A solution to achieve sequencing from SARS-CoV-2 specimens with low viral loads: concatenation of reads from independent reactions.

ABSTRACT:

Background

During the pandemic, whole genome sequencing was critical to characterize SARS-CoV-2 for surveillance, clinical and therapeutical purposes. However, low viral loads in specimens often led to suboptimal sequencing, making lineage assignment and phylogenetic analysis difficult. We propose an alternative approach to sequencing these specimens that involves sequencing in triplicate and concatenation of the reads obtained using bioinformatics. This proposal is based on the hypothesis that the uncovered regions in each replicate differ and that concatenation would compensate for these gaps and recover a larger percentage of the sequenced genome.

Results

Whole genome sequencing was performed in triplicate on 30 samples with Ct > 32 and the benefit of replicate read conca

SUBMITTER: Cerro-Monje A 

PROVIDER: S-EPMC11137936 | biostudies-literature | 2024 May

REPOSITORIES: biostudies-literature