Detection of SARS-CoV-2 infection by saliva and nasopharyngeal sampling in frontline healthcare workers: An observational cohort study

  1. Naomi F. Walker
  2. Rachel L. Byrne
  3. Ashleigh Howard
  4. Elissavet Nikolaou
  5. Madlen Farrar
  6. Sharon Glynn
  7. Katerina S. Cheliotis
  8. Ana I. Cubas Atienzar
  9. Kelly Davies
  10. Jesús Reiné
  11. Zalina Rashid-Gardner
  12. Esther L. German
  13. Carla Solórzano
  14. Tess Blandamer
  15. Lisa Hitchins
  16. Christopher Myerscough
  17. Bradford D. Gessner
  18. Elizabeth Begier
  19. Andrea M. Collins
  20. Mike Beadsworth
  21. Stacy Todd
  22. Helen Hill
  23. Catherine F. Houlihan
  24. Eleni Nastouli
  25. Emily R. Adams
  26. Elena Mitsi
  27. Daniela M. Ferreira
  28. on behalf of the SAFER investigators

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Abstract

The SARS-CoV-2 pandemic has caused an unprecedented strain on healthcare systems worldwide, including the United Kingdom National Health Service (NHS). We conducted an observational cohort study of SARS-CoV-2 infection in frontline healthcare workers (HCW) working in an acute NHS Trust during the first wave of the pandemic, to answer emerging questions surrounding SARS-CoV-2 infection, diagnosis, transmission and control.

Methods

Using self-collected weekly saliva and twice weekly combined oropharyngeal/nasopharyngeal (OP/NP) samples, in addition to self-assessed symptom profiles and isolation behaviours, we retrospectively compared SARS-CoV-2 detection by RT-qPCR of saliva and OP/NP samples. We report the association with contemporaneous symptoms and isolation behaviour.

Results

Over a 12-week period from 30 th March 2020, 40·0% (n = 34/85, 95% confidence interval 31·3–51·8%) HCW had evidence of SARS-CoV-2 infection by surveillance OP/NP swab and/or saliva sample. Symptoms were reported by 47·1% (n = 40) and self-isolation by 25·9% (n = 22) participants. Only 44.1% (n = 15/34) participants with SARS-CoV-2 infection reported any symptoms within 14 days of a positive result and only 29·4% (n = 10/34) reported self-isolation periods. Overall agreement between paired saliva and OP/NP swabs was 93·4% (n = 211/226 pairs) but rates of positive concordance were low. In paired samples with at least one positive result, 35·0% (n = 7/20) were positive exclusively by OP/NP swab, 40·0% (n = 8/20) exclusively by saliva and in only 25·0% (n = 5/20) were the OP/NP and saliva result both positive.

Conclusions

HCW are a potential source of SARS-CoV-2 transmission in hospitals and symptom screening will identify the minority of infections. Without routine asymptomatic SARS-CoV-2 screening, it is likely that HCW with SARS-CoV-2 infection would continue to attend work. Saliva, in addition to OP/NP swab testing, facilitated ascertainment of symptomatic and asymptomatic SARS-CoV-2 infections. Combined saliva and OP/NP swab sampling would improve detection of SARS-CoV-2 for surveillance and is recommended for a high sensitivity strategy.

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  1. Version published to 10.1371/journal.pone.0280908
  2. ScreenIT

    SciScore for 10.1101/2021.04.23.21255964: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: All participants provided written informed consent.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    The isolate REMRQ0001/human/2020/Liverpool propagated in VERO E6 cells and maintained as previously described (Patterson et al., 2020) was used for the serial dilutions.
    VERO E6
    suggested: None
    Software and Algorithms
    SentencesResources
    Statistical analysis: Analysis was in R (version 4.0.4) and Prism 8 (Graphpad).
    Graphpad
    suggested: (GraphPad, RRID:SCR_000306)

    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:
    Resource limitations reducing access to routine diagnostic testing possibly impacted on staff isolation and test-seeking behaviour in the first wave of the UK COVID-19 pandemic. Occupational testing first became available to symptomatic HCW at Liverpool University Hospitals NHS Foundation Trust on 2nd April 2020. However, presenteeism in HCW may be a contributory factor, even in the context of a global respiratory pandemic (Tartari et al., 2020). Clarification on and reinforcement of self-isolation and testing policies for HCW when symptomatic is advisable, especially given symptomatic infections are likely more transmissible (Buitrago-Garcia et al., 2020). Limitations of this study include some loss to follow up and withdrawal of participants with resulting missing data. However, the overall retention in the study was good (over 80% at week 8) and return of samples was overall high. There was possible inconsistency of self-sampling technique as participants were not supervised. Sample processing, which required one freeze-thaw cycle (NP swab) or two freeze-thaw cycles (saliva) prior to RNA extraction, possibly reduced the overall yield of the PCR assay. In summary, we report a high prevalence of SARS-CoV-2 infection in asymptomatic and symptomatic HCWs, attending work during the first wave of the COVID-19 pandemic in UK, as detected by saliva and NP surveillance sampling. However, there was limited agreement between the two sampling methods. Detection of SARS-CoV-2 by survei...

    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 10.1101/2021.04.23.21255964 on medRxiv