Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19

  1. Giselle Ibette Lopez-Lopes
  2. Cintia Ahagon
  3. Margarete Aparecida Benega
  4. Daniela Bernardes Borges da Silva
  5. Valéria Oliveira Silva
  6. Katia Corrêa de Oliveira Santos
  7. Lincoln Spinazola do Prado
  8. Fabiana Pereira dos Santos
  9. Audrey Cilli
  10. Claudia Saraceni
  11. Núria Borges da Cruz
  12. Ana Maria Sardinha Afonso
  13. Maria do Carmo Timenetsky
  14. Luís Fernando de Macedo Brígido
  15. the IAL-COVID working group

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Abstract

Background

SARS-CoV-2 RNA detection with real time PCR is currently the central diagnostic tool to determine ongoing active infection. Nasopharyngeal and oral swabs are the main collection tool of biological material used as the source of viral RNA outside a hospital setting. However, limitation in swabs availability, trained health professional with proper PPE and potential risk of aerosols may hinder COVID diagnosis. Self-collection with swabs, saliva and throat wash to obtain oropharyngeal wash has been suggested as having comparable performance of regular swab. We performed throat wash (TW) based surveillance with laboratory heath workers and other employees (LHW) at a laboratory research institute.

Methods

Consecutive volunteer testing of LWH and external household and close contacts were included. TW self-collection was performed in 5 mL of sterile saline that was returned to original vial after approximate 5 secs of gargle. RNA extraction and rtPCR were performed as part of routine COVID protocols using Allplex (Seegene, Korea).

Results

Four hundred and twenty two volunteers, 387 (93%) LHW and 43 (7%) contacts participated in the survey. One or more positive COVID rtPCR was documented in 63 (14.9% CI95 12%-19%) individuals. No correlation was observed between with direct activities with COVID samples to positivity, with infection observed in comparable rates among different laboratory areas, administrative or supportive activities. Among 63 with detected SARS-CoV-2 RNA, 59 with clinical information, 58% reported symptoms at a median of 4 days prior to collection, most with mild disease. Over a third (38%) of asymptomatic cases developed symptoms 1-3 days after collection. Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs.

Conclusions

The study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. The proportion of asymptomatic and pre-symptomatic cases is elevated and reinforces the need of universal precautions and frequent surveys to limit the spread of the disease.

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  1. ScreenIT

    SciScore for 10.1101/2020.07.29.20163998: (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.
    Cell Line AuthenticationAuthentication: The extracted RNA (Bio Gene, Quibasa or by automated Extraction, Abbott M2000) was tested for COVID-19 using the commercial kit Allplex (Seegene, Korea), which is based on the Charité protocol (Corman, 2020).

    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 findings described here have to take these limitations into account. Another important point is the selection of throat wash (TW) as the mode of sample collection. The practicality of the method, previous local experience of its use for influenza and mumps, and literature support (Guo 2020, Saito 2020) were the main reasons for this choice. Saliva would also be an option (Azzi 2020), but swabs, the validated method for collection, was simply not available. Self-collection was performed in 5 mL of sterile saline that was returned to original vial after approximate 5 secs of gargle. The variability of this procedure in each volunteer and the fact that it was done without direct observation might had influence the results. We opt to use a lower volume, 5 mL, whereas the literature suggest up to 20mL (Guo 2020). We felt this volume was adequate and maybe provided a more concentrate wash. Volunteers from different areas of the institute participated in the study. One or more positive COVID rtPCR was documented in about 15% of case, 11% if only first testing is considered. This rates are higher than the “target levels” of 5 % (WHO 2020) for reopening services. It is also higher than some surveys among Health Care Workers in Italy, 2.3% (Lahner 2020) and US, 5% (Barrett 2020), but lower than that observed for some community outbreaks as in Washington, USA (Kimball 2020), where 30% residents had positive test results. The proportion of asymptomatic cases at this community study (...

    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

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  2. Version published to 10.1101/2020.07.29.20163998 on medRxiv