SGS

Duration: January - December 2023

Partner countries: Countries with approved GHPP projects

Partner institutions: Institutions in GHPP partner countries

Involved RKI units: ZIG 4, MF 1, MF 2

Source: RKI

Challenges addressed by the project

The COVID-19 pandemic has exposed the potential strengths but also challenges for genomics in public health surveillance systems. Unfortunately, the scale of genomic surveillance (GS) remains largely weak in parts of the world and the aim is here to build up GS capacities in countries in the context of COVID-19 and lessons learned from the pandemic.

The challenge and global aim is to shift genomics from academic research into routine public health practice, to make informed evidence-based decisions on the management of pathogens with pandemic and epidemic potential. Participants from GHPP partner countries will be invited to engage in workshops with experts in the field of GS. The workshops will also include discussions to address the gaps and barriers in the public health system in terms of genomic surveillance capacities.

Objectives

Genomic surveillance is crucial for the monitoring of known and newly emerging pathogens and for the efficient response to infectious disease threats with pandemic and epidemic potential. Through GS the public health action is transformed by providing a deeper understanding of pathogens, their evolution and circulation within the human population. The workshop delivered in the course of this project will strengthen strategic public health workforce within different GHPP partner countries. The workshop will be designed to build on previous experience and tailored towards specific needs. Participants will be recruited from different GHPP project partner countries. Therefore, the workshop will also provide a platform for participants from different countries to connect and open the potential for further south-south collaborations, exchanges, or support.

The project will provide partners with a basic skill set in sequencing and bioinformatics to respond and manage not only the current SARS-CoV-2 pandemic but lay grounds to respond to other emerging or re-emerging pathogens.

Our overall objectives for this project are to increase knowledge on Next-Generation Sequencing (NGS) and Bioinformatics, thereby also setting grounds to fostering networking between partners from different GHPP projects. We will offer two training modules to colleagues from GHPP partner countries who will be visiting the Robert Koch Institute (RKI) for a GS workshop. GHPP working groups will be able to use this offer to strengthen their existing projects with an add-on GS training package. The training offered will be structured to include individuals with no or limited experience to participate. If successful, we aim to perpetuate the trainings to allow for sustainable knowledge exchange and growth within the GHPP projects or applying countries.

Overview of activities

The project will consist of two training modules, one week per module.

Training Module 1: Next Generation and Nanopore Sequencing

The Next Generation and Nanopore Sequencing training module will cover all parts of the sequencing library preparation and sequencing process in theory and practice, with the aim to teach the participants how to independently generate sequencing data that will be further analysed in the Bioinformatics Module 2. In some of the theoretical parts and presentations of this module, the RKI unit MF 1 will be involved in terms of the considerations required before a sequencing run to generate a sufficient quantity and quality of data output. In principle, both modules are designed closely together. According to the participants' pre-knowledge or given laboratory infrastructure in the respective country, the taught sequencing technique will be Illumina or Oxford Nanopore.

Training Module 2: Bioinformatics and data analysis

The Bioinformatics training module will comprise all basic tasks to perform an efficient genomic surveillance based on Next-Generation and Nanopore Sequencing data. In general, we will explain and illustrate basic concepts using SARS-CoV-2 sequencing data as example, however, the same or similar methods can be also applied to data from other pathogens. The participants will learn how to control the quality of raw data produced in Module 1, how to analyse the data to answer different surveillance questions (Is this an outbreak cluster? Is this a recombinant virus?), and how to visualize their results e.g. to inform public health authorities. We will compare and teach advantages and disadvantages of the two major sequencing technologies: Illumina and Oxford Nanopore.

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