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OBJECTIVE: To analyze SARS-CoV-2 whole genome reported of Pakistan and compare them with other viral strains collected from other world region to better understand the origin and genetic characterization of the virus.
METHODS: All the available genomic information of SARS-CoV-2 including Pakistani strains were collected from various online sources. Phylogenetic analysis of 131 sequences from 11 countries (Brazil, China, India, Italy, Nepal, Pakistan, Spain, Sweden, Taiwan, USA and Viet-Nam) were performed and compared with other related coronaviruses to find the evolution of virus and its origin. Individual SARS-CoV-2 gene, spike (S) glycoprotein and the receptor binding domain (RBD) with closely related coronaviruses were compared to further explore genetic variations and the likely RBD properties of the virus.
RESULTS: The analysis shows that genome of all analyzed 131 SARS-CoV-2 strains collected from different geographical area were extremely similar, exhibiting >99% sequence identity. Notably, genome of the SARS-CoV-2 has high similarity (89.1% sequence identity) with the two bat-derived severe acute respiratory syndrome (SARS) like betacoronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21 but was sufficiently divergent from SARS-CoV (82.3% similarity) and MERS-CoV (50% similarity). Phylogenetic analysis shows that the SARS-CoV-2 has relatively similar spike glycoprotein with bat-SL-CoVZC45, however, the RBD was more like that of SARS-CoVGZ02.
CONCLUSION: Using different bioinformatics tools, we determined that SARS-CoV-2 has high similarities to bat-derived SARS like betacoronaviruses than SARS-CoV at the whole genome level, however, the RBD was more like that of SARS-CoVGZ02, which shows that they use similar ACE2 as a cell receptor.
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