期刊论文详细信息
BMC Medical Genomics
Despite low viral titer in saliva samples, Sanger-based SARS-CoV-2 spike gene sequencing is highly applicable for the variant identification
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
PDF
【 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

【 预 览 】
附件列表
Files Size Format View
RO202309153846840ZK.pdf 2107KB PDF download
40517_2023_266_Article_IEq58.gif 1KB Image download
Fig. 1 75KB Image download
【 图 表 】

Fig. 1

40517_2023_266_Article_IEq58.gif

【 参考文献 】
  • [1]
  • [2]
  • [3]
  • [4]
  • [5]
  • [6]
  • [7]
  • [8]
  • [9]
  • [10]
  • [11]
  • [12]
  • [13]
  • [14]
  • [15]
  • [16]
  • [17]
  • [18]
  • [19]
  • [20]
  • [21]
  • [22]
  • [23]
  • [24]
  • [25]
  • [26]
  • [27]
  • [28]
  • [29]
  • [30]
  • [31]
  • [32]
  • [33]
  • [34]
  文献评价指标  
  下载次数:1次 浏览次数:0次