tetano
Editor, Senior Moderator
Methods Mol Biol
. 2026:2981:157-201.
doi: 10.1007/978-1-0716-4836-0_8.
Methods to Characterize Mutant Spectra of RNA Viruses: The Case of SARS-CoV-2
Celia Perales[SUP] 1 2 [/SUP], María Eugenia Soria[SUP] 3 4 [/SUP], Ana Isabel de Ávila[SUP] 4 [/SUP], Brenda Martínez-González[SUP] 3 4 [/SUP], Isabel Gallego[SUP] 4 [/SUP], Carlos García-Crespo[SUP] 4 [/SUP], Pilar Somovilla[SUP] 4 5 [/SUP], Pablo Mínguez[SUP] 6 7 8 [/SUP], Ignacio Gadea[SUP] 3 9 [/SUP], Esteban Domingo[SUP] 10 [/SUP]
Affiliations
Viral isolates consist of complex mixtures of many variants that are termed mutant spectra, distributions, clouds or swarms. They include information on virus behavior that is not captured by consensus sequences. Here, we describe experimental procedures, a bioinformatics pipeline, and calculations to characterize the mutant spectrum of RNA viruses. The data are obtained through the high-resolution MiSeq Illumina ultra-deep sequencing platform. We describe protocols for SARS-CoV-2 patients' isolates and laboratory populations, which can be adapted to other RNA viral pathogens. Precautions for sample handling to avoid cross-contaminations and controls for mutation and deletion detection reliability are also outlined.
Keywords: COVID-19; Deletion; MiSeq Illumina; Mutation; RNA quantification; Ultra-deep sequencing; Viral quasispecies; cDNA amplification.
. 2026:2981:157-201.
doi: 10.1007/978-1-0716-4836-0_8.
Methods to Characterize Mutant Spectra of RNA Viruses: The Case of SARS-CoV-2
Celia Perales[SUP] 1 2 [/SUP], María Eugenia Soria[SUP] 3 4 [/SUP], Ana Isabel de Ávila[SUP] 4 [/SUP], Brenda Martínez-González[SUP] 3 4 [/SUP], Isabel Gallego[SUP] 4 [/SUP], Carlos García-Crespo[SUP] 4 [/SUP], Pilar Somovilla[SUP] 4 5 [/SUP], Pablo Mínguez[SUP] 6 7 8 [/SUP], Ignacio Gadea[SUP] 3 9 [/SUP], Esteban Domingo[SUP] 10 [/SUP]
Affiliations
- PMID: 42056692
- DOI: 10.1007/978-1-0716-4836-0_8
Viral isolates consist of complex mixtures of many variants that are termed mutant spectra, distributions, clouds or swarms. They include information on virus behavior that is not captured by consensus sequences. Here, we describe experimental procedures, a bioinformatics pipeline, and calculations to characterize the mutant spectrum of RNA viruses. The data are obtained through the high-resolution MiSeq Illumina ultra-deep sequencing platform. We describe protocols for SARS-CoV-2 patients' isolates and laboratory populations, which can be adapted to other RNA viral pathogens. Precautions for sample handling to avoid cross-contaminations and controls for mutation and deletion detection reliability are also outlined.
Keywords: COVID-19; Deletion; MiSeq Illumina; Mutation; RNA quantification; Ultra-deep sequencing; Viral quasispecies; cDNA amplification.