Rapid genome surveillance of SARS-CoV-2 and study of risk factors using shipping container laboratories and portable DNA sequencing technology

  1. Sara Farahi Bilooei
  2. Dejana Jovicevic
  3. Arash Iranzadeh
  4. Anthony Thomas
  5. Ivan Muscat
  6. Cynthia Mpofu
  7. Helene Steiner
  8. Thomas Meany

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Abstract

In this paper we report on genome sequencing of 154 SARS-CoV-2 samples between June and July 2021 (Summer outbreak) in the Bailiwick of Jersey, a UK channel island. We have analysed extensive data collected on 598,155 RT-qPCR tests that identified 8,950 positive cases as part of public health surveillance from September 2020 to August 2021. Our study implemented an amplicon-based sequencing approach using the Oxford Nanopore Technology (ONT) portable device. This revealed the emergence of twelve AY sublineages and were clustered into the Delta sub-clades 21I and 21J. This was integrated alongside an existing RT-qPCR diagnostic laboratory to provide a sample-to-sequence turnaround time of approximately 30 hours with significant scope for optimisation. Owing to the geographic remoteness of the island from large scale sequencing infrastructure, this presents an opportunity to provide policy makers with near real-time sequencing findings. Our analysis suggests that age and sex remained a substantial risk factor for mortality. We observe viral loads are higher in advanced ages and unvaccinated individuals. The median age of SARS-CoV-2 positive individuals was higher during winter than the summer outbreak, and the contact tracing program showed that younger individuals stayed positive for longer.

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  1. ScreenIT

    SciScore for 10.1101/2022.02.25.22271277: (What is this?)

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

    Table 1: Rigor

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

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Basecalling, assembly, and variant calling: Basecalling was performed on fast5 raw sequence data generated with MinION MK1C using Guppy v.4.2.2 (ONT) with the high-accuracy base-call setting (model dna_r9.4.1_450bps_hac).
    MinION
    suggested: (MinION, RRID:SCR_017985)
    Frameshift mutations and misplaced stop codons were polished manually by aligning genomes to the reference using MAFFT 30 and visualising the alignment files by Aliview 31.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)

    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:
    This study has several limitations. The samples selected for sequencing only contained Ct values below 30, as it is difficult to sequence very low viral load samples. The sex of individual positive cases was missing, and only total positive cases for each month were considered. The vaccine status of positive cases in the community was unknown and therefore was not considered in the Ct value study. Infected inbound passenger individuals with either 1 or 2 doses of vaccine were categorised in one group. We compared the median Ct value of the summer outbreak to winter; however, the community’s variants during summer can not be confirmed. While the dominant variant present during winter in the UK is the Alpha variant, this can not be confirmed as no sequencing has been carried out on samples during that time.

    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.

    Results from scite Reference Check: We found no unreliable references.

    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 10.1101/2022.02.25.22271277 on medRxiv