Ultrasensitive Isothermal Detection of SARS-CoV‑2 Based on Self-Priming Hairpin-Utilized Amplification of the G‑Rich Sequence

• Published in: Analytical chemistry (Washington) Vol. 94; no. 50; pp. 17448 - 17455
• Main Authors: Li, Yan, Kim, Hansol, Ju, Yong, Park, Yeonkyung, Kang, Taejoon, Yong, Dongeun, Park, Hyun Gyu
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 20.12.2022
• Subjects: Amplification; Chemistry; Coronaviruses; COVID-19; Fluorescence; gRNA; Humans; Molecular Diagnostic Techniques - methods; Nucleic Acid Amplification Techniques - methods; Nucleotide sequence; Pandemics; Priming; RNA, Viral - genetics; SARS-CoV-2 - genetics; Selectivity; Sensitivity and Specificity; Severe acute respiratory syndrome coronavirus 2; Viral diseases
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/acs.analchem.2c03442

The outbreak of the novel coronavirus disease 2019 (COVID-19) pandemic induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of fatalities all over the world. Unquestionably, the effective and timely testing for infected individuals is the most imperative for the prevention of the ongoing pandemic. Herein, a new method was established for detecting SARS-CoV-2 based on the self-priming hairpin-utilized isothermal amplification of the G-rich sequence (SHIAG). In this strategy, the target RNA binding to the hairpin probe (HP) was uniquely devised to lead to the self-priming-mediated extension followed by the continuously repeated nicking and extension reactions, consequently generating abundant G-rich sequences from the intended reaction capable of producing fluorescence signals upon specifically interacting with thioflavin T (ThT). Based on the unique isothermal design concept, we successfully identified SARS-CoV-2 genomic RNA (gRNA) as low as 0.19 fM with excellent selectivity by applying only a single HP and further verified its practical diagnostic capability by reliably testing a total of 100 clinical specimens for COVID-19 with 100% clinical sensitivity and specificity. This study would provide notable insights into the design and evolution of new isothermal strategies for the sensitive and facile detection of SARS-CoV-2 under resource constraints.