D2.1 Review of existing i) laboratory surveillance systems and ii) outbreak detection systems or methods of participating countries

This deliverable report summarizes the work carried out under Work Package (WP) 2 “Outbreak Detection” 
during the first ten months for task 1 and the first twelve months for task 2 of the Joint Action 
UNITED4Surveillance. Additionally, the report describes work that is still planned for the remainder of the project 
period. WP2 is divided into two tasks: task 1 “Improving Laboratory-Based Reporting”, covered in sections 
3 and 4, and task 2 “Outbreak and Signal Detection”, covered in section 5 and 6. 

Section 3.3.1 provides a high-level review/inventory of existing laboratory surveillance systems of seven 
countries that were active partners in this subtask (Denmark, Finland, Germany, Latvia, Netherlands, Norway and 
Slovenia). Countries provided information on the context of infectious disease surveillance in their country, 
described how laboratory-based surveillance is organized and which stakeholders are involved, elaborated on 
the data flow, reflected on challenges, needs and gaps and gave an outlook on planned developments to 
improve laboratory-based reporting in their national setting. 

Section 3.3.2 entails a description of results from a needs and gaps survey with respect to laboratory-based 
reporting across 23 countries of the UNITED4Surveillance consortium. The survey focused on general, legal, 
policy and organizational, technical [data and information technology (IT)], as well as financial aspects of 
laboratory-based surveillance. Concrete gaps in all surveyed aspects were identified that could be further 
explored and addressed in the future.

Section 4 describes the scope and status of national pilots that have been initiated in four countries (Denmark, 
Finland, Netherlands and Norway) with the aim to address previously identified gaps and thereby improve 
reporting of laboratory-based data. The pilots will be concluded in September 2024.

Section 5.3.1 entails a description of results from a needs and gaps survey regarding automated outbreak 
detection methods for routine surveillance data of infectious diseases. The survey was jointly developed by 
national public health institutes in Hungary, Lithuania, Spain and Germany. The survey covered questions on 
types of surveillance systems with existing automated outbreak detection tools including the methods and an 
overview of the systems with a potential for automated outbreak detection in 21 countries of the 
UNITED4Surveillance consortium. 

Section 5.3.2 and 5.3.4 provide preliminary results of the evaluation of outbreak detection methods and the 
tool development process. The tool is developed by data scientists from Austria, Denmark, Finland and Germany 
as an open source software process on GitHub in form of an R-package that contains a R-shiny app that can be 
used to perform signal detection on surveillance data. 

Section 6 gives a comprehensive overview of the pilot surveillance systems, in which the developed automated 
outbreak detection tool will be deployed from March 2024 onwards. The pilot countries includu Denmark, 
Finland, Hungary, Ireland, Malta, Netherlands, Poland, Slovenia, Latvia, Lithuania and Portugal. The identified use 
cases are mainly gastroenteritis and respiratory diseases.