Consolidation of SARS-CoV-2 Genomic Surveillance and Expansion to other Pathogens at RKI

The IMS-HERA2 project aims to strengthen the German national infrastructures for the integrated genomic surveillance (IGS) of respiratory pathogens and to contribute to an improved regional, national and European capacity for genome-based outbreak investigation.

The COVID-19 pandemic has highlighted the importance and absolute necessity of systematic genomic surveillance of SARS-CoV-2, especially when sequencing data can be combined with clinical and epidemiological data sets. In view of the high virulence, rapid evolution and demonstrated capacity for immune escape of SARS-CoV-2, there is no doubt that close and continuous integrated genomic surveillance of this pathogen will be a public health imperative for years to come. Therefore, there is an urgent need for sustainable infrastructures and efficient public sector processes that enable long-term diagnostic and molecular surveillance of SARS-CoV-2.

The primary goal of IMS-HERA2 is to strengthen our infrastructure for WGS and data analysis of SARS-CoV-2, and then to expand our capacity to other important respiratory pathogens as a logical next step towards a comprehensive pathogen surveillance system in Germany.

IMS-HERA2 in numbers

Funding statement

Co-funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Commission. Neither the European Union nor the granting authority can be held responsible for them.

Background

Genomic surveillance is an effective tool used in public health to keep track of infectious diseases and to rapidly install countermeasures to protect the general population. A central component of successful pathogen surveillance and rapid detection of potential threats is understanding the spread of a pathogen and its pathogenic properties. Knowledge of the pathogen genome is an important source of information here. The detection of mutations in the genome of a pathogen makes it possible to reconstruct relationships, uncover transmission routes and predict resistances.

IGS combines data from multiple sources. First, the genomes of pathogen isolate from patient samples are decoded using advanced DNA sequencing techniques, namely whole genome sequencing (WGS). Next, the results of sequencing data analysis are linked with epidemiological and clinical data that is obtained together with the initial pathogen sample. This allows the monitoring of pathogen spread, identification of abnormal infection clusters e.g. outbreaks and detection of new pathogen variants with increased transmissibility or virulence. The benefits of IGS in the detection of viral variants were impressively demonstrated during the COVID-19 pandemic.

Given the high virulence, rapid evolution and proven ability of this pathogen to escape the immune system, there is no question that close and continuous integrated genomic surveillance of SARS-CoV­‑2 will be essential for public health in the coming years. Therefore, there is an urgent need for sustainable infrastructures and efficient public sector processes to enable reliable long-term diagnostic and molecular surveillance of SARS-CoV-2. Several of the infrastructure components, like sample preparation, WGS and data analysis pipelines were established for SARS-CoV-2 during the first HERA funding period and are generic in nature.

The second funding phase of IMS-HERA2 will further develop these structures to miniaturize and automate sample preparation, WGS and data analysis to increase sample throughput capacity and cost effectiveness.

In addition, the methods are being adapted for systematic genomic surveillance of other respiratory pathogens of high public health relevance, such as influenza virus and respiratory syncytial virus (RSV).

Goals

• In the short-term, contribution to the establishment of a sustainable, efficient and high capacity WGS infrastructure and sample/data processes for national public health microbiology;
• In the short/medium-term, contribution to early detection and enhanced monitoring of Influenza A/B virus and RSV, and laying the groundwork for the surveillance of other respiratory pathogens at the national and the EU/EEA levels;
• In the medium/long-term, contribution to enhanced genomic-based infectious disease outbreak investigation capacities at regional, national and/or EU/EEA levels

The proposed actions will have an impact not only at the national and EU levels, but also at the regional level.

Work packages

Project Coordination

Robert Koch Institute, MF1 Genome Competence Center
For information, comments and suggestions, please contact us at IGS@rki.de.

Participants

• MF1, RKI, Berlin
• FG17, RKI, Berlin
• NRZ Influenza, RKI, Berlin

Project key figures

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