Methods to Characterize Mutant Spectra of RNA Viruses: The Case of SARS-CoV-2

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.