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Rapid identification of SARS-CoV-2 strains via isothermal enzymatic recombinase amplification and nanopore sequencing

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Abstract

Surveillance of the SARS-CoV-2 genome has become a crucial technique in the management of COVID-19, aiding the pandemic response and supporting effective public health interventions. Typically, whole-genomic sequencing is used along with PCR-based target enrichment techniques to identify SARS-CoV-2 variants, which is a complicated and time-consuming process that requires central laboratory facilities. Thus, there is an urgent need to develop rapid and cost-effective tools for precise on-site detection and identification of SARS-CoV-2 strains. In this study, we demonstrate the rapid diagnosis of COVID-19 and identification of SARS-CoV-2 variants by amplification and sequencing of the entire SARS-CoV-2 S gene using isothermal enzymatic recombinase amplification combined with the advanced Oxford nanopore sequencing technique. The entire procedure, from sampling to sequencing, takes less than 8 hours and can be performed with limited resources. The newly developed method has noteworthy implications for examining the transmission dynamics of the virus, detecting novel genetic variants, and assessing the effect of mutations on diagnostic approaches, antiviral treatments, and vaccines.

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The data supporting the findings of this study are presented in the article and its supplementary materials and are available from the corresponding author upon request.

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Author information

Authors and Affiliations

  1. NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam

    Diem Hong Tran, Hoang Dang Khoa Do, Hau Thi Tran, Trang Nguyen Minh Pham, Hoang Danh Nguyen, Minh Thiet Vu & Huong Thi Thu Phung

  2. Medical Device Testing Center, Pasteur Institute, Ho Chi Minh City, Vietnam

    Hoang Thuy Linh

  3. University Medical Center, Ho Chi Minh City, Vietnam

    Hoang Thuy Linh

  4. Directorial Board, Pasteur Institute, Ho Chi Minh City, Vietnam

    Hoang Quoc Cuong

  5. Department of Health, Can Tho City, Vietnam

    Hoang Quoc Cuong

Authors
  1. Diem Hong Tran
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  2. Hoang Dang Khoa Do
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  3. Hau Thi Tran
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  4. Trang Nguyen Minh Pham
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  5. Hoang Danh Nguyen
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  6. Hoang Thuy Linh
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  7. Hoang Quoc Cuong
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  8. Minh Thiet Vu
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  9. Huong Thi Thu Phung
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Contributions

HTTP and MTV led the conceptualization and design of the study, formulated the research questions, and supervised the laboratory work. DHT conducted the major experimental procedures and collected the data. HDKD and HDN performed sequencing data analysis and interpretation. HTT and TNMP provided technical support in the laboratory and assisted in data interpretation. HTL and HQC provided the samples, assisted in experimental design, and contributed to manuscript editing. DHT, HDKD, MTV, and HTTP contributed to manuscript writing, editing, and critical revisions. All authors contributed to the intellectual content and approved the final version of the manuscript.

Corresponding authors

Correspondence to Minh Thiet Vu or Huong Thi Thu Phung.

Ethics declarations

Ethical approval

The study was approved by the Research Ethics Committee of Pasteur Institute in Ho Chi Minh City, Vietnam.

Conflict of interest

The authors declare that they have no conflicts of interest.

Additional information

Communicated by Pablo Pineyro

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Tran, D.H., Do, H.D.K., Tran, H.T. et al. Rapid identification of SARS-CoV-2 strains via isothermal enzymatic recombinase amplification and nanopore sequencing. Arch Virol 169, 87 (2024). https://doi.org/10.1007/s00705-024-06012-8

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  • DOI: https://doi.org/10.1007/s00705-024-06012-8

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