Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay

  1. Cecilia Salazar
  2. Florencia Díaz-Viraqué
  3. Marianoel Pereira-Gómez
  4. Ignacio Ferrés
  5. Pilar Moreno
  6. Gonzalo Moratorio
  7. Gregorio Iraola

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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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  1. ScreenIT

    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 Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    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.
    MinION
    suggested: (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.
    RAMPART
    suggested: (Rampart, RRID:SCR_016742)
    Briefly, genomes were aligned using MAFFT [6] and a phylogeny was reconstructed with IQ-TREE [7].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    IQ-TREE
    suggested: (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.

    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 checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2020.05.09.086223v1 on bioRxiv