If the reproduction number isn't so useful when case numbers are very low, what other metrics can we look at? 1/
(By 'very low' case numbers, I'm talking about a handful of reported cases per day. When we adjust for under-reporting, many European countries probably still have thousands of cases per day, so unfortunately R is still very relevant.) 2/
One useful metric at low numbers is the proportion of cases that can be linked to known outbreak clusters. It's clearly more concerning to have 20 scattered local cases that don't have clear sources than a cluster of 20 linked cases that can all be traced to an imported case. 3/
Detailed contact tracing and phylogenetic data (e.g. nejm.org/doi/full/10.10…) can both be useful here, helping identify cases that aren't linked, and hence could represent undetected chains of transmission 4/
If there's a new flare up, it's also possible to use detailed contact tracing data to estimate the distribution of secondary cases (i.e. the individual-level version of R) before the flare up was brought under control nature.com/articles/natur… 5/
If individual-level transmission is particularly high in certain settings, it may point to interactions that could be changed to reduce risk. Reducing this potential superspreading could also enhance effectiveness of contact tracing, as we outline here medrxiv.org/content/10.110… 6/6
