Evidence map›Paper›PMID 34537361›Full record

ArticleClinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases2022

Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants.

Joachim Mertens, Jasmine Coppens, Katherine Loens, Marie Le Mercier, Basil Britto Xavier, Christine Lammens, Sarah Vandamme, Hilde Jansens, Herman Goossens, Veerle Matheeussen

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Article in Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.

0numbers the graph read from it
0cells of the map it votes in
19citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

19 citing papers in PubMed.

  1. Observational
  2. Molecular mechanisms of SARS-CoV-2 entry: implications for biomedical strategies.Microbiology and molecular biology reviews : MMBR · 2025
    Review
  3. Article
  4. Article
  5. Article
  6. Article
  7. Review
  8. Review
  9. Article
  10. Review
  11. Spike protein of SARS-CoV-2 variants: a brief review and practical implications.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2022
    Review
  12. Article
  13. Article
  14. Review
  15. Article
  16. Article
  17. Review
  18. Testing Antigens, Antibodies, and Immune Cells in COVID-19 as a Public Health Topic-Experience and Outlines.International journal of environmental research and public health · 2021
    Review
  19. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Joachim MertensDepartment of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium; Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Antwerp, Belgium.
Jasmine CoppensDepartment of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium; Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium.
Katherine LoensDepartment of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium; Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium.
Marie Le MercierDepartment of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium.
Basil Britto XavierLaboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium.
Christine LammensLaboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium.
Sarah VandammeDepartment of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium.
Hilde JansensDepartment of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium; Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium.
Herman GoossensDepartment of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium; Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium.
Veerle MatheeussenDepartment of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium; Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Antwerp, Belgium; Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium. Electronic address: veerle.matheeussen@uza.be.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

objectivesTo evaluate a testing algorithm for the rapid identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that includes the use of PCR-based targeted single nucleotide polymorphism (SNP) detection assays preceded by a multiplex PCR sensitive to S-Gene Target Failure (SGTF).

methodsPCR SNP assays targeting SARS-CoV-2 S-gene mutations ΔH69-V70, L452R, E484K, N501Y, H655Y and P681R using melting curve analysis were performed on 567 samples in which SARS-CoV-2 viral RNA was detected by a multiplex PCR. Viral whole-genome sequencing (WGS) was performed to confirm the presence of SNPs and to identify the Pangolin lineage. Additionally, 1133 SARS-CoV-2 positive samples with SGTF were further assessed by WGS to determine the presence of ΔH69-V70.

resultsThe N501Y-specific assay (n = 567) had an overall percentage agreement (OPA) of 98.5%. The ΔH69-V70-specific (n = 178) and E484K-specific (n = 401) assays had OPA of 96.6% and 99.7%, respectively. Assessment of H655Y (n = 139) yielded a 100.0% concordance when applied in the proposed algorithm. The L452R-specific (n = 67) and P681R-specific (n = 62) assays had an OPA of 98.2% and 98.1%, respectively. The proposed algorithm identified six variants of concern/interest (VOC/VOI)-Alpha (n = 149), Beta (n = 65), Gamma (n = 86), Delta (n = 49), Eta (n = 6), Kappa (n = 6)-and 205 non-VOC/VOI strains-including the variants under monitoring B.1.214.2 (n = 43) and B.1.1.318 (n = 18) and Epsilon (n = 1). An excellent concordance was observed for the identification of all SARS-CoV-2 lineages evaluated.

conclusionsWe present a flexible testing algorithm for the rapid detection of current and emerging SARS-CoV-2 VOC/VOIs, which can be easily adapted based on the local endemicity of specific variants.

Indexed as

Polymorphism, Single NucleotideAlgorithmsCOVID-19HumansMultiplex Polymerase Chain ReactionMutationPandemicsPolymerase Chain ReactionSARS-CoV-2Spike Glycoprotein, CoronavirusSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2Coronavirus disease 2019Melting curve analysisNucleic acid testingPolymerase chain reactionSevere acute respiratory syndrome coronavirus 2Severe acute respiratory syndrome coronavirus 2 variantsTesting algorithmWhole-genome sequencing

Identifiers

PMID34537361
PMCPMC8444474

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Registered trials

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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.