WHOLE GENOME SEQUENCING OF SARS‐CoV‐2: COMPARISON OF TARGET CAPTURE AND AMPLICON SINGLE MOLECULAR REAL TIME SEQUENCING PROTOCOLS

alexandrossfakianakis shared this article with you from Inoreader WHOLE GENOME SEQUENCING OF SARS‐CoV‐2: COMPARISON OF TARGET CAPTURE AND AMPLICON SINGLE MOLECULAR REAL TIME SEQUENCING PROTOCOLS via Journal of Medical Virology 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 Molecular 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% [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 w ith Ct>17 (p<0.01). Pacbio SMRT sequencing protocols appears to be suitable for WGS, genotyping and detecting mutations of SARS-CoV-2. This article is protected by copyright. All rights reserved. View on Web

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