Investigating the origin of the Belgian second SARS-CoV-2 wave by using (pre)admission screening samples

  1. Reinout Naesens
  2. Laura Heireman
  3. Sarah Vandamme
  4. Philippe Willems
  5. Bruno Van Herendael
  6. Walter Verstrepen
  7. Pieter De Schouwer
  8. Peggy Bruynseels

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Abstract

The goal of this study was to estimate rates of SARS-CoV-2 carriership and viral loads in the general Antwerp population and to compare the estimated prevalences and incidences with governmental data (numbers of detected positive cases, stringency measure index) in order to evaluate the dynamics leading to the second wave. We used (pre)admission screening results from the major Antwerp hospitals for estimating community prevalences and incidences. 43.545 samples were included (April – November 2020). High SARS-CoV-2 carriership rates (mean week prevalence of 1.3%) were found in the general Antwerp population. 35.4% of positive cases carried high viral loads. Only a small proportion (15.3%) of the viral circulation was detected by the nationally implemented testing policy. In the weeks before the second Belgian wave, increasing prevalences and incidences were found, together with country-wide easing of restriction measures. In our opinion these findings have led to origin of the second viral wave.

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  1. ScreenIT

    SciScore for 10.1101/2020.12.09.20246462: (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

    No key resources detected.

    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:
    The limitations of this study include that (weak positive) asymptomatic cases could have corrresponded to previous infections with persistant existence of detectable RNA. This may have biased the results. However, the rapid decrease of positivity ratios after the implementation of extra measures (second pandemic wave) suggests we predominantly included active infections. Although the phenomenon of prolonged shedders does certainly exist, our data suggest that it is relatively insignificant and does not affect the major findings in this paper. Also, the median duration of positive results has been shown to be two to three weeks4. Another limitation is that we did not follow up positive/negative cases. We did not link the data to secondary COVID-19 cases, thus not establishing the contagiousness of positive cases. The screenings were linked to hospital procedures/admissions. Although we can accept these screenings as random samples from the community, the cohort is not a representative sample from the community: data points were not equally distributed in the Antwerp province, and age distributions were not representative for the Antwerp province (underestimation of younger age groups, and overestimation of older age groups). In conclusion, we found that SARS-CoV-2 was significantly present in the Antwerp province population in the period after the first wave. The virus circulated in all age groups with a predomincance in the elderly. 1.3% of the investigated cohort tested posi...

    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.

  2. Version published to 10.1101/2020.12.09.20246462 on medRxiv