ArticleJournal of virological methods2022
Development of a simple genotyping method based on indel mutations to rapidly screen SARS-CoV-2 circulating variants: Delta, Omicron BA.1 and BA.2.
Article in Journal of virological methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 19 citations in OpenAlex.
- Article
- Two-Stage Mixed-Dye-Based Isothermal Amplification with Ribonuclease-Cleavable Enhanced Probes for Dual-Visualization Detection of SARS-CoV-2 Variants of Interest.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- The evaluation of risk factors for prolonged viral shedding during anti-SARS-CoV-2 monoclonal antibodies and long-term administration of antivirals in COVID-19 patients with B-cell lymphoma treated by anti-CD20 antibody.BMC infectious diseases · 2024Article
- Multiplexed RT-qPCR Coupled with Whole-Genome Sequencing to Monitor a SARS-CoV-2 Omicron Variant of Concern in a Hospital Laboratory Setting in Latvia.Diagnostics (Basel, Switzerland) · 2023Article
- A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing.Microbiology spectrum · 2023Article
- "Nano COVID-19": Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern.Experimental biology and medicine (Maywood, N.J.) · 2023Article
- Rapid Detection of SARS-CoV-2 Variants of Concern by Genomic Surveillance Techniques.Advances in experimental medicine and biology · 2023Article
- Article
Corrections and comments
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Authors and funding
13 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The high need of rapid and flexible tools that facilitate the identification of circulating SARS-CoV-2 Variants of Concern (VOCs) remains crucial for public health system monitoring. Here, we develop allele-specific (AS)-qPCR assays targeting three recurrent indel mutations, ΔEF156-157, Ins214EPE and ΔLPP24-26, in spike (S) gene to identify the Delta VOC and the Omicron sublineages BA.1 and BA.2, respectively. After verification of the analytical specificity of each primer set, two duplex qPCR assays with melting curve analysis were performed to screen 129 COVID-19 cases confirmed between December 31, 2021 and February 01, 2022 in Sfax, Tunisia. The first duplex assay targeting ΔEF156-157 and Ins214EPE mutations successfully detected the Delta VOC in 39 cases and Omicron BA.1 in 83 cases. All the remaining cases (n = 7) were identified as Omicron BA.2, by the second duplex assay targeting Ins214EPE and ΔLPP24-26 mutations. The results of the screening method were in perfect concordance with those of S gene partial sequencing. In conclusion, our findings provide a simple and flexible screening method for more rapid and reliable monitoring of circulating VOCs. We highly recommend its implementation to guide public health policies.
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