SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis

  1. Sully Márquez
  2. Belén Prado-Vivar
  3. Juan José Guadalupe
  4. Mónica Becerra-Wong
  5. Bernardo Gutierrez
  6. Clinical COVID-19 Ecuador Consortium
  7. Juan Carlos Fernández-Cadena
  8. Derly Andrade-Molina
  9. Gabriel Morey-Leon
  10. Miguel Moncayo
  11. Rommel Guevara
  12. Josefina Coloma
  13. Gabriel Trueba
  14. Michelle Grunauer
  15. Verónica Barragán
  16. Patricio Rojas-Silva
  17. Paúl Cárdenas

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Abstract

SARS-CoV-2, the etiological agent of COVID-19, was first described in Wuhan, China in December 2019 and has now spread globally. Ecuador was the second country in South America to confirm cases and Guayaquil was one of the first cities in the world to experience high mortality due to COVID-19. The aim of this study was to describe the lineages circulating throughout the country and to compare the mutations in local variants, to the reference strain. In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the whole SARS-CoV-2 genomes of 119 patients from all provinces of Ecuador, using the ARTIC network protocols. Our data from lineage assignment of the one hundred and nineteen whole genomes revealed twenty different lineages. All genomes presented differences in the S gene compared to the Wuhan reference strain, being the D614G amino acid replacement the most common change. The B.1.1.119 lineage was the most frequent and was found in several locations in the Coast and Andean region. Three sequences were assigned to the new B.1.1.7 lineage. Our work is an important contribution to the understanding of the epidemiology of SARS-CoV-2 in Ecuador and South America.

Highlights

  • All 119 genomes showed mutations compared to the reference strain, which could be important to understand the virulence, severity and transmissibility of the virus.

  • Until January 17, three sequences were assigned to the new B.1.1.7 lineage.

  • Our findings suggest that there were at least twenty independent introductions of SARS-CoV-2 to Ecuador.

Article Summary Line

We report 119 sequences of SARS-CoV-2 across all Ecuadorian provinces, 20 different lineages were found until January 17 th , including B.1.1.7.

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  1. ScreenIT

    SciScore for 10.1101/2021.03.19.21253620: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIRB: The use of samples was approved by the Bioethics Committee of Universidad San Francisco de Quito (CEISH No. 1234).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    . cDNA MinION library preparation was performed using the Rapid Barcoding kit (SQK-RBK004), native barcoding kit (NB-114) with ligation sequencing kit (LSK-109) following manufacturer instructions and then loaded into a MinION flow cell (FLO-MIN 106).
    MinION
    suggested: (MinION, RRID:SCR_017985)
    Also, the RAMPART software (v1.0.5) from the ARTIC Network (https://github.com/artic-network/rampart) was used to monitor sequencing in real-time.
    RAMPART
    suggested: (Rampart, RRID:SCR_016742)
    Sequence quality scoring, demultiplexing and adapter removal was performed with the NanoPlot (13) and Porechop (version 0.2.4) algorithms, respectively (https://github.com/rrwick/Porechop).
    Porechop
    suggested: (Porechop, RRID:SCR_016967)
    A maximum likelihood phylogenetic reconstruction was performed with GTR substitution model and 1000 bootstrap resampling using IQtree 2.1.1.
    IQtree
    suggested: None

    Results from OddPub: Thank you for sharing your data.

    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.
    • Thank you for including a protocol registration statement.

    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 10.1101/2021.03.19.21253620 on medRxiv