Rapid monitoring of SARS-CoV-2 variants of concern through high-resolution melt analysis.

Autor: Diotallevi A; Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy. aurora.diotallevi@uniurb.it., Buffi G; Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy., Barocci S; Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy., Ceccarelli M; Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy.; Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy., Bencardino D; Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy., Andreoni F; Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy.; Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy., Orlandi C; Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy., Ferri M; Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy., Vandini D; Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy., Menzo S; Virology Laboratory, Azienda Ospedaliero Universitaria delle Marche, 60126, Ancona, AN, Italy., Carlotti E; Department of Prevention, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino Marche, 61029, Urbino, PU, Italy., Casabianca A; Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy., Magnani M; Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy., Galluzzi L; Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2023 Dec 07; Vol. 13 (1), pp. 21598. Date of Electronic Publication: 2023 Dec 07.
DOI: 10.1038/s41598-023-48929-1
Abstrakt: The current global pandemic of COVID-19 is characterized by waves of infection due to the emergence of new SARS-CoV-2 variants carrying mutations on the Spike (S) protein gene. Since autumn 2020 many Variants of Concern (VOC) have been reported: Alpha/B.1.1.7, Beta/B.1.351, Gamma/P.1, Delta/B.1.617.2, Omicron/B.1.1.529, and sublineages. Surveillance of genomic variants is currently based on whole-genome sequencing (WGS) of viral genomes on a random fraction of samples positive to molecular tests. WGS involves high costs, extended analysis time, specialized staff, and expensive instruments compared to a PCR-based test. To rapidly identify the VOCs in positive samples, six assays based on real-time PCR and high-resolution melting (HRM) were designed on the S gene and applied to 120 oro/nasopharyngeal swab samples collected from October 2020 to June 2022 (106 positive and 14 negative samples). Overall, the assays showed 100% specificity and sensitivity compared with commercial PCR tests for COVID-19. Moreover, 104 samples out of 106 (98.1%) were correctly identified as follows: 8 Wuhan (wild type), 12 Alpha, 23 Delta, 46 Omicron BA.1/BA.1.1, 15 Omicron BA.2/BA.4/BA.5. With our lab equipment, about 10 samples can be processed every 3 h at the cost of less than € 10 ($ 10.60) per sample, including RNA extraction. The implementation of this approach could help local epidemiological surveillance and clinical decision-making.
(© 2023. The Author(s).)
Databáze: MEDLINE
Externí odkaz:
Nepřihlášeným uživatelům se plný text nezobrazuje