Workpackage 1

Risk assessment and risk-based strategies for sample and data collection

WP leader: Emma Snary, DEFRA/APHA (10)
co-leader: Christian Gortazar, UCLM (18)

Overall task: To develop risk assessment models and risk-based sampling and data collection strategies for NGS-based analyses of foodborne and (re-) emerging infections.

1. To develop methodology for risk assessment including NGS outputs:

1.1 To develop a generic and spatial risk assessment framework to identify which regions and species are at an increased risk of incursion and further spread of novel pathogens.

1.2 To develop a generic food chain risk assessment framework based on NGS data.

1.3 To develop tools for epidemiological transmission modeling and rapid spatial risk assessment.

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. As part of this task, a review of automated tools for rapid assessment of key transmission parameters and rates of spread estimates has been undertaken and will be made available in the Library.

2. To develop risk-based sampling algorithms and data collection strategies for early detection and investigation of unusual patterns of infectious disease outbreaks: in the fields of Task 2.1) unusual clinical symptoms in humans and domestic animals in medical and veterinary practice; Task 2.2) early detection of emerging and re-emerging infections coming from wild or feral animals; Task 2.3) human pathogen circulation in the absence of recognized illness; and Task 2.4) food-level sampling strategies for surveillance as well as foodborne outbreak investigation.

Understanding the extent of current sampling of food, human and animal populations, 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. An inventory of existing, and where possible harmonised, sampling 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.


Emma Snary
Animal and Plant Health Agency


Christian Gortazar
Universidad de Castilla - La Mancha
14 DECEMBER 2018