues in the RBD that are significant in facilitating binding between SARS-CoV-2 and ACE2. RmYN02 and RaTG13 were found to only share one of the residues with SARS-CoV-2. This demonstrates a complex selection and recombination taking place leading to SARS-CoV-2. 

Receptor-binding domain differences between RmYN02 and SARS-CoV-2

What separates SARS-CoV-2 from other betacoronaviruses is that the S protein of SARS-CoV-2 has four amino-acid insertion at the junction of S1 and S2. In contrast, RmYN02 has a three amino acid PAA insertions. Presence of insertions, although slightly different between SARS-CoV-2 and RmYN02, demonstrates the the RmYN02 is a likely relative of SARS-CoV-2 and suggests the natural zoonotic origin of SARS-CoV-2.

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