Comparative study of SARS, MERS, BAT-SARS and SARS-CoV-2

Scientists have found that several viruses that belong to the Coronaviridae family can infect a wide range of hosts, including birds, humans and other mammals. These viruses are single-stranded, positive-stranded RNA viruses, whose size varies between 27-32 kb. They are divided into four categories, namely, alpha, beta, delta and gamma.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the ongoing 2019 coronavirus disease pandemic (COVID-19), and was first identified in Wuhan province, China, in December 2019 Due to its high infectivity and mortality rate, the World Health Organization announced COVID-19 to be a pandemic on March 11, 2020.

As viruses undergo genomic mutation, it is extremely important to identify the mutation site for the development of the vaccine. Several phylogenetic tree-based analyzes were conducted to understand the evolutionary relationship of SARS-CoV-2 with other beta coronaviruses. A previous study built a phylogenetic tree and found that the genomic sequence for SARS-CoV-2 is 88% identical to BAT-CoV. In another study, scientists isolated about 70 SARS-CoV-2 genomic sequences from patients with COVID-19 and studied the peak glycoprotein gene. This study also reported that the BetaCoV-bat-Yunnan-RaTG13-2013 virus is almost identical to SARS-CoV-2.

Although a comparative study of the genomic sequences of SARS-CoV, MERS-CoV and SARS-CoV-2 is available, there is a gap in the research regarding the comparison between four types of coronavirus, namely, SARS-CoV, MERS- CoV, BAT-CoV and SARS-CoV-2. A new study, which deals with the genomic comparison between the sequence of the four types of coronavirus mentioned above, was published in Journal of Medical Virology. This study used several genetic markers, including single nucleotide polymorphisms (SNPs), phylogeny of the entire genome sequence, mutations in proteins and microsatellites. These were compared with the reference genomic reference sequence SARS-CoV-2 which is known as the Wuhan strain (Wuhan-Wu-I). All sequences were obtained from NCBI Genbank.

The SARS-CoV, MERS-CoV and SARS-CoV-2 sequences were obtained from Homo sapiens (host), while BAT-CoV sequences were collected from eight different types of bats. The results of this study are described below.

Phylogenetic analysis

For the phylogenetic analysis of the different coronavirus sequences, a maximum likelihood approach with 1000 initialized values ​​was used. Phylogenetic analysis revealed different strains of coronavirus. All phylogenetic analysis based on the genome showed that MERS-CoV belongs to species in the outer group, while the other three were classified as species in the inner group. Within the inner group, two strains were found, namely, a strain consisting of SARS-CoV-2 and another consisting of SARS-CoV and BAT-CoV. The branches of the phylogenetic tree indicated that SARS-CoV had diverged very early from BAT-CoV. The tree also revealed an independent divergence from SARS-CoV-2 from BAT-CoV. Phylogeny also showed that SARS-CoV-2 is more related to BAT-CoV and SARS-CoV than MERS-CoV. Simplot software was used to visualize the similarity graph between the four selected species. It revealed about 98% BAT-CoV homology with the reference sequence, that is, the Wuhan stain of SARS-CoV-2. However, 92% similarity was obtained between SARS-CoV and the reference sequence, and 58% similarity between MERS-CoV and the Wuhan strain.

Analysis of genetic variants

Variant-based analysis showed that the MERS-CoV genome differed from the reference Wuhan strain at 134.21 sites, the BAT-CoV genome differed at 136.72 sites, the SARS-CoV genome differed at 26.64 sites, and the genome SARS-CoV-2 differed by 0.66 sites. In addition, the current study also revealed that the likelihood of mutations at the MERS-CoV and SARS-CoV-2 missense sites is greater compared to SARS-CoV and BAT-CoV. This is due to the reduced number of missense variations in SARS-CoV and BAT-CoV, which occurred due to selection pressure on missense sites.

The number of mutations in the Spike protein (S), Envelope protein (E), membrane protein (M), Nucleocapsid protein (N) and structural proteins were calculated. The SNPs were filtered from the S, M, E and N gene regions by a python script. The S, M, E and N genes revealed the presence of a varied number of SNPs. The online tool Multialin was used to detect similarities between four coronaviruses selected for the current study.

Microsatellite analysis

Microsatellite analysis is used to determine repetitive sequences in the genome. These sequences have a significant impact on the onset of diseases and their evolution. In this study, microsatellite analysis was performed using the online tools IMEX (Imperfect Microsatellite Extractor) and FMSD (Fast Microsatellite Discovery). No significant presence of microsatellites was found using IMEX. However, the FMSD revealed the presence of more microsatellites in the MERS-CoV. The SARS-CoV-2 genome showed the presence of the highest incidence of compound microsatellites.

In summary, the analysis of the phylogenetic tree showed that SARS-CoV-2 is closely related to BAT-CoV and its second closest relative is SARS-CoV. All strains of MERS-CoV showed a distal relationship with SARS-CoV-2. In the analysis of the genetic variants, more mutations were found in MERS-CoV compared to SARS-CoV and BAT-CoV. Phylogenetic analysis, study of genetic variation, multisequence and analysis of microsatellites, showed that the bat is the native host of SARS-CoV-2. In addition, it also concluded that BAT-CoV is closely related to SARS-CoV-2. There is the possibility of the presence of an intermediate host to initiate the transmission of the COVID-19 from BAT to man. However, more research is needed to validate this assumption. The FMSD tool revealed that SARS-CoV is more associated with SARS-CoV-2 than BAT-CoV.