![]() Therefore, rapid detection and identification of SARS-CoV-2 variants and monitoring of their prevalence are critical and necessary. However, a small minority of mutations can confer a selective advantage and new features to the virus in terms of increased transmissibility 1, vaccine response 2, 3, pathogenicity or greater severity of the associated disease 4, and response to monoclonal antibody therapy 5. Most changes have little or no impact on the virus phenotype. RNA viruses, including SARS-CoV-2, the causative agent of the twenty-first-century COVID-19 pandemic, constantly evolve through genome modifications. The implementation of this approach could help local epidemiological surveillance and clinical decision-making. 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. 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. Overall, the assays showed 100% specificity and sensitivity compared with commercial PCR tests for COVID-19. 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). WGS involves high costs, extended analysis time, specialized staff, and expensive instruments compared to a PCR-based test. 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. ![]() 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. 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. ![]()
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