GIGA COVID-19 task force: 2 months into the pandemic
More than 175 GIGA members have joined what has become a “task force” with members of FARAH, the faculty of medicine, science and engineering for a total of 200. Here is a brief overview of what has been achieved so far.
RT-PCR testing platform
One of the major contributions of the COVID-19 task force was to establish, faster than anyone else in Belgium, an accredited testing platform with a capacity of 3,000 samples per day. This was to a large extend made possible by the expertise of the GIGA genomics platform and the Greenmat laboratory (Rudi Cloots), the dedication of Laurent Gillet (FARAH), and the determination of Fabrice Bureau (ULiege Vice-rector for research). It has been one of the pillars of the national task force. So far, RT-PCR required tedious upfront decontamination of arriving samples. Eight teams totalling 75 volunteers have rolled up their sleeves to handle up to 3,000 samples day in and day out, 7/7. Their team leaders have been awesome. Pre-processed samples are then shipped to the faculty of veterinary medicine (FARAH) for RNA extraction, RT-PCR and data-processing. This has made for long evenings for x teams totalling … volunteers from GIGA and the faculty of veterinary medicine. An impressive achievement. Congratulations to you all.
Next generation testing
RT-PCR based testing is unlikely to provide the testing capacity needed to allow society’s return to normalcy in the safest conditions. GIGA members helped by people from the faculties of science and engineering are working on faster - yet equally accurate - tests for the presence of the viral genome using LAMP, Cas12/13, pooling, and next generation sequencing. Testing for the presence of the virus is advantageously complemented by testing for circulating anti-SARS-CoV-2 antibodies. Currently available serological tests do not distinguish between neutralizing (possibly conferring protection) and non-neutralizing antibodies. GIGA members are engaged with local companies to develop such tests.
Too much remains unknown about the pathophysiology of COVID-19. Why are some people developing a lethal disease when others easily overcome the infection? Is there a genetic predisposition to COVID-19? What is the nature of the immune response and immuno-pathology? What is the impact of previous exposures to infectious agents on the outcome of COVID-19? There will be ample opportunities for GIGA scientists to study these and other fundamental questions provided that study material is available. Thirty-six GIGA members have put on PPE’s and have entered L3 labs to process samples collected weekly from the >250 COVID-19 patients that have been hospitalized at the CHU or Mont Legia ICU. How widespread is COVID-19 and how rapidly does it penetrate the population? How many of us have been exposed to the virus and have developed a protective immune response? To address such essential questions, the CHU of Liège has initiated a large experiment based on the collection of samples from >3,000 people working on the CHU sub-campus (including GIGA). Members from the GIGA-Consciousness and GIGA-CRC thematic research units have assisted Stéphanie Gofflot’s team to process the thousands of bloods. All samples, whether from patients or healthy people, are being deposited in the BHUL (Biothèque Hospitalo-Universitaire de Liège) to support future research efforts by the local community, often in the context of international consortia.
One option to treat the most severe COVID-19 cases that is being explored in many countries (including Belgium) are transfusions with plasma from convalescents. Yet the presumptive plasmas need to be tested for their ability to neutralize the virus. Through the laboratories of Dr. Daniel Desmecht and Mutien Garigliany of FARAH, ULiège has the exceptional capability to perform these tests. Ten GIGA members have been trained in the manipulation of SARS-CoV-2 to test plasmas provided by the Belgian Red Cross.
Sequencing the viral genome
Is the severity of COVID-19 in a way related to the SARS-CoV-2 strain? Does the sequence of the viral genome changes as disease progresses and extends to different tissues? Can we better monitor the epidemy by tracking viral strains? Two GIGA members from Dr. Vincent Bours’ team have sequenced more SARS-CoV-2 genomes than any other Belgian laboratory (nextrain.org) using Oxford Nanopore technology. The plan is to sequence the viral genome from all CHU COVID-19 patients.
Getting the COVID-19 task force up and running required enormous assistance and support at many levels. GIGA administration has been there, responding to the demands of the community without counting hours, committed to help us all through these unusual times. Many volunteers have brought exotic meals, pastry, food and other goodies for the doctors and nurses on the front-line.
We are going together through a once in-a-lifetime crisis. It looks like we are past the epidemic’s peak, yet COVID-19 is not over. We will still have to deal with security measures for a while. Thank you to all of these people for their almost inexhaustible investment with such positive spirit. This pandemic demonstrates more than ever that the interdisciplinarity, interactions and complementarity, at the basis of the concept of GIGA, are the best solutions for moving forward!