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Detection of SARS-CoV-2 spike protein D614G mutation using μTGGE

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A Correction to this article was published on 25 April 2024

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Abstract

Background

The accurate and expeditious detection of SARS-CoV-2 mutations is critical for monitoring viral evolution, assessing its impact on transmission, virulence, and vaccine efficacy, and formulating public health interventions. In this study, a detection system utilizing micro temperature gradient gel electrophoresis (μTGGE) was developed for the identification of the D614 and G614 variants of the SARS-CoV-2 spike protein.

Methods

The in vitro synthesized D614 and G614 gene fragments of the SARS-CoV-2 spike protein were amplified via polymerase chain reaction and subjected to μTGGE analysis.

Results

The migration patterns exhibited by the D614 and G614 variants on the polyacrylamide gel were distinctly dissimilar and readily discernible by μTGGE. In particular, the mid-melting pattern of D614 was shorter than that of G614.

Conclusions

Our results demonstrate the capability of μTGGE for the rapid, precise, and cost-effective detection of SARS-CoV-2 spike protein D614 and G614 variants without the need for sequencing. Therefore, this approach holds considerable potential for use in point-of-care mutation assays for SARS-CoV-2 and other pathogens.

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Data availability

All data are available in case of need.

Change history

Abbreviations

CCM:

Chemical cleavage of mismatch

COVID-19:

Coronavirus disease

DGGE:

Denaturing temperature gel electrophoresis

DHPLC:

Denaturing high-performance liquid chromatography

HA:

Heteroduplex analysis

μTGGE:

Micro temperature gradient gel electrophoresis

PCR:

Polymerase chain reaction

PTT:

Protein truncation test

SARS-CoV-2:

Severe acute respiratory syndrome coronavirus 2

SSCP:

Single-strand conformation polymorphism

ssDNA:

Single-stranded DNA

TGGE:

Temperature gradient gel electrophoresis

T m :

Melting temperature

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Acknowledgements

We acknowledge Ms. Emi Arikawa and Mr. Masayuki Yamagata for technical assistance.

Funding

This work was supported in part by Grants-in-Aid for Scientific Research (no. 23KJ1201 for K.J., no. 18KK0285 for T.T. and K.Y., 18K19839 for M.B. and K.Y., and no. 22H03332 for T.T. and K.Y.) from Japan Society for the Promotion of Science, Emerging/re-emerging infectious disease project of Japan (grant no. 20he0622020h0001 for T.T. and K.Y. and 23hk0302011h0203 for M.B. and K.K.) from Japan Agency for Medical Research and Development, and A-Step (no. JPMJTR20UU for K.Y.) from Japan Science and Technology Agency.

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Authors and Affiliations

  1. Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan

    Kevin Maafu Juma, Kenta Morimoto, Teisuke Takita & Kiyoshi Yasukawa

  2. BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Lab, Ashahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan

    Vishnu Sharma, Kirti Sharma, Radhika Biyani & Manish Biyani

  3. Biyani BioSolutions Pvt. Ltd., R-4, Sector 3, Vidhyadharnagar, Jaipur, 302023, India

    Vishnu Sharma & Manish Biyani

  4. Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan

    Manish Biyani

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  1. Kevin Maafu Juma
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Contributions

KMJ, MB, and KY designed the research; KMJ, KM, VS, KS, RS, MB, KY performed the research; KMJ, MB, TT, and KY analyzed data; KMJ, MB, and KY wrote the manuscript.

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Correspondence to Manish Biyani or Kiyoshi Yasukawa.

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Juma, K.M., Morimoto, K., Sharma, V. et al. Detection of SARS-CoV-2 spike protein D614G mutation using μTGGE. Mol Biol Rep 51, 289 (2024). https://doi.org/10.1007/s11033-023-09065-1

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