Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2

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Abstract

Epidemiological and genomic analyses uncover viral mutational dynamics and transmission bottleneck size during the early COVID-19 pandemic in Austria.

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  1. SciScore for 10.1101/2020.07.15.204339: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Read pairs were mapped on the combined Hg38 and SARS-CoV-2 genome (GenBank: MN908947.3) using the BWA-MEM software package (v 0.7.17) (43).
    BWA-MEM
    suggested: (Sniffles, RRID:SCR_017619)
    From the viral reads BAM file, the consensus FASTA file was generated using the Samtools (v 1.9) (45), mpileup, Bcftools (v 1.9) (46), and SEQTK (https://github.com/lh3/seqtk).
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    For calling low frequency variants the viral read alignment file was realigned using the Viterbi method provided by LoFreq (v 2.1.2) (47).
    LoFreq
    suggested: (LoFreq, RRID:SCR_013054)
    Annotations of the variants was performed with SnpEff (v 4.3) (49) and SnpSift (v 4.3) (50).
    SnpEff
    suggested: (SnpEff, RRID:SCR_005191)
    SnpSift
    suggested: (SnpSift, RRID:SCR_015624)
    Phylogenetic analysis and inference of transmission lines: Phylogenetic analysis was conducted using the Augur package (version 7.0.2) (51).
    Augur
    suggested: None
    We reconstructed the phylogeny with the augur pipeline using IQ-Tree (52) and further processed the resulting trees with treetime to infer ancestral traits of the nodes (53).
    IQ-Tree
    suggested: (IQ-TREE, RRID:SCR_017254)
    The consequence type of the mutations was annotated using a customized implementation of the Ensembl Variant Effect Predictor (VEP version 92) using the first SARS-CoV-2 sequenced genome (NCBI ID: NC_045512v2) as a reference.
    Ensembl Variant Effect Predictor
    suggested: None
    Variant
    suggested: (VARIANT, RRID:SCR_005194)

    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.

    About SciScore

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