Deletion detection in SARS-CoV-2 genomes from COVID-19 patients: elimination of false positives.

ABSTRACT: Deletions are prevalent in the genomes of SARS-CoV-2 isolates from COVID-19 patients, but their roles in the severity, transmission, and persistence of disease are poorly understood. Millions of COVID-19 swab samples from patients have been sequenced and made available online, offering an unprecedented opportunity to study such deletions. Multiplex-PCR sequencing (amplicon-seq) has been the most widely used method for sequencing clinical COVID-19 samples. However, through experiments with negative control samples and existing bioinformatics methods, we find that this protocol introduces large numbers of false-positive deletions. These false positives commonly occur in short alignments, at low frequency and depth, and near primer binding sites used for whole-genome amplification. To address

SUBMITTER: Jiang N 

PROVIDER: S-EPMC12900060 | biostudies-literature | 2026

REPOSITORIES: biostudies-literature