Molecular characterization, its mutation pattern and the molecular surveillance of SARS-CoV-2 in Hiroshima

• Project/Area Number: 21K21113
• Research Category: Grant-in-Aid for Research Activity Start-up
• Allocation Type: Multi-year Fund
• Review Section: 0908:Society medicine, nursing, and related fields
• Research Institution: Hiroshima University
• Principal Investigator: KO KO 広島大学, 医系科学研究科(医), 助教 (80910299)
• Project Period (FY): 2021-08-30 – 2023-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2022: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2021: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
• Keywords: SARS-CoV-2 / Surveillance / Infection control / variant screening / Sanger sequencing / Variants screening / Sanger method / Molecular Surveillance / Epidemiology / Mutation / Infectious Diseases

Outline of Research at the Start

Using total 667 saliva samples of COVID-19 confirmed cases in Hiroshima collected between September 2020 and April 2021, the applicant can clarify the following facts in this study.
1) The molecular characters and the mutation pattern of SARS-CoV-2 in Hiroshima
2) The mutation rate between third and fourth wave outbreak
3) Identification of notable SARS-CoV-2 mutant variants
4) Notification of other type of mutations apart from above mentioned mutant variants
5) Validation of newly formulated screening method over NGS sequencing for mutation screening

Outline of Final Research Achievements

A study on development of Sanger based SARS-CoV-2 variants classification by partial spike sequencing among 734 stocked samples provided 99.6% successful amplification and 96.9% genomic data which allowed for variant identification and molecular surveillance of SARS-CoV-2 variants in Hiroshima. The findings of this study demonstrate that Sanger sequencing is a reliable and effective approach for screening a large number of samples to detect significant SARS-CoV-2 variants. In comparison to Next Generation Sequencing (NGS), our method offers a practical and universally applicable tool that is both low-cost and time-efficient, particularly in regions where NGS is not readily accessible. Our method enables the identification not only of existing variants but also the examination of uncommon mutations or newly emerged variants, making it invaluable for pandemic prevention and control efforts.

Academic Significance and Societal Importance of the Research Achievements

This study introduced the possibility of SARS-CoV-2 variant screening by partial sequencing at spike region which has higher screening rate then next generation sequencing and applicable to the resource limited setting for molecular surveillance and pandemic control.

Research Products

• [Journal Article] Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan (2022)
  • Author(s): K Ko, K Takahashi, S Nagashima, B E, S Ouoba, MRA Hussain, T Akita, A Sugiyama, T Sakaguchi, H Tahara, H Ohge, H Ohdan, T Kubo, N Ishikawa, T Takafuta, Y Fujii, M Mimori, F Okada, E Kishita, K Ariyoshi, M Kuwabara, J Tanaka
  • Journal Title: Scientific Reports Volume: 12 Issue: 1 Pages: 2419-2419
  • DOI: 10.1038/s41598-022-04952-2
  • Peer Reviewed / Open Access / Int'l Joint Research