Tracking SARS-CoV-2 Variants Using a Rapid Typification Strategy: A Key Tool for Early Detection and Spread Investigation of Omicron in Argentina

Abstract

SARS-CoV-2 variants of concern (VOC) and interest (VOI) present mutations in reference to the original virus, being more transmissible. We implemented a rapid strategy for the screening of SARS-CoV-2 VOC/VOIs using real time RT-PCR and performed monitoring and surveillance of the variants in our region. Consecutive real-time RT-PCRs for detection of the relevant mutations/deletions present in the Spike protein in VOC/VOIs (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems) were implemented. A total of 6,640 SARS-CoV-2 RNA samples (Cts < 30) from infected individuals in Central Argentina during 2021 were analyzed using different algorithms that were gradually adapted to the changing scenarios of local variant circulation. The strategy developed allowed the early detection and the identification of VOC/VOIs that circulated through the year, with a 100% of concordance with the WGS. The analyses of the samples showed introductions of VOCs Alpha and Gamma in February and March 2021, respectively. Gamma showed an exponential increase, with a peak of detection in July (72%), being responsible of the second wave of COVID19 in Argentina. Since VOC Delta entered into the region, it increased gradually, together with VOI Lambda, replacing VOC Gamma, until being the main variant (84.9%) on November. By December, these variants were replaced by the emergent VOC Omicron in a term of 2 weeks, producing the third wave. We report a useful tool for VOC/VOI detection, capable to quickly and cost-effectively monitor currently recognized variants in resource-limited settings, which allowed to track the recent expansion of Omicron in our region, and contributed to the implementation of public health measures to control the disease spread.

Bridging the Sequencing Gap: N501Y SNP RT-qPCR Assay Detects First SARS-CoV-2 Beta Variant in the Philippines

“…However, both sequencing approaches were time-consuming which resulted in delayed identification of variants. They then established an algorithm using an RT-qPCR strategy that targeted the N501Y, E484K, and L452 mutations (17). Similarly, our optimized assay would have been a useful tool for more rapid identification of variants in the country had it been included in our surveillance initiatives as a screening step.…”

“…An RT-qPCR assay that targets variant-specific SNP mutations like N501Y can be used as a screening tool for early variant classification (11). Laboratory-developed SNP RT-qPCR assays were implemented in the surveillance measures in several countries, which allowed them to screen and identify probable variants rapidly (13)(14)(15)(16)(17). In this paper, we optimized and used a SNP RT-qPCR assay to screen for the variant-associated N501Y amino acid substitution in banked SARS-CoV-2 samples.…”

Differentiation of SARS-CoV-2 Variants Using RT-qPCRs by Targeting Recurrent Mutation Sites: A Diagnostic Laboratory Experience from Multi-Center Regional Study, August 2020–December 2021, Poland

“…Although the NGS is the gold standard for differentiating SARS-CoV-2 variants, due to its long turnaround time and high cost per sample, its use is less feasible by diagnostic laboratories [ 26 ]. Therefore, RT-qPCR assays detecting VOCs-specific mutations appear to be a better option for timely clinical applications and population surveillance [ 26 , 38 , 39 , 40 , 41 ]. The present study applied just this method to test a set of more than 1000 samples for SARS-CoV-2 variants.…”

Multicenter Diagnostic Evaluation of OnSite COVID-19 Rapid Test (CTK Biotech) among Symptomatic Individuals in Brazil and the United Kingdom

“…The RT-qPCR mixture was prepared, and samples were tested for the presence of each S-gene mutation. The mutation panel was customized to detect each variant as follows: Alpha (P681H[+], E484K[−], K417N[−], L452R[−], T20N[−], P681R[−], L452Q[−]), Beta (E484K[+], K417N[+], P681H[−], L452R[−], T20N[−], P681R[−], L452Q[−]), Gamma (E484K[+], T20N[+], K417N[−], L452R[−], P681H[−], P681R[−], L452Q[−]), Delta and Kappa (L452R[+], P681R[+], E484K[−], K417N[−], T20N[−], P681H[−], L452Q[−]), Zeta (E484K[+], K417N[−], L452R[−], T20N[−], P681H[−], P681R[−], L452Q[−]), and Lambda (L452Q[+], E484K[−], K417N[−], P681H[−], L452R[−], T20N[−], P681R[−]) ( 28 – 30 ). Data were analyzed by QuantStudio design and analysis software v2.5.1.…”