Your browser doesn't support javascript.
Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants.
Mertens, Joachim; Coppens, Jasmine; Loens, Katherine; Le Mercier, Marie; Xavier, Basil Britto; Lammens, Christine; Vandamme, Sarah; Jansens, Hilde; Goossens, Herman; Matheeussen, Veerle.
  • Mertens J; Department 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.
  • Coppens J; Department 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.
  • Loens K; Department 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.
  • Le Mercier M; Department of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium.
  • Xavier BB; Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium.
  • Lammens C; Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium.
  • Vandamme S; Department of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium.
  • Jansens H; Department 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.
  • Goossens H; Department 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.
  • Matheeussen V; Department 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 Med
Clin Microbiol Infect ; 28(1): 124-129, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1479592
ABSTRACT

OBJECTIVES:

To 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).

METHODS:

PCR 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.

RESULTS:

The 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.

CONCLUSIONS:

We 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.
Subject(s)
Keywords

Full text: Available Collection: International databases Database: MEDLINE Main subject: Polymorphism, Single Nucleotide / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies Topics: Variants Limits: Humans Language: English Journal: Clin Microbiol Infect Journal subject: Communicable Diseases / Microbiology Year: 2022 Document Type: Article Affiliation country: J.cmi.2021.09.007

Similar

MEDLINE

...
LILACS

LIS


Full text: Available Collection: International databases Database: MEDLINE Main subject: Polymorphism, Single Nucleotide / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies Topics: Variants Limits: Humans Language: English Journal: Clin Microbiol Infect Journal subject: Communicable Diseases / Microbiology Year: 2022 Document Type: Article Affiliation country: J.cmi.2021.09.007