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

ongoing

The COVID-19 pandemic has revealed the importance and absolute necessity of a systematic genomic surveillance of SARS-CoV-2, especially when sequencing data can be combined with clinical and epidemiological datasets. Given this pathogen’s high virulence, rapid evolution and demonstrated capacity for immune escape, there is no question that close and continuous integrated molecular surveillance of SARS-CoV-2 will remain a public health imperative for years to come. Therefore, sustainable infrastructures and efficient processes in the public sector that enable long-term diagnostic and molecular SARS-CoV-2 surveillance are urgently needed. Several of the infrastructure components and processes have been established for SARS-CoV-2 during the first HERA funding phase have a generic character. They can be adapted for the systematic genomic surveillance of other important pathogens, opening up further possibilities to prevent and combat infectious diseases with high public health relevance. Therefore, we propose to address the most relevant topics for enhancing whole genome sequencing (WGS) and reverse transcription polymerase chain reaction (RT-PCR) national infrastructures and capacities, pursuing three specific objectives: • 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.