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...

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Detalles Bibliográficos
Autores: 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
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
Descripción
Sumario: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

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