ArticlePLoS biology2021
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.
Article in PLoS biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 144 papers.
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Who cites it
144 citing papers in PubMed.
- Immunogenicity and safety of the CoronaVac inactivated vaccine in patients with autoimmune rheumatic diseases: a phase 4 trial.Nature medicine · 2021Trial
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- Epitope-Resolved Digital SERS Profiling of Structurally Dynamic Antigens via a Multi-Epitope Bispecific Antibody Framework.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- SARS-CoV-2 Point-of-Care Testing Modalities: Integrating Molecular, Immunological, Biosensor, and AI Approaches.Diagnostics (Basel, Switzerland) · 2026Review
- Targeted ORF8-N Sanger Sequencing as a SARS-CoV-2 Surveillance Contingency During Supply Shortages.Revista da Sociedade Brasileira de Medicina Tropical · 2026Article
- Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are unbiased and robust to differential shedding.Nature communications · 2025Article
- Integrated Analysis of the 2022 SARS-CoV-2 Omicron Lineage Replacement Dynamics in Connecticut, US.Viruses · 2025Article
- Using machine learning models to predict the impact of template mismatches on polymerase chain reaction assay performance.Scientific reports · 2025Article
- Topologically constrained DNA-mediated one-pot CRISPR assay for rapid detection of viral RNA with single nucleotide resolution.EBioMedicine · 2025Article
- Reality check: testing theFrontiers in cellular and infection microbiology · 2025Article
- Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant.OBM genetics · 2025Article
- Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections.PLoS computational biology · 2024Article
- Enhancing the epidemiological surveillance of SARS-CoV-2 using Sanger sequencing to identify circulating variants and recombinants.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- Retrospective Analysis of Omicron in Minas Gerais, Brazil: Emergence, Dissemination, and Diversification.Microorganisms · 2024Article
- Observational
- Article
- NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples.Pathogens (Basel, Switzerland) · 2024Article
- SARS-CoV-2 variant survey: Comparison of RT-PCR screening with TGS and variant distribution across two divisions of Bangladesh.PloS one · 2024Article
- A meta-analysis highlights the idiosyncratic nature of tradeoffs in laboratory models of virus evolution.Virus evolution · 2024Article
- An Open One-Step RT-qPCR for SARS-CoV-2 detection.PloS one · 2024Article
84 more citing papers are in PubMed but not listed here.
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Authors and funding
41 authors.
Funding
Abstract
With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69-70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.
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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.