Modeling within-host and aerosol dynamics of SARS-CoV-2: The relationship with infectiousness

  1. Nora Heitzman-Breen
  2. Stanca M. Ciupe

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Abstract

The relationship between transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the amount of virus present in the proximity of a susceptible host is not understood. Here, we developed a within-host and aerosol mathematical model and used it to determine the relationship between viral kinetics in the upper respiratory track, viral kinetics in the aerosols, and new transmissions in golden hamsters challenged with SARS-CoV-2. We determined that infectious virus shedding early in infection correlates with transmission events, shedding of infectious virus diminishes late in the infection, and high viral RNA levels late in the infection are a poor indicator of transmission. We further showed that viral infectiousness increases in a density dependent manner with viral RNA and that their relative ratio is time-dependent. Such information is useful for designing interventions.

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  1. Version published to 10.1371/journal.pcbi.1009997
  2. ScreenIT

    SciScore for 10.1101/2022.03.08.483569: (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
    We use the ’fminserach’ algorithm in matlab and the resulting estimates are given in Tables 1 and 2.
    matlab
    suggested: (MATLAB, RRID:SCR_001622)

    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:
    Our study has several limitations. We assumed that both infectious virus clearance and RNA degradation rates are known, with infectious virus clearance set at influenza levels c + d = 10 per day (corresponding to life-span of 2.4 hours) and the degradation rate set arbitrarily at d = 1 per day (corresponding to life-span of one day). Using sensitivity analysis we have found that changing the clearance rates to c + d = 15 and c + d = 5 does not influence the results (not shown). In all instances, however, the RNA degradation needs to be small, d = 1 or smaller, to explain the differences between infectious virus and viral RNA decay. Moreover, we had too include and estimate an additional removal of the aerosol infectious virus, which we assumed was due to infectious viral inactivation due to the elements. We have also considered that all neutralized virus leads to RNA production. Further information is needed to determine the biological processes leading to increased degradation of infectious virus in aerosols compared to upper respiratory tract and leading to the persistence of RNA in upper respiratory tract and aerosols after infectious virus is lost. Lastly, due to limited aerosol data in the females (with some subjects having just one data point above the limit of detection) we could not properly identify sex-specific differences and excluded this group from some of the analyses. In conclusion, we have developed a within-host and aerosol model for SARS-CoV-2 infection in g...

    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 10.1101/2022.03.08.483569v1 on bioRxiv