The Impact of Cocirculating Pathogens on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/Coronavirus Disease 2019 Surveillance: How Concurrent Epidemics May Introduce Bias and Decrease the Observed SARS-CoV-2 Percentage Positivity

  1. Aleksandra Kovacevic
  2. Rosalind M Eggo
  3. Marc Baguelin
  4. Matthieu Domenech de Cellès
  5. Lulla Opatowski

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Abstract

Background

Circulation of seasonal non–severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) respiratory viruses with syndromic overlap during the coronavirus disease 2019 (COVID-19) pandemic may alter the quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures.

Methods

Using a multipathogen susceptible-exposed-infectious-recovered (SEIR) transmission model formalizing cocirculation of SARS-CoV-2 and another respiratory virus, we assessed how an outbreak of secondary virus may affect 2 COVID-19 surveillance indicators: testing demand and positivity. Using simulation, we assessed to what extent the use of multiplex polymerase chain reaction tests on a subsample of symptomatic individuals can help correct the observed SARS-CoV-2 percentage positivity and improve surveillance quality.

Results

We find that a non–SARS-CoV-2 epidemic strongly increases SARS-CoV-2 daily testing demand and artificially reduces the observed SARS-CoV-2 percentage positivity for the duration of the outbreak. We estimate that performing 1 multiplex test for every 1000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percentage positivity.

Conclusions

This study showed that cocirculating respiratory viruses can distort SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex polymerase chain reaction tests, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.

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  1. Version published to 10.1093/infdis/jiab459
  2. ScreenIT

    SciScore for 10.1101/2021.06.08.21258533: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    R (version 4.0.3) and RStudio (version 1.3.1093) were used for modelling transmission, testing, and all statistical analyses [25, 26].
    RStudio
    suggested: (RStudio, RRID:SCR_000432)

    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:
    To keep our model simple, the mechanisms are a simplification of the real processes, and therefore, there are limitations. We did not incorporate testing capacity within this model, and we assumed that all symptomatic individuals requesting testing on a given day will be able to do so. Additionally, we assumed that interactions between viruses were neutral, meaning that the presence of one of the viruses did not affect (promote nor protect against) infection with the other virus. Recent studies have suggested some possible protection from COVID-19 infection conferred by rhinovirus interference with SARS-CoV-2 replication kinetics and this may warrant further exploration at the population level [33]. We proposed a method to correct the observed positivity rate of SARS-CoV-2 during an outbreak of another respiratory virus, to help reduce the overall underestimation of SARS-CoV-2 in the population. Clinical sensitivities between tests can differ markedly depending on the test manufacturer and in the case of multiplex PCR testing, sensitivity also depends on the pathogen being detected [30, 34]. With the overall high sensitivity of both SARS-CoV-2 and multiplex PCR tests, correcting the observed positivity rate could be a very effective way of minimizing the underestimation of the true COVID-19 burden in the community. Furthermore, multiplex testing, which in France is generally performed by ‘Sentinelles’ physicians on patients seen in the consultation to test for various respira...

    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.

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  3. Version published to 10.1101/2021.06.08.21258533v1 on medRxiv