ArticleVirology journal2023
Discrimination of SARS-CoV-2 omicron variant and its lineages by rapid detection of immune-escape mutations in spike protein RBD using asymmetric PCR-based melting curve analysis.
Article in Virology journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- A single mutation may contribute to accelerated evolution of SARS-CoV-2 toward Omicron.Nature communications · 2025Article
- Conformational Dynamics and Binding Interactions of SARS-CoV-2 Spike Protein Variants: Omicron, XBB.1.9.2, and EG.5.Journal of chemical information and modeling · 2025Article
- Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.The Journal of infection · 2024Article
- RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution.medRxiv : the preprint server for health sciences · 2024Article
- An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern.Scientific reports · 2023Article
- A novel assay based on DNA melting temperature for multiplexed identification of SARS-CoV-2 and influenza A/B viruses.Frontiers in microbiology · 2023Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe SARS-CoV-2 Omicron strain has multiple immune-escape mutations in the spike protein receptor-binding domain (RBD). Rapid detection of these mutations to identify Omicron and its lineages is essential for guiding public health strategies and patient treatments. We developed a two-tube, four-color assay employing asymmetric polymerase chain reaction (PCR)-based melting curve analysis to detect Omicron mutations and discriminate the BA.1, BA.2, BA.4/5, and BA.2.75 lineages.
methodsThe presented technique involves combinatory analysis of the detection of six fluorescent probes targeting the immune-escape mutations L452R, N460K, E484A, F486V, Q493R, Q498R, and Y505H within one amplicon in the spike RBD and probes targeting the ORF1ab and N genes. After protocol optimization, the analytical performance of the technique was evaluated using plasmid templates. Sensitivity was assessed based on the limit of detection (LOD), and reliability was assessed by calculating the intra- and inter-run precision of melting temperatures (T
resultsAll genotypes were sensitively identified using the developed method with a LOD of 39.1 copies per reaction. The intra- and inter-run coefficients of variation for the T
conclusionThe developed assay can provide accurate, reliable, rapid, simple and low-cost detection of the immune-escape mutations located in the spike RBD to detect the Omicron variant and discriminate its lineages, and its use can be easily generalized in clinical laboratories with a fluorescent PCR platform.
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