The course will be conducted by the National Institute of Health Doutor Ricardo Jorge (INSA), Portugal, parter of the consortium “AURORAE - lAboratory sUppoRt fOr influenza and coRonA for Europe”, under contract of European Centre for Disease Prevention and Control (ECDC).
The development of INSaFLU-TELEVIR and the expansion of its computational capacity have been co-funded by INSA and various projects promoted by the European Union, namely TELEVIR, GENEO and DURABLE.
Duration: 2-hour webinar on 29th October 2024, 10:00-12:00 CET.
Audience: The INSaFLU-TELEVIR (https://insaflu.insa.pt/) platform is a free, versatile and user-friendly bioinformatics suite for virus next- and third-generation sequencing data analysis. As the platform does not require advanced expertise in bioinformatics, this training session can be particularly fit to beginners to intermediate learners in the field of bioinformatics (such as, laboratory technicians, microbiologists or even epidemiologists) working in surveillance of viral pathogens, with emphasis on influenza, SARS-CoV-2, RSV, or other viral respiratory pathogens. Notwithstanding, other professionals with particular interest in viral metagenomics detection and genomic epidemiology can benefit from this INSaFLU-TELEVIR training course.
Objectives: After completing this training, the participants should be able to:
- Understand the workflow of INSaFLU-TELEVIR for viral metagenomics detection and routine genomic surveillance of viruses, with emphasis on SARS-CoV-2, Influenza and other respiratory virus
- Describe the steps to yield meaningful genomic surveillance data through the INSaFLU-TELEVIR platform, from raw next- and third-generation sequencing data to mutation detection, consensus generation, virus classification, alignments, phylogenetics, integrative Nextstrain phylogeographical and temporal analysis, etc
- Recognise advantages and limitations of the tool.
Tools and Files: Various tools (including INSaFLU-TELEVIR) and their respective documentation are already available within the EVA page of this webinar, under "Prepare for the Webinar" section, for you to explore.
Participation: This training is open for self-enrolment on EVA.
Biosafety and quality assurance in a public health laboratory 2024 - AURORAE
This is a webinar on biosafety and quality assurance in a public health laboratory. It aims to deepen the understanding of implementation of biosafety measures in a laboratory and the need for continuous quality control. This training activity is part of the AURORAE training program which has the objective to support countries in building capacities in the areas of diagnosis, detection, identification and characterization of primarily influenza, RSV and SARS-CoV-2 viruses.
Dates and duration: 16th December 2024 13:00-15:00 (CET).
Location: Online.
Audience: The webinar is designed for beginner to intermediate learners with previous knowledge of and working experience with laboratory techniques. The participants should be or plan to be involved in the microbiological surveillance of influenza.
Objectives: After completing this training, the participants should be able to:
- Understand the requirements for the control of the risks associated with the pathogens being handled.
- Describe standard laboratory practices as well as the different biosafety levels (1-4)
- Recognize the need for verification or validation of a new molecular assay in a laboratory and the need for continuous quality control.
- Understand the differentiation between the concepts of verification and validation and through specific statistical techniques and analyses to detect trends and shifts in order to review the results of the laboratory tests conducted.
- Understand the requirements for the development and maintenance of a viral biobank facility.
Participation: This webinar is open for self-enrolment.
The aim of this virtual training is to provide participants with an in-depth understanding of whooping cough (pertussis) epidemiology, surveillance, and vaccination strategies. Participants will learn how genomic tools are used for surveillance, examine the epidemiology of recent outbreaks, and explore the public health impacts of vaccination, particularly in the context of pregnancy and early infancy. Additionally, practical sessions will provide hands-on experience in the rapid genotyping of Bordetella pertussis.
Dates and duration:
Monday 4th November from 9:00 to 12:30 (Session 1) and
Tuesday 5th November from 9:00 to 12:00 (Session 2).
Audience: Public health microbiologists, epidemiologists and bioinformaticians.
Objectives: Upon completion of this workshop, participants will be able to:
- Understand the global and European epidemiology of whooping cough and the structure of surveillance systems.
- Describe the genomic evolution of Bordetella pertussis and Bordetella parapertussis under vaccine pressure.
- Recognize the spatial dynamics of Bordetella pertussis and its fitness changes induced by vaccines.
- Use genomic tools, including BIGSdb and GrapeTree, for rapid genotyping of B. pertussis to analyse vaccine antigens, antibiotic resistance, and genomic comparisons.
- Analyse the public health impact of vaccination, particularly maternal vaccination strategies to prevent infant pertussis.
Participation: This course is open for public enrolment.
The aim of this virtual training is to provide participants with comprehensive knowledge on the health risks associated with seafood products. The focus will be on understanding norovirus in shellfish, exploring the genomic and epidemiological surveillance for seafood products, examining the French REMI network for shellfish production areas surveillance, and engaging in a practical session to address outbreak scenarios. Additionally, participants will gain insights into the specific risks posed by marine pathogens (Vibrio, Hepatitis A, Phytotoxin (Paralytic Shellfish Poisoning - PSP), the challenges in quantitative microbial risk assessment, and the epidemiology and detection of parasites in seafood, with practical case studies to enhance understanding. Finally, EU surveillance systems for seafood products will be discussed focusing on risk assessment of parasites in fishery products, on the future AMR monitoring in seafood and the notifications related to seafood.
Dates: 10 September (09:00 – 12:00 CEST) and 12 September (14:00 – 17:00 CEST) 2024.
Duration: Two half-days.
Location: Online - Find the link after enrolment.
Audience: Public health microbiologists, epidemiologists and bioinformaticians.
Objectives - Upon completion of this workshop, participants will be able to:
- Understand the key health risks associated with seafood products.
- Explain the role of norovirus in shellfish and the methods used for genomic and epidemiological surveillance.
- Describe the structure and function of the French REMI network for shellfish production areas surveillance.
- Apply epidemiological principles to manage and respond to seafood-related health outbreaks.
- Explain principles of Quantitative risk assessment with application to marine toxins and pathogens Vibrio, Hepatitis A, PSP, with a focus on dose-response, relationships with epidemiological data and pathogen virulence and challenges in data collection for risk assessment.
- Identify and understand the diversity of parasites in seafood, and learn about epidemiological and molecular techniques for their detection and study.
- Understand the risk assessment of parasites in fishery products
- Comprehend the future of AMR monitoring in seafood
- Understand the notification system for seafood-related Issues
Participation: This course is open for public enrolment from 26th August 2024.
This virtual training workshop is part of the Genetic Epidemiology and Bioinformatics Training Programme (GenEpi-BioTrain). The aim of this virtual training is to introduce participants to the theoretical and practical aspects of waterborne disease surveillance, using Leptospirosis as an example. Participants will gain insight into surveillance tools and the state of the art in human Leptospirosis. They will also gain knowledge on Leptospirosis surveillance from an animal perspective. Additionally, in a second session, microbiological assessment of water quality will be covered. Participants will be first introduced to water monitoring before delving into the design of molecular tools and bathing water monitoring.
Dates: 22 and 24 July 2024.
Duration: Two half-days from 09:00 to 12:00 (CET).
Location: Online - Find the link after enrolment.
Audience: Public health microbiologists, epidemiologists and bioinformaticians.
Objectives - Upon completion of this workshop, participants will be able to:
Explain the basics of Leptospirosis, including the disease, pathogens, transmission, treatment, and dissemination.
Describe the state of the art in human Leptospirosis.
Understand the surveillance tools in place against Leptospirosis in human and animal cases.
Explain the impact of Leptospirosis in animals.
Describe the microbiological assessment of water quality and the molecular tools in place.
Be familiar with the WHO quantitative analysis for water quality.
Understand the importance of water quality assessment, for example, in an environmental aspect or in the context of international events such as the Olympic Games in Paris (La Seine).
Participation: This course is open for public enrolment from 1st July 2024.
The aim of this virtual training is to introduce participants to working in Unix and creating Conda environments for running simple bioinformatics tasks. The training is divided into three sessions. In the first session, participants will be introduced to the Unix ecosystem and basic Unix commands useful for inspecting various files. In the second session, participants will focus on file manipulation and consolidate their understanding of the command line interface. The third session aims to enhance participants’ ability to perform bioinformatics tasks in the command line by setting up and using Conda environments.
Duration: Three half-days on 20, 21 and 22 August 2024 from 10:00 to 14:00 (CET)
Location: Online - Find the link after enrolment.
Audience: Public health microbiologists, epidemiologist, or beginners in bioinformatics interested in learning about the power of the command line interface and setting up separate environments with bioinformatics tools.
Objectives:
Upon completion of this workshop, participants will be able to:
- Understand and recognize Unix as an ecosystem
- Execute several basic commands in the terminal
- Navigate in Unix
- Run simple commands for inspecting files
- Manipulate file contents from command line
- Understand the differences between file locations and running commands in the terminal
- Understand principles behind package management in separate environments
- Have a basic understanding of the Conda ecosystem for handling environments and packages
- Download and install Mamba on Ubuntu
- Use Mamba - A Conda ecosystem package manager
- Create and activate environments
- Install a bioinformatics software
- Run a bioinformatics analysis
Participation: This course is open for public enrolment from 29 July 2024.
The aim of this virtual training is to provide participants with in-depth knowledge of RSV (Respiratory Syncytial Virus), including its genomic diversity, evolution, available treatments, and emerging vaccine strategies. The focus will be on how genomic data informs public health responses, the impact of RSV on vulnerable populations, and ongoing advancements in treatment and prevention. The training will also explore regulatory frameworks and public health strategies for managing RSV outbreaks.
Dates and duration: 10 and 13 December 2024 (Two half-days)
Audience: Public health microbiologists, epidemiologists and bioinformaticians.
Objectives: Upon completion of this workshop, participants will be able to:
- Understand the virology, epidemiology, and clinical impact of RSV on global health.
- Explain RSV genomic diversity, evolutionary trends, and their implications for public health.
- Use bioinformatics tools to analyse RSV genomic sequences, variants, and interpret phylogenetic data.
- Analyse genomic data to better understand RSV transmission patterns and outbreaks.
- Describe current RSV treatment options and advancements in monoclonal antibodies.
- Understand the status and challenges in developing RSV vaccines, particularly for vulnerable groups like pregnant women.
Participation: This course is open for public enrolment.
This virtual training workshop is part of the Genetic Epidemiology and Bioinformatics Training Programme (GenEpi-BioTrain). The aim of this virtual training is to introduce participants to theoretical and practical aspects of alignments and phylogenetics. Participants will gain a basic understanding of what a phylogeny is, and how it can be generated and assessed for quality and trustworthiness.
Dates: 19 and 20 March 2024.
Duration: Two half-days from 12:30 to 16:00 (CET).
Location: Online - Find the link after enrolment.
Audience: Public health microbiologists, epidemiologists and bioinformaticians interested in discussing concepts of phylogenies and in interpreting phylogenetic trees.
Objectives - Upon completion of this workshop, participants will be able to:
- Describe what phylogeny is;
- Generate phylogenies using state-of-the-art tools for alignments and phylogenetic inference;
- Evaluate the quality and trustworthiness of a phylogeny.
Participation: This course is open for public enrolment from 5 to 19 March 2024.
This virtual training workshop is part of the Genetic Epidemiology and Bioinformatics Training Programme (GenEpi-BioTrain). It's organised as part of Wave 1 dedicated to Influenza and SARS-CoV-2.
The aim of this virtual training is to introduce participants to theoretical and practical aspects of analysing SARS-CoV-2 in wastewater. Participants will get insights into the laboratory work, the interpretation of SARS-CoV-2 levels in wastewater and the variant analysis with examples from the Danish SARS-CoV-2 wastewater surveillance.
Duration: Three half-days on 20, 21 and 22 August 2024 from 10:00 to 14:00 (CET)
Location: Online - Find the link after enrolment.
Audience: Public health microbiologists and bioinformaticians interested in discussing concepts of wastewater surveillance, data quality control, measuring viral concentrations in wastewater and normalising and interpreting levels of SARS-CoV-2.
Objectives:
Upon completion of this workshop, participants will be able to:
- Describe the concept of wastewater surveillance.
- Discuss the advantages and disadvantages of SARS-CoV-2 wastewater surveillance.
- Describe the laboratory workflow for measuring viral concentrations in wastewater, including relevant quality control measures.
- Describe how wastewater samples
can be prepared for sequencing.
- Discuss
how SARS-CoV-2 levels in wastewater can be normalised and interpreted.
- Have a basic understanding of the analysis steps (including quality control) to investigate lineage abundance from sequencing data using bioinformatic command line tools.
- Discuss how wastewater analysis can complement other types of surveillance.
Participation: This course is open for public enrolment from 10 to 24 January 2024.