Transmission dynamics of SARS-CoV-2 in the hospital setting

  1. Yin Mo
  2. David W. Eyre
  3. Sheila F. Lumley
  4. Timothy M. Walker
  5. Robert H. Shaw
  6. Denise O’Donnell
  7. Lisa Butcher
  8. Katie Jeffery
  9. Christl A. Donnelly
  10. Oxford COVID infection review team
  11. Ben S. Cooper

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Abstract

Background

SARS-CoV-2 can spread efficiently in hospitals, but the transmission pathways amongst patients and healthcare workers are unclear.

Methods

We analysed data from four teaching hospitals in Oxfordshire, UK, from January to October 2020. Associations between infectious SARS-CoV-2 individuals and infection risk were quantified using logistic, generalised additive and linear mixed models. Cases were classified as community- or hospital-acquired using likely incubation periods.

Results

Nine-hundred and twenty of 66184 patients who were hospitalised during the study period had a positive SARS-CoV-2 PCR test within the same period (1%). Out of these, 571 patients had their first positive PCR tests while hospitalised (62%), and 97 of these occurred at least seven days after admission (11%). Amongst the 5596 healthcare workers, 615 (11%) tested positive during the study period using PCR or serological tests. For susceptible patients, one day in the same ward with another patient with hospital-acquired SARS-CoV-2 was associated with an additional eight infections per 1000 susceptible patients (95%CrI 6-10). Exposure to an infectious patient with community-acquired COVID-19 or to an infectious healthcare worker was associated with substantially lower infection risks (2/1000 susceptible patients/day, 95%CrI 1-2). As for healthcare worker infections, exposure to an infectious patient with hospital-acquired SARS-CoV-2 or to an infectious healthcare worker were both associated with an additional one infection per 1000 susceptible healthcare workers per day (95%CrI 1-2). Exposure to an infectious patient with community-acquired SARS-CoV-2 was associated with half this risk (0.5/1000 susceptible healthcare workers/day, 95%CrI 0.3-0.7).

Interpretation

Exposure to patients with hospital-acquired SARS-CoV-2 poses a substantial infection risk. Infection control measures to limit nosocomial transmission must be optimised to protect both staff and patients from SARS-CoV-2 infection.

Funding

National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Oxford University in partnership with Public Health England (PHE) (NIHR200915). Medical Research Council, Nosocomial transmission of SARS-CoV-2 (MR/V028456/1).

Research in context

Evidence before this study

We searched the PubMed database using the search terms (”COVID-19” OR ”SARS-CoV-2”) AND (”nosocomial” OR ”hospital”) AND (”transmission”) in either the abstracts or titles, for English-language articles published up to March 31, 2021. This returned 748 results, out of which ten reported transmission events in the hospital setting quantitatively. These publications can be broadly categorised to epidemiological descriptions of isolated outbreaks (5) or contact tracing of patients exposed to infected healthcare workers (1), retrospective cohort studies involving a particular group of patients, e.g., patients who underwent surgical procedures (2), and using genomic sequencing to identify transmission clusters (2). None of the studies reported the comparative transmission rates of SARS-CoV-2 amongst patients and staff.

Added value of this study

This study reports the analysis of a large observational dataset collected from a group of hospitals in the UK over eight months, consisting of both hospitalised patients and healthcare workers. Based on these detailed individual-level data, we quantified the associations between patient and healthcare worker characteristics and risks for acquiring nosocomial SARS-CoV-2 infection after adjusting for their exposures to SARS-CoV-2. Over the study period, we describe how risk of acquisition changes both with calendar time and over a patient’s hospital stay. By linking the presence of infected and susceptible patients and healthcare workers by time and ward locations, we quantify the relative importance of the transmission pathways for both the susceptible patients and healthcare workers.

Implications of all the available evidence

Nosocomial transmission of SARS-CoV-2 is common. Identifying the drivers of SARS-CoV-2 transmissions in the hospital setting is essential for designing infection prevention and control policies to minimise the added pressure from such events on our health systems. We found that newly infected patients who acquired SARS-CoV-2 in the hospital pose the highest risk of onward transmission to other patients and healthcare workers. Infection control and prevention efforts need to be enhanced around these patients to prevent further transmissions and studies assessing the effectiveness of these policies are needed.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2021.04.28.21256245: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Deidentified patient data and data from HCW testing were obtained from electronic healthcare records using the Infections in Oxfordshire Research Database (IORD) which has generic Research Ethics Committee, Health Research Authority and Confidentiality Advisory Group approvals (19/SC/0403, 19/CAG/0144).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Additionally, probable infections prior to widespread availability of testing were identified in staff without a positive PCR result, but who were either anti-nucleocapsid or anti-spike IgG antibody positive and recalled a date of onset of symptoms consistent with COVID-19.
    anti-nucleocapsid
    suggested: None
    anti-spike IgG
    suggested: None

    Results from OddPub: Thank you for sharing your code.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    There are several limitations in our analysis. Firstly, the dates on which the infected patients first developed symptoms were not available. Hence, we needed to assume that the PCR test swabs were taken on the symptom onset dates. While this assumption is reasonable based on the analysis of a subset of data early in the pandemic, it is not true from phase three onwards when weekly screening of patients regardless of symptoms was implemented. We addressed this by performing sensitivity analysis comparing model outputs when using data collected during phase one and two versus phase three (supplementary material section 5). Secondly, we assumed that HCW were absent from work after the dates on which their first positive PCR test swabs were taken or COVID-19 symptoms were first self-reported. However, where HCW experienced minimal or no symptoms they may have continued to work. These issues could be further explored using HCW absentee data in subsequent analysis. A key challenge in this analysis is that the times of infection are unknown. This has led to the adoption of various arbitrary cut-offs on length of stay prior to infection to define nosocomial infection. Further analysis using data augmentation methods may potentially overcome this to produce estimates that better account for different sources of uncertainty. Other drivers of SARS-CoV-2 transmissions in the hospital setting not fully explained by infection pressures, which we did not capture in the analysis, may includ...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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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  2. Version published to 10.1101/2021.04.28.21256245v1 on medRxiv