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Development of highly adaptable RT-PCR methods for identifying Delta and BA.1 variants in inactivated COVID-19 vaccines

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Abstract

Background The emergence and rapid spread of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), poses a significant threat to human health and public safety. While next-generation sequencing (NGS) is capable of detecting and tracking new COVID-19 variants for disease diagnosis and prevention, its high cost and time-consuming nature limit its widespread use. In this study, our aim was to develop a highly adaptable and accurate RT-PCR method for identifying the Delta or BA.1 variants in inactivated COVID-19 vaccine. We devised three two-plex RT-PCR methods targeting specific mutation sites: S: Δ156–157, S: N211-, L212I, and S: Δ142–144, Y145D. The RT-PCR method targeting the S: Δ156–157 mutation site was able to distinguish the Delta variant from other COVID-19 virus strains, while the RT-PCR methods targeting the S: N211-, L212I or S: Δ142–144, Y145D mutation sites were able to distinguish the BA.1 variant from other COVID-19 virus strains. We separately validated these three two-plex RT-PCR methods, and the results demonstrated good linearity, repeatability, reproducibility, and specificity for each method. Moreover, all three methods can be applied in the production of SARS-CoV-2 variant inactivated vaccines, enabling the identification of Delta or BA.1 variants in virus cultures as well as in inactivated vaccine stocks. This study presents a systematic approach to identify COVID-19 variants using multiple RT-PCR methods. We successfully developed three two-plex RT-PCR methods that can identify Delta and BA.1 variants based on specific mutation sites, and we completed the validation of these three methods.

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  1. Zhanhui Wang and Yao He contributed equally to this work.

Authors and Affiliations

  1. Beijing Institute of Biological Products Company Limited, Beijing, 100176, China

    Zhanhui Wang, Yao He, Zhenyu He, Yancen Guo, Yuxiu Zhao & Yuntao Zhang

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  1. Zhanhui Wang
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  2. Yao He
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Contributions

Y.Z. and Y.Z. are the corresponding author and coordinate the strains and experimental sites used in this study. Z.W. and Y.H. conceived and designed this study. Z.W. prepared the manuscript. Z.W. Y.H. Z.H. and Y.G. performed all experiments. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Yuxiu Zhao or Yuntao Zhang.

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Wang, Z., He, Y., He, Z. et al. Development of highly adaptable RT-PCR methods for identifying Delta and BA.1 variants in inactivated COVID-19 vaccines. Mol Biol Rep 51, 892 (2024). https://doi.org/10.1007/s11033-024-09799-6

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