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Applying modern analytical techniques to historical outbreaks enhances our understanding of past pandemics. Thanks to @charlotteperlant.bsky.social and our coauthors @fxweill.bsky.social, @paolobosetti.bsky.social and Mirabelle Scipioni !

In Apr-Jun, transmissions concentrated around Paris, mostly with short-range events. In Jul-Sep, long-range transmissions drove the spread to the north, where local hubs formed. Mean transmission distance declined in Oct. We estimate cholera was introduced in 10 major ports from outside France.

Spread was well captured by a gravity model, highlighting human mobility's role. Transmission rose by 2.5-fold in Aug., compensated by a drop in duration of infectivity of municipalities, likely due to interventions. Commercial ports played a key role both as points of introduction/local hubs.

The epidemic started in April in Paris area and expanded mostly to the North of France, with a peak in September. Infected municipalities clustered around major commercial ports.

The report provides a linelist of >4000 cholera deaths that occurred across France, along with detailed descriptions of control measures and maps documenting local outbreaks.

Simplicity is a key strength of the package: it only takes a few lines of code to run and compare different types of models! Dev by Nathanael Hoze, with contributions from Marga Pons, @jessmetcalf.bsky.social, @mtwhite.bsky.social, @hsalje.bsky.social.

Rsero is useful to determine optimal designs for serosurveys depending on context. For example, should you target the general population, children <10y.o. or <20y.o.? This will depend on the expected annual probability of infection (FOI)...

You can also use Rsero to evaluate the impact of interventions, here mass drug administration on Trachoma prevalence in Nepal.

Rsero can assess how infection risk may vary with individual characteristics, e.g. gender and location.

Rsero can help you determine if your data are more consistent with a scenario of endemic ‘constant’ circulation, or with the occurrence of 1, 2 or 3 outbreaks in the last 50 years. It can estimate the year when these outbreaks occurred.

Done!