This is a common space to all nominated participants of any training activity of the AURORAE Training Programme 2022-2025.
The overall objectives of the AURORAE trainings are to support countries in building capacities in the areas of diagnosis, detection, identification and characterisation of primarily influenza and SARS-CoV-2 viruses. Courses may include topics like diagnostic methods, molecular typing, sampling strategies for disease surveillance and for detection, use and limitation of test methods, testing strategies, test interpretation, bioinformatics, biosafety issues, shipment of infectious material, quality assurance, as well as capacity gaps identified through EQAs and/or surveys.
The training formats include face-to-face training courses (wetlab and drylab), twinning visits of various durations, and virtual trainings (webinars, instructive videos, self-paced online trainings).
It contains links to training events and to the respective training materials. Click here to read more about AURORAE.
- Face-to-face trainings (3-5 days).
- This type of training will give a broad overview and is therefore targeted to participants that will benefit most from such a broad competency training
- The learning objectives are related to influenza and/or SARS-CoV-2 public health laboratory methods and basic genomic epidemiology and bioinformatic essentials
- The aim is to offer one face-to-face training on influenza and one on SARS-CoV-2 per year
- Participants should have a microbiology or related background and familiar with common molecular techniques (such as PCR)
- Up to ten participants per course
- Twinning visits (2, 5 or 10 days)
- This type of training will give an in-depth focussed training on a selection of specific methods.
- For the twinning visits, usually one participant will visit a twinning institute for a tailored training. Therefore, the exact training content will depend on both the twinning institute and the participant and will be discussed and agreed before the start of the training.
- The learning objectives are related to influenza and/or SARS-CoV-2 public health laboratory methods and basic genomic epidemiology and bioinformatic essentials
- Virtual trainings
- Range of formats possible from webinars to instructional videos or self-paced online courses
- The learning objectives are related to influenza and/or SARS-CoV-2 public health laboratory methods and basic genomic epidemiology and bioinformatic essentials
- Virtual trainings will be hosted on the EVA platform
The European Centre for Disease Prevention and Control (ECDC) relies on the European Union (EU)/European Economic Area (EEA) Member States’ expertise and laboratory capacities to support its public health core functions and disease specific work within its mandate.
AURORAE is a consortium of 12 institutions in 8 EU/EEA member states that ECDC procured to provide support to microbiology-related activities and capacity building
focusing on COVID-19 and influenza in the EU/EEA, the Western Balkans and
Türkiye by providing:
- EQA and ring trial activities
- Centralised laboratory support for influenza and SARS-CoV-2 viruses in-depth characterisation for timely pandemic response
- Training activities for detection, characterisation and response.
By providing training and encouraging cooperation between expert and reference laboratories, ECDC aims to foster the development of sufficient capacity within the Community, enhance data sharing and collaborations between public health institutions and ECDC, and facilitate networking activities and cross-border collaborations.
AURORAE offers ECDC procured trainings that focus on influenza and SARS-CoV-2. The training programme was initiated in July 2022 and will continue over four years.
Experts of twelve institutes from eight European countries together were awarded a new framework contract by the ECDC in 2022, to provide "support to microbiology-related activities and capacity building focusing on COVID-19 and influenza in the EU/EEA, the Western Balkans and Türkiye. Laboratory support, training, and standardisation”. The consortium was named AURORAE (lAboratory sUppoRt fOr influenza and SARS coRonAvirus 2 for Europe) and activities started on 23rd June 2022 and will run over a four year period.
The Consortium is coordinated by National Institute for Public Health and the Environment (RIVM), Netherlands. The project coordinator is Adam Meijer (RIVM, Netherlands).
AURORAE is composed of the following institutes:
- Sciensano (SCIN), Belgium
- Institut Pasteur (IP), France
- Hospices Civils de Lyon (HCL), France
- Charité – Universitätsmedizin Berlin (CU), Germany
- Robert Koch-Institute (RKI), Germany
- Aristotle University of Thessaloniki (AUTH), Greece
- Hellenic Pasteur Institute (HPI), Greece
- Laboratoire National de Santé (LNS), Luxembourg
- National Institute for Public Health and the Environment (RIVM), Netherlands
- Erasmus University Medical Center Rotterdam (EMC), Netherlands
- Norwegian Institute of Public Health (NIPH), Norway
- National Institute of Health Dr. Ricardo Jorge (INSA), Portugal
- Professionals working in public health institutions with a background in public health microbiology or related and who are or will be involved in the molecular/genomic surveillance of influenza and/or SARS-CoV-2 viruses including laboratory assays for detection and characterisation of the viruses as well as production, handling, or analysis of next generation sequence data.
Participants should be part of the ECDC ERLI-Net and/or ECOVID-LabNet or a national public health institute or associated institute in countries of the EU/EEA, the Western Balkan (Albania, Kosovo, Montenegro, Serbia, North Macedonia, Bosnia and Herzegovina) or Türkiye.
- In due time before training activities are planned, ECDC will announce by email to the National Focal Points for viral respiratory diseases the opportunities to express interest in these training activities.
- Expressions of interest for participation are collected and a selection of participants is made by ECDC.
- Priority will be given to participants who have not yet participated in a recent ECDC or WHO funded course covering similar topics and based on training needs identified through past EQAs or surveys if applicable.
- More than one applicant from the same country will be accepted only based on available seats.
This is a common space to all nominated participants of any block of any wave of the Genetic Epidemiology Training Programme (GenEpi-BioTrain) 2023-2026.
It contains links to training events and to the respective training materials. Click here to read more about GenEpi-BioTrain.
Information session 20 October 2023.
- Face-to-face workshops “Bridging the gaps in bioinformatics” (2 weeks).
- The objective of this training is to strengthen programming knowledge and skills, database management, use and development of bioinformatic tools and increase awareness about application for use in the public health context
- Trainees have basic/limited bioinformatics skills
- The curriculum covers overview of sequencing technologies, genome assembly and analysis, QC, coding best practices, pipeline development, etc.
- Face-to-face workshops “Interdisciplinary genomic epidemiology and public health bioinformatics” (2 weeks)
- The aim is to improve the knowledge of and capacity for applied genomic epidemiology and bioinformatics for public health action
- Each workshop may include up to ten “country teams” of one bioinformatician, one microbiologist, one epidemiologist to promote the collaboration of inter-disciplinary teams within the public health institutions
- The curriculum will be developed around case studies (e.g. common outbreak scenarios) to be solved by leveraging on interdisciplinary collaboration
- Exchange visits for bioinformaticians (either one, two or three weeks)
- Participants from one EU/EEA country go to a public health institution of another EU/EEA country
- The trainee shall have clearly defined public health bioinformatics-related learning needs and goals that the exchange visit is expected to address.
- Face-to-face trainings on specific topics in genomic epidemiology and/or public health bioinformatics (3 days)
- Specific topics (to be defined according to training needs and interests from Member States) in genomic epidemiology aimed at different proficiency levels.
- Virtual training sessions/webinars (1 day or 2 half-days)
- Specific topics (to be defined according to training needs and interests from Member States) in genomic epidemiology aimed at different proficiency levels.
Since 2021, ECDC in collaboration with the European Commission has made substantial investments to increase the capacity of Member States public health laboratories to perform whole genome sequencing (WGS) and reverse transcription polymerase chain reaction (RT-PCR) (ECDC supports EU/EEA Member States in rapid detection of SARS-CoV-2 variants (europa.eu)).
To ensure efficient use of WGS infrastructure investments and to further strengthen Member States laboratory capacity, ECDC offers a training programme in genomic epidemiology and public health bioinformatics. The programme is launched in parallel to the WGS infrastructure support and should facilitate the use of genomic data in EU level surveillance and outbreak response.
The training programme, the “GenEpi-BioTrain”, was initiated in January 2023 and will continue over the next four years.
The contract project managers for the GenEpi-BioTrain are Rene Hendriksen, DTU (main) and Anders Rhod Larsen, SSI (deputy).
The consortium includes:
- DTU & SSI (DK),
- Institut Pasteur (FR),
- Research Centre Borstel (DE),
- THL (FI) and
- Karolinska Institutet & University Hospital (SE).
The overall objectives of the trainings are to support countries in building up their capacity in genomic epidemiology and bioinformatics for public health purposes, and to increase the interdisciplinary collaboration between bioinformaticians, epidemiologists and microbiologists within a country to facilitate the routine use of genomic information for surveillance, preparedness, and outbreak response. Activities shall also enhance data sharing and collaborations between public health institutions and ECDC, and enhanced networking activities will foster cross-border collaborations.
- To allow the professionals with a background in computational biology and bioinformatics to:
- enhance and extend their skills to strengthen their capacity in the field of public health bioinformatics.
- better understand the needs and concepts of epidemiology and public health microbiology, with a focus on the inputs and outputs needed by their counterparts (i.e., microbiologists, epidemiologists, professionals in public health surveillance and response) to take rapid and informed public health action.
- To allow the professionals without a background in computational biology/bioinformatics to:
- gain a better understanding of how genomic epidemiology can be applied in a public health context with special focus on how traditional and genomic data can be jointly analysed, interpreted and used for public health purposes.
- become more familiar with the concepts, formats and conventions commonly used in microbial genomics, and get a better understanding of how the structure and format of the data can be used to streamline the data analysis process.
- better understand the concepts behind and use of the most common bioinformatic tools and pipelines used for epidemiological analyses, including limitations and possible alternatives; and
- gain a better overview of the basic principles, options for and best practices of data storage, management and sharing, with a specific focus on sequencing data and associated metadata.
- To allow professionals with a background in microbiology and epidemiology to:
- enhance and extend their understanding of the field of public health bioinformatics.
- better understand the needs and concepts of bioinformatics, with a focus on the inputs and outputs needed by these counterparts to take rapid and informed public health action.
- Professionals working in public health institutions with a background in computational biology and bioinformatics who are/are going to analyse genomic data for public health surveillance purposes. This group may come from diverse backgrounds and fields of study, including bioinformatics, biology, computer science, biochemistry, microbial genomics, metagenomics, algorithm development, microbiology, molecular genetics, biomedical sciences, forensic biology, comparative and molecular bioscience, epidemiology etc; and
- Professionals working in public health institutions who do not have a specific background in bioinformatics but need to understand and interpret genomic data for surveillance (i.e. microbiologists, epidemiologists, professionals in public health response and surveillance).
The ECDC will liaises with the National Focal points for Microbiology in coordination with National Focal Points of relevant disease groups are kindly invited to select participants.
All training materials produced to deliver the training activities of this programme will be made available in the Library of Training Materials after events take place. Anyone can consult these materials, learn from them and share and adapt them to teach others. The materials are ECDC property and licenced as Creative Commons (CC BY 4.0). Read here more about licencing.