Measuring Basic Reproduction Number to Assess Effects of Nonpharmaceutical Interventions on Nosocomial SARS-CoV-2 Transmission

George Shirreff; Jean-Ralph Zahar; Simon Cauchemez; Laura Temime; Lulla Opatowski


Emerging Infectious Diseases. 2022;28(7):1345-1354. 

In This Article

Abstract and Introduction


Outbreaks of SARS-CoV-2 infection frequently occur in hospitals. Preventing nosocomial infection requires insight into hospital transmission. However, estimates of the basic reproduction number (R0) in care facilities are lacking. Analyzing a closely monitored SARS-CoV-2 outbreak in a hospital in early 2020, we estimated the patient-to-patient transmission rate and R0. We developed a model for SARS-CoV-2 nosocomial transmission that accounts for stochastic effects and undetected infections and fit it to patient test results. The model formalizes changes in testing capacity over time, and accounts for evolving PCR sensitivity at different stages of infection. R0 estimates varied considerably across wards, ranging from 3 to 15 in different wards. During the outbreak, the hospital introduced a contact precautions policy. Our results strongly support a reduction in the hospital-level R0 after this policy was implemented, from 8.7 to 1.3, corresponding to a policy efficacy of 85% and demonstrating the effectiveness of nonpharmaceutical interventions.


Despite sweeping control measures, SARS-CoV-2 continues to pose a major threat to older persons and persons with comorbidities, both of whom can have poorer clinical outcomes.[1,2] Thus, hospitals and long-term care facilities (LTCFs) must be particularly vigilant to prevent the spread of SARS-CoV-2 infection among their patients. Nosocomial spread has been an issue since the pandemic began in 2020, and many outbreaks have occurred in hospitals and healthcare facilities, often with high attack and mortality rates.[3]

To control nosocomial spread, healthcare facilities have progressively implemented preventive measures, such as generalized masking, testing campaigns among patients and staff, isolation, visitor restrictions,[3] and more recently vaccination.[4] However, the risk for viral transmission among hospital patients and staff and the effectiveness of control measures remain unclear, and outbreaks still occur.[3,5,6]

The basic reproduction number (R0) refers to the number of secondary infections caused by a single index infection in an otherwise susceptible population. R0 has been widely used as an indicator of SARS-CoV-2 epidemic risk and has also proved valuable for evaluating testing strategies and other preventive measures within healthcare settings.[7,8] R0 likely varies between types of healthcare facilities and differs considerably from estimates in the general community.[9] However, estimating R0 in healthcare settings is more challenging than estimating R0 in the community. The populations in institutions are small and epidemics are highly stochastic. More data usually are available from hospitals or wards that have more cases. Healthcare facilities rarely test patients randomly or at multiple times during their hospitalizations. Most available data from hospital outbreaks consist of distributions of positive tests over time in a context of evolving testing policy and capacity.

At the beginning of the pandemic, most countries had no standard strategy or recommendation on how surveillance should be carried out and tests distributed. Testing was mostly conducted on symptomatic patients, and surveillance consisted of possible contact tracing around detected cases. However, unreported asymptomatic cases could represent a substantial fraction of transmissions, and little data on the testing policy are available to estimate how many cases fell through the gaps.

Here, we propose a new framework to analyze detailed hospital test data by using a stochastic transmission model explicitly accounting for testing policy. We estimated R0 in the context of a large SARS-CoV-2 outbreak in a LTCF. The outbreak had a high initial R0, and we reconstructed the unobserved epidemic to assess effectiveness of nonpharmaceutical interventions.