Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. (January 2022)

• Record Type: Journal Article
• Authors: Mertens, Joachim; Coppens, Jasmine; Loens, Katherine; Le Mercier, Marie; Xavier, Basil Britto; Lammens, Christine; Vandamme, Sarah; Jansens, Hilde; Goossens, Herman; Matheeussen, Veerle
• Is Part Of: Clinical microbiology and infection. Volume 28:Number 1(2022)
• Page Start: 124
• Page End: 129
• Publication Date: 2022-01
• Subjects: Coronavirus disease 2019 -- Melting curve analysis -- Nucleic acid testing -- Polymerase chain reaction -- Severe acute respiratory syndrome coronavirus 2 -- Severe acute respiratory syndrome coronavirus 2 variants -- Testing algorithm -- Whole-genome sequencing; Medical microbiology -- Periodicals; Diagnostic microbiology -- Periodicals; Communicable diseases -- Periodicals; Infection -- Periodicals; 616.01
• DOI: 10.1016/j.cmi.2021.09.007
• Languages: English
• ISSNs: 1198-743X

Abstract

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.