Variation in synonymous evolutionary rates in the SARS-CoV-2 genome
IntroductionCoronavirus disease 2019 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Influential variants and mutants of this virus continue to emerge, and more effective virus-related information is urgently required for identifying and predicting ne...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1136386/full |
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| author | Qianru Sun Qianru Sun Jinfeng Zeng Jinfeng Zeng Kang Tang Kang Tang Haoyu Long Haoyu Long Chi Zhang Chi Zhang Jie Zhang Jie Zhang Jing Tang Jing Tang Yuting Xin Yuting Xin Jialu Zheng Jialu Zheng Litao Sun Litao Sun Siyang Liu Siyang Liu Xiangjun Du Xiangjun Du Xiangjun Du |
| author_facet | Qianru Sun Qianru Sun Jinfeng Zeng Jinfeng Zeng Kang Tang Kang Tang Haoyu Long Haoyu Long Chi Zhang Chi Zhang Jie Zhang Jie Zhang Jing Tang Jing Tang Yuting Xin Yuting Xin Jialu Zheng Jialu Zheng Litao Sun Litao Sun Siyang Liu Siyang Liu Xiangjun Du Xiangjun Du Xiangjun Du |
| author_sort | Qianru Sun |
| collection | DOAJ |
| description | IntroductionCoronavirus disease 2019 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Influential variants and mutants of this virus continue to emerge, and more effective virus-related information is urgently required for identifying and predicting new mutants. According to earlier reports, synonymous substitutions were considered phenotypically silent; thus, such mutations were frequently ignored in studies of viral mutations because they did not directly cause amino acid changes. However, recent studies have shown that synonymous substitutions are not completely silent, and their patterns and potential functional correlations should thus be delineated for better control of the pandemic.MethodsIn this study, we estimated the synonymous evolutionary rate (SER) across the SARS-CoV-2 genome and used it to infer the relationship between the viral RNA and host protein. We also assessed the patterns of characteristic mutations found in different viral lineages.ResultsWe found that the SER varies across the genome and that the variation is primarily influenced by codon-related factors. Moreover, the conserved motifs identified based on the SER were found to be related to host RNA transport and regulation. Importantly, the majority of the existing fixed-characteristic mutations for five important virus lineages (Alpha, Beta, Gamma, Delta, and Omicron) were significantly enriched in partially constrained regions.DiscussionTaken together, our results provide unique information on the evolutionary and functional dynamics of SARS-CoV-2 based on synonymous mutations and offer potentially useful information for better control of the SARS-CoV-2 pandemic. |
| first_indexed | 2024-04-10T05:11:06Z |
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| id | doaj.art-fccda825b20c4e4c871c8cf643887b15 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-10T05:11:06Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-fccda825b20c4e4c871c8cf643887b152023-03-09T07:25:02ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-03-011410.3389/fmicb.2023.11363861136386Variation in synonymous evolutionary rates in the SARS-CoV-2 genomeQianru Sun0Qianru Sun1Jinfeng Zeng2Jinfeng Zeng3Kang Tang4Kang Tang5Haoyu Long6Haoyu Long7Chi Zhang8Chi Zhang9Jie Zhang10Jie Zhang11Jing Tang12Jing Tang13Yuting Xin14Yuting Xin15Jialu Zheng16Jialu Zheng17Litao Sun18Litao Sun19Siyang Liu20Siyang Liu21Xiangjun Du22Xiangjun Du23Xiangjun Du24School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaKey Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, ChinaIntroductionCoronavirus disease 2019 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Influential variants and mutants of this virus continue to emerge, and more effective virus-related information is urgently required for identifying and predicting new mutants. According to earlier reports, synonymous substitutions were considered phenotypically silent; thus, such mutations were frequently ignored in studies of viral mutations because they did not directly cause amino acid changes. However, recent studies have shown that synonymous substitutions are not completely silent, and their patterns and potential functional correlations should thus be delineated for better control of the pandemic.MethodsIn this study, we estimated the synonymous evolutionary rate (SER) across the SARS-CoV-2 genome and used it to infer the relationship between the viral RNA and host protein. We also assessed the patterns of characteristic mutations found in different viral lineages.ResultsWe found that the SER varies across the genome and that the variation is primarily influenced by codon-related factors. Moreover, the conserved motifs identified based on the SER were found to be related to host RNA transport and regulation. Importantly, the majority of the existing fixed-characteristic mutations for five important virus lineages (Alpha, Beta, Gamma, Delta, and Omicron) were significantly enriched in partially constrained regions.DiscussionTaken together, our results provide unique information on the evolutionary and functional dynamics of SARS-CoV-2 based on synonymous mutations and offer potentially useful information for better control of the SARS-CoV-2 pandemic.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1136386/fullbinding motifcodon usagedominant variantsSARS-CoV-2synonymous evolutionary rate |
| spellingShingle | Qianru Sun Qianru Sun Jinfeng Zeng Jinfeng Zeng Kang Tang Kang Tang Haoyu Long Haoyu Long Chi Zhang Chi Zhang Jie Zhang Jie Zhang Jing Tang Jing Tang Yuting Xin Yuting Xin Jialu Zheng Jialu Zheng Litao Sun Litao Sun Siyang Liu Siyang Liu Xiangjun Du Xiangjun Du Xiangjun Du Variation in synonymous evolutionary rates in the SARS-CoV-2 genome Frontiers in Microbiology binding motif codon usage dominant variants SARS-CoV-2 synonymous evolutionary rate |
| title | Variation in synonymous evolutionary rates in the SARS-CoV-2 genome |
| title_full | Variation in synonymous evolutionary rates in the SARS-CoV-2 genome |
| title_fullStr | Variation in synonymous evolutionary rates in the SARS-CoV-2 genome |
| title_full_unstemmed | Variation in synonymous evolutionary rates in the SARS-CoV-2 genome |
| title_short | Variation in synonymous evolutionary rates in the SARS-CoV-2 genome |
| title_sort | variation in synonymous evolutionary rates in the sars cov 2 genome |
| topic | binding motif codon usage dominant variants SARS-CoV-2 synonymous evolutionary rate |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1136386/full |
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