Microbiology

To meet the urgent need to strengthen Member States capacity for detecting and monitoring new variants of the SARS-CoV-2 virus, ECDC had set up in 2020 an emergency contract to support, in particular but not exclusively, Member States with limited or no whole genome sequencing capacity. In collaboration with the European Commission, a second contract for whole genome sequencing services became operational in March 2021, providing support to all countries for sequencing of SARS-CoV-2 positive isolates. More than 120,000 samples from 11 EU/EEA Member States and four Western Balkan countries were processed between February and December 2021.

Alongside with the direct sequencing services, ECDC initiated the implementation of the laboratory capacity building activities under the EU Health Emergency Preparedness and Response Authority (HERA) Incubator Action Area 1: Rapid detection of SARS-CoV-2 variants. In September 2021, ECDC awarded more than 77 M€ to 24 EU/ EEA countries to strengthen whole genome sequencing and RT-PCR infrastructures within the countries' national public health programmes. The immediate objective was to reinforce countries' capacities for early detection and enhanced monitoring of emergent and known SARS-CoV-2 variants.

ECDC continued to provide technical support to public health reference laboratory networks across the EU/EEA and enlargement countries, taking into account WHO networks’ reference laboratory activities. The Centre continued benchmarking microbiological capacities in countries, facilitating the development of rapid communication of laboratory-based information for surveillance and alert, and supporting Member States in strengthening their microbiology capacity, based on gaps identified by the EULabCap indicators and EQA schemes. ECDC offered as well need-based sequencing support to Member States that have not yet fully transitioned to WGS-based surveillance. ECDC and the European Commission are continuing to provide EU/EEA Member States and Western Balkan countries with access to outsourced whole genome sequencing services for SARS-CoV-2 samples. More than 120,000 samples from 11 EU/EEA Member States and 4 Western Balkan countries were processed between February and December 2021. Timely and secure WGS data sharing and storage are secured by customised protected workspaces for WGS data management.

ECDC continued to collaborate with EFSA on the detection and public health risk assessment of foodborne outbreaks.