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

CASTRO, GONZALO; SICILIA, PAOLA; BOLZON, LAURA; LOPEZ, LAURA; BARBAS, GABRIELA; PISANO MARÍA BELÉN; VIVIANA, RÉ

Frontiers in Medicine

Frontiers Media S.A

Año: 2022

SARS-CoV-2 variants of concern (VOC) and interest (VOI) present mutations in referenceto the original virus, being more transmissible. We implemented a rapid strategy for thescreening of SARS-CoV-2 VOC/VOIs using real time RT-PCR and performed monitoringand surveillance of the variants in our region. Consecutive real-time RT-PCRs fordetection of the relevant mutations/deletions present in the Spike protein in VOC/VOIs(TaqManTM SARS-CoV-2 Mutation Panel, Applied Biosystems) were implemented.A total of 6,640 SARS-CoV-2 RNA samples (Cts < 30) from infected individuals inCentral Argentina during 2021 were analyzed using different algorithms that weregradually adapted to the changing scenarios of local variant circulation. The strategydeveloped allowed the early detection and the identification of VOC/VOIs that circulatedthrough the year, with a 100% of concordance with the WGS. The analyses of thesamples showed introductions of VOCs Alpha and Gamma in February and March2021, respectively. Gamma showed an exponential increase, with a peak of detection inJuly (72%), being responsible of the second wave of COVID19 in Argentina. Since VOCDelta entered into the region, it increased gradually, together with VOI Lambda, replacingVOC Gamma, until being the main variant (84.9%) on November. By December, thesevariants were replaced by the emergent VOC Omicron in a term of 2 weeks, producingthe third wave. We report a useful tool for VOC/VOI detection, capable to quickly andcost-effectively monitor currently recognized variants in resource-limited settings, whichallowed to track the recent expansion of Omicron in our region, and contributed to theimplementation of public health measures to control the disease spread.