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

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(5), P. e0321581 - e0321581

Published: May 5, 2025

Monitoring the emergence and propagation of SARS-COV2 variants, especially Omicron remains a major concern in developing countries, including Tunisia. We here report lessons simple approaches used to track prevalent variants city district Sfax, Tunisia, between June 2022 April 2023. Initially, screening approach was designed by selecting verifying key SARS-CoV-2 mutations using publicly available sequencing data. Then, analytical performance tests rigorously assessed before being implemented on 227 confirmed COVID-19 cases. In first stage, from September 2022, allele-specific (AS)-qPCR detection deletions ΔHV69-70 (S gene) ΔKSF141-143 (ORF1a allowed identification BA.5 as predominant variant (128 out 165 cases; 77.5%) which quickly replaced pre-existing lineages BA.4 (15.7%) BA.2 (6.7%). second October 2023, circulation additional demonstrated concomitant new relevant PCR-RFLP (n=62). Detection Y264H (ORF1b) V445P/G446S resulted 38 cases BQ.1 14 XBB variant, respectively. Further restriction analysis S gene conducted screen more recent sublineages, CH.1.1. For all sequenced (n=115), our rapid assays showed perfect concordance with results identifying variants. These findings highlight potential simple, cheap proven methods for genotyping monitoring Therefore, these appear valuable tools effective infection control prevention countries.

Language: Английский

The sensitivity and specificity of Abbott Panbio™ COVID 19 Ag Rapid test in the context of four SARS-CoV-2 variants

Heliyon, Journal Year: 2023, Volume and Issue: 10(1), P. e23475 - e23475

Published: Dec. 9, 2023

Rapid antigen tests for the detection of SARS-CoV-2 are commonly used diagnosis Covid-19. Previously published data showed a wide range sensitivity and specificity RATs, but these studies were performed on relatively small numbers samples using only limited virus variants. The aim study was to evaluate main parameters RAT 4 different variants in comparison with PCR.

Language: Английский