Infokiri

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European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

ECDC AURORAE training programme

2024 catalogue of ECDC AURORAE laboratory

influenza and SARS-CoV-2 trainings

This catalogue contains all laboratory influenza and SARS-CoV-2 in-person training course and twinning visit trainings which the ECDC is offering through the AURORAE programme in 2024. The training activities are endorsed and funded by the ECDC and conducted through the AURORAE consortium.

Expressions of interest for these training activities are collected through the EU survey tool under the following link:

https://ec.europa.eu/eusurvey/runner/EoI_2024_ECDC_InflSC2_training

The password to access the survey is “Training2024”.

The training activities are free-of-charge and accommodation, and travel arrangements will be covered by

ECDC through the AURORAE consortium framework contract.

All the trainings are subject to ECDC budget availability. All trainings will be held in English. Please find here a general description of the AURORAE training program for influenza and SARS-CoV-2 wet and dry laboratory trainings: https://eva.ecdc.europa.eu/course/view.php?id=816

If you have any further questions or remarks, please contact [email protected]

Training target audience:

The target audience of the training programme are professionals with background in microbiology or similar

fields. Eligibility criteria include:

• The participants should be or will be involved in the microbiological surveillance of respiratory viruses

(e.g. SARS-CoV-2 and/or influenza) and should be able to actively apply skills acquired as part of the training.

• The participants should be part of the European Influenza Surveillance Network (EISN) and/or

European COVID-19 surveillance network (ECOVID-Net) or must currently be employed in the public health sector in one of the EU/EEA countries, the Western Balkan (Albania, Kosovo, Montenegro,

Serbia, North Macedonia, Bosnia and Herzegovina) or Türkiye.

Training formats:

The training formats include face-to-face training courses (wetlab and drylab) and twinning visits of various

durations.

Face-to-face trainings.

• The in-person courses on wet-dry laboratory aspects of respiratory virus surveillance are designed for a

specific target audience of ten participants each.

2/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

• Please observe pre-requisites for participation and the expected expertise level for participation to

ensure all participants will benefit from an aligned learning experience.

Twinning visits

• One participant or trainer will visit the twinning institute for a tailored training. Therefore, the exact training content will depend on the participant and will be discussed and agreed before the start of the

training.

• This training allows for an in-depth focussed training on a selection of specific methods.

• It is expected that participants are already knowledgeable in the respective training content and fulfil the pre-requisites required for each training.

• The participants should use the visits to deepen their knowledge, exchange best-practise, and to be

enabled to cascade the training content at their home institutes.

Content

Content .................................................................................................................................................. 2

Face 2 face courses ................................................................................................................................. 3

Course Title: Summer school on respiratory viruses laboratory surveillance methods and reporting ...................... 3

Course Title: A practical introduction to NGS data analysis ........................................................................... 4

Course Title: Wet-/Dry-lab influenza virus NGS course ................................................................................. 5

Course Title: Influenza laboratory methods and reporting ............................................................................. 6

Course Title: Detection and typing of seasonal and zoonotic influenza ............................................................ 7

Twinning visits: 5 days ............................................................................................................................ 8

Course Title: SARS-CoV-2 whole genome sequencing and basic bioinformatics ................................................ 8

Course Title: Intensive 5-day training influenza surveillance laboratory methods and reporting ............................. 9

Twinning visits: 2 days .......................................................................................................................... 10

Course Title: Focused 2-day training on influenza surveillance laboratory methods and reporting ........................ 10

3/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Face 2 face courses

Course Title: Summer school on respiratory viruses laboratory surveillance methods and reporting

Format Face-to-face training for 10 participants

Dates/duration 26 June -02 July 2024 (5 working days summer school incl. weekend)

Location Hellenic Pasteur Institute, Athens, Greece

Description

Summer school of five-day training on respiratory viruses surveillance laboratory methods and reporting with a focus on influenza. The training will begin on a Wednesday and end on a Tuesday, thereby including a weekend with no training activities but time to network and explore nearby areas of Greece.

Objectives/intended learning outcomes

By the end of this course, the learner will be able to:

Describe and apply laboratory methods used in the microbiological surveillance of respiratory viruses.

The course will cover basic knowledge on the below areas: - multiplex respiratory real-time PCR implementation - detection and typing - subtype/lineage determination for seasonal influenza strains from

human specimens - sequencing - basic bioinformatic analysis of influenza virus/ use of bioinformatics

tools - clade assignment for seasonal influenza and zoonotic (avian/swine)

strains - genetic antiviral resistance determination - phylogenetic analyses - antigenic characterisation - biosafety and quality assurance - validation of molecular assays

Operate the reporting of results to ECDC TESSy databases and to public databases such as GISAID.

This course aims to provide an introductory training on Respiratory viruses and influenza surveillance laboratory methods and reporting. A weekend between course days will allow for more network and other activities.

Target audience

The training is designed for ten participants with beginner-level knowledge who

will be actively involved in the microbiological surveillance of influenza and other

respiratory viruses. The training is for participants who should have sufficient expertise in relevant laboratory methods and be able to cascade the training at

their institute. The training is considered beginner-level.

4/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Course Title: A practical introduction to NGS data analysis

Format In-person course

Dates/duration 13-17 May 2024 (4 working days)

Location Robert-Koch-Institut, Berlin, Germany

Description Four day dry-lab course giving a general practical introduction to NGS data analysis with examples of SARS-CoV-2.

Pre-course material GenEpi-BioTrain - Virtual Training 3: SARS-CoV-2 amplicon sequencing data (europa.eu)

Objectives/intended learning outcomes

By the end of this course, the learner will be able to:

Understand and explain the theory of SARS-CoV-2 NGS.

Execute bioinformatic analyses using Ugene and Conda environment including:

- consensus sequence generation - quality assessment - genotypic assignment of Pangolin/Nextclade lineages - genotypic assessment of antiviral resistance - phylogenetic analyses

Operate the reporting of results to ECDC TESSy databases and submitting data to public databases such as GISAID or the COVID-19 data portal.

Target audience

This course is designed for participants with no or little experience in analysing

NGS data. Previous knowledge of Linux and bioinformatics is not required. Participants should have fundamental understanding of molecular biology and

basic knowledge in NGS theory and background. The training is considered

beginner level.

Workstations (laptops) will be provided during the training.

5/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Course Title: Wet-/Dry-lab influenza virus NGS course

Format In-person course

Dates/duration 1 – 4 October 2024 (4 working days)

Location Aristotle University of Thessaloniki, Thessaloniki, Greece

Description Four-day wet-/dry-lab course

Objectives/intended learning outcomes

By the end of this course, the learner will be able to:

Apply laboratory methods for influenza virus NGS from sample to sequence (Nanopore, Ion Torrent)

Execute bioinformatic analyses including - phylogenetic analyses - genotypic assignment of influenza clades of seasonal and zoonotic

influenza (from human specimens) - genotypic assessment of antiviral resistance

Operate the reporting of results to ECDC TESSy databases and submitting data to public databases such as GISAID.

Target audience

This course is designed for staff with prior knowledge and experience of standard laboratory techniques such as PCR and understanding of NGS technologies and

beginner/advanced sequence analysis and manipulation skills.

The training is considered advanced to expert level.

6/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Course Title: Influenza laboratory methods and reporting

Format In-person course

Dates/duration 4–7 June 2024 (4 working days)

Location Aristotle University of Thessaloniki, Thessaloniki, Greece

Description Four day wet-lab course on laboratory methods used in the microbiological surveillance of influenza virus.

Objectives/intended learning outcomes

By the end of this course, the learner will be able to:

Apply laboratory methods used in the microbiological surveillance of influenza virus including

- Isolation (cell culture and on embryonated eggs); - Antigenic characterisation (HA) (Hemagglutinin inhibition assay, HAI); - Phenotypic antiviral resistance assessment (neuraminidase inhibition

NAI);

Operate the reporting of results to TESSy.

Target audience This course is designed for laboratory staff with prior knowledge and experience of standard laboratory techniques such as PCR, cell culture, and handling of

infectious materials. The training is considered advanced to expert level.

7/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Course Title: Detection and typing of seasonal and zoonotic influenza

Format In-person course

Dates/duration December 2024 (4 working days)

Location Robert-Koch-Institut, Berlin, Germany

Description Four-day wet-lab course

Objectives/intended learning outcomes

By the end of this course, the learner will be able to:

Understand and apply laboratory methods used in the microbiological surveillance of influenza virus for the detection and typing (subtype/lineage determination) of seasonal and zoonotic influenza from human specimens.

Understand and explain the concept of respiratory virus multiplex assays to detect at least influenza, SARS-CoV-2 and RSV.

Operate the reporting of results to TESSy.

Target audience This course is designed for laboratory staff with prior knowledge and experience of standard laboratory techniques such as PCR. The training is considered

advanced level.

8/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Twinning visits: 5 days

Course Title: SARS-CoV-2 whole genome sequencing and basic bioinformatics

Format In-person course

Dates/duration 5 days. The training is available 4 times.

Location Laboratoire National De Santé, Dudelange, Luxembourg

Description Five-day twinning visit on SARS-CoV-2 whole genome sequencing and bioinformatics

Objectives/intended learning outcomes

By the end of this course, the learner will be able to:

Apply the WGS workflow from sample to sequence and methods for variant determination.

Analyse and visualise for example variant proportions over time from own data and using online resources such as Nextstrain and others to assess global data.

Operate the reporting of results to ECDC TESSy databases and to public databases such as GISAID or the COVID-19 data portal.

Explain the purpose and limitations of the Illumina and Nanopore techniques.

This twinning visit offers the trainee the possibility to discover two different techniques (Illumina and Nanopore) used in the Microbiology department of the trainer in the national genomic surveillance with

the downstream data analysis and reporting. The training will be tailored to the trainer and the trainee’s needs.

Target audience

This course is designed for laboratory staff with prior knowledge and experience of standard laboratory techniques such as PCR, Sanger sequencing, and

understanding of NGS technologies. The training is for one participant who

should have sufficient knowledge on relevant laboratory methods to gain the greatest benefit from this training and be able to cascade the training at their

institute. The training is considered advanced to expert level.

9/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Course Title: Intensive 5-day training influenza surveillance laboratory methods and reporting

Format In-person course

Dates/duration 5 days. The training is available 4 times (tentative in April, May, September, October).

Location Hellenic Pasteur Institute, Athens, Greece

Description Five-day twinning visit on intensive training influenza surveillance laboratory methods and reporting or Integrated Respiratory virus multiplex qRT-PCR implementation.

Objectives/intended learning outcomes

The exact training content will be agreed with the training participant.

By the end of this course, the learner will be able to:

Describe and apply laboratory methods used in the microbiological surveillance of influenza virus. Depending on training needs, content will cover one of the two below areas with a focus on trainees’ needs: 1. Intensive training influenza surveillance laboratory methods and reporting:

- detection and typing by real-time PCR - subtype/lineage determination for seasonal influenza and zoonotic

(avian/swine) strains from human specimens - validation of molecular assays - genetic antiviral resistance determination - phenotypic antiviral resistance testing - antigenic characterisation - virus microneutralization assay - biosafety and quality assurance

2. Respiratory virus multiplex qRT-PCR implementation and surveillance:

- multiplex respiratory real-time PCR implementation - detection and typing - subtype/lineage determination for seasonal influenza and zoonotic

(avian/swine) strains from human specimens - biosafety and quality assurance - validation of molecular assays - sequencing - basic bioinformatic analysis of influenza virus/ use of bioinformatics

tools - clade assignment for seasonal influenza and zoonotic (avian/swine)

strains - phylogenetic analyses

Operate the reporting of results to ECDC TESSy databases and to public databases such as GISAID.

This twinning visit aims to provide an intensive training on influenza surveillance laboratory methods and reporting. The training will be tailored to the trainer and the trainee’s needs.

Target audience

The training is for one participant who should have sufficient knowledge on relevant laboratory methods to gain the greatest benefit from this training and

be able to cascade the training at their institute. The training is considered advanced to expert level.

10/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Twinning visits: 2 days

Course Title: Focused 2-day training on influenza surveillance laboratory methods and reporting

Format In-person course

Dates/duration 2 days. The training is available 4 times (tentative in April, June, October, November).

Location Hellenic Pasteur Institute, Athens, Greece

Description Two-day twinning visit on focused training influenza surveillance laboratory methods and reporting

Objectives/intended learning outcomes

The exact training content will be agreed with the training participant.

By the end of this course, the learner will be able to:

Describe and apply laboratory methods used in the microbiological surveillance of influenza. Depending on training needs, content will cover one of the below areas with a focus on trainees’ needs: 1. Molecular assays

- multiplex respiratory real-time PCR implementation - detection and typing - subtype/lineage determination for seasonal influenza and zoonotic

(avian/swine) strains from human specimens - validation of molecular assays

2. Genetic and Phenotypic Antiviral resistance - genetic antiviral resistance determination - phenotypic antiviral resistance testing

3. Neutralization and Antigenic characterization assays - virus microneutralization assay - antigenic characterisation

4. Bioinformatics Analysis - Basic bioinformatic analysis of influenza virus / use of bioinformatics

tools - clade assignment for seasonal influenza and zoonotic (avian/swine)

strains - genetic antiviral resistance determination - phylogenetic analyses - reporting of results to public databases such as GISAID

Operate the reporting of results to ECDC TESSy databases.

This twinning visit aims to provide a focused training on certain aspects of influenza surveillance laboratory methods and reporting. The training will be tailored to the trainee’s needs.

Target audience

The training is for one participant who should have sufficient knowledge on relevant laboratory methods to gain the greatest benefit from this training and

be able to cascade the training at their institute. The training is considered

advanced to expert level.

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European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

ECDC AURORAE training programme

Laboratory influenza and SARS-CoV-2 trainings

18 February 2024, Solna

Background:

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 the 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, the ECDC

aims to foster the development of sufficient capacity within the Community, enhance data sharing and collaborations between public health institutions and the ECDC, and facilitate networking activities and cross-

border collaborations.

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 programme was initiated in July 2022.

Of note: there will be no costs for training activities for the participants or countries, all costs for training, accommodation, and travel arrangements will be covered by ECDC through the

AURORAE consortium framework contract.

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European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Training formats:

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).

Face-to-face trainings (3-5 days).

• This type of training will give a broad overview and is therefore targeted to participants that

with beginner or advanced subject knowledge

• Participants should have a microbiology or related background and should be familiar with relevant common molecular techniques

• 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 participants with advanced or expert subject knowledge and also aims to enable cascading

of the training.

• For the twinning visits, usually one participant will visit a twinning institute for a tailored

training. Therefore, the exact training content will depend on the participant and will be discussed and agreed before the start of the training.

Virtual trainings

• A range of formats can be used, including webinars, instructional videos, and self-paced online courses

• Virtual trainings will be hosted on the EVA platform and usually are open to everyone.

Training target audience:

The target audience of the training programme are professionals with background in microbiology or similar

fields. Eligibility criteria include:

• The participants should be or will be involved in the microbiological surveillance of respiratory viruses

(e.g. SARS-CoV-2 and/or influenza) and should be able to actively apply skills acquired as part of the training.

• The participants should be part of the European Influenza Surveillance Network (EISN) and/or

European COVID-19 surveillance network (ECOVID-Net) or must currently be employed in the public health sector in one of the EU/EEA countries, the Western Balkan (Albania, Kosovo, Montenegro,

Serbia, North Macedonia, Bosnia and Herzegovina) or Türkiye.

Exact pre-requisites for participation may vary by course, specifically in terms of subject knowledge, and

training activities are marked as “Beginner”, “Advanced”, or “Expert” level courses.

Expression of interest process:

The EISN and ECOVID-Net are informed by the ECDC about upcoming training activities by a call for

expression of interest and the responses are collected through the EU survey tool.

• ECDC will send out invitation letters to the National Focal Points (NFP) for Respiratory viruses.

• The NFPs specified above are kindly asked to invite appropriate staff/colleagues to submit their

expressions of interest for training activities.

• The EU survey tool should be filled out separately for each individual.

• For individuals expressing interest in trainings the following should apply: o their work should include tasks to actively apply skills acquired as part of the training.

o they should be selected to ensure the maximum impact of the training on the public health sector they serve, taking into consideration their projected period of implementation of skills

at the institute, and possibilities of potentially cascading training nationally and direct use of

the acquired skills. o they will need to submit a short version of their resume (one page CV) and their motivation

for their participation in the respective training activities. o in addition, the country’s NFP for Respiratory viruses should submit a short paragraph (letter

of endorsement) endorsing that participant and describing how the host institute can benefit from their participation in the selected training activities.

3/3

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Selection process:

• ECDC will review expressions of interest after the deadline for submission has passed.

• ECDC strives to respect equal opportunities for countries, but priority may be given to countries with

larger identified training needs as identified through past EQAs, surveys, or similar if applicable.

• Participants will be selected based on professional background, maximum impact, and course

availability and previous participation in similar ECDC-funded training activities within the last 2

years.

• More than one applicant from the same country can be accepted for the same training activity, but

acceptance depends on availability of seats.

• ECDC and AURORAE aim to send notification letters to all candidates within two weeks after the end

of the submission period.

Replacement of participants:

In the event, that a selected participant cannot attend a scheduled training for a justifiable reason (e.g. sickness), the AURORAE partner conducting the training and the ECDC need to be informed at the earliest time possible. The NFP for Respiratory viruses of the selected participants institute or country may propose a replacement candidate to participate in the training instead. The NFPs are to ensure that the replacement candidate has comparable qualifications and expected benefit of the training activity as the initially selected individual.

1/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

ECDC AURORAE training programme

2024 catalogue of ECDC AURORAE laboratory

influenza and SARS-CoV-2 trainings

This catalogue contains all laboratory influenza and SARS-CoV-2 in-person training course and twinning visit trainings which the ECDC is offering through the AURORAE programme in 2024. The training activities are endorsed and funded by the ECDC and conducted through the AURORAE consortium.

Expressions of interest for these training activities are collected through the EU survey tool under the following link:

https://ec.europa.eu/eusurvey/runner/EoI_2024_ECDC_InflSC2_training

The password to access the survey is “Training2024”.

The training activities are free-of-charge and accommodation, and travel arrangements will be covered by

ECDC through the AURORAE consortium framework contract.

All the trainings are subject to ECDC budget availability. All trainings will be held in English. Please find here a general description of the AURORAE training program for influenza and SARS-CoV-2 wet and dry laboratory trainings: https://eva.ecdc.europa.eu/course/view.php?id=816

If you have any further questions or remarks, please contact [email protected]

Training target audience:

The target audience of the training programme are professionals with background in microbiology or similar

fields. Eligibility criteria include:

• The participants should be or will be involved in the microbiological surveillance of respiratory viruses

(e.g. SARS-CoV-2 and/or influenza) and should be able to actively apply skills acquired as part of the training.

• The participants should be part of the European Influenza Surveillance Network (EISN) and/or

European COVID-19 surveillance network (ECOVID-Net) or must currently be employed in the public health sector in one of the EU/EEA countries, the Western Balkan (Albania, Kosovo, Montenegro,

Serbia, North Macedonia, Bosnia and Herzegovina) or Türkiye.

Training formats:

The training formats include face-to-face training courses (wetlab and drylab) and twinning visits of various

durations.

Face-to-face trainings.

• The in-person courses on wet-dry laboratory aspects of respiratory virus surveillance are designed for a

specific target audience of ten participants each.

2/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

• Please observe pre-requisites for participation and the expected expertise level for participation to

ensure all participants will benefit from an aligned learning experience.

Twinning visits

• One participant or trainer will visit the twinning institute for a tailored training. Therefore, the exact training content will depend on the participant and will be discussed and agreed before the start of the

training.

• This training allows for an in-depth focussed training on a selection of specific methods.

• It is expected that participants are already knowledgeable in the respective training content and fulfil the pre-requisites required for each training.

• The participants should use the visits to deepen their knowledge, exchange best-practise, and to be

enabled to cascade the training content at their home institutes.

Content

Content .................................................................................................................................................. 2

Face 2 face courses ................................................................................................................................. 3

Course Title: Summer school on respiratory viruses laboratory surveillance methods and reporting ...................... 3

Course Title: A practical introduction to NGS data analysis ........................................................................... 4

Course Title: Wet-/Dry-lab influenza virus NGS course ................................................................................. 5

Course Title: Influenza laboratory methods and reporting ............................................................................. 6

Course Title: Detection and typing of seasonal and zoonotic influenza ............................................................ 7

Twinning visits: 5 days ............................................................................................................................ 8

Course Title: SARS-CoV-2 whole genome sequencing and basic bioinformatics ................................................ 8

Course Title: Intensive 5-day training influenza surveillance laboratory methods and reporting ............................. 9

Twinning visits: 2 days .......................................................................................................................... 10

Course Title: Focused 2-day training on influenza surveillance laboratory methods and reporting ........................ 10

3/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Face 2 face courses

Course Title: Summer school on respiratory viruses laboratory surveillance methods and reporting

Format Face-to-face training for 10 participants

Dates/duration 26 June -02 July 2024 (5 working days summer school incl. weekend)

Location Hellenic Pasteur Institute, Athens, Greece

Description

Summer school of five-day training on respiratory viruses surveillance laboratory methods and reporting with a focus on influenza. The training will begin on a Wednesday and end on a Tuesday, thereby including a weekend with no training activities but time to network and explore nearby areas of Greece.

Objectives/intended learning outcomes

By the end of this course, the learner will be able to:

Describe and apply laboratory methods used in the microbiological surveillance of respiratory viruses.

The course will cover basic knowledge on the below areas: - multiplex respiratory real-time PCR implementation - detection and typing - subtype/lineage determination for seasonal influenza strains from

human specimens - sequencing - basic bioinformatic analysis of influenza virus/ use of bioinformatics

tools - clade assignment for seasonal influenza and zoonotic (avian/swine)

strains - genetic antiviral resistance determination - phylogenetic analyses - antigenic characterisation - biosafety and quality assurance - validation of molecular assays

Operate the reporting of results to ECDC TESSy databases and to public databases such as GISAID.

This course aims to provide an introductory training on Respiratory viruses and influenza surveillance laboratory methods and reporting. A weekend between course days will allow for more network and other activities.

Target audience

The training is designed for ten participants with beginner-level knowledge who

will be actively involved in the microbiological surveillance of influenza and other

respiratory viruses. The training is for participants who should have sufficient expertise in relevant laboratory methods and be able to cascade the training at

their institute. The training is considered beginner-level.

4/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Course Title: A practical introduction to NGS data analysis

Format In-person course

Dates/duration 13-17 May 2024 (4 working days)

Location Robert-Koch-Institut, Berlin, Germany

Description Four day dry-lab course giving a general practical introduction to NGS data analysis with examples of SARS-CoV-2.

Pre-course material GenEpi-BioTrain - Virtual Training 3: SARS-CoV-2 amplicon sequencing data (europa.eu)

Objectives/intended learning outcomes

By the end of this course, the learner will be able to:

Understand and explain the theory of SARS-CoV-2 NGS.

Execute bioinformatic analyses using Ugene and Conda environment including:

- consensus sequence generation - quality assessment - genotypic assignment of Pangolin/Nextclade lineages - genotypic assessment of antiviral resistance - phylogenetic analyses

Operate the reporting of results to ECDC TESSy databases and submitting data to public databases such as GISAID or the COVID-19 data portal.

Target audience

This course is designed for participants with no or little experience in analysing

NGS data. Previous knowledge of Linux and bioinformatics is not required. Participants should have fundamental understanding of molecular biology and

basic knowledge in NGS theory and background. The training is considered

beginner level.

Workstations (laptops) will be provided during the training.

5/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Course Title: Wet-/Dry-lab influenza virus NGS course

Format In-person course

Dates/duration 1 – 4 October 2024 (4 working days)

Location Aristotle University of Thessaloniki, Thessaloniki, Greece

Description Four-day wet-/dry-lab course

Objectives/intended learning outcomes

By the end of this course, the learner will be able to:

Apply laboratory methods for influenza virus NGS from sample to sequence (Nanopore, Ion Torrent)

Execute bioinformatic analyses including - phylogenetic analyses - genotypic assignment of influenza clades of seasonal and zoonotic

influenza (from human specimens) - genotypic assessment of antiviral resistance

Operate the reporting of results to ECDC TESSy databases and submitting data to public databases such as GISAID.

Target audience

This course is designed for staff with prior knowledge and experience of standard laboratory techniques such as PCR and understanding of NGS technologies and

beginner/advanced sequence analysis and manipulation skills.

The training is considered advanced to expert level.

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European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Course Title: Influenza laboratory methods and reporting

Format In-person course

Dates/duration 4–7 June 2024 (4 working days)

Location Aristotle University of Thessaloniki, Thessaloniki, Greece

Description Four day wet-lab course on laboratory methods used in the microbiological surveillance of influenza virus.

Objectives/intended learning outcomes

By the end of this course, the learner will be able to:

Apply laboratory methods used in the microbiological surveillance of influenza virus including

- Isolation (cell culture and on embryonated eggs); - Antigenic characterisation (HA) (Hemagglutinin inhibition assay, HAI); - Phenotypic antiviral resistance assessment (neuraminidase inhibition

NAI);

Operate the reporting of results to TESSy.

Target audience This course is designed for laboratory staff with prior knowledge and experience of standard laboratory techniques such as PCR, cell culture, and handling of

infectious materials. The training is considered advanced to expert level.

7/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Course Title: Detection and typing of seasonal and zoonotic influenza

Format In-person course

Dates/duration December 2024 (4 working days)

Location Robert-Koch-Institut, Berlin, Germany

Description Four-day wet-lab course

Objectives/intended learning outcomes

By the end of this course, the learner will be able to:

Understand and apply laboratory methods used in the microbiological surveillance of influenza virus for the detection and typing (subtype/lineage determination) of seasonal and zoonotic influenza from human specimens.

Understand and explain the concept of respiratory virus multiplex assays to detect at least influenza, SARS-CoV-2 and RSV.

Operate the reporting of results to TESSy.

Target audience This course is designed for laboratory staff with prior knowledge and experience of standard laboratory techniques such as PCR. The training is considered

advanced level.

8/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Twinning visits: 5 days

Course Title: SARS-CoV-2 whole genome sequencing and basic bioinformatics

Format In-person course

Dates/duration 5 days. The training is available 4 times.

Location Laboratoire National De Santé, Dudelange, Luxembourg

Description Five-day twinning visit on SARS-CoV-2 whole genome sequencing and bioinformatics

Objectives/intended learning outcomes

By the end of this course, the learner will be able to:

Apply the WGS workflow from sample to sequence and methods for variant determination.

Analyse and visualise for example variant proportions over time from own data and using online resources such as Nextstrain and others to assess global data.

Operate the reporting of results to ECDC TESSy databases and to public databases such as GISAID or the COVID-19 data portal.

Explain the purpose and limitations of the Illumina and Nanopore techniques.

This twinning visit offers the trainee the possibility to discover two different techniques (Illumina and Nanopore) used in the Microbiology department of the trainer in the national genomic surveillance with

the downstream data analysis and reporting. The training will be tailored to the trainer and the trainee’s needs.

Target audience

This course is designed for laboratory staff with prior knowledge and experience of standard laboratory techniques such as PCR, Sanger sequencing, and

understanding of NGS technologies. The training is for one participant who

should have sufficient knowledge on relevant laboratory methods to gain the greatest benefit from this training and be able to cascade the training at their

institute. The training is considered advanced to expert level.

9/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Course Title: Intensive 5-day training influenza surveillance laboratory methods and reporting

Format In-person course

Dates/duration 5 days. The training is available 4 times (tentative in April, May, September, October).

Location Hellenic Pasteur Institute, Athens, Greece

Description Five-day twinning visit on intensive training influenza surveillance laboratory methods and reporting or Integrated Respiratory virus multiplex qRT-PCR implementation.

Objectives/intended learning outcomes

The exact training content will be agreed with the training participant.

By the end of this course, the learner will be able to:

Describe and apply laboratory methods used in the microbiological surveillance of influenza virus. Depending on training needs, content will cover one of the two below areas with a focus on trainees’ needs: 1. Intensive training influenza surveillance laboratory methods and reporting:

- detection and typing by real-time PCR - subtype/lineage determination for seasonal influenza and zoonotic

(avian/swine) strains from human specimens - validation of molecular assays - genetic antiviral resistance determination - phenotypic antiviral resistance testing - antigenic characterisation - virus microneutralization assay - biosafety and quality assurance

2. Respiratory virus multiplex qRT-PCR implementation and surveillance:

- multiplex respiratory real-time PCR implementation - detection and typing - subtype/lineage determination for seasonal influenza and zoonotic

(avian/swine) strains from human specimens - biosafety and quality assurance - validation of molecular assays - sequencing - basic bioinformatic analysis of influenza virus/ use of bioinformatics

tools - clade assignment for seasonal influenza and zoonotic (avian/swine)

strains - phylogenetic analyses

Operate the reporting of results to ECDC TESSy databases and to public databases such as GISAID.

This twinning visit aims to provide an intensive training on influenza surveillance laboratory methods and reporting. The training will be tailored to the trainer and the trainee’s needs.

Target audience

The training is for one participant who should have sufficient knowledge on relevant laboratory methods to gain the greatest benefit from this training and

be able to cascade the training at their institute. The training is considered advanced to expert level.

10/10

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Twinning visits: 2 days

Course Title: Focused 2-day training on influenza surveillance laboratory methods and reporting

Format In-person course

Dates/duration 2 days. The training is available 4 times (tentative in April, June, October, November).

Location Hellenic Pasteur Institute, Athens, Greece

Description Two-day twinning visit on focused training influenza surveillance laboratory methods and reporting

Objectives/intended learning outcomes

The exact training content will be agreed with the training participant.

By the end of this course, the learner will be able to:

Describe and apply laboratory methods used in the microbiological surveillance of influenza. Depending on training needs, content will cover one of the below areas with a focus on trainees’ needs: 1. Molecular assays

- multiplex respiratory real-time PCR implementation - detection and typing - subtype/lineage determination for seasonal influenza and zoonotic

(avian/swine) strains from human specimens - validation of molecular assays

2. Genetic and Phenotypic Antiviral resistance - genetic antiviral resistance determination - phenotypic antiviral resistance testing

3. Neutralization and Antigenic characterization assays - virus microneutralization assay - antigenic characterisation

4. Bioinformatics Analysis - Basic bioinformatic analysis of influenza virus / use of bioinformatics

tools - clade assignment for seasonal influenza and zoonotic (avian/swine)

strains - genetic antiviral resistance determination - phylogenetic analyses - reporting of results to public databases such as GISAID

Operate the reporting of results to ECDC TESSy databases.

This twinning visit aims to provide a focused training on certain aspects of influenza surveillance laboratory methods and reporting. The training will be tailored to the trainee’s needs.

Target audience

The training is for one participant who should have sufficient knowledge on relevant laboratory methods to gain the greatest benefit from this training and

be able to cascade the training at their institute. The training is considered

advanced to expert level.

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European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

ECDC AURORAE training programme

Laboratory influenza and SARS-CoV-2 trainings

18 February 2024, Solna

Background:

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 the 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, the ECDC

aims to foster the development of sufficient capacity within the Community, enhance data sharing and collaborations between public health institutions and the ECDC, and facilitate networking activities and cross-

border collaborations.

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 programme was initiated in July 2022.

Of note: there will be no costs for training activities for the participants or countries, all costs for training, accommodation, and travel arrangements will be covered by ECDC through the

AURORAE consortium framework contract.

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European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Training formats:

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).

Face-to-face trainings (3-5 days).

• This type of training will give a broad overview and is therefore targeted to participants that

with beginner or advanced subject knowledge

• Participants should have a microbiology or related background and should be familiar with relevant common molecular techniques

• 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 participants with advanced or expert subject knowledge and also aims to enable cascading

of the training.

• For the twinning visits, usually one participant will visit a twinning institute for a tailored

training. Therefore, the exact training content will depend on the participant and will be discussed and agreed before the start of the training.

Virtual trainings

• A range of formats can be used, including webinars, instructional videos, and self-paced online courses

• Virtual trainings will be hosted on the EVA platform and usually are open to everyone.

Training target audience:

The target audience of the training programme are professionals with background in microbiology or similar

fields. Eligibility criteria include:

• The participants should be or will be involved in the microbiological surveillance of respiratory viruses

(e.g. SARS-CoV-2 and/or influenza) and should be able to actively apply skills acquired as part of the training.

• The participants should be part of the European Influenza Surveillance Network (EISN) and/or

European COVID-19 surveillance network (ECOVID-Net) or must currently be employed in the public health sector in one of the EU/EEA countries, the Western Balkan (Albania, Kosovo, Montenegro,

Serbia, North Macedonia, Bosnia and Herzegovina) or Türkiye.

Exact pre-requisites for participation may vary by course, specifically in terms of subject knowledge, and

training activities are marked as “Beginner”, “Advanced”, or “Expert” level courses.

Expression of interest process:

The EISN and ECOVID-Net are informed by the ECDC about upcoming training activities by a call for

expression of interest and the responses are collected through the EU survey tool.

• ECDC will send out invitation letters to the National Focal Points (NFP) for Respiratory viruses.

• The NFPs specified above are kindly asked to invite appropriate staff/colleagues to submit their

expressions of interest for training activities.

• The EU survey tool should be filled out separately for each individual.

• For individuals expressing interest in trainings the following should apply: o their work should include tasks to actively apply skills acquired as part of the training.

o they should be selected to ensure the maximum impact of the training on the public health sector they serve, taking into consideration their projected period of implementation of skills

at the institute, and possibilities of potentially cascading training nationally and direct use of

the acquired skills. o they will need to submit a short version of their resume (one page CV) and their motivation

for their participation in the respective training activities. o in addition, the country’s NFP for Respiratory viruses should submit a short paragraph (letter

of endorsement) endorsing that participant and describing how the host institute can benefit from their participation in the selected training activities.

3/3

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Selection process:

• ECDC will review expressions of interest after the deadline for submission has passed.

• ECDC strives to respect equal opportunities for countries, but priority may be given to countries with

larger identified training needs as identified through past EQAs, surveys, or similar if applicable.

• Participants will be selected based on professional background, maximum impact, and course

availability and previous participation in similar ECDC-funded training activities within the last 2

years.

• More than one applicant from the same country can be accepted for the same training activity, but

acceptance depends on availability of seats.

• ECDC and AURORAE aim to send notification letters to all candidates within two weeks after the end

of the submission period.

Replacement of participants:

In the event, that a selected participant cannot attend a scheduled training for a justifiable reason (e.g. sickness), the AURORAE partner conducting the training and the ECDC need to be informed at the earliest time possible. The NFP for Respiratory viruses of the selected participants institute or country may propose a replacement candidate to participate in the training instead. The NFPs are to ensure that the replacement candidate has comparable qualifications and expected benefit of the training activity as the initially selected individual.