Despite low viral titer in saliva samples, Sanger-based SARS-CoV-2 spike gene sequencing is highly applicable for the variant identification

BMC Medical Genomics

Research

Junko Tanaka¹  Tomoyuki Akita¹  Aya Sugiyama¹  Shintaro Nagashima¹  Ko Ko¹  Kazuaki Takahashi¹  Golda Ataa Akuffo¹  Bunthen E²  Serge Ouoba³  Yoshihiro Kitahara⁴  Mafumi Okimoto⁴  Noriaki Ito⁴  Toshiro Takafuta⁴  Kei Miwata⁴ 

[1] Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, 734-8551, Hiroshima, Japan;Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, 734-8551, Hiroshima, Japan;Payment Certification Agency (PCA), Ministry of Health, Phnom Penh, Cambodia;Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, 734-8551, Hiroshima, Japan;Unité de Recherche Clinique de Nanoro (URCN), Institut de Recherche en Science de La Santé (IRSS), Nanoro, Burkina Faso;Hiroshima City Funairi Citizens Hospital, Hiroshima, Japan;

关键词: SARS-CoV-2;    Sanger method;    Next generation sequencing;    Amplification;    Variants;    Screening;    Japan;   

DOI  :  10.1186/s12920-023-01633-5

 received in 2023-06-15, accepted in 2023-08-16,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundThis 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.MethodsUsing 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.ResultsAmong 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.ConclusionsOur 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.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

【 图 表 】

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