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J Clin Microbiol
. 2022 Apr 25;e0017822.
doi: 10.1128/jcm.00178-22. Online ahead of print.
Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification
Priscilla S-W Yeung # 1 , Hannah Wang # 1 , Mamdouh Sibai 1 , Daniel Solis 1 , Fumiko Yamamoto 1 , Naomi Iwai 2 , Becky Jiang 2 , Nathan Hammond 3 , Bernadette Truong 2 , Selamawit Bihon 2 , Suzette Santos 2 , Marilyn Mar 2 , Claire Mai 3 , Kenji O Mfuh 2 , Jacob A Miller 4 , ChunHong Huang 1 , Malaya K Sahoo 1 , James L Zehnder 1 , Benjamin A Pinsky 1 2 5
Affiliations
- PMID: 35465708
- DOI: 10.1128/jcm.00178-22
Abstract
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: COVID-19; Omicron; SARS-CoV-2; variant.