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

Abstract

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.

• Authors: Aurora Diotallevi, Gloria Buffi, Simone Barocci, Marcello Ceccarelli, Daniela Bencardino, Francesca Andreoni, Chiara Orlandi, Marilisa Ferri, Daniela Vandini, Stefano Menzo, Eugenio Carlotti, Anna Casabianca, Mauro Magnani, Luca Galluzzi
• Journal: Scientific reports (Sci Rep) Vol. 13 Issue 1 Pg. 21598 (12 07 2023) ISSN: 2045-2322 [Electronic] England
• PMID: 38062105 (Publication Type: Journal Article)
• Copyright: © 2023. The Author(s).

Topics

• Humans
• SARS-CoV-2 (genetics)
• COVID-19 (epidemiology)
• Real-Time Polymerase Chain Reaction
• Biological Assay