Abstract
The transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of paramount importance in controlling and combating the coronavirus disease 2019 (COVID-19) pandemic. Currently, over 15,000 SARS-CoV-2 single mutations have been recorded, which have a great impact on the development of diagnostics, vaccines, antibody therapies, and drugs. However, little is known about SARS-CoV-2’s evolutionary characteristics and general trend. In this work, we present a comprehensive genotyping analysis of existing SARS-CoV-2 mutations. We reveal that host immune response via APOBEC and ADAR gene editing gives rise to near 65% of recorded mutations. Additionally, we show that children under age five and the elderly may be at high risk from COVID-19 because of their overreaction to the viral infection. Moreover, we uncover that populations of Oceania and Africa react significantly more intensively to SARS-CoV-2 infection than those of Europe and Asia, which may explain why African Americans were shown to be at increased risk of dying from COVID-19, in addition to their high risk of COVID-19 infection caused by systemic health and social inequities. Finally, our study indicates that for two viral genome sequences of the same origin, their evolution order may be determined from the ratio of mutation type, C > T over T > C.
Highlights
The ongoing outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to tremendous human mortality and economic hardship
There are two well-known deaminase RNA editing mechanisms in human cells: the APOBEC [26] and the adenosine deaminases acting on RNA (ADAR) [27]
To reveal that C > T and A > G mutations are driven by RNA-APOBEC and RNA-ADAR
Summary
The ongoing outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to tremendous human mortality and economic hardship. As of 31 July 2020, over 17,106,007 confirmed COVID-19 cases have been reported worldwide and 668,910 deaths have occurred from the disease [1]. To mitigate this devastating pandemic, we have to control its spread by sufficient testing, social distancing, contact tracking, and developing effective diagnosis tools, efficacious antiviral drugs, antibody therapies, and preventive vaccines. SARS-CoV-2 is a positive-sense, single-strand RNA virus that belongs to the beta coronavirus genus [2]. It has a genome size of 29.82 kb, which encodes multiple non-structural and structural proteins. The ORF1ab encode non-structural proteins for RNA replication and transcription
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