An effective COVID-19 response in South America: the Uruguayan Conundrum
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Abstract
Background
South America has become the new epicenter of the COVID-19 pandemic with more than 1.1M reported cases and >50,000 deaths (June 2020). Conversely, Uruguay stands out as an outlier managing this health crisis with remarkable success.
Methods
We developed a molecular diagnostic test to detect SARS-CoV-2. This methodology was transferred to research institutes, public hospitals and academic laboratories all around the country, creating a “ COVID-19 diagnostic lab network ”. Uruguay also implemented active epidemiological surveillance following the “Test, Trace and Isolate” (TETRIS) strategy coupled to real-time genomic epidemiology.
Results
Three months after the first cases were detected, the number of positive individuals reached 826 (23 deaths, 112 active cases and 691 recovered). The Uruguayan strategy was based in a close synergy established between the national health authorities and the scientific community. In turn, academia rapidly responded to develop national RT-qPCR tests. Consequently, Uruguay was able to perform ∼1,000 molecular tests per day in a matter of weeks. The “ COVID-19 diagnostic lab network ” performed more than 54% of the molecular tests in the country. This, together with real- time genomics, were instrumental to implement the TETRIS strategy, helping to contain domestic transmission of the main outbreaks registered so far.
Conclusions
Uruguay has successfully navigated the first trimester of the COVID-19 health crisis in South America. A rapid response by the scientific community to increase testing capacity, together with national health authorities seeking out the support from the academia were fundamental to successfully contain, until now, the COVID-19 outbreak in the country.
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SciScore for 10.1101/2020.07.24.20161802: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources These primer/probe sets were subjected to BLAST searching to ensure that they did not align to sequences other than SARS-CoV. BLASTsuggested: (BLASTX, RRID:SCR_001653)Effective reproduction number (Re) calculation: Re was estimated using a discretized generation time distribution assuming a shifted gamma distribution (discr_si function) implemented on EpiEstim package1–3, with serial interval (k) ranging from 0 to 30, mean µ = 3.95 and standard deviation σ = 4.75 as … SciScore for 10.1101/2020.07.24.20161802: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources These primer/probe sets were subjected to BLAST searching to ensure that they did not align to sequences other than SARS-CoV. BLASTsuggested: (BLASTX, RRID:SCR_001653)Effective reproduction number (Re) calculation: Re was estimated using a discretized generation time distribution assuming a shifted gamma distribution (discr_si function) implemented on EpiEstim package1–3, with serial interval (k) ranging from 0 to 30, mean µ = 3.95 and standard deviation σ = 4.75 as parameters4,5. EpiEstimsuggested: (EpiEstim, RRID:SCR_018538)SARS-CoV-2 genomes from cases reported in Uruguay were sequenced with different technologies, including Illumina and the ARTIC Network protocol using the MinION platform (Oxford Nanopore). MinIONsuggested: (MinION, RRID:SCR_017985)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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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.
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SciScore for 10.1101/2020.07.24.20161802: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Of note, and consistently with observations made worldwide12, men appeared to be more affected than women with 5.9% of men requiring critical care assistance vs. 1.7% of women (Table 1). Table 2: Resources
Software and Algorithms Sentences Resources These primer/probe sets were subjected to BLAST searching to ensure that they did not align to sequences other than SARS-CoV. BLASTsuggested: (BLASTX, SCR_001653)Effective reproduction number (Re) calculation Re was estimated using a … SciScore for 10.1101/2020.07.24.20161802: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Of note, and consistently with observations made worldwide12, men appeared to be more affected than women with 5.9% of men requiring critical care assistance vs. 1.7% of women (Table 1). Table 2: Resources
Software and Algorithms Sentences Resources These primer/probe sets were subjected to BLAST searching to ensure that they did not align to sequences other than SARS-CoV. BLASTsuggested: (BLASTX, SCR_001653)Effective reproduction number (Re) calculation Re was estimated using a discretized generation time distribution assuming a shifted gamma distribution (discr_si function) implemented on EpiEstim package 1–3, with serial interval (k) ranging from 0 to 30, mean µ = 3.95 and standard deviation σ = 4.75 as parameters4,5. EpiEstimsuggested: (EpiEstim, SCR_018538)SARS-CoV-2 genomes from cases reported in Uruguay were sequenced with different technologies, including Illumina and the ARTIC Network protocol using the MinION platform (Oxford Nanopore). MinIONsuggested: (MinION, SCR_017985)Data from additional tools added to each annotation on a weekly basis.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
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