I’m super happy to present a very cool project I’ve been working on with Alistair Antonopoulos and the BIOSECURE folks: PARAMETRA, a livestock pathogens parameters database that we just published. It’s a curated collection of epidemiological parameters for 20 livestock pathogens, in an effort to help modelers stop spending countless hours searching through literature for that transmission rate or test sensitivity value. Here, we have collected over 2,000 parameter values from published studies and plan to keep it growing.
In this heatmap, you can see an overview of the parameters available in PARAMETRA by pathogen. Not surprisingly, avian influenza and African swine fever had the highest number of modeling parameters published. Across all diseases, the most frequently reported disease parameters were basic reproduction number, transmission parameters from compartmental models, and test sensitivity and specificity.
PARAMETRA entries – By pathogen and parameter
Looking at the parameter references by year, we could see how articles reporting pathogen parameters tend to jump up after outbreaks happen, like with Coxiella burnetti after the Netherlands outbreak in 2008 or African Swine Fever after it appeared in Lithuania in 2014.
Articles referenced in PARAMETRA – By year and pathogen
In the next plot we can see the basic reproduction number (R0) of the pathogens included in the database. The values show huge variability because they were measured in different contexts and study types. This is why we encourage PARAMETRA users to look up the original articles for each parameter to better understand which values will be most appropriate for their models.
Basic reproduction number (R0) – By pathogen and study type
The gaps in PARAMETRA
Although we could find R0 values for most of this priority diseases, if you go back to the first plot, we also see lots of blank spaces, as some of these priority diseases (such as contagious agalactia) have little to no available information for many modelling parameters, making them nearly impossible to model in a quantitative way.
Now we’re calling on researchers to help fill these gaps! Some disease parameters may have escaped our literature review, others will likely be published in the future (or may have been published since January 2024). If you know of parameters that would be nice additions to PARAMETRA, please submit them through our PARAMETRA submission form. Our plan is to continue developing PARAMETRA into something useful for veterinary epidemiology modelers, updating and improving it over the coming years.
The publication
Antonopoulos, A., Ciria, N., Regan, Á., Tubay, J., Ciaravino, G., Hayes, B., Lambert, S., Vergne, T., Velkers, F., Biebaut, E., Viltrop, A., Dewulf, J., Charlier, J., Fischer, E., & Palau, A. A. (2025). PARAMETRA: A transmission modelling database for livestock diseases. Preventive Veterinary Medicine, 245, 106668. https://doi.org/10.1016/j.prevetmed.2025.106668
The website – biosecure-eu.github.io/parametra