ArticleJournal of clinical microbiology2022
A Method for Variant Agnostic Detection of SARS-CoV-2, Rapid Monitoring of Circulating Variants, and Early Detection of Emergent Variants Such as Omicron.
Article in Journal of clinical microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it, 23 citations in OpenAlex.
- The relative prevalence of the Omicron variant within SARS-CoV-2 infected cohorts in different countries: A systematic review.Human vaccines & immunotherapeutics · 2023Pooled it
- A 1-year study on SARS-CoV-2 variant shifts in wastewater using dPCR: comparison with clinical and GISAID data.mSystems · 2025Article
- A User-Centered Service Model for Accelerating COVID-19 Diagnostic Innovation: The RADx-rad Dx Core Approach.IEEE open journal of engineering in medicine and biology · 2025Article
- An SNP-based diagnostic method forFrontiers in veterinary science · 2025Article
- A micro-disc-based multiplex method for monitoring emerging SARS-CoV-2 variants using the molecular diagnostic tool Intelli-OVI.Communications medicine · 2024Article
- Omicron and Delta variant prevalence detection and identification during the fourth COVID-19 wave in Mexico using wastewater-based epidemiology.IJID regions · 2024Article
- A response playbook for early detection and population surveillance of new SARS-CoV-2 variants in a regional public health laboratory.BMC public health · 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
- Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing.Scientific reports · 2023Article
- Article
- Detection of SARS-CoV-2 Variants via Different Diagnostics Assays Based on Single-Nucleotide Polymorphism Analysis.Diagnostics (Basel, Switzerland) · 2023Article
- Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR.Frontiers in public health · 2023Article
- Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination.Med (New York, N.Y.) · 2022Article
- A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants.Microbiology spectrum · 2022Article
- Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy.Microorganisms · 2022Article
- A robust, highly multiplexed mass spectrometry assay to identify SARS-CoV-2 variants.medRxiv : the preprint server for health sciences · 2022Article
- Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform.Frontiers in public health · 2022Article
Corrections and comments
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Authors and funding
26 authors at 5 institutions in 1 country.
Funding
Abstract
The rapid emergence of SARS-CoV-2 variants raised public health questions concerning the capability of diagnostic tests to detect new strains, the efficacy of vaccines, and how to map the geographical distribution of variants to understand transmission patterns and loads on healthcare resources. Next-generation sequencing (NGS) is the primary method for detecting and tracing new variants, but it is expensive, and it can take weeks before sequence data are available in public repositories. This article describes a customizable reverse transcription PCR (RT-PCR)-based genotyping approach which is significantly less expensive, accelerates reporting, and can be implemented in any lab that performs RT-PCR. Specific single-nucleotide polymorphisms (SNPs) and indels were identified which had high positive-percent agreement (PPA) and negative-percent agreement (NPA) compared to NGS for the major genotypes that circulated through September 11, 2021. Using a 48-marker panel, testing on 1,031 retrospective SARS-CoV-2 positive samples yielded a PPA and NPA ranging from 96.3 to 100% and 99.2 to 100%, respectively, for the top 10 most prevalent World Health Organization (WHO) lineages during that time. The effect of reducing the quantity of panel markers was explored, and a 16-marker panel was determined to be nearly as effective as the 48-marker panel at lineage assignment. Responding to the emergence of Omicron, a genotyping panel was developed which distinguishes Delta and Omicron using four highly specific SNPs. The results demonstrate the utility of the condensed panel to rapidly track the growing prevalence of Omicron across the US in December 2021 and January 2022.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.