3.8. Genomic Comparison
CoVs are RNA viruses and contain the largest genomes of all RNA viruses [87]. CoVs belong to the subfamily Coronavirinae in the family of Coronaviridae of the order Nidovirales, and this subfamily includes four genera: α-coronavirus, β-coronavirus, γ-coronavirus, and δ-coronavirus [88]. Both SARS-CoV-2 and SARS-CoV are in the coronavirus family, β-coronavirus genera [89]. The genome of SARS-CoV-2 is more than 85% similar to the genome of the SARS-like virus ZC45 (bat-SL-CoVZC45, MG772933.1), and together these types of viruses form a unique Orthocoronavirinae subfamily with another SARS-like virus ZXC21 in the sarbecovirus subgenus [35]. All the three viruses show typical β-coronavirus gene structure. Human SARS-CoV and a genetically similar bat coronavirus (bat-SL-CoVZXC21, MG772934) from southwest of China have formed another clade within the sarbecovirus [35].
We also performed comparative genomic analyses of SARS-CoV-2 and SARS-CoV by zpicture. The results showed that the genomic sequences of SARS-CoV-2 and SARS-CoV have extremely high homology at the nucleotide level (Figure 4a,b). There are six regions of difference (RD) in the genome sequence between SARS-CoV and SARS-CoV-2, and the RDs are named according to the order of discovery. RD1, RD2, and RD3 (448nt, 55nt, and 278nt, respectively) are partial coding sequences of the orf lab gene; RD4 and RD5 (315nt and 80nt, respectively) are partial coding sequences of the S gene; RD6 is 214nt in size and is part of the coding sequence of the orf7b and orf8 genes. These RDs may provide new molecular markers for the identification of SARS-CoV-2 and SARS-CoV, and also help to develop new drugs against SARS-CoV-2.
To analyze the homogeneity of SARS-CoV, MERS-CoV, and SARS-CoV-2, an evolutionary tree was constructed based on the genomes of 35 SARS-CoV-2 strains from different data submission units, one SARS-CoV strain, and two MERS-CoV strains (Figure S1). Phylogenetic analysis showed that the distance of SARS-CoV (AY274119) is closer to SARS-CoV-2 strains than MERS-CoV (KC164505, JX869059).