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Article

Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data.

Molecular biology and evolution - 1 Sept 2026

Anker Klara Marie, Evans Pena Rosario, Kemp Steven A, Clarke Joseph, Zhao Lele, Bonsall David, Grayson Nicholas, Bashton Matthew, Walker Ann Sarah, Golubchik Tanya, Hall Matthew, Lythgoe Katrina

Abstract excerpt

Deep-sequencing data are increasingly used to study within-host viral diversity and to inform evolutionary inference. For SARS-CoV-2, analyses based on intra-host single-nucleotide variants (iSNVs) have been widely applied to quantify within-host diversity and infer transmission dynamics. However, these applications critically depend on the reliable identification of low-frequency variants, which remain...

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Topics

Humans
SARS-CoV-2
High-Throughput Nucleotide Sequencing
Artifacts
COVID-19

Methodology Data sources Editorial policy Privacy Delete account & data About Contact Helena Bioinformatics

Polymorphism, Single Nucleotide

Genome, Viral

Genetic Variation

Gene Frequency

Source

Open in PubMed Open full text

Identifiers

PMID: 42610621
DOI: 10.1093/molbev/msag209
PMCID: PMC13533334

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