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- Title
Whole‐genome sequencing of SARS‐CoV‐2: Comparison of target capture and amplicon single molecule real‐time sequencing protocols.
- Authors
Nicot, Florence; Trémeaux, Pauline; Latour, Justine; Jeanne, Nicolas; Ranger, Noémie; Raymond, Stéphanie; Dimeglio, Chloé; Salin, Gérald; Donnadieu, Cécile; Izopet, Jacques
- Abstract
Fast, accurate sequencing methods are needed to identify new variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) genome. Single‐molecule real‐time (SMRT) Pacific Biosciences (PacBio) provides long, highly accurate sequences by circular consensus reads. This study compares the performance of a target capture SMRT PacBio protocol for whole‐genome sequencing (WGS) of SARS‐CoV‐2 to that of an amplicon PacBio SMRT sequencing protocol. The median genome coverage was higher (p < 0.05) with the target capture protocol (99.3% [interquartile range, IQR: 96.3–99.5]) than with the amplicon protocol (99.3% [IQR: 69.9–99.3]). The clades of 65 samples determined with both protocols were 100% concordant. After adjusting for Ct values, S gene coverage was higher with the target capture protocol than with the amplicon protocol. After stratification on Ct values, higher S gene coverage with the target capture protocol was observed only for samples with Ct > 17 (p < 0.01). PacBio SMRT sequencing protocols appear to be suitable for WGS, genotyping, and detecting mutations of SARS‐CoV‐2.
- Subjects
SARS-CoV-2; NUCLEOTIDE sequencing; SINGLE molecules
- Publication
Journal of Medical Virology, 2023, Vol 95, Issue 1, p1
- ISSN
0146-6615
- Publication type
Article
- DOI
10.1002/jmv.28123