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

Autor: Tran DH; NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam., Do HDK; NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam., Tran HT; NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam., Pham TNM; NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam., Nguyen HD; NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam., Linh HT; Medical Device Testing Center, Pasteur Institute, Ho Chi Minh City, Vietnam.; University Medical Center, Ho Chi Minh City, Vietnam., Cuong HQ; Directorial Board, Pasteur Institute, Ho Chi Minh City, Vietnam.; Department of Health, Can Tho City, Vietnam., Vu MT; NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam. vmthiet@ntt.edu.vn., Phung HTT; NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam. ptthuong@ntt.edu.vn.
Jazyk: angličtina
Zdroj: Archives of virology [Arch Virol] 2024 Apr 02; Vol. 169 (5), pp. 87. Date of Electronic Publication: 2024 Apr 02.
DOI: 10.1007/s00705-024-06012-8
Abstrakt: 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.
(© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)
Databáze: MEDLINE
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