Use of allele-specific qPCR and PCR-RFLP analysis for rapid detection of the SARS-CoV-2 variants in Tunisia: A cheap flexible approach adapted for developing countries.

ABSTRACT: Monitoring the emergence and propagation of SARS-COV2 variants, especially Omicron variants, remains a major concern in developing countries, including Tunisia. We here report lessons of simple approaches used to track prevalent Omicron variants in the city and district of Sfax, Tunisia, between June 2022 and April 2023. Initially, the screening approach was designed by selecting and verifying key SARS-CoV-2 mutations using publicly available sequencing data. Then, the analytical performance of the screening tests was rigorously assessed before being implemented on 227 confirmed COVID-19 cases. In a first stage, from June to September 2022, allele-specific (AS)-qPCR detection of deletions ΔHV69-70 (S gene) and ΔKSF141-143 (ORF1a gene) allowed identification of BA.5 as the predominant varia

SUBMITTER: Ayadi W 

PROVIDER: S-EPMC12052121 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature