key: cord-0722085-0g0spxwg authors: Castro, G. M.; Sicilia, P.; Bolzon, M. L.; Lopez, L.; Barbas, M. G.; Pisano, M. B.; Re, V. E. title: 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 date: 2021-11-20 journal: nan DOI: 10.1101/2021.11.16.21266265 sha: 1ecf916a836b61349dccc9c7e23c411f1815e41e doc_id: 722085 cord_uid: 0g0spxwg Background: 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. Methods: 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. 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. Results: the 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%. Conclusions: we 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. Background: SARS-CoV-2 variants of concern (VOC) and interest (VOI) present 25 mutations in reference to the original virus, being more transmissible. We 26 implemented a rapid strategy for the screening of SARS-CoV-2 VOC/VOIs using real 27 time RT-PCR and performed monitoring and surveillance of the variants in our region. 36 The analyses of the samples showed introductions of VOCs Alpha and Gamma in 37 February and March 2021, respectively. Since then, Alpha presented a low to 38 moderate circulation (1.7% of the SARS-CoV-2 currently detected). Gamma showed an 39 exponential increase, with a peak of detection in July (72%), until reaching a current 40 frequency of 41.1%. VOC Delta was first detected in July in travellers and currently 41 represents 35% of detections in the community. VOI Lambda presented a gradual 42 increase, showing a current frequency of 29%. 43 Conclusions: we report a useful tool for VOC/VOI detection, innovative for Argentina, 44 capable to quickly and cost-effectively monitor currently recognized variants. It was 45 key in the early detection of Delta, being able to implement measures to delay its 46 dissemination. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Figure 1A) . 74 Over the last few months, several variants were classified as of interest (VOI), but later 75 demonstrated to no longer pose a major added risk to global public health compared 76 to other circulating SARS-CoV-2 variants, so they were re-classified as variants under is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 20, 2021. ; https://doi.org/10.1101/2021.11.16.21266265 doi: medRxiv preprint 5 concern in public health due to the emergent variants, in the last months there has 97 been a rapidly growing demand for WGS. In February 2021, the strategy of partial 98 sequencing of the S gene was implemented for the search of VOC/VOIs in our region, 99 and VOCs Alpha and Gamma, as well as former VOI Zeta were detected for the first is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 20, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 20, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 20, 2021. ; https://doi.org/10.1101/2021.11.16.21266265 doi: medRxiv preprint 9 Once this strategy was implemented, the processing of the samples began, and a total 173 of 3941 samples was tested. Figure 2 shows changes in VOC/VOIs distribution within 174 SARS-CoV-2 infections among the community in Córdoba during the studied period. 175 VOCs Alpha and Gamma were first detected in our region in the months of February 176 and March, respectively. From that moment, they began to circulate in the population. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 20, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 20, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 20, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint 249 On the other hand, this strategy was also a very useful tool for the surveillance of is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint probably as a consequence of the increase of VOC Delta in the community. In the 276 coming weeks we will be able to observe if VOC Delta definitely displaces the rest of is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 20, 2021. ; https://doi.org/10.1101/2021.11.16.21266265 doi: medRxiv preprint In conclusion, we report a valid strategy based on real time RT-PCR for VOC/VOI 295 detection, first implemented in Argentina, which balance cost and time processing, 296 capable to monitor currently recognized variants of concern. In the present moment 297 requiring rapid strain typing to guide public health measures, such a rapid and 298 accessible approach is essential. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 20, 2021. ; https://doi.org/10.1101/2021.11.16.21266265 doi: medRxiv preprint . CC-BY-ND 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 20, 2021. ; https://doi.org/10.1101/2021.11.16.21266265 doi: medRxiv preprint Official hCoV-19 Reference Sequence World Health Organization (WHO) SARS-CoV-2 Variant 324 Classifications and Definitions Rapid 327 screening method for the detection of SARS-CoV-2 variants of concern Emerging Viral Diseases. Novel SARS-CoV-2 variants: the pandemics within the 331 pandemic. Microbiol and Infect Outbreak info. Variants of concern reports CoV-2 variant monitoring using PCR confirmed by whole genome 338 sequencing in a high-volume diagnostic laboratory Proyecto Argentino Interinstitucional de genómica de SARS-CoV-2 341 (Consorcio proyecto PAIS) Vigilancia de variantes de SARS-CoV-2 en la CABA Proyecto Argentino Interinstitucional de genómica de SARS-CoV-2 (Consorcio proyecto 345 PAIS) Situación de nuevas Variantes CoV-2 en Argentina SE30/2021. Informe técnico Hughes, and the Center for Viral Systems Biology. 354 outbreak.info, Brazil Mutation Report and Chile Mutation Report Mutation-Specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of 358 Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation Government of the Province of Cordoba It is made available under a perpetuity.is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprintThe copyright holder for this this version posted November 20, 2021. ; https://doi.org/10.1101/2021.11.16.21266265 doi: medRxiv preprint