Excessive G-U transversions in novel allele variants in SARS-CoV-2 genomes

PeerJ
Alexander Y Panchin, Yuri V Panchin

Abstract

SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission. We used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variations. These frequencies were compared with relative substitutions frequencies between SARS-CoV-2 and related animal coronaviruses. A similar analysis was performed for human coronaviruses SARS-CoV and HKU1. We found a 9-fold excess of G-U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). This suggests that mutation patterns of SARS-CoV-2 have changed after transmission to humans. The excess of G-U transversions was much smaller in a similar analysis for SARS-CoV and non-existent for HKU1. Remarkably, we did not find a similar excess of complementary C-A mutati...Continue Reading

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Citations

Mar 23, 2021·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Alexander Tyshkovskiy, Alexander Y Panchin
Apr 26, 2021·Genome Biology and Evolution·Nicola De MaioNick Goldman
Jun 10, 2021·European Journal of Medical Research·SeyedAhmad SeyedAlinaghi Shayesteh Jahanfar
Jul 15, 2021·BioMed Research International·Abdelmalek HakmaouiBrahim Admou
Sep 15, 2021·Briefings in Bioinformatics·Diego ForniManuela Sironi
Oct 27, 2021·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Alexander Tyshkovskiy, Alexander Y Panchin

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Datasets Mentioned

BETA
MN996532.1
MT040335.1
KY417146.1
DQ648856.1
MH687968.1
KT368891.1

Methods Mentioned

BETA
deamination

Software Mentioned

perl scripts
Clustal Omega
BLASTn

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