Despite low viral titer in saliva samples, Sanger-based SARS-CoV-2 spike gene sequencing is highly applicable for the variant identification
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Published:2023-08-24
Issue:1
Volume:16
Page:
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ISSN:1755-8794
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Container-title:BMC Medical Genomics
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language:en
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Short-container-title:BMC Med Genomics
Author:
Ko Ko,Takahashi Kazuaki,Ito Noriaki,Sugiyama Aya,Nagashima Shintaro,Miwata Kei,Kitahara Yoshihiro,Okimoto Mafumi,Ouoba Serge,Akuffo Golda Ataa,E Bunthen,Akita Tomoyuki,Takafuta Toshiro,Tanaka Junko
Abstract
Abstract
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.
Funder
Japan Agency for Medical Research and Development
Publisher
Springer Science and Business Media LLC
Subject
Genetics (clinical),Genetics
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