Despite low viral titer in saliva samples, Sanger-based SARS-CoV-2 spike gene sequencing is highly applicable for the variant identification
© 2023. BioMed Central Ltd., part of Springer Nature..
BACKGROUND: This study aimed to compare the performance of Sanger-based SARS-CoV-2 spike gene sequencing and Next Generation Sequencing (NGS)-based full-genome sequencing for variant identification in saliva samples with low viral titer.
METHODS: Using 241 stocked saliva samples collected from confirmed COVID-19 patients between November 2020 and March 2022 in Hiroshima, SARS-CoV-2 spike gene sequencing (nt22735-nt23532) was performed by nested RT-PCR and Sanger platform using in-house primers. The same samples underwent full-genome sequencing by NGS using Illumina NextSeq2000.
RESULTS: Among 241 samples, 147 were amplified by both the Sanger and the Illumina NextSeq2000 NGS, 86 by Sanger only, and 8 were not amplified at all. The overall amplification rates of Illumina NextSeq2000 NGS and Sanger were 61% and 96.7%, respectively. At low viral titer (< 103 copies/mL), Illumina NextSeq2000 NGS provided 19.2% amplification, while Sanger was 89.7% (p < 0.0001). Both platforms identified 38 wild type, 54 Alpha variants, 84 Delta variants, and 57 Omicron variants.
CONCLUSIONS: Our study provided evidence to expand the capacity of Sanger-based SARS-CoV-2 spike gene sequencing for variants identification over full-genome by Illumina NextSeq2000 NGS for mass screening. Therefore, the feasible and simple Sanger-based SARS-CoV-2 spike gene sequencing is practical for the initial variants screening, which might reduce the gap between the rapid evolution of SARS-CoV-2 and its molecular surveillance.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:16 |
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| Enthalten in: |
BMC medical genomics - 16(2023), 1 vom: 24. Aug., Seite 199 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Ko, Ko [VerfasserIn] |
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| Links: |
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| Themen: |
Amplification |
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| Anmerkungen: |
Date Completed 28.08.2023 Date Revised 21.11.2023 published: Electronic Citation Status MEDLINE |
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| doi: |
10.1186/s12920-023-01633-5 |
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| Förderinstitution / Projekttitel: |
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| 520 | |a © 2023. BioMed Central Ltd., part of Springer Nature. | ||
| 520 | |a BACKGROUND: This study aimed to compare the performance of Sanger-based SARS-CoV-2 spike gene sequencing and Next Generation Sequencing (NGS)-based full-genome sequencing for variant identification in saliva samples with low viral titer | ||
| 520 | |a METHODS: Using 241 stocked saliva samples collected from confirmed COVID-19 patients between November 2020 and March 2022 in Hiroshima, SARS-CoV-2 spike gene sequencing (nt22735-nt23532) was performed by nested RT-PCR and Sanger platform using in-house primers. The same samples underwent full-genome sequencing by NGS using Illumina NextSeq2000 | ||
| 520 | |a RESULTS: Among 241 samples, 147 were amplified by both the Sanger and the Illumina NextSeq2000 NGS, 86 by Sanger only, and 8 were not amplified at all. The overall amplification rates of Illumina NextSeq2000 NGS and Sanger were 61% and 96.7%, respectively. At low viral titer (< 103 copies/mL), Illumina NextSeq2000 NGS provided 19.2% amplification, while Sanger was 89.7% (p < 0.0001). Both platforms identified 38 wild type, 54 Alpha variants, 84 Delta variants, and 57 Omicron variants | ||
| 520 | |a CONCLUSIONS: Our study provided evidence to expand the capacity of Sanger-based SARS-CoV-2 spike gene sequencing for variants identification over full-genome by Illumina NextSeq2000 NGS for mass screening. Therefore, the feasible and simple Sanger-based SARS-CoV-2 spike gene sequencing is practical for the initial variants screening, which might reduce the gap between the rapid evolution of SARS-CoV-2 and its molecular surveillance | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Amplification | |
| 650 | 4 | |a Japan | |
| 650 | 4 | |a Next generation sequencing | |
| 650 | 4 | |a SARS-CoV-2 | |
| 650 | 4 | |a Sanger method | |
| 650 | 4 | |a Screening | |
| 650 | 4 | |a Variants | |
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| 700 | 1 | |a Ito, Noriaki |e verfasserin |4 aut | |
| 700 | 1 | |a Sugiyama, Aya |e verfasserin |4 aut | |
| 700 | 1 | |a Nagashima, Shintaro |e verfasserin |4 aut | |
| 700 | 1 | |a Miwata, Kei |e verfasserin |4 aut | |
| 700 | 1 | |a Kitahara, Yoshihiro |e verfasserin |4 aut | |
| 700 | 1 | |a Okimoto, Mafumi |e verfasserin |4 aut | |
| 700 | 1 | |a Ouoba, Serge |e verfasserin |4 aut | |
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| 700 | 1 | |a Takafuta, Toshiro |e verfasserin |4 aut | |
| 700 | 1 | |a Tanaka, Junko |e verfasserin |4 aut | |
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