Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay
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Abstract
After its emergence in China in December 2019, the new coronavirus disease (COVID-19) caused by SARS-CoV-2, has rapidly spread infecting more than 3 million people worldwide. South America is among the last regions hit by COVID-19 pandemic. In Uruguay, first cases were detected on March 13 th 2020 presumably imported by travelers returning from Europe.
Methods
We performed whole-genome sequencing of 10 SARS-CoV-2 from patients diagnosed during the first week (March 16 th to 19 th ) of COVID-19 outbreak in Uruguay. Then, we applied genomic epidemiology using a global dataset to reconstruct the local spatio-temporal dynamics of SARS-CoV-2.
Results
Our phylogeographic analysis showed three independent introductions of SARS-CoV-2 from different continents. Also, we evidenced regional circulation of viral strains originally detected in Spain. Introduction of SARS-CoV-2 in Uruguay could date back as early as Feb 20 th . Identification of specific mutations showed rapid local genetic differentiation.
Conclusions
We evidenced early independent introductions of SARS-CoV-2 that likely occurred before first cases were detected. Our analysis set the bases for future genomic epidemiology studies to understand the dynamics of SARS-CoV-2 in Uruguay and the Latin America and the Caribbean region.
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SciScore for 10.1101/2020.05.09.086223: (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 Sequencing of SARS-CoV-2 positive samples was performed according to the primalseq [5] approach on the MinION sequencing platform (Oxford Nanopore Technologies, United Kingdom) using the V2 primer pools. MinIONsuggested: (MinION, RRID:SCR_017985)The RAMPART software from the ARTIC Network (https://github.com/artic-network/rampart) was used to monitor the sequencing run in real time, estimate coverage across samples and check barcoding. RAMPARTsuggested: (Rampart, RRID:SCR_016742)Br… SciScore for 10.1101/2020.05.09.086223: (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 Sequencing of SARS-CoV-2 positive samples was performed according to the primalseq [5] approach on the MinION sequencing platform (Oxford Nanopore Technologies, United Kingdom) using the V2 primer pools. MinIONsuggested: (MinION, RRID:SCR_017985)The RAMPART software from the ARTIC Network (https://github.com/artic-network/rampart) was used to monitor the sequencing run in real time, estimate coverage across samples and check barcoding. RAMPARTsuggested: (Rampart, RRID:SCR_016742)Briefly, genomes were aligned using MAFFT [6] and a phylogeny was reconstructed with IQ-TREE [7]. MAFFTsuggested: (MAFFT, RRID:SCR_011811)IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)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.
- No funding statement was detected.
- No protocol registration statement was detected.
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