High-Throughput Adaptable SARS-CoV-2 Screening for Rapid Identification of Dominant and Emerging Regional Variants

  1. Zita Hubler
  2. Xiao Song
  3. Cameron Norris
  4. Mehul Jani
  5. David Alouani
  6. Maureen Atchley
  7. Lisa Stempak
  8. Sarah Cherian
  9. Christine Schmotzer
  10. Navid Sadri

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Abstract

Objectives

Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant strains can be associated with increased transmissibility, more severe disease, and reduced effectiveness of treatments. To improve the availability of regional variant surveillance, we describe a variant genotyping system that is rapid, accurate, adaptable, and able to detect new low-level variants built with existing hospital infrastructure.

Methods

We used a tiered high-throughput SARS-CoV-2 screening program to characterize variants in a supraregional health system over 76 days. Combining targeted reverse transcription–polymerase chain reaction (RT-PCR) and selective sequencing, we screened SARS-CoV-2 reactive samples from all hospitals within our health care system for genotyping dominant and emerging variants.

Results

The median turnaround for genotyping was 2 days using the high-throughput RT-PCR–based screen, allowing us to rapidly characterize the emerging Delta variant. In our population, the Delta variant is associated with a lower cycle threshold value, lower age at infection, and increased vaccine-breakthrough cases. Detection of low-level and potentially emerging variants highlights the utility of a tiered approach.

Conclusions

These findings underscore the need for fast, low-cost, high-throughput monitoring of regional viral sequences as the pandemic unfolds and the emergence of SARS-CoV-2 variants increases. Combining RT-PCR–based screening with selective sequencing allows for rapid genotyping of variants and dynamic system improvement.

Article activity feed

  1. Version published to 10.1093/ajcp/aqab212
  2. Version published to 10.1101/2021.08.31.21262625v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.08.31.21262625: (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
    Data Analysis: For this study, variant call from the qPCR-based Variant Screen and the sequencing results were combined and analyzed using Excel, R, and GraphPad Prism.
    Excel
    suggested: None
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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:
    [15, 18] Nevertheless, monitoring variants by exclusively sequencing is not feasible for most clinical laboratories due to cost and resource limitations. Overall, neither qPCR screening nor unbiased population sequencing is optimized for detecting novel low-level variants on a regional basis which may delay the identification of emerging clinically important strains. To accommodate these limitations, we implemented a pipeline with a qPCR-based screen for the most common variants and subsequent sequencing of select samples. Examples of sequenced samples include: ambiguous qPCR expression profiles, clinically interesting cases, or quality control samples. Depending on available resources, sequencing can be performed in-house or commercially. In short, this tiered approach matches the strengths of each technology to the most informative samples. One significant advantage of the tiered approach is its dynamic feedback and iterative improvement. As the virus evolves, so too must the tests we use to detect it. In our workflow, the variant calling results are used to adjust the primers and the screening ruleset to reflect variability in the regional level of variants. For example, if a variant of concern is noted in another country, we can incorporate primers to detect it before the variant arrives in our population. Or, if a novel mutation is seen in the quality control samples from a dominant strain, the ruleset can be adjusted to account for the new subtype. The current setup wil...

    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

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  4. Version published to 10.1101/2021.08.31.21262625v1 on medRxiv