Early Identification of SARS-CoV-2 Emergence in the DoD via Retrospective Analysis of 2019-2020 Upper Respiratory Illness Samples

  1. Richard R. Chapleau
  2. Monica Christian
  3. Benjamin Connors
  4. Christa Premo
  5. Tim C. Chao
  6. Juan Rodriguez
  7. Shana Huntsberger
  8. Jennifer Meyer
  9. Amanda Javorina
  10. Kenney Reynolds
  11. David Riddle
  12. Mark Lisanby
  13. Clarise Starr

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Abstract

The first case of non-travel related SARS-COV-2 was detected late February 2020 in California, however the delay of diagnostic testing and initial stringent testing criteria made it difficult to identify those who could have acquired it through community spread. There was speculation by many that the virus may have been circulating at least a month earlier [1], and environmental sampling has suggested that versions of this virus were found many months before the first human samples were identified [2]. Here we performed a retrospective study from residual samples collected from a global DoD Respiratory Surveillance Program to establish a tentative timeline by which this virus was circulating in our DoD population. We performed RT-PCR for SARS-COV-2 and compared to the dates of these cases to the first cases identified in respective states and counties using the Johns Hopkins COVID tracker website. Twenty-four positive samples were identified out of approximately 7,000 tested. Although we found some early cases in certain regions, we did not see circulation before late February in samples collected both in the US and outside the USA.

SUMMARY

What is already known about this topic?

We know that the first reported case of SARS-COV-2 was mid-January; however, there has been conjecture that the virus was found in the community before this date.

What is added by this report?

Here we took samples collection from a global respiratory surveillance program and evaluated for the presence of SARS-COV-2 RNA. The first case we found in the surveillance program was approximately 30-60 days before the first case was identified on military installations via diagnostic testing, however was not earlier than the mid-January reported case in California.

What are the implications for public health practice?

The implementation of new and emerging pathogen detection assays into already established surveillance programs could detect early community spread and possibly reduce spread of pathogen among vulnerable populations.

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  1. ScreenIT

    SciScore for 10.1101/2021.02.18.21251368: (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:
    Due to early resource limitations in the global molecular testing supply chain, we began testing our early samples using the SYBRgreen detection method. Several of the samples ran out of material prior to establishing consistent supply chain provisions for probe-based detection using the CDC assay and Superscript real-time detection. One of these samples was the detected sample from late February. While we tested more than 7,000 samples, the number of independent test sites is small and heavily favored by one Service. We expected a high proportion of samples to originate from NORTHCOM facilities, as most of the DoD MTFs are located there, however representation overseas is limited with only ten Air Force installations and one Army installation. In a demonstration of collaboration, we did receive samples from six Coast Guard clinics, too. Additionally, we did not receive any samples from Southern Command and less than 10 samples from Central Command, so the impact of the epidemic in our military members stationed in those regions is unknown. In order to provide adequate surveillance during normal operations and epidemics, the Military Health System, and the Defense Health Agency by extension, must increase the participation of sentinel sites in the Respiratory Surveillance Program. With 475 military hospitals and medical clinics across the globe, the DoD is the only healthcare system that is equipped to monitor worldwide infectious diseases before they enter the homeland. The ...

    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 10.1101/2021.02.18.21251368 on medRxiv