SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation?
Introduction: SARS-CoV-2 isolates of a given clade may contain low frequency genomes that encode amino acids or deletions which are typical of a different clade. Methods: Here we use high resolution ultra-deep sequencing to analyze SARS-CoV-2 mutant spectra. Results: In 6 out of 11 SARS-CoV-2 isolat...
| Autores: | , , , , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Fecha de publicación: | 2024 |
| País: | España |
| Institución: | Universidad Autónoma de Madrid |
| Repositorio: | Biblos-e Archivo. Repositorio Institucional de la UAM |
| Idioma: | inglés |
| OAI Identifier: | oai:repositorio.uam.es:10486/718222 |
| Acceso en línea: | http://hdl.handle.net/10486/718222 https://dx.doi.org/10.3389/fmicb.2024.1358258 |
| Access Level: | acceso abierto |
| Palabra clave: | COVID-19 ultra-deep sequencing variant of concern viral emergence viral quasispecies clade-discordant residues Biología y Biomedicina / Biología |
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| dc.title.none.fl_str_mv |
SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation? |
| title |
SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation? |
| spellingShingle |
SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation? Martínez-González, Brenda COVID-19 ultra-deep sequencing variant of concern viral emergence viral quasispecies clade-discordant residues Biología y Biomedicina / Biología |
| title_short |
SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation? |
| title_full |
SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation? |
| title_fullStr |
SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation? |
| title_full_unstemmed |
SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation? |
| title_sort |
SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation? |
| dc.creator.none.fl_str_mv |
Martínez-González, Brenda Soria, Maria Eugenia Mínguez, Pablo Lorenzo Redondo, Ramón Salar Vidal, Llanos López García, Alberto Esteban Muñoz, Mario Durán Pastor, Antoni Somovilla Crespo, Pilar García Crespo, Carlos Ávila, Ana Isabel de Gomez, Jordi Esteban Moreno, Jaime Fernández Roblas, Ricardo Gadea Gironés, Ignacio Domingo, Esteban Perales, Celia |
| author |
Martínez-González, Brenda |
| author_facet |
Martínez-González, Brenda Soria, Maria Eugenia Mínguez, Pablo Lorenzo Redondo, Ramón Salar Vidal, Llanos López García, Alberto Esteban Muñoz, Mario Durán Pastor, Antoni Somovilla Crespo, Pilar García Crespo, Carlos Ávila, Ana Isabel de Gomez, Jordi Esteban Moreno, Jaime Fernández Roblas, Ricardo Gadea Gironés, Ignacio Domingo, Esteban Perales, Celia |
| author_role |
author |
| author2 |
Soria, Maria Eugenia Mínguez, Pablo Lorenzo Redondo, Ramón Salar Vidal, Llanos López García, Alberto Esteban Muñoz, Mario Durán Pastor, Antoni Somovilla Crespo, Pilar García Crespo, Carlos Ávila, Ana Isabel de Gomez, Jordi Esteban Moreno, Jaime Fernández Roblas, Ricardo Gadea Gironés, Ignacio Domingo, Esteban Perales, Celia |
| author2_role |
author author author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Departamento de Biología Molecular Facultad de Ciencias |
| dc.subject.none.fl_str_mv |
COVID-19 ultra-deep sequencing variant of concern viral emergence viral quasispecies clade-discordant residues Biología y Biomedicina / Biología |
| topic |
COVID-19 ultra-deep sequencing variant of concern viral emergence viral quasispecies clade-discordant residues Biología y Biomedicina / Biología |
| description |
Introduction: SARS-CoV-2 isolates of a given clade may contain low frequency genomes that encode amino acids or deletions which are typical of a different clade. Methods: Here we use high resolution ultra-deep sequencing to analyze SARS-CoV-2 mutant spectra. Results: In 6 out of 11 SARS-CoV-2 isolates from COVID-19 patients, the mutant spectrum of the spike (S)-coding region included two or more amino acids or deletions, that correspond to discordant viral clades. A similar observation is reported for laboratory populations of SARS-CoV-2 USA-WA1/2020, following a cell culture infection in the presence of remdesivir, ribavirin or their combinations. Moreover, some of the clade-discordant genome residues are found in the same haplotype within an amplicon. Discussion: We evaluate possible interpretations of these findings, and reviewed precedents for rapid selection of genomes with multiple mutations in RNA viruses. These considerations suggest that intra-host evolution may be sufficient to generate minority sequences which are closely related to sequences typical of other clades. The results provide a model for the origin of variants of concern during epidemic spread─in particular Omicron lineages─that does not require prolonged infection, involvement of immunocompromised individuals, or participation of intermediate, non-human hosts |
| publishDate |
2024 |
| dc.date.none.fl_str_mv |
2024 2024-03-14 |
| dc.type.none.fl_str_mv |
research article http://purl.org/coar/resource_type/c_2df8fbb1 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
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info:eu-repo/semantics/article |
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article |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10486/718222 https://dx.doi.org/10.3389/fmicb.2024.1358258 |
| url |
http://hdl.handle.net/10486/718222 https://dx.doi.org/10.3389/fmicb.2024.1358258 |
| dc.language.none.fl_str_mv |
Inglés eng |
| language_invalid_str_mv |
Inglés |
| language |
eng |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 Attribution 4.0 International http://creativecommons.org/licenses/by/4.0/ |
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info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 Attribution 4.0 International http://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf |
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Frontiers Media SA |
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Frontiers Media SA |
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reponame:Biblos-e Archivo. Repositorio Institucional de la UAM instname:Universidad Autónoma de Madrid |
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Universidad Autónoma de Madrid |
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Biblos-e Archivo. Repositorio Institucional de la UAM |
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Biblos-e Archivo. Repositorio Institucional de la UAM |
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1869424243533414400 |
| spelling |
SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation?Martínez-González, BrendaSoria, Maria EugeniaMínguez, PabloLorenzo Redondo, RamónSalar Vidal, LlanosLópez García, AlbertoEsteban Muñoz, MarioDurán Pastor, AntoniSomovilla Crespo, PilarGarcía Crespo, CarlosÁvila, Ana Isabel deGomez, JordiEsteban Moreno, JaimeFernández Roblas, RicardoGadea Gironés, IgnacioDomingo, Esteban Perales, CeliaCOVID-19ultra-deep sequencingvariant of concernviral emergenceviral quasispeciesclade-discordant residuesBiología y Biomedicina / BiologíaIntroduction: SARS-CoV-2 isolates of a given clade may contain low frequency genomes that encode amino acids or deletions which are typical of a different clade. Methods: Here we use high resolution ultra-deep sequencing to analyze SARS-CoV-2 mutant spectra. Results: In 6 out of 11 SARS-CoV-2 isolates from COVID-19 patients, the mutant spectrum of the spike (S)-coding region included two or more amino acids or deletions, that correspond to discordant viral clades. A similar observation is reported for laboratory populations of SARS-CoV-2 USA-WA1/2020, following a cell culture infection in the presence of remdesivir, ribavirin or their combinations. Moreover, some of the clade-discordant genome residues are found in the same haplotype within an amplicon. Discussion: We evaluate possible interpretations of these findings, and reviewed precedents for rapid selection of genomes with multiple mutations in RNA viruses. These considerations suggest that intra-host evolution may be sufficient to generate minority sequences which are closely related to sequences typical of other clades. The results provide a model for the origin of variants of concern during epidemic spread─in particular Omicron lineages─that does not require prolonged infection, involvement of immunocompromised individuals, or participation of intermediate, non-human hostsThe author(s) declare financial support was received for the research, authorship, and/or publication of this article. The study was supported by the Spanish Ministry of Science and Innovation, grants PID2020-113888RB-I00/AEI/10.13039/501100011033 and 202220 I116 and by the European Commission-Next Generation EU (regulation EU 2020/2024) through the CSIC’s Global Health Platform (PTI Salud Global). The work was also funded by grants PI21/00139 funding from Instituto de Salud Carlos III (ISCIII), co-funded by the European Union, CSIC-COV19-014 from Consejo Superior de Investigaciones Científicas (CSIC) and project 525/C/2021 from Fundació La Marató de TV3, grants 202136-30 and 202136-31. We also acknowledge the project S2018/BAA-4370 (PLATESA2 from Comunidad de Madrid/FEDER). Institutional grants from the Fundación Ramón Areces and Banco Santander to the CBMSO are also acknowledged. The team at CBMSO belongs to the Global Virus Network (GVN). BM-G is supported by predoctoral contract PFIS FI19/00119 from Instituto de Salud Carlos III cofinanced by Fondo Social Europeo (FSE), “El FSE invierte en tu futuro.” PM is supported by the Miguel Servet program of the Instituto de Salud Carlos III (CPII21/00015), cofinanced by the European Regional Development Fund (ERDF). AD-P is supported by the contract 13-2022-008566 cofinanced by the Comunidad de Madrid, through the Programa Investigo, en el marco del Plan de Recuperación, Transformación y Resiliencia, financed by the European Union - Next Generation EU. PS is supported by postdoctoral contract Margarita Salas, CA1/RSUE/2021 from MCIU. CG-C is supported by predoctoral contract PRE2018-083422 from MCIUFrontiers Media SADepartamento de Biología MolecularFacultad de Ciencias20242024-03-14research articlehttp://purl.org/coar/resource_type/c_2df8fbb1VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10486/718222https://dx.doi.org/10.3389/fmicb.2024.1358258reponame:Biblos-e Archivo. Repositorio Institucional de la UAMinstname:Universidad Autónoma de MadridInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositorio.uam.es:10486/7182222026-06-23T12:46:27Z |
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