In light of the COVID-19 pandemic, there has been much research conducted into the origins of the SARS-CoV-2 virus and similar viruses to establish a greater understanding. The researchers compare SARS-CoV-2 and RaTG13, a coronavirus found in bats, with the aim of calculating the divergence between the two strains. The Short Communication article is published as part of the Special Focus Issue ‘COVID-19: studying the global pandemic’ in Future Virology.
Aim: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the world. There is urgent need to understand the phylogeny, divergence and origin of SARS-CoV-2. Materials & methods: A recent study claimed that there was 17% divergence between SARS-CoV-2 and RaTG13 (a SARS-related coronaviruses) on synonymous sites by using sequence alignment. We re-analyzed the sequences of the two coronaviruses with the same methodology. Results: We found that 87% of the synonymous substitutions between the two coronaviruses could be potentially explained by the RNA modification system in hosts, with 65% contributed by deamination on cytidines (C-T mismatches) and 22% contributed by deamination on adenosines (A-G mismatches). Conclusion: Our results demonstrate that the divergence between SARS-CoV-2 and RaTG13 has been overestimated.
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