Pratik Goswami1,2, Martin Bartas3, Matej Lexa4, Natália Bohálová1,5, Adriana Volná6, Jiří Červeň3, Veronika Červeňová7, Petr Pečinka3, Vladimír Špunda6,8, Miroslav Fojta1, Václav Brázda1. 1. Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic. 2. National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic. 3. Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic. 4. Faculty of Informatics, Masaryk University, Brno, Czech Republic. 5. Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic. 6. Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic. 7. Department of Mathematics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic. 8. Global Change Research Institute of the Czech Academy of Sciences, Brno, Czech Republic.
Abstract
SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 genome. In this study, we inspected high-frequency mutations of SARS-CoV-2 and carried out systematic analyses of their overlay with inverted repeat (IR) loci and CpG islands. The main conclusion of our study is that SARS-CoV-2 hot-spot mutations are significantly enriched within both IRs and CpG island loci. This points to their role in genomic instability and may predict further mutational drive of the SARS-CoV-2 genome. Moreover, CpG islands are strongly enriched upstream from viral ORFs and thus could play important roles in transcription and the viral life cycle. We hypothesize that hypermethylation of these loci will decrease the transcription of viral ORFs and could therefore limit the progression of the disease.
SARS-CoV-2 is aene">n inten class="Gene">nsively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 genome. In this study, we inspected high-frequency mutations of SARS-CoV-2 and carried out systematic analyses of their overlay with inverted repeat (IR) loci and CpG islands. The main conclusion of our study is that SARS-CoV-2hot-spot mutations are significantly enriched within both IRs and CpG island loci. This points to their role in genomic instability and may predict further mutational drive of the SARS-CoV-2 genome. Moreover, CpG islands are strongly enriched upstream from viral ORFs and thus could play important roles in transcription and the viral life cycle. We hypothesize that hypermethylation of these loci will decrease the transcription of viral ORFs and could therefore limit the progression of the disease.
Authors: Martin Bartas; Pratik Goswami; Matej Lexa; Jiří Červeň; Adriana Volná; Miroslav Fojta; Václav Brázda; Petr Pečinka Journal: Brief Bioinform Date: 2021-04-09 Impact factor: 11.622