Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution.
Nearly two decades after the last epidemic caused by a severe acute respiratory syndrome coronavirus (SARS-CoV), newly emerged SARS-CoV-2 quickly spread in 2020 and precipitated an ongoing global public health crisis. Both the continuous accumulation of point mutations, owed to the naturally imposed...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0268389 |
| _version_ | 1828330003935264768 |
|---|---|
| author | Danilo Rosa Nunes Carla Torres Braconi Louisa F Ludwig-Begall Clarice Weis Arns Ricardo Durães-Carvalho |
| author_facet | Danilo Rosa Nunes Carla Torres Braconi Louisa F Ludwig-Begall Clarice Weis Arns Ricardo Durães-Carvalho |
| author_sort | Danilo Rosa Nunes |
| collection | DOAJ |
| description | Nearly two decades after the last epidemic caused by a severe acute respiratory syndrome coronavirus (SARS-CoV), newly emerged SARS-CoV-2 quickly spread in 2020 and precipitated an ongoing global public health crisis. Both the continuous accumulation of point mutations, owed to the naturally imposed genomic plasticity of SARS-CoV-2 evolutionary processes, as well as viral spread over time, allow this RNA virus to gain new genetic identities, spawn novel variants and enhance its potential for immune evasion. Here, through an in-depth phylogenetic clustering analysis of upwards of 200,000 whole-genome sequences, we reveal the presence of previously unreported and hitherto unidentified mutations and recombination breakpoints in Variants of Concern (VOC) and Variants of Interest (VOI) from Brazil, India (Beta, Eta and Kappa) and the USA (Beta, Eta and Lambda). Additionally, we identify sites with shared mutations under directional evolution in the SARS-CoV-2 Spike-encoding protein of VOC and VOI, tracing a heretofore-undescribed correlation with viral spread in South America, India and the USA. Our evidence-based analysis provides well-supported evidence of similar pathways of evolution for such mutations in all SARS-CoV-2 variants and sub-lineages. This raises two pivotal points: (i) the co-circulation of variants and sub-lineages in close evolutionary environments, which sheds light onto their trajectories into convergent and directional evolution, and (ii) a linear perspective into the prospective vaccine efficacy against different SARS-CoV-2 strains. |
| first_indexed | 2024-04-13T20:33:31Z |
| format | Article |
| id | doaj.art-b8f922b766cb4fefa33f3fad835199a3 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T20:33:31Z |
| publishDate | 2022-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-b8f922b766cb4fefa33f3fad835199a32022-12-22T02:31:06ZengPublic Library of Science (PLoS)PLoS ONE1932-62032022-01-01175e026838910.1371/journal.pone.0268389Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution.Danilo Rosa NunesCarla Torres BraconiLouisa F Ludwig-BegallClarice Weis ArnsRicardo Durães-CarvalhoNearly two decades after the last epidemic caused by a severe acute respiratory syndrome coronavirus (SARS-CoV), newly emerged SARS-CoV-2 quickly spread in 2020 and precipitated an ongoing global public health crisis. Both the continuous accumulation of point mutations, owed to the naturally imposed genomic plasticity of SARS-CoV-2 evolutionary processes, as well as viral spread over time, allow this RNA virus to gain new genetic identities, spawn novel variants and enhance its potential for immune evasion. Here, through an in-depth phylogenetic clustering analysis of upwards of 200,000 whole-genome sequences, we reveal the presence of previously unreported and hitherto unidentified mutations and recombination breakpoints in Variants of Concern (VOC) and Variants of Interest (VOI) from Brazil, India (Beta, Eta and Kappa) and the USA (Beta, Eta and Lambda). Additionally, we identify sites with shared mutations under directional evolution in the SARS-CoV-2 Spike-encoding protein of VOC and VOI, tracing a heretofore-undescribed correlation with viral spread in South America, India and the USA. Our evidence-based analysis provides well-supported evidence of similar pathways of evolution for such mutations in all SARS-CoV-2 variants and sub-lineages. This raises two pivotal points: (i) the co-circulation of variants and sub-lineages in close evolutionary environments, which sheds light onto their trajectories into convergent and directional evolution, and (ii) a linear perspective into the prospective vaccine efficacy against different SARS-CoV-2 strains.https://doi.org/10.1371/journal.pone.0268389 |
| spellingShingle | Danilo Rosa Nunes Carla Torres Braconi Louisa F Ludwig-Begall Clarice Weis Arns Ricardo Durães-Carvalho Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution. PLoS ONE |
| title | Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution. |
| title_full | Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution. |
| title_fullStr | Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution. |
| title_full_unstemmed | Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution. |
| title_short | Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution. |
| title_sort | deep phylogenetic based clustering analysis uncovers new and shared mutations in sars cov 2 variants as a result of directional and convergent evolution |
| url | https://doi.org/10.1371/journal.pone.0268389 |
| work_keys_str_mv | AT danilorosanunes deepphylogeneticbasedclusteringanalysisuncoversnewandsharedmutationsinsarscov2variantsasaresultofdirectionalandconvergentevolution AT carlatorresbraconi deepphylogeneticbasedclusteringanalysisuncoversnewandsharedmutationsinsarscov2variantsasaresultofdirectionalandconvergentevolution AT louisafludwigbegall deepphylogeneticbasedclusteringanalysisuncoversnewandsharedmutationsinsarscov2variantsasaresultofdirectionalandconvergentevolution AT clariceweisarns deepphylogeneticbasedclusteringanalysisuncoversnewandsharedmutationsinsarscov2variantsasaresultofdirectionalandconvergentevolution AT ricardoduraescarvalho deepphylogeneticbasedclusteringanalysisuncoversnewandsharedmutationsinsarscov2variantsasaresultofdirectionalandconvergentevolution |