tetano
Editor, Senior Moderator
J Med Virol
. 2023 Feb 9.
doi: 10.1002/jmv.28564. Online ahead of print.
WHOLE-GENOME SINGLE MOLECULE REAL-TIME SEQUENCING OF SARS-CoV-2 OMICRON
Florence Nicot[SUP] 1 [/SUP], Pauline Trémeaux[SUP] 1 [/SUP], Justine Latour[SUP] 1 [/SUP], Romain Carcenac[SUP] 1 [/SUP], Sofia Demmou[SUP] 1 [/SUP], Nicolas Jeanne[SUP] 1 [/SUP], Noémie Ranger[SUP] 1 [/SUP], Clémentine De Smet[SUP] 1 [/SUP], Stéphanie Raymond[SUP] 1 2 [/SUP], Chloé Dimeglio[SUP] 1 2 [/SUP], Jacques Izopet[SUP] 1 2 [/SUP]
Affiliations
Abstract
New variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can only be identified using accurate sequencing methods. Single molecule real-time (SMRT) sequencing has been used to characterize Alpha and Delta variants, but not Omicron variants harbouring numerous mutations in the SARS-CoV-2 genome. This study assesses the performance of a target capture SMRT sequencing protocol for whole genome sequencing (WGS) of SARS-CoV-2 Omicron variants and compared it to that of an amplicon SMRT sequencing protocol optimized for Omicron variants. The failure rate of the target capture protocol (6%) was lower than that of the amplicon protocol (34%, p<0.001) on our dataset, and the median genome coverage with the target capture protocol (98.6% [IQR: 86-99.4]) was greater than that with the amplicon protocol (76.6% [IQR: 66-89.6], (p<0.001)). The percentages of samples with >95% whole genome coverage were 64% with the target capture protocol and 19% with the amplicon protocol (p<0.05). The clades of 96 samples determined with both protocols were 93% concordant and the lineages of 59 samples were 100% concordant. Thus, target capture SMRT sequencing appears to be an efficient method for WGS, genotyping and detecting mutations of SARS-CoV-2 Omicron variants. This article is protected by copyright. All rights reserved.
Keywords: Omicron; SARS-CoV-2 genotyping; SMRT sequencing; long read sequencing; whole genome sequencing.
. 2023 Feb 9.
doi: 10.1002/jmv.28564. Online ahead of print.
WHOLE-GENOME SINGLE MOLECULE REAL-TIME SEQUENCING OF SARS-CoV-2 OMICRON
Florence Nicot[SUP] 1 [/SUP], Pauline Trémeaux[SUP] 1 [/SUP], Justine Latour[SUP] 1 [/SUP], Romain Carcenac[SUP] 1 [/SUP], Sofia Demmou[SUP] 1 [/SUP], Nicolas Jeanne[SUP] 1 [/SUP], Noémie Ranger[SUP] 1 [/SUP], Clémentine De Smet[SUP] 1 [/SUP], Stéphanie Raymond[SUP] 1 2 [/SUP], Chloé Dimeglio[SUP] 1 2 [/SUP], Jacques Izopet[SUP] 1 2 [/SUP]
Affiliations
- PMID: 36756931
- DOI: 10.1002/jmv.28564
Abstract
New variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can only be identified using accurate sequencing methods. Single molecule real-time (SMRT) sequencing has been used to characterize Alpha and Delta variants, but not Omicron variants harbouring numerous mutations in the SARS-CoV-2 genome. This study assesses the performance of a target capture SMRT sequencing protocol for whole genome sequencing (WGS) of SARS-CoV-2 Omicron variants and compared it to that of an amplicon SMRT sequencing protocol optimized for Omicron variants. The failure rate of the target capture protocol (6%) was lower than that of the amplicon protocol (34%, p<0.001) on our dataset, and the median genome coverage with the target capture protocol (98.6% [IQR: 86-99.4]) was greater than that with the amplicon protocol (76.6% [IQR: 66-89.6], (p<0.001)). The percentages of samples with >95% whole genome coverage were 64% with the target capture protocol and 19% with the amplicon protocol (p<0.05). The clades of 96 samples determined with both protocols were 93% concordant and the lineages of 59 samples were 100% concordant. Thus, target capture SMRT sequencing appears to be an efficient method for WGS, genotyping and detecting mutations of SARS-CoV-2 Omicron variants. This article is protected by copyright. All rights reserved.
Keywords: Omicron; SARS-CoV-2 genotyping; SMRT sequencing; long read sequencing; whole genome sequencing.