Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification
- 25 April 2022
- journal article
- research article
- Published by American Society for Microbiology in Journal of Clinical Microbiology
- Vol. 60 (5), e0017822
- https://doi.org/10.1128/jcm.00178-22
Abstract
Y The ability to distinguish between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) is of ongoing interest due to differences in transmissibility, responses to vaccination, clinical prognosis, and therapy. Although detailed genetic characterization requires whole-genome sequencing (WGS), targeted nucleic acid amplification tests can serve a complementary role in clinical settings, as they are more rapid and accessible than sequencing in most laboratories. We designed and analytically validated a two-reaction multiplex reverse transcription-quantitative PCR (RT-qPCR) assay targeting spike protein mutations L452R, E484K, and N501Y in reaction 1 and del69-70, K417N, and T478K in reaction 2. This assay had 95 to 100% agreement with WGS for 502 upper respiratory tract swab samples collected between 26 April 2021 and 1 August 2021, consisting of 43 Alpha, 2 Beta, 20 Gamma, 378 Delta, and 59 non-VOC infections. Validation in a separate group of 230 WGS-confirmed Omicron variant samples collected in December 2021 and January 2022 demonstrated 100% agreement. This RT-qPCR-based approach can be implemented in clinical laboratories already performing SARS-CoV-2 nucleic acid amplification tests to assist in local epidemiological surveillance and clinical decision-making.Keywords
This publication has 45 references indexed in Scilit:
- Emergence of a Novel SARS-CoV-2 Variant in Southern CaliforniaJAMA, 2021
- Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine seraCell, 2021
- Neutralization of SARS-CoV-2 lineage B.1.1.7 pseudovirus by BNT162b2 vaccine–elicited human seraScience, 2021
- Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United StatesPublished by Cold Spring Harbor Laboratory ,2021
- 40 minutes RT-qPCR Assay for Screening Spike N501Y and HV69-70del MutationsPublished by Cold Spring Harbor Laboratory ,2021
- Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020Eurosurveillance, 2021
- On the evolutionary epidemiology of SARS-CoV-2Current Biology, 2020
- Nextstrain: real-time tracking of pathogen evolutionBioinformatics, 2018
- TreeTime: Maximum-likelihood phylodynamic analysisVirus Evolution, 2018
- STARD 2015: an updated list of essential items for reporting diagnostic accuracy studiesBMJ, 2015