Rapid Detection of SARS-CoV-2 Variants of Concern, Including B.1.1.28/P.1, British Columbia, Canada

To screen all severe acute respiratory syndrome coronavirus 2–positive samples in Vancouver, British Columbia, Canada, and determine whether they represented variants of concern, we implemented a real-time reverse transcription PCR–based algorithm. We rapidly identified 77 samples with variants: 57 with B.1.1.7, 7 with B.1.351, and an epidemiologic cluster of 13 with B.1.1.28/P.1.

A robust surveillance system for early identifi cation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) is of critical public health value. VOCs have demonstrated in vitro evasion of antibody neutralization ( Given the potential for VOCs to enhance transmission, increase deaths, and possibly evade natural or vaccine-induced immune responses, identifying cases of coronavirus disease (COVID-19) caused by VOCs and monitoring their prevalence is critical. We propose a rapid VOC surveillance strategy that uses multiple rRT-PCRs to screen all samples positive for SARS-CoV-2. This study was approved by the Providence Health Care/University of British Columbia and Simon Fraser University Research Ethics Boards (H20-01055).

The Study
During January 26-March 1, 2021, the clinical virology laboratory at St. Paul's Hospital, Vancouver, British Columbia, Canada, conducted VOC testing on nasopharyngeal swab and saliva/mouth rinse samples in which SARS-CoV-2 was detected at any cycle threshold (C t ) value. SARS-CoV-2 detection was performed by using the LightMix SarbecoV E-gene plus EAV control assay (TIB To screen all severe acute respiratory syndrome coronavirus 2-positive samples in Vancouver, British Columbia, Canada, and determine whether they represented variants of concern, we implemented a real-time reverse transcription PCR-based algorithm. We rapidly identifi ed 77 samples with variants: 57 with B.
During  During the study period, VOC detection among diagnostic samples rapidly increased (Figure). Of note, identified VOCs included a large cluster of the B.1.1.28/P.1 variant not previously identified in British Columbia. All B.1.1.28/P.1 variants were initially suspected from the K417N assay, for which PCR products were identified at a lower melting temperature than expected. All suspected B.1.1.28/P.1 variants were confirmed when rescreened by using the V1176F target. The

Conclusions
Implementation of a PCR-based algorithm to detect VOCs has enabled our laboratory to rapidly detect new variants that are in the early stages of community transmission. Our protocol enabled detection of VOCs within 24 hours of COVID-19 diagnosis, a marked advantage over sequencing-based surveillance strategies. VOC positivity rate was 3.2%, but detection rates increased markedly over time, as might be expected with exponential growth observed in other countries.
Although WGS has been the primary modality for VOC surveillance, universal sequencing of SARS-CoV-2-positive specimens is limited by both laboratory and bioinformatics capacity (6). Because of the volume of VOC testing and the limited capacity for high complexity WGS, turnaround times by WGS may be days to weeks. Since the onset of the CO-VID-19 pandemic, molecular diagnostics (i.e., PCR) have been increasingly adopted by laboratories to promptly identify SARS-CoV-2, and infrastructure has been established for this testing modality. A PCRbased algorithm for the molecular detection of VOCs could be rapidly adopted, providing almost real-time results to inform infection prevention and control and public health measures (3,7,8). PCR may also be more sensitive because WGS is challenging to perform on samples with low viral loads (C t >30) (9). Compared with WGS, PCR screening enhanced sensitivity for VOC detection by >10%.
Although the most prevalent VOCs worldwide harbor N501Y, this mutation is not present in all variants (10). A PCR-based algorithm for identifying VOCs that use N501Y as the initial screening target must acknowledge this limitation. Given the rapid emergence of new variants, ongoing surveillance is key, and laboratories considering a PCRbased algorithm would need to adapt the algorithm as VOC prevalence changes. For example, our initial screening PCR targeted N501Y, but because of rising rates of B.1.1.7, we adjusted our laboratorydeveloped test to include N501Y and delHV69/70 in a duplexed assay.
PCR-based methods for rapid VOC detection should not replace broader VOC surveillance with WGS, which enables identification of non-N501Y VOCs and can characterize emerging mutations in known VOCs. This ability is critical for enabling laboratories to revise their PCR targets in an ongoing manner to keep pace with local VOC circulation.