Epidemiological Datasets

Inventory of harmonised sampling and storage protocols
Reina Sikkema, Lineke Begeman, Lidewij Wiersma, Stephanie Lim, Marion Koopmans, Thijs Kuiken

An inventory of existing, and where possible harmonised, protocols has been developed in order to map the types of samples that are currently recommended at the EU or international level for known diseases of public and veterinary health importance. This approach provides a foundation for the development of novel risk-based sampling algorithms and protocols described in Workpackage 1. It represents a first step in achieving the COMPARE objective to improve the rapid identification of emerging infectious diseases, and allows for the exploration of novel integrated forms of surveillance for emerging infectious disease (EID). Understanding the extent of current sampling of food, human and animal populations through this inventory of known, and in some cases, notifiable pathogens helps to predict the characteristics of samples that are likely to be supplied or made available through existing surveillance systems. If known/notifiable pathogens are not identified upon conventional analysis of these samples, the samples may become the substrate for NGS laboratory protocols that are the subject of COMPARE Workpackage 2.

Available soon
Any comments, please contact Reina S. Sikkema, r.sikkema@erasmusmc.nl

Automated tools for rapid assessment of key transmission parameters and rates of spread estimates
Bram van Bunnik, Mark Woolhouse
Version:  18/09/2017

An aim within Workpackage 1 is to search and catalogue tools for the rapid assessment of key transmission parameters and rate of spread estimates. Model-fitting in real time has proven potential to inform risk assessment and policy responses to outbreaks, provided there is rapid access to epidemiological and genome sequence data. Implementing these models for real-time outbreak use in the appropriate software (e.g. specific programming language or software program) for further use by others is often a job that requires specialist skills in programming and/or mathematics and can take up valuable time. In order to find out which tools (models / frameworks) are available, an online search was performed to identify relevant open-source models or modelling frameworks that can be readily used (or adapted) to investigate an outbreak situation. This catalogue was created of these models/frameworks and specific information on the models was extracted from the model/framework documentation to help identify the correct model for a specific situation.

Any comments, please contact bram.vanbunnik@ed.ac.uk


Emma Snary
Animal and Plant Health Agency
16 JULY 2024