2021 Fiscal Year Research-status Report
Molecular characterization, its mutation pattern and the molecular surveillance of SARS-CoV-2 in Hiroshima
| Project/Area Number |
21K21113
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| Research Institution | Hiroshima University |
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Principal Investigator |
KO KO 広島大学, 医系科学研究科(医), 助教 (80910299)
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| Project Period (FY) |
2021-08-30 – 2023-03-31
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| Keywords | SARS-CoV-2 / Variants screening / Sanger method |
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| Outline of Annual Research Achievements |
Total 239 saliva samples from the confirmed cases of COVID-19 collected from 2020.12.1 to 2022.3.14 in Hiroshima were screened for SARS-CoV-2 variants using Sanger based sequencing method. 159 out of 239 samples had been amplified using in-house primer set targeting the S1 spike gene of SARS-CoV-2 (22,735nt~23,532nt) and the variants were identified through the unique checkpoints in the targeted gene. The viral titer ranges from 8 to 5E+8 copies/mL with an average of 8E+6 copies/mL. There is no significant difference in viral titer by variants. No mutation at spike gene was 16 (10%), E484K mutation (R.1) was 3 (1.9%), Alpha (B.1.1.7) was 33 (20.8%), Delta (B.1.627) was 65 (40.9%) and Omicron (B.1.1.529) was 42 (26.4%). The remaining 80 samples were now ongoing for the variant screening.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
159 out of 239 samples from confirmed cases of COVID-19 in Hiroshima had been performed Sanger based variant screening targeting the S1 spike gene of SARS-CoV-2. 66.5% of samples were completed for variant screening. Now, the amplification of remaining 80 samples were completed and now proceed to sequencing. 40% of remaining work had been completed.
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| Strategy for Future Research Activity |
The remaining 80 samples were ongoing for the variants screening. Then, the genomes data will be analyzed using Genetynx Mac and the validation of Sanger sequencing will be performed by homology analysis of genomes data from Sanger and Next generation Sequencing of each single sample. After finalizing the result, the complete report will be done.
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| Causes of Carryover |
The variant screening of samples included this study was performed using the existing reagents and primers of another project. Therefore, the usage of this grant is less than expected. But, from now, the new reagents and other laboratory equipment will be bought in order to continue the research.
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[Journal Article] Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan2022
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
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Journal Title
Scientific Reports
Volume: 12
Pages: 2419
DOI
Peer Reviewed / Open Access / Int'l Joint Research
