Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes
Background 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 compariso...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2020-07-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/9648.pdf |
| _version_ | 1797420558411890688 |
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| author | Alexander Y. Panchin Yuri V. Panchin |
| author_facet | Alexander Y. Panchin Yuri V. Panchin |
| author_sort | Alexander Y. Panchin |
| collection | DOAJ |
| description | Background 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. Methods 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. Results 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 mutations in SARS-CoV-2. We discuss possible explanations for these observations. |
| first_indexed | 2024-03-09T07:04:10Z |
| format | Article |
| id | doaj.art-5e2bdef053544bbaa818fe8f95c52741 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:04:10Z |
| publishDate | 2020-07-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-5e2bdef053544bbaa818fe8f95c527412023-12-03T09:45:53ZengPeerJ Inc.PeerJ2167-83592020-07-018e964810.7717/peerj.9648Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomesAlexander Y. PanchinYuri V. PanchinBackground 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. Methods 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. Results 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 mutations in SARS-CoV-2. We discuss possible explanations for these observations.https://peerj.com/articles/9648.pdfSARS-CoV-2COVID-19MutationsTransversionsEvolutionMutagenesis |
| spellingShingle | Alexander Y. Panchin Yuri V. Panchin Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes PeerJ SARS-CoV-2 COVID-19 Mutations Transversions Evolution Mutagenesis |
| title | Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes |
| title_full | Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes |
| title_fullStr | Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes |
| title_full_unstemmed | Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes |
| title_short | Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes |
| title_sort | excessive g u transversions in novel allele variants in sars cov 2 genomes |
| topic | SARS-CoV-2 COVID-19 Mutations Transversions Evolution Mutagenesis |
| url | https://peerj.com/articles/9648.pdf |
| work_keys_str_mv | AT alexanderypanchin excessivegutransversionsinnovelallelevariantsinsarscov2genomes AT yurivpanchin excessivegutransversionsinnovelallelevariantsinsarscov2genomes |