Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2.
Identifying drivers of viral diversity is key to understanding the evolutionary as well as epidemiological dynamics of the COVID-19 pandemic. Using rich viral genomic data sets, we show that periods of steadily rising diversity have been punctuated by sudden, enormous increases followed by similarly...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-02-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1010896 |
| _version_ | 1811158375063355392 |
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| author | Bjarke Frost Nielsen Chadi M Saad-Roy Yimei Li Kim Sneppen Lone Simonsen Cécile Viboud Simon A Levin Bryan T Grenfell |
| author_facet | Bjarke Frost Nielsen Chadi M Saad-Roy Yimei Li Kim Sneppen Lone Simonsen Cécile Viboud Simon A Levin Bryan T Grenfell |
| author_sort | Bjarke Frost Nielsen |
| collection | DOAJ |
| description | Identifying drivers of viral diversity is key to understanding the evolutionary as well as epidemiological dynamics of the COVID-19 pandemic. Using rich viral genomic data sets, we show that periods of steadily rising diversity have been punctuated by sudden, enormous increases followed by similarly abrupt collapses of diversity. We introduce a mechanistic model of saltational evolution with epistasis and demonstrate that these features parsimoniously account for the observed temporal dynamics of inter-genomic diversity. Our results provide support for recent proposals that saltational evolution may be a signature feature of SARS-CoV-2, allowing the pathogen to more readily evolve highly transmissible variants. These findings lend theoretical support to a heightened awareness of biological contexts where increased diversification may occur. They also underline the power of pathogen genomics and other surveillance streams in clarifying the phylodynamics of emerging and endemic infections. In public health terms, our results further underline the importance of equitable distribution of up-to-date vaccines. |
| first_indexed | 2024-04-10T05:23:35Z |
| format | Article |
| id | doaj.art-60e6ac8315c74e3288ac9599ef3805f4 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-04-10T05:23:35Z |
| publishDate | 2023-02-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-60e6ac8315c74e3288ac9599ef3805f42023-03-08T05:30:41ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582023-02-01192e101089610.1371/journal.pcbi.1010896Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2.Bjarke Frost NielsenChadi M Saad-RoyYimei LiKim SneppenLone SimonsenCécile ViboudSimon A LevinBryan T GrenfellIdentifying drivers of viral diversity is key to understanding the evolutionary as well as epidemiological dynamics of the COVID-19 pandemic. Using rich viral genomic data sets, we show that periods of steadily rising diversity have been punctuated by sudden, enormous increases followed by similarly abrupt collapses of diversity. We introduce a mechanistic model of saltational evolution with epistasis and demonstrate that these features parsimoniously account for the observed temporal dynamics of inter-genomic diversity. Our results provide support for recent proposals that saltational evolution may be a signature feature of SARS-CoV-2, allowing the pathogen to more readily evolve highly transmissible variants. These findings lend theoretical support to a heightened awareness of biological contexts where increased diversification may occur. They also underline the power of pathogen genomics and other surveillance streams in clarifying the phylodynamics of emerging and endemic infections. In public health terms, our results further underline the importance of equitable distribution of up-to-date vaccines.https://doi.org/10.1371/journal.pcbi.1010896 |
| spellingShingle | Bjarke Frost Nielsen Chadi M Saad-Roy Yimei Li Kim Sneppen Lone Simonsen Cécile Viboud Simon A Levin Bryan T Grenfell Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2. PLoS Computational Biology |
| title | Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2. |
| title_full | Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2. |
| title_fullStr | Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2. |
| title_full_unstemmed | Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2. |
| title_short | Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2. |
| title_sort | host heterogeneity and epistasis explain punctuated evolution of sars cov 2 |
| url | https://doi.org/10.1371/journal.pcbi.1010896 |
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