Whole-genome sequencing of SARS-CoV-2 : Comparison of target capture and amplicon single molecule real-time sequencing protocols
© 2022 The Authors. Journal of Medical Virology published by Wiley Periodicals LLC..
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:95 |
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| Enthalten in: |
Journal of medical virology - 95(2023), 1 vom: 30. Jan., Seite e28123 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Nicot, Florence [VerfasserIn] |
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| Links: |
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| Themen: |
Journal Article |
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| Anmerkungen: |
Date Completed 10.01.2023 Date Revised 08.02.2023 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1002/jmv.28123 |
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| 520 | |a © 2022 The Authors. Journal of Medical Virology published by Wiley Periodicals LLC. | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
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| 700 | 1 | |a Trémeaux, Pauline |e verfasserin |4 aut | |
| 700 | 1 | |a Latour, Justine |e verfasserin |4 aut | |
| 700 | 1 | |a Jeanne, Nicolas |e verfasserin |4 aut | |
| 700 | 1 | |a Ranger, Noémie |e verfasserin |4 aut | |
| 700 | 1 | |a Raymond, Stéphanie |e verfasserin |4 aut | |
| 700 | 1 | |a Dimeglio, Chloé |e verfasserin |4 aut | |
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| 700 | 1 | |a Izopet, Jacques |e verfasserin |4 aut | |
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