National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel

  1. Itay Bar-Or
  2. Victoria Indenbaum
  3. Merav Weil
  4. Michal Elul
  5. Nofar Levi
  6. Irina Aguvaev
  7. Zvi Cohen
  8. Virginia Levy
  9. Roberto Azar
  10. Batya Mannasse
  11. Rachel Shirazi
  12. Efrat Bucris
  13. Orna Mor
  14. Alin Sela Brown
  15. Danit Sofer
  16. Neta S. Zuckerman
  17. Ella Mendelson
  18. Oran Erster

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Abstract

In this report, we describe a national-scale monitoring of the SARS-CoV-2 (SC-2) variant dynamics in Israel, using multiple-time sampling of 13 wastewater treatment plants. We used a combination of inclusive and selective quantitative PCR assays that specifically identify variants A19/A20 or B.1.1.7 and tested each sample for the presence and relative viral RNA load of each variant. We show that between December 2020 and March 2021, a complete shift in the SC-2 variant circulation was observed, where the B.1.1.7 replaced the A19 in all examined test points. We further show that the normalized viral load (NVL) values and the average new cases per week reached a peak in January 2021 and then decreased gradually in almost all test points, in parallel with the progression of the national vaccination campaign, during February–March 2021. This study demonstrates the importance of monitoring SC-2 variant by using a combination of inclusive and selective PCR tests on a national scale through wastewater sampling, which is far more amendable for high-throughput monitoring compared with sequencing. This approach may be useful for real-time dynamics surveillance of current and future variants, such as the Omicron (BA.1, BA.2) and other variants.

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  1. Version published to 10.3390/v14061229
  2. ScreenIT

    SciScore for 10.1101/2021.12.26.21268420: (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
    The reaction was run using Bio-Rad CFX96 instrument (https://www.bio-rad.com/en-us/product/cfx96-touch-real-time-pcr-detection-system?ID=LJB1YU15).
    https://www.bio-rad.com/en-us/product/cfx96-touch-real-time-pcr-detection-system
    suggested: (Bio-Rad CFX96 Real-Time PCR Detection System, RRID:SCR_018064)
    Analysis of the results were performed using the Bio-Rad CFX Maestro software (https://www.bio-rad.com/en-us/product/cfx96-touch-deep-well-real-time-pcr-detection-system?ID=LZJTUJ15). 2.5.
    Bio-Rad CFX Maestro
    suggested: None
    CFX
    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: 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.

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

    About SciScore

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  3. Version published to 10.1101/2021.12.26.21268420v1 on medRxiv