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

Abstract

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 Córdoba, 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.

SARS-CoV-2 genomic surveillance enables the identification of Delta/Omicron co-infections in Argentina

“…VOC Delta was first described in our province on July 2021, when it was detected in a traveler and his close contacts. Due to the efforts carried out by the health authorities of the province, which included tracking and isolating Delta positive cases and its close contacts, the spread of this VOC was delayed, so its increase was gradual, until reaching its highest proportion of circulation (85%) in November 2021 (Castro et al 2021), but without a substantial increase in the number of cases (Gobierno de la provincia de Córdoba 2022).…”

“…A strategy of SARS-CoV-2 VOC/VOI typing was implemented in the province of Cordoba, Argentina, during 2021, which varied throughout the year according to the the local profile of circulating variants (Castro et al 2021). By the beginning of December 2021, with a major presence of Delta circulating in the community, the strategy included a first screening of L452R and P681R mutations, followed by detections of P681H, K417N, L452Q (the second round of mutation detection was carried out depending on the results of the first screening) (Castro et al 2021, Gobierno de la provincia de Cordoba 2022). TaqMan™ SARS-CoV-2 Mutation Panel (Applied Biosystems) was used for detection of the relevant mutations/deletions.…”

“…But then, given the increase in the number of COVID-19 cases, the appearance of VOC/VOIs and the need for rapid results that enable the public health decision-making, some provinces implemented different strategies based on real-time RT-PCRs for detection of VOC/VOIs relevant mutations, as additional techniques to the WGS. This was the case of the province of Córdoba, in the central region of the country, where a strategy that combined detection of point mutations was developed (Castro et al 2021). This strategy served for molecular surveillance of SARS-CoV-2 variants during 2021, enabling the typing of a greater number of samples in less processing time (Castro et al 2021, Gobierno de la provincia de Cordoba 2022).…”

“…This was the case of the province of Córdoba, in the central region of the country, where a strategy that combined detection of point mutations was developed (Castro et al 2021). This strategy served for molecular surveillance of SARS-CoV-2 variants during 2021, enabling the typing of a greater number of samples in less processing time (Castro et al 2021, Gobierno de la provincia de Cordoba 2022). Moreover, this strategy allowed the detection of Omicron variant for the first time in Cordoba on December 2021, when the third wave of COVID-19 started in the country, displacing VOC Delta, the major variant circulating at that time (Gobierno de la provincia de Córdoba 2022).…”

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

“…A preliminary version of this manuscript has been posted as a preprint at medRxiv ( 17 ), https://doi.org/10.1101/2021.11.16.21266265 .…”