Tradeoffs between proliferation and transmission in virus evolution- insights from evolutionary and functional analyses of SARS-CoV-2.
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| Format: | Artículo científico |
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Virology journal
2025
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| author | Tai, Jui-Hung Lee, Ding-Chin Lin, Hsin-Fu Chao, Tai-Ling Ruan, Yongsen Cheng, Ya-Wen Chou, Yu-Chi Lin, You-Yu Chang, Sui-Yuan Chen, Pei-Jer Yeh, Shiou-Hwei Wang, Hurng-Yi |
| author_facet | Tai, Jui-Hung Lee, Ding-Chin Lin, Hsin-Fu Chao, Tai-Ling Ruan, Yongsen Cheng, Ya-Wen Chou, Yu-Chi Lin, You-Yu Chang, Sui-Yuan Chen, Pei-Jer Yeh, Shiou-Hwei Wang, Hurng-Yi Tai, Jui-Hung Lee, Ding-Chin Lin, Hsin-Fu Chao, Tai-Ling Ruan, Yongsen Cheng, Ya-Wen Chou, Yu-Chi Lin, You-Yu Chang, Sui-Yuan Chen, Pei-Jer Yeh, Shiou-Hwei Wang, Hurng-Yi |
| collection | PubMed - marine biology |
| contents | Tradeoffs between proliferation and transmission in virus evolution- insights from evolutionary and functional analyses of SARS-CoV-2. Tai, Jui-Hung Lee, Ding-Chin Lin, Hsin-Fu Chao, Tai-Ling Ruan, Yongsen Cheng, Ya-Wen Chou, Yu-Chi Lin, You-Yu Chang, Sui-Yuan Chen, Pei-Jer Yeh, Shiou-Hwei Wang, Hurng-Yi SARS-CoV-2 COVID-19 Humans Evolution, Molecular Mutation Spike Glycoprotein, Coronavirus Genetic Variation Selection, Genetic To be successful, a virus must maintain high between-host transmissibility while also effectively adapting within hosts. The impact of these potentially conflicting demands on viral genetic diversity and adaptation remains largely unexplored. These modes of adaptation can induce uncorrelated selection, bring mutations that enhance certain fitness aspects at the expense of others to high freqency, and contribute to the maintenance of genetic variation. The vast wealth of SARS-CoV-2 genetic data gathered from within and across hosts offers an unparalleled opportunity to test the above hypothesis. By analyzing a large set of SARS-CoV-2 sequences (~ 2 million) collected from early 2020 to mid-2021, we found that high frequency mutations within hosts are sometimes detrimental during between-host transmission. This highlights potential inverse selection pressures within- versus between-hosts. We also identified a group of nonsynonymous changes likely maintained by pleiotropy, as their frequencies are significantly higher than neutral expectation, yet they have never experienced clonal expansion. Analyzing one such mutation, spike M1237I, reveals that spike I1237 boosts viral assembly but reduces in vitro transmission, highlighting its pleiotropic effect. Though they make up about 2% of total changes, these types of variants represent 37% of SARS-CoV-2 genetic diversity. These mutations are notably prevalent in the Omicron variant from late 2021, hinting that pleiotropy may promote positive epistasis and new successful variants. Estimates of viral population dynamics, such as population sizes and transmission bottlenecks, assume neutrality of within-host variation. Our demonstration that these changes may affect fitness calls into question the robustness of these estimates. |
| format | Artículo científico |
| id | pubmed_40253323 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Virology journal |
| record_format | pubmed |
| spellingShingle | Tradeoffs between proliferation and transmission in virus evolution- insights from evolutionary and functional analyses of SARS-CoV-2. Tai, Jui-Hung Lee, Ding-Chin Lin, Hsin-Fu Chao, Tai-Ling Ruan, Yongsen Cheng, Ya-Wen Chou, Yu-Chi Lin, You-Yu Chang, Sui-Yuan Chen, Pei-Jer Yeh, Shiou-Hwei Wang, Hurng-Yi SARS-CoV-2 COVID-19 Humans Evolution, Molecular Mutation Spike Glycoprotein, Coronavirus Genetic Variation Selection, Genetic Tradeoffs between proliferation and transmission in virus evolution- insights from evolutionary and functional analyses of SARS-CoV-2. Tai, Jui-Hung Lee, Ding-Chin Lin, Hsin-Fu Chao, Tai-Ling Ruan, Yongsen Cheng, Ya-Wen Chou, Yu-Chi Lin, You-Yu Chang, Sui-Yuan Chen, Pei-Jer Yeh, Shiou-Hwei Wang, Hurng-Yi SARS-CoV-2 COVID-19 Humans Evolution, Molecular Mutation Spike Glycoprotein, Coronavirus Genetic Variation Selection, Genetic To be successful, a virus must maintain high between-host transmissibility while also effectively adapting within hosts. The impact of these potentially conflicting demands on viral genetic diversity and adaptation remains largely unexplored. These modes of adaptation can induce uncorrelated selection, bring mutations that enhance certain fitness aspects at the expense of others to high freqency, and contribute to the maintenance of genetic variation. The vast wealth of SARS-CoV-2 genetic data gathered from within and across hosts offers an unparalleled opportunity to test the above hypothesis. By analyzing a large set of SARS-CoV-2 sequences (~ 2 million) collected from early 2020 to mid-2021, we found that high frequency mutations within hosts are sometimes detrimental during between-host transmission. This highlights potential inverse selection pressures within- versus between-hosts. We also identified a group of nonsynonymous changes likely maintained by pleiotropy, as their frequencies are significantly higher than neutral expectation, yet they have never experienced clonal expansion. Analyzing one such mutation, spike M1237I, reveals that spike I1237 boosts viral assembly but reduces in vitro transmission, highlighting its pleiotropic effect. Though they make up about 2% of total changes, these types of variants represent 37% of SARS-CoV-2 genetic diversity. These mutations are notably prevalent in the Omicron variant from late 2021, hinting that pleiotropy may promote positive epistasis and new successful variants. Estimates of viral population dynamics, such as population sizes and transmission bottlenecks, assume neutrality of within-host variation. Our demonstration that these changes may affect fitness calls into question the robustness of these estimates. |
| title | Tradeoffs between proliferation and transmission in virus evolution- insights from evolutionary and functional analyses of SARS-CoV-2. |
| topic | SARS-CoV-2 COVID-19 Humans Evolution, Molecular Mutation Spike Glycoprotein, Coronavirus Genetic Variation Selection, Genetic |
| url | https://pubmed.ncbi.nlm.nih.gov/40253323/ |