A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusion
Abstract The ability of SARS-CoV-2 to rapidly mutate represents a remarkable complicancy. Quantitative evaluations of the effects that these mutations have on the virus structure/function is of great relevance and the availability of a large number of SARS-CoV-2 sequences since the early phases of t...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-12-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-04147-1 |
| _version_ | 1819283136838631424 |
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| author | Nicole Balasco Gianluca Damaggio Luciana Esposito Flavia Villani Rita Berisio Vincenza Colonna Luigi Vitagliano |
| author_facet | Nicole Balasco Gianluca Damaggio Luciana Esposito Flavia Villani Rita Berisio Vincenza Colonna Luigi Vitagliano |
| author_sort | Nicole Balasco |
| collection | DOAJ |
| description | Abstract The ability of SARS-CoV-2 to rapidly mutate represents a remarkable complicancy. Quantitative evaluations of the effects that these mutations have on the virus structure/function is of great relevance and the availability of a large number of SARS-CoV-2 sequences since the early phases of the pandemic represents a unique opportunity to follow the adaptation of the virus to humans. Here, we evaluated the SARS-CoV-2 amino acid mutations and their progression by analyzing publicly available viral genomes at three stages of the pandemic (2020 March 15th and October 7th, 2021 February 7th). Mutations were classified in conservative and non-conservative based on the probability to be accepted during the evolution according to the Point Accepted Mutation substitution matrices and on the similarity of the encoding codons. We found that the most frequent substitutions are T > I, L > F, and A > V and we observe accumulation of hydrophobic residues. These findings are consistent among the three stages analyzed. We also found that non-conservative mutations are less frequent than conservative ones. This finding may be ascribed to a progressive adaptation of the virus to the host. In conclusion, the present study provides indications of the early evolution of the virus and tools for the global and genome-specific evaluation of the possible impact of mutations on the structure/function of SARS-CoV-2 variants. |
| first_indexed | 2024-12-24T01:26:41Z |
| format | Article |
| id | doaj.art-ed6f49649a2f4946a07c836ce014213c |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-24T01:26:41Z |
| publishDate | 2021-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-ed6f49649a2f4946a07c836ce014213c2022-12-21T17:22:29ZengNature PortfolioScientific Reports2045-23222021-12-0111111410.1038/s41598-021-04147-1A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusionNicole Balasco0Gianluca Damaggio1Luciana Esposito2Flavia Villani3Rita Berisio4Vincenza Colonna5Luigi Vitagliano6Institute of Biostructures and Bioimaging, National Research Council (CNR)Institute of Genetics and Biophysics, National Research Council (CNR)Institute of Biostructures and Bioimaging, National Research Council (CNR)Institute of Genetics and Biophysics, National Research Council (CNR)Institute of Biostructures and Bioimaging, National Research Council (CNR)Institute of Genetics and Biophysics, National Research Council (CNR)Institute of Biostructures and Bioimaging, National Research Council (CNR)Abstract The ability of SARS-CoV-2 to rapidly mutate represents a remarkable complicancy. Quantitative evaluations of the effects that these mutations have on the virus structure/function is of great relevance and the availability of a large number of SARS-CoV-2 sequences since the early phases of the pandemic represents a unique opportunity to follow the adaptation of the virus to humans. Here, we evaluated the SARS-CoV-2 amino acid mutations and their progression by analyzing publicly available viral genomes at three stages of the pandemic (2020 March 15th and October 7th, 2021 February 7th). Mutations were classified in conservative and non-conservative based on the probability to be accepted during the evolution according to the Point Accepted Mutation substitution matrices and on the similarity of the encoding codons. We found that the most frequent substitutions are T > I, L > F, and A > V and we observe accumulation of hydrophobic residues. These findings are consistent among the three stages analyzed. We also found that non-conservative mutations are less frequent than conservative ones. This finding may be ascribed to a progressive adaptation of the virus to the host. In conclusion, the present study provides indications of the early evolution of the virus and tools for the global and genome-specific evaluation of the possible impact of mutations on the structure/function of SARS-CoV-2 variants.https://doi.org/10.1038/s41598-021-04147-1 |
| spellingShingle | Nicole Balasco Gianluca Damaggio Luciana Esposito Flavia Villani Rita Berisio Vincenza Colonna Luigi Vitagliano A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusion Scientific Reports |
| title | A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusion |
| title_full | A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusion |
| title_fullStr | A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusion |
| title_full_unstemmed | A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusion |
| title_short | A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusion |
| title_sort | global analysis of conservative and non conservative mutations in sars cov 2 detected in the first year of the covid 19 world wide diffusion |
| url | https://doi.org/10.1038/s41598-021-04147-1 |
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