Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic

  1. Wenjuan Zhang
  2. John Paul Govindavari
  3. Brian D. Davis
  4. Stephanie S. Chen
  5. Jong Taek Kim
  6. Jianbo Song
  7. Jean Lopategui
  8. Jasmine T. Plummer
  9. Eric Vail

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Abstract

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  1. Version published to 10.1001/jamanetworkopen.2020.24191
  2. ScreenIT

    SciScore for 10.1101/2020.06.12.20129999: (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
    Duplicated reads are labelled with Picard (http://broadinstitute.github.io/picard/) and BCFtools14 was used to generate consensus sequence.
    Picard
    suggested: (Picard, RRID:SCR_006525)
    Multiple sample alignment (MSA) was performed with MAFFT (v7.464)15 and phylogenetic tree was generated with FastTree (v2.1)16 implementing generalized time-reversible (GTR) model.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    FastTree
    suggested: (FastTree, RRID:SCR_015501)

    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:
    A caveat to our sample collection is that the emergency department admissions are less frequent for younger patients and biased to patients greater than 18 years old. Despite this, the average age of CSMC patients was ∼60 years old, which is consistent with other observations that older adults are susceptible to COVID1910. Patient samples by diagnostic RT-qPCR that had lower cycle numbers e.g. higher viral copies generally had poorer outcomes. Moreover, patients with higher viral loads detected by RT-qPCR also correlated to a higher percent SARS-CoV-2 genome coverage by sequencing. From a technical perspective, 48 of 192 patients which had poorer quality sequencing coverage (<50%) and also were diagnostically positive by RT-qPCR at >30 cycles. The remaining144 patients passed all quality control metrics for sequencing and alignment generally <25 cycles of RT-qPCR19. Hence, when using NGS approaches for diagnostic purposes, a potential caveat is that genome sequencing favors those patients with higher viral titers and may not capture those who have low viral copy numbers. The local phylogenetic tree demonstrated two large clusters which were mainly defined by six high frequency mutations. Phylogenetic analysis of these samples by collection date, reveals the main variants which define these two large clusters were observed throughout March and April and were present in the community prior to the collection start date. This study presents a snapshot of the molecular characteris...

    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.

  3. Version published to 10.1101/2020.06.12.20129999v1 on medRxiv