Strategy for a rapid screening and surveillance of SARS-CoV-2 variants by real time RT-PCR: a key tool that allowed control and delay in Delta spread in Cordoba, Argentina

BackgroundSARS-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. Methodsconsecutive 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. An algorithm was established and 3941 SARS-CoV-2 RNA samples (Cts<30) obtained from oropharyngeal swabs from infected individuals in Cordoba, Argentina, between January and October 2021, were analyzed. Resultsthe strategy of choice included a first screening of 3 mutations (N501Y, E484K, L452R) followed by the detection of other mutations/deletions based on the results. The analyses of the samples showed introductions of VOCs Alpha and Gamma in February and March 2021, respectively. Since then, Alpha presented a low to moderate circulation (1.7% of the SARS-CoV-2 currently detected). Gamma showed an exponential increase, with a peak of detection in July (72%), until reaching a current frequency of 41.1%. VOC Delta was first detected in July in travellers and currently represents 35% of detections in the community. VOI Lambda presented a gradual increase, showing a current frequency of 29%. Conclusionswe report a useful tool for VOC/VOI detection, innovative for Argentina, capable to quickly and cost-effectively monitor currently recognized variants. It was key in the early detection of Delta, being able to implement measures to delay its dissemination.