Cresswell, R., Augustin, D., Bouros, I., Farm, H. J., Miao, S., Ahern, A., Robinson, M., Lemenuel-Diot, A., Gavaghan, D. J., Lambert, B. and Thompson, Robin N. (2022) Heterogeneity in the onwards transmission risk between local and imported cases affects practical estimates of the time-dependent reproduction number. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380 (2233). 20210308. doi:10.1098/rsta.2021.0308 ISSN 1364-503X.

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Abstract

During infectious disease outbreaks, inference of summary statistics characterizing transmission is essential for planning interventions. An important metric is the time-dependent reproduction number (Rt), which represents the expected number of secondary cases generated by each infected individual over the course of their infectious period. The value of Rt varies during an outbreak due to factors such as varying population immunity and changes to interventions, including those that affect individuals' contact networks. While it is possible to estimate a single population-wide Rt, this may belie differences in transmission between subgroups within the population. Here, we explore the effects of this heterogeneity on Rt estimates. Specifically, we consider two groups of infected hosts: those infected outside the local population (imported cases), and those infected locally (local cases). We use a Bayesian approach to estimate Rt, made available for others to use via an online tool, that accounts for differences in the onwards transmission risk from individuals in these groups. Using COVID-19 data from different regions worldwide, we show that different assumptions about the relative transmission risk between imported and local cases affect Rt estimates significantly, with implications for interventions. This highlights the need to collect data during outbreaks describing heterogeneities in transmission between different infected hosts, and to account for these heterogeneities in methods used to estimate Rt.

Item Type:	Journal Article
Subjects:	Q Science > QR Microbiology R Medicine > RA Public aspects of medicine R Medicine > RC Internal medicine
Divisions:	Faculty of Science, Engineering and Medicine > Science > Mathematics
Library of Congress Subject Headings (LCSH):	COVID-19 (Disease) , COVID-19 (Disease) -- Transmission -- Mathematical models, Communicable diseases -- Epidemiology -- Mathematical models, Viruses -- Reproduction
Journal or Publication Title:	Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
Publisher:	The Royal Society Publishing
ISSN:	1364-503X
Official Date:	3 October 2022
Dates:	Date Event 3 October 2022 Published 15 August 2022 Available 4 May 2022 Accepted
Volume:	380
Number:	2233
Article Number:	20210308
DOI:	10.1098/rsta.2021.0308
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Date of first compliant deposit:	4 May 2022
Date of first compliant Open Access:	5 May 2022
RIOXX Funder/Project Grant:	Project/Grant ID RIOXX Funder Name Funder ID EP/V053507/1 UK Research and Innovation http://dx.doi.org/10.13039/100014013 EP/S024093/1 [EPSRC] Engineering and Physical Sciences Research Council http://dx.doi.org/10.13039/501100000266 Clarendon Fund Oxford University UNSPECIFIED UNSPECIFIED Roche Pharmaceutical https://www.roche.co.uk/
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