SARS-CoV-2 mutant spectra as variant of concern nurseries : endless variation?
Copyright © 2024 Martínez-González, Soria, Mínguez, Lorenzo-Redondo, Salar-Vidal, López-García, Esteban-Muñoz, Durán-Pastor, Somovilla, García-Crespo, de Ávila, Gómez, Esteban, Fernández-Roblas, Gadea, Domingo and Perales..
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:15 |
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| Enthalten in: |
Frontiers in microbiology - 15(2024) vom: 27., Seite 1358258 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Martínez-González, Brenda [VerfasserIn] |
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| Links: |
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| Themen: |
COVID-19 |
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| Anmerkungen: |
Date Revised 03.04.2024 published: Electronic-eCollection Citation Status PubMed-not-MEDLINE |
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| doi: |
10.3389/fmicb.2024.1358258 |
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| 520 | |a Copyright © 2024 Martínez-González, Soria, Mínguez, Lorenzo-Redondo, Salar-Vidal, López-García, Esteban-Muñoz, Durán-Pastor, Somovilla, García-Crespo, de Ávila, Gómez, Esteban, Fernández-Roblas, Gadea, Domingo and Perales. | ||
| 520 | |a 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 | ||
| 520 | |a Methods: Here we use high resolution ultra-deep sequencing to analyze SARS-CoV-2 mutant spectra | ||
| 520 | |a 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 | ||
| 520 | |a 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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| 650 | 4 | |a clade-discordant residues | |
| 650 | 4 | |a ultra-deep sequencing | |
| 650 | 4 | |a variant of concern | |
| 650 | 4 | |a viral emergence | |
| 650 | 4 | |a viral quasispecies | |
| 700 | 1 | |a Soria, María Eugenia |e verfasserin |4 aut | |
| 700 | 1 | |a Mínguez, Pablo |e verfasserin |4 aut | |
| 700 | 1 | |a Lorenzo-Redondo, Ramón |e verfasserin |4 aut | |
| 700 | 1 | |a Salar-Vidal, Llanos |e verfasserin |4 aut | |
| 700 | 1 | |a López-García, Alberto |e verfasserin |4 aut | |
| 700 | 1 | |a Esteban-Muñoz, Mario |e verfasserin |4 aut | |
| 700 | 1 | |a Durán-Pastor, Antoni |e verfasserin |4 aut | |
| 700 | 1 | |a Somovilla, Pilar |e verfasserin |4 aut | |
| 700 | 1 | |a García-Crespo, Carlos |e verfasserin |4 aut | |
| 700 | 1 | |a de Ávila, Ana Isabel |e verfasserin |4 aut | |
| 700 | 1 | |a Gómez, Jordi |e verfasserin |4 aut | |
| 700 | 1 | |a Esteban, Jaime |e verfasserin |4 aut | |
| 700 | 1 | |a Fernández-Roblas, Ricardo |e verfasserin |4 aut | |
| 700 | 1 | |a Gadea, Ignacio |e verfasserin |4 aut | |
| 700 | 1 | |a Domingo, Esteban |e verfasserin |4 aut | |
| 700 | 1 | |a Perales, Celia |e verfasserin |4 aut | |
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