In 2021, the Department of Microbiology of the Laboratoire national de santé (LNS) continued its contribution to the national response to the COVID-19 pandemic by supporting Luxembourg and its people through multiple outreach activities and its genomic surveillance programme. At the same time, the Microbiology team also identified its sustainable highlights of excellence beyond Corona.
One of the main milestones of 2021 was the nomination as the National Reference Laboratory for acute respiratory infections in Luxembourg by the Ministry of Health, until January 2028. This nomination constituted a further achievement as the LuxMicrobiobank was also nominated to represent Luxembourg in the World Health Organization’s (WHO) BioHub initiative, and the department was awarded the HERA (Health Emergency Preparedness and Response Authority) incubator grant, worth 4.8 million euros from the European Centre for Disease Prevention and Control (ECDC), in order to expand and widen the spectrum of its reference activities provided by LNS Luxembourg Genomic and Molecular Microbiology Unit (LUX-GEMM) in response to the COVID-19 pandemic.
Designation as the National Reference Laboratory – a mandate to provide reference functions in the public health sector
Dr Tamir Abdelrahman, head of the LNS Department of Microbiology, explains that the appointment as the National Reference Laboratory for acute respiratory infection consolidates the various activities that the department has undertaken over the past years, especially during the COVID-19 pandemic: “This nomination is also a mandate to provide reference functions in the public health microbiology sector and a step forward in coordinating national efforts with the Health Directorate (DISA) and partner laboratories. The new National Reference Laboratory is built on several pillars. It provides excellent clinical microbiology services, a strong research and development arm to identify the state-of-the-art diagnostic technology to be rolled out to laboratories across the country, public health microbiology, training and education and international collaboration.”
Dr Trung-Nguyen Nguyen, head of the Virology and Serology service, welcomed the perfect timing of the nomination that came in just as the department was expanding the national genomics surveillance programme, launched in March 2020, to hospitalised patients. Plans are also underway to introduce further phylodynamics studies matching the international standards of data collection: “The implications for the initiative for national seroprevalence studies and vaccination follow-up programmes are significant. Although most efforts were directed toward COVID-19, it should also be mentioned that we implemented the “ReViLux” surveillance programme for all respiratory viruses, which will expand to bacterial pathogens in the next phase.”
LNS Biobank first to deliver COVID-19 virus samples to WHO BioHub
Since the identification of the first SARS-CoV-2 in Luxembourg, there was a plan to establish a dedicated microbial biobank to ensure storage of clinical samples in a timely manner in order to facilitate the rapid characterisation of the virus, either via sequencing or virus culture. The LuxMicroBiobank was launched by the LNS in May 2020 to host all positive SARS-CoV-2 samples and to serve as a resource for validation of new diagnostic methods in Luxembourg by offering fair and equitable access to anonymised clinical samples to all partners based on public health needs. The already LuxMicroBiobank hosts 83 106 SARS-CoV-2 positive samples (since Mars 2020). The Ministry of Health has recognised the success of the LuxMicroBiobank through its nomination to represent Luxembourg in the WHO BioHub initiative. Luxembourg has thus joined a small group of countries (including Italy, Egypt, Thailand, Switzerland, Japan, El Salvador, South Africa, UK, Portugal, and Peru) to participate in the pilot phase of the BioHub project, dedicated to SARS-CoV-2. The Grand Duchy was the first to provide COVID-19 virus samples to the new hub in the framework of the initiative.
The LNS becomes one of the main public health microbiology hubs in Europe
Another very notable event of the year was the European Centre for Disease Prevention and Control (ECDC) awarding LNS – Microbiology the HERA incubator grant (4.8 million euros) to expand and widen the spectrum of activities provided by LNS LUX-GEMM in response to the COVID-19 pandemic. On 17 February 2021, the European Commission launched the “HERA Incubator” programme as a new EU bio-defence preparedness plan against SARS-CoV-2 variants making substantial investments to increase Member States’ capacity to identify and characterise variants. In April 2020, the Ministry of Health nominated the LNS as project lead for the national capacity building grant view to the existing infrastructure and ongoing whole-genomic sequencing activities for SARS-CoV-2. The LNS is also participating in the development of regional data hubs in order to facilitate the timely reporting of whole-genome sequencing (WGS) and reverse transcription polymerase chain reaction (RT-PCR) data to the ECDC.The HERA incubator grant offers a major boost to the national drive-in capacity building, enhances the cross-border pandemic preparedness and response cooperation, and it establishes LNS-Microbiology as one of the main public health microbiology hubs in Europe.
” The department of microbiology had delivered successful projects in 2021, which is due to the excellent expertise and cooperation within the team”, states Tamir Abdelrahman, “as well as the strong collaboration with our many external partners. I am sure that we have created a very strong basis to successfully continue our work towards internationally recognised scientific excellence for Luxembourg and its people.”
In 2021, the LNS Microbiology team also continued to play its major role as Fighters against Covid-19 in Luxembourg through several sequencing and outreach activities
Below are selected highlights of activities in 2021:
- Long-term care facilities: the LNS deployed 13 outreach teams, each composed of one administrator and one nurse to perform systematic RT-PCR testing in nursing homes in Luxembourg. The visits were planned in 3-week cycles. An urgent intervention team was set up if a cluster was identified by the Inspection Sanitaire. The systematic testing was complementary to frequent rapid diagnostic testing using antigen detection tests introduced earlier during the year.
- National COVID-19 Seroprevalence programme: serological testing was performed upon invitation to monitor the seroprevalence of anti-SARS-CoV-2 antibodies in the population. Individuals were invited to one of the three DBS (Dried Blood Spots) Centers; Centre de Prélèvement (CDP) of the LNS, Maison Médicale Val Fleuri Luxembourg and Maison Médicale Ettelbruck.
- School Testing: The department of microbiology helped implement the Ministry of Education’s testing strategy in schools with PCR testing targeting primary schools as the younger population (< 12 years old) were not vaccinated. The LNS deployed on average 12 teams working on the school testing.
- The national programme “COVID-19 vaccination Serology follow up – COVVAC Sero” (COVVAC SERO): The program was launched on 15 June 2021, in partnership with DISA to evaluate the development of antibodies post-vaccination and to create a national database for vaccination follow-up in nursing homes. For the sampling, a less invasive method was chosen, namely the DBS test. Patient were only required to provide a few drops of blood. The goal was to test interested individuals from the 66 different nursing homes in Luxembourg every 3 months to establish their antibody levels and to evaluate the effectiveness of the different types of vaccines that were currently used against the different SARS-CoV-2 variants.
- CORONAVAR: Detection of SARS-CoV-2 variants of concern in wastewater – The LNS department of microbiology participated in the CORONAVAR project (the Luxembourg National Research Fund (FNR) COVID-19 project) coordinated by the Luxembourg Institute of Science and Technology (LIST), which consisted in detecting and characterising SARS-CoV-2 variants circulating in Luxembourg wastewater. The data collected during the project provided the prevalence of SARS-CoV-2 new variants of interest (VOI) and of concern (VOC) in wastewater samples from approximately 75% of the Luxembourg population. This information was essential to help policy makers manage the health crisis and to set up or lift different protective measures for the population based on the prevalence estimates at the wastewater treatment plants.