The Coronavirus Calendar (CoronaCal): a Simplified SARS-CoV-2 Test System for Sampling and Retrospective Analysis

  1. David S. Thaler
  2. Manija A. Kazmi
  3. Karina C. Åberg
  4. Jordan M. Mattheisen
  5. Thomas Huber
  6. Thomas P. Sakmar

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Abstract

Background

The testing of saliva samples for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA has become a useful and common method to diagnose coronavirus disease 2019 (Covid-19). However, there are limited examples of serial testing with correlated clinical metadata, especially in the outpatient setting.

Method

We developed a method to collect serial saliva samples on ordinary white printer paper, which can be subsequently analyzed for the presence of SARS-CoV-2 RNA using established polymerase chain reaction (PCR) procedures. The collection systems consisted of a biological diary (CoronaCal) where subjects dab their saliva onto ovals printed onto paper. The dried samples are covered with a sticker that includes a symptom checklist to create a biological diary. Each sheet of letter paper can accommodate up to 14 serial samples.

Results

In a pilot study, ten subjects used CoronaCals for durations of nine to 44 days. SARS-CoV-2 RNA was extracted and detected in CoronaCals from nine of nine people with either Covid-19 symptoms or exposure to someone with Covid-19, and in zero of one asymptomatic person. The CoronaCals were stored for up to 70 days at room temperature during collection and then frozen for up to four months before analysis, suggesting that SARS-CoV-2 RNA is stable once dried onto paper. Interestingly, the temporal pattern of symptoms was not well correlated with SARS-CoV-2 RNA in serial daily collections for up to 44 days. In addition, SARS-CoV-2 positivity was discontinuous over time in most cases but persisted for up to 24 days.

Conclusions

We conclude that sampling of saliva on simple paper CoronaCals may provide a useful method to study the natural history and epidemiology of Covid-19. The CoronaCal collection and testing method we developed is also easy to implement, inexpensive, non-invasive, and scalable. More broadly, the approach can be used to archive biological samples for retrospective analysis to deepen epidemiological understanding during viral disease outbreaks and to provide information about the natural history of emerging infections.

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  1. ScreenIT

    SciScore for 10.1101/2022.03.03.22271769: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The protocol for the collection of the biological diaries described in this study was reviewed by the Institutional Review Board (IRB) at Rockefeller University and was deemed not to be human-subjects research.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Apparatus: The Agilent AriaMx qPCR instrument was used for RT-qPCR measurements.
    Agilent AriaMx
    suggested: (Agilent AriaMx Real-time PCR System, RRID:SCR_019469)

    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:
    One caveat is that not all testing detected both N1 and N2. In addition, the presence of small amounts of detectable SARS-CoV-2 RNA does not confirm the presence of infectious viral particles. The relationship between self-reported symptoms and SARS-CoV-2 RNA signal is of interest. Large studies have shown that positive PCR tests are not always associated with symptoms and conversely, that symptoms can occur during the absence of a PCR signal [12]. The CoronaCals presented here demonstrate these possibilities directly during the time courses of infections in individuals. The CoronaCal method relies totally on self-reporting and self-collection. The study team had no direct contact with the volunteer participants to instruct or influence their use of the diaries or to attempt to increase compliance. Although participants were provided with enough materials to collect up to 84 days of samples, the longest diaries collected were from 44 days. The shortest diary collected was for 10 days. Compliance is an issue for any self-collection and reporting system, and although compliance was not uniform, a tremendous amount of information could be obtained if the strategy were to be scaled-up to larger numbers of participants. In addition, more information could be obtained if participants could be interviewed, or if everyone in a particular household, for example, completed a CoronaCal diary contemporaneously. Such a study would require informed consent, however, and was not our aim for...

    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

    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 10.1101/2022.03.03.22271769 on medRxiv