Tracking SARS-CoV-2 Variants Using a Rapid Typification Strategy: A Key Tool for Early Detection and Spread Investigation of Omicron in Argentina
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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.
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SciScore for 10.1101/2021.11.16.21266265: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization Samples were randomly selected from all the province and from all the months studied in order to monitor VOC/VOI circulation in the community. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The strategy described here present some limitations: a)-some samples show inconclusive results, b)-samples with Ct values >30 …
SciScore for 10.1101/2021.11.16.21266265: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization Samples were randomly selected from all the province and from all the months studied in order to monitor VOC/VOI circulation in the community. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The strategy described here present some limitations: a)-some samples show inconclusive results, b)-samples with Ct values >30 cannot be typified, c)-many diagnostic PCR platforms can deplete swab material, leaving an inadequate volume of residual sample for a multitube mutation screen [Wang et al. 2021], d)-since VOC/VOI classification is dynamic and is constantly changing [WHO 2021], the strategy must be constantly reviewed and evaluated in order to corroborate whether the algorithm used is adequate for a correct VOC typing, e)-it is not possible to find mutations other than those specifically searched for, which leads to not being able to detect new emerging VOC/VOIs. These limitations show that WGS cannot be replaced by real time RT-PCR specific for VOC/VOI. Furthermore, these methodologies complement each other. While specific real time RT-PCRs for mutations of interest are a useful tool for rapid VOC/VOI screening, WGS-based parallel surveillance is critical to detect new emerging variants and to study phylogeographic relationships between circulating viruses. In conclusion, we report a valid strategy based on real time RT-PCR for VOC/VOI detection, first implemented in Argentina, which balance cost and time processing, capable to monitor currently recognized variants of concern. In the present moment requiring rapid strain typing to guide public health measures, such a rapid and accessible approach is essential.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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