Genomic analysis reveals local transmission of SARS-CoV-2 in early pandemic phase in Peru

  1. Carlos Padilla-Rojas
  2. Karolyn Vega-Chozo
  3. Marco Galarza-Perez
  4. Henri Bailon Calderon
  5. Priscila Lope-Pari
  6. Johanna Balbuena-Torres
  7. David Garcia Neyra
  8. Maribel Huaringa-Nuñez
  9. Nancy Rojas-Serrano
  10. Omar A. Caceres-Rey

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Abstract

The dissemination of cases of the new SAR-COV-2 coronavirus represents a serious public health problem for Latin America and Peru. For this reason, it is important to characterize the genome of the isolates that circulate in Latin America. To characterize the complete genome of first samples of the virus circulating in Peru, we amplified seven overlapping segments of the viral genome by RT-PCR and sequenced using Miseq platform. The results indicate that the genomes of the Peruvian SARS-COV-2 samples belong to the genetic groups G and S. Likewise, a phylogenetic and MST analysis of the isolates confirm the introduction of multiple isolates from Europe and Asia that, after border closing, were transmitted locally in the capital and same regions of the country. These Peruvian samples (56%) grouped into two clusters inside G clade and share B.1.1.1 lineage. The characterization of these isolates must be considered for the use and design of diagnostic tools, and effective treatment and vaccine formulations.

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  1. ScreenIT

    SciScore for 10.1101/2020.09.05.284604: (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
    The fastq files generated were cleaned using Groomer and Trimmomatic (https://usegalaxy.org/).
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    The reads mapped to the Wuhan-Hu-1 reference genome available at the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/nuccore/?term=Severe+acute+respiratory+syndrome+coronavirus+2+AND+Wuhan) using BWA-ME (https://usegalaxy.org).
    BWA-ME
    suggested: None
    Finally, the genomes were assembled using SPAdes and compared to the reference genome using CONTIGuator (http://contiguator.sourceforge.net/).
    SPAdes
    suggested: (SPAdes, RRID:SCR_000131)
    Nucleotide and amino acid variations were detected using snpEff (http://snpeff.sourceforge.net/SnpEff_manual.html).
    snpEff
    suggested: (SnpEff, RRID:SCR_005191)
    Likewise, a manual edition of the genomes was done using the Geneious Prime software (https://www.geneious.com/).
    https://www.geneious.com/
    suggested: (Geneious, RRID:SCR_010519)
    The MCC tree was visualized and edited using FigTree (http://tree.bio.ed.ac.uk/software/figtree/).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    Additionally, to detect local transmission of the virus we performed Maximum Likelihood analysis with 1000 bootstraps of confidence using MEGA X (https://www.megasoftware.net).
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    A minimum spanning tree (MST) analysis using BioNumerics version 7.6 (
    BioNumerics
    suggested: None

    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:
    An important limitation of our study is the uneven spatial and temporal sampling scheme, most SARS-CoV-2 sequences recovered in the present study were from Lima and a few samples of north and south regions of Peru. These sampling does not represent the viral diversity in other regions of Peru. More accurate reconstructions of the origin and regional spread of the clade B.1.1.1 will require a denser sampling from Peru and neighboring South American countries, particularly during the very early phase of the epidemic. It is crucial to analyze more cases by whole genome sequencing of the SARS-CoV-2 virus from different regions of the country, to better understand the spread and evolution of this new coronavirus in Perú. It is also important to integrate the information from the laboratory diagnosis and the genomic analysis of the virus with the clinical and epidemiological data to depict the clinical epidemiology and infection mechanisms of this coronavirus in Peru.

    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.

    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 10.1101/2020.09.05.284604v1 on bioRxiv