Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA

This is the repository associated with the paper "Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA" Nature Communications (2022).

We investigated whether sentinel surveillance of recently symptomatic individuals receiving an outpatient diagnostic test for SARS-CoV-2 infection could accurately assess the instantaneous reproductive number R(t) and provide early warning of changes in transmission.

Figure 1. Timing of indicators relative to infection.

• Reliable indicators of SARS-CoV-2 transmission and infection prevalence are necessary for timely intervention
• Case-based indicators (e.g. incident cases in the general population) are subject to bias due to differences in access to and demand for testing^1,3
• Hospital-based indicators (e.g. emergency department visits, hospitalizations) lag infection by several weeks^1,2,4,5
• Symptom onset occurs relatively soon after infection and symptomatic individuals are far more likely to receive a diagnostic test^1,2,3

References

1. Evaluating Data Types: A Guide for Decision Makers using Data to Understand the Extent and Spread of COVID-19. 2020, The National Academies Press. 15.
2. Lauer, S.A., et al., Annals of internal medicine, 2020. 172(9): p. 577-582.
3. Brauner, J.M., et al., Science, 2021. 371(6531): p. eabd9338
4. Faes, C., et al., International journal of environmental research and public health, 2020. 17(20): p. 7560
5. Hawryluk, I., et al Journal of the Royal Society Interface 17.172 (2020): 20200596.