Laureate Philippe LEMEY

Ceremony of the Francqui-Collen Prizes 2023 by His Majesty the King
at the Palais des Académies on June 6, 2023 (by invitation only).

Philippe LEMEY
Clinical & Translational Research

Career– Research – Report of the Jury – Speeches

His career

Philippe Lemey was born in Kortrijk on August 10, 1977. After secondary education at the St.-Jozefsinstituut in Kortrijk, he studied Pharmaceutical Sciences at the KU Leuven where he graduated magna cum laude in 2000. During an internship at the Department of Clinical and Epidemiological Virology at the Rega Institute under the supervision of Prof. dr. Marc Van Ranst, he developed an interest in viruses and became fascinated by the role of bioinformatics in genetic research. Therefore, he decided to start a PhD at this department, this time under the supervision of Prof. Anne-Mieke Vandamme, for which he was awarded a grant by the agency for Innovation by Science and Technology (IWT). Philippe studied the evolution of human retroviruses and unraveled, among other things, the origin and epidemic spread of specific variants of the human immunodeficiency virus (HIV). To further develop his knowledge in computational analyses, he combined his PhD with a Master of Bioinformatics training at KU Leuven.

After completing his PhD in 2005, he continued his career as a postdoctoral researcher at the Department of Zoology, University of Oxford, supported first by a grant from the European Organization of Molecular Biology (EMBO) and then by a European Marie-Curie grant. In this new environment, he focused even more on computational analysis of various viruses and began to work on the second edition of ‘The Phylogenetic Handbook’, a comprehensive book on the theory and practice of phylogenetic and population genetic analysis that was finally published in 2009. This book became a reference work in its discipline. Before returning to the Rega Institute, Philippe joined the Isaac Newton Institute for Mathematical Sciences in Cambridge during the Phylogenetics Program in 2007.

After a postdoctoral fellowship supported by the Research Foundation – Flanders (FWO) at KU Leuven, Philippe started his own multidisciplinary research group at the Rega Institute in 2010. Supported by an ERC starting grant from the European Research Council, he and his team developed computational methodology to map the spread of viruses based on their genetic information. With the help of an ERC consolidator grant, this was further expanded and applied to various viruses such as Ebola, rabies, influenza and SARS-CoV-2. He also integrated molecular biological techniques in his research to produce viral genetic data. The importance of this work for molecular epidemiology and epidemic response represents a crucial translational impact. Philippe’s research was rewarded with the prize ‘Dr. Luc Broeckaert and Mrs. Annie Depreeuw 2014’ awarded by the Royal Academy of Medicine, the prize of the ‘Centre d’Études Princess Joséphine-Charlotte’ (2017), and the international ‘Mitchell Prize’ in Bayesian statistics.

Philippe Lemey is married to Lieve Van Hoovels, Clinical Biologist. They have two wonderful daughters, Hanne (13 years old) and Margot (9 years old).

 

His research

Where do new viruses come from and how are we exposed to them? How do they adapt in a new host and how do they evade immune responses? How do they evolve and spread? These are some of the questions that attracted Philippe to study viruses based on their genetic information. He initially had a strong focus on HIV, and using evolutionary reconstructions he showed where, when and under what conditions the two main types of this virus began to spread in the human population. He also showed how the evolution of the virus within the host is related to disease development.

This research and the emergence of new technologies to obtain genetic data motivated Philippe to develop new statistical and computational techniques to accurately extract a maximum amount of information from sequence data. With new models that were implemented in a popular software, he and his team showed how the spread of viruses can be mapped in extensive detail. In addition, new data integration methods were applied to identify the factors underlying their spread. This methodology was widely applicable and allowed, for example, to unravel the worldwide spread of the seasonal flu virus and to relate the difference in success of different variants to the way they evolve. The methods could also be applied to create a ‘genomic anatomy’ of the Ebola virus outbreak and to demonstrate how this virus could spread on a large scale. In a follow-up work, he illustrated how such techniques also allow for the evaluation of intervention strategies. When this virus reappeared in 2021, Philippe contributed evolutionary analyzes to show that this was due to a persistent infection with reduced replication or latency.

During the Ebola outbreak in West Africa, it became clear that viral genomic information can play an important role in the epidemic response. Philippe’s team therefore conducted further methodological research and developed a way to efficiently incorporate new information into evolutionary reconstructions. In addition, he also supported molecular surveillance using portable sequencing technology. An example of this is a collaboration with the Bernard-Nocht Institute in Hamburg that aimed to explain the increased incidence of Lassa virus in Nigeria. This could be attributed to an increased spill-over from the rodent reservoir and was therefore not due to human transmission of specific virus strains. This provided important information for local health authorities to help contain the spread of Lassa.

The COVID-19 pandemic has shown how vulnerable our society is to new viruses and what efforts are needed to combat them. Philippe has made several contributions to our knowledge of the SARS-CoV-2 virus and how this epidemic originated. Together with colleagues, the evolutionary history of this virus in the bat reservoir was unraveled and conspiracy theories about the origin of the virus were disproved. Philippe developed new methods to integrate travel history and human mobility in evolutionary reconstructions. Using these, he mapped the early global spread of the virus and then showed how the second wave arose in Europe through a large number of new introductions associated with summer vacation travel. In addition, Philippe also supported research of his colleagues, such as vaccine research at the Rega Institute, and provided advice to the World Health Organization. Philippe considers it important that other researchers, especially the new generation of researchers, have access to the methods developed by his team and therefore supports several international workshops.

 

Report of the Jury (April 25, 2023)

The 2023 Francqui Prize in Clinical and Translational Research is awarded to Professor Philippe Lemey who is undoubtedly among a handful of global leaders in the field of computational biology specialised in viral phylogeny and phylodynamic analysis. Trained both in pharmaceutical sciences and in bioinformatics, he combines insights in infection biology with the development of computational tools to understand origins and evolution of viruses of global public health importance. Basic insights from his fundamental research on viral replication processes have been incorporated in the development of software tools that within a short period of time have become the working horses of virology, viral bioinformatics, and viral epidemiology.  He has developed and co-developed key bioinformatics tools that have revolutionised the field of virology and our understanding of how viruses evolve, spread, cause impact and can be controlled.

In addition to its methodological value, his work has facilitated broad uptake, thanks to the user friendliness of the software produced, the open sharing of code, and his highly valued courses. Philippe Lemey has been a core teacher, training the new leaders in this field globally. His publication record testifies to the global impact of his work, addressing key questions in our understanding of emergence, spread, evolution and effectiveness of control measures of several major viral pathogens. These include the viruses causing Covid-19, dengue fever, Ebola haemorrhagic fever, acquired human immunodeficiency syndrome, Lassa fever, measles, rabies, rinderpest, swine influenza, West Nile fever and yellow fever.

The field of viral genomics is one of the most rapidly evolving fields in science, raising important new challenges that require fundamentally new ways of exploring viral evolution. Philippe Lemey is well positioned to continue to lead the field in a new era of big data applications needed to understand virology now and in the future.

Members of the international jury :

Hans Clevers obtained his MD degree in 1984 and his PhD degree in 1985 from the University Utrecht, the Netherlands. His postdoctoral work (1986-1989) was done with Cox Terhorst at the Dana-Farber Cancer Institute of Harvard University, Boston, USA. From 1991-2002 Hans Clevers was Professor in Immunology at the University Utrecht and, since 2002, Professor in
Molecular Genetics. From 2002-2012 he was director of the Hubrecht Institute in Utrecht. From 2012-2015 he was President of the Royal Netherlands Academy of Arts and Sciences (KNAW). From June 2015-2019 he was director Research of the Princess Máxima Center for pediatric oncology. Since March 2022, Hans Clevers is Head of Pharma Research and Early Development (pRED) of Roche, Basel Switzerland.

– Chairman of the Jury

and

Azad Bonni serves in an executive leadership role at Roche as Senior Vice President and Global Head of Neuroscience and Rare Diseases in pRED. He oversees a rich and differentiated portfolio from research to completion of Phase 2 trials. Before Roche, Azad was Head of Neuroscience at Washington University in St Louis, and prior to that Professor of Neurobiology at Harvard. Azad is an international leader in neuroscience who has made fundamental discoveries on mechanisms of neuronal connectivity in the brain. He received his MD at Queen’s University, neurology residency at McGill University, and PhD and postdoctoral training at Harvard University. Azad has trained over 40 exceptional graduate students and postdoctoral fellows, many of whom have launched their own independent laboratories at prestigious institutions. He has received numerous honors and awards including election to the American Association for the Advancement of Science, Royal Society of Canada, and National Academy of Medicine.

Boudewijn Burgering is professor in Signal transduction at the Center of Molecular Medicine ( University Medical Center Utrecht, the Netherlands ). His research revolves around the role of PI3K signaling in disease and ageing, with a focus on the role of the kinase PKB/AKT and the transcription factor family FOXO. He made some high impact discoveries in this field and is EMBO member and member of Dutch consortium Oncode, acting on various reviewing committees, including ERC and organizer of international meetings.

Anne Grapin-Botton studied at Ecole Normale Superieure (Cachan) and University Paris 7. She obtained a PhD from University Paris 6, focusing on nervous system development and studied endoderm development as a post-doc in Harvard University. Anne Grapin-Botton and her group investigate the impact of the cellular and organ architecture on the cells’ fate choices and how single cells act in a community to generate an organ. To do so, they use mouse genetics, live imaging in 3D and they developed 3D in vitro “organoid” culture systems modelling development. More recently they used human in vitro stem cell models investigate human development. These studies are intended to gain insight into human syndromes impairing pancreas development and they guide the generation of replacement beta cells for Diabetes therapy.

Guido Kroemer is currently Professor at the Faculty of Medicine of the University of Paris-Cité, Director of the research team « Metabolism, Cancer and Immunity » of the French Medical Research Council (INSERM), Director of the Metabolomics and Cell Biology platforms of the Gustave Roussy Comprehensive Cancer Center, and Hospital Practitioner at the Hôpital Européen George Pompidou, Paris, France. Dr. Kroemer’s work focuses on the pathophysiological implications of cell stress and death in the context of aging, cancer and inflammation. »

Akiko Iwasaki, Ph.D. is a Sterling Professor of Immunobiology at the Yale University School of Medicine. Her research focuses on the mechanisms of immune defense against viruses at mucosal surfaces, which are a major site of entry for infectious agents. Professor Iwasaki received her Ph.D. in Immunology from the University of Toronto and completed her postdoctoral training with the National Institutes of Health before joining Yale’s faculty in 2000. She has received many awards and honors and has been a Howard Hughes Medical Institute Investigator since 2014. She was elected to the National Academy of Sciences in 2018, to the National Academy of Medicine in 2019 and to the American Academy of Arts and Sciences in 2021. Professor Iwasaki has been a leading scientific voice during the COVID-19 pandemic and is also well known for her Twitter advocacy on women and underrepresented minorities in the science and medicine fields and has been named to the 2023 STATUS list of the ultimate list of leaders in life sciences.

Marion Koopmans is director of the Department of Viroscience at Erasmus Medical Centre in The Netherlands, the WHO collaborating centre for Emerging Infectious Diseases (EID), director for EID of the Netherlands Centre for One Health NCOH and scientific director of the Pandemic and Disaster Preparedness Centre in Rotterdam/Delft, The Netherlands.

Her research focuses on emerging infections with special emphasis on unravelling pathways of disease emergence and spread at the human animal interface. Koopmans coordinates the EU funded consortium VEO, which develops risk based innovative early warning surveillance in a One Health context, and is deputy coordinator of a recently awarded HERA funded network of centres of excellence for EID research preparedness.

Ton Logtenberg is an immunologist and professor in the Center for Translational Immunology in the University Medical Center Utrecht, The Netherlands. Ton is the founder and former President and CEO of Merus, a Nasdaq listed clinical-stage biotechnology company advancing targeted treatments based on multi-specific antibodies to address the unmet needs of cancer patients. He is the Chairman of the Board of biotechnology companies Synox Therapeutics and Mestag Therapeutics and a Board member of the Forbion European Acquisition Corporation. Ton is a Venture Parture at Forbion Capital Partners, a Dutch VC firm that invests in Life Science companies.

Tamara Schikowski is an Environmental Epidemiologist and is currently head of the research group ‘Environmental epidemiology of lung, brain, and skin aging’ at the IUF-Leibniz Research Institute of Environmental Medicine in Duesseldorf, Germany.
Her research is directed at understanding how long-term exposure to air pollution and other environmental influences can cause diseases in populations, in particular in vulnerable groups such as the elderly and children. She is PI of several large-scale cohort studies and is involved in many national and international projects in China, India, and Japan. She is an executive board member of the German National Cohort (NAKO).

– Members of the Jury

 

(Translated) Speech of Count Herman Van Rompuy
President of the Francqui Foudation

It feels good to be here with many, in contrast to the corona days. Back then we were only a few to be present here, though always in the presence of His Majesty the King, who insisted on personally presenting the highest scientific awards in our country. I say this because one of our two laureates, Professor Philippe Lemey, is being awarded for his pioneering research to combat the spread of viral infections. So at the Francqui Foundation we have not forgotten the pandemic. We must not fall into the trap of contemporary « actualism » where a page is turned too quickly and where sometimes too few lessons are drawn from history, even from recent history. Sometimes one draws conclusions too quickly, sometimes one forgets too quickly. For better or worse, we must remain lucid and judge each fact correctly. This is called wisdom.

In general, we must continue to think about the longer term. We must not give in to the great impatience that demands immediate results, including from research. Scientific research and development are the greatest investments in the future, both fundamental and applied research. This is why the work on the spread of cancer by our other Francqui-Collen Prize laureate Professor Sarah-Maria Fendt is so important. She, too, works at the KU Leuven. We are a country of major manufacturing pharmaceutical industries, both in the North and in the South of Belgium, but we are also in the koppelet in terms of medical research. The pandemic has affected us all and the fight against cancer has great support among the people, partially thanks to the actions of « Kom op tegen kanker ». Thus, the Francqui-Collen Prize closely matches the concerns and fears of a large majority of our compatriots. There is no gap between our agenda and that of the citizens of this country.

We owe this especially to the international jury headed by Professor Hans Clevers, himself a very distinguished researcher at the university and beyond. The jury does not take into account our many internal subtle balances but chooses the best, ‘merit based’. We also thank Professor Pierre van Moerbeke who guided the jury process from beginning to end. And we thank Professor Désiré Collen for his generosity and his support for scientific research in which he himself excelled.

The international jury awarded the two prizes after extensive deliberations. Their decisions are as follows.

Sarah-Maria Fendt focuses her fundamental research on cancer cell metastasis, in particular on the nutrients cancer cells need to proliferate in other parts of the body. Sarah-Maria Fendt and her team have discovered that these cells feed differently depending on where they spread. This process is known as metastasis. In addition, her research has shown that by targeting nutrient processing, it is possible to reduce cancer cell multiplication and proliferation in distant organs. Today, most cancer patients die of metastatic disease. The findings of Professor Fendt and her team pave the way for new, life-saving treatments.

Professor Fendt is not only interested in the nutrition of proliferating cancer cells, but also in the nutrition of patients. In her research on mice, she has found that a high-fat diet promotes the spread of cancer. In a forthcoming study, Professor Fendt and her team aim to discover that certain diets can also prevent the spread of cancer.

Scientific discoveries can sometimes be dangerous. Think of the atomic bomb or some forms of artificial intelligence, but with cancer research there is no doubt. The goal is to save an untold number of human lives or preserve the quality of life. That is meaningful in itself. And when I say meaningful it means that it serves other people. That could include you and me, because disease does not discriminate between people.

Thanks to his applied research, Philippe Lemey has developed important tools to combat the spread of viruses. These tools, implemented in the « BEAST » software program, map the genetic code of viruses in real time, enabling governments and health professionals to rapidly gain a clearer picture of the appearance of a virus, and take immediate action to halt its spread. For example, the program played a decisive role during the Ebola epidemic in West Africa (2014-2016) and the Lassa epidemic in Central Africa (2018).

Today, the software to which Philippe Lemey has contributed since 2004, is considered the global workhorse of genomic epi-demiology. It has revolutionized virology and our understanding of how viruses evolve, spread, impact and can be controlled.

The pandemic helped us discover virology and virologists. Together with the governments and thanks to the discipline of the vast majority of our fellow citizens, they have saved millions of lives around the world. Here too, there is no need to question the point of scientific research. It is self-evident.

The rationality of science contrasts sharply with the irrationality we too often find elsewhere. There is no rational or ethical argument to justify a war of conquest, or to envisage such a war. Today, there are even threats of nuclear war. Nostalgic or imperial nationalism is a disease we thought belonged to yesterday’s world. We were mistaken. Of course, we must respond to fear and uncertainty, but we must not contribute to reinforcing these negative emotions.

Reason and fairness together with the classical virtues of prudence, courage, moderation and justice, are the only chance for a good life for all. Only in that climate can there be creativity, innovation and open-minded inquiry. Only in that spiritual climate can we tackle the greatest problem of our time – the climate itself. The universities have the vocation to continue working on this. Much is at stake. We do not live in « business as usual » time.

The scientists we honor today are not only exceptional researchers but also demonstrate an ethical drive to do the right thing. We are all at the service of people’s health and well-being, at the service of the common good, the bonum commune. The Francqui-Collen Prize also serves this idea and this ideal.

All of us gathered here, and many others outside this room, are proud to see that our men and women are recognized far beyond our borders. We want to thank them today in their own countries.

I congratulate them once again.

 

(Translated) Speech of Professor Philippe Lemey

Sire,

First and foremost, I want to thank You for continuing to support this meeting with your presence. It is an important sign of appreciation for science in this country, especially in times when society’s trust in science is not readily apparent.

Geachte voorzitter, zeer geachte Dames en Heren, Chers Mesdames et Messieurs,

The list of laureates in past years for this prestigious Francqui-Collen Prize is nothing short of impressive, so it is with great humility that I am able to stand here today. Viruses have been in the news often, perhaps far too often, in recent years. We have all witnessed how they can turn the world upside down, affect our health and disrupt our society. But we are not helpless against them either. Tremendous efforts have been made from health care and science to combat COVID-19, and the Rega Institute in Leuven also made important contributions.

Viruses are the most widespread biological entities on earth. They exist in every form of life we know, and probably appeared very early in the evolution of the first life forms. Some have been circulating among humankind for a very long time, while others have only recently appeared. For many viruses, an important part of their success lies in the speed at which they evolve. This enables them to adapt rapidly to a new host and bypass our immune defenses. But it also makes their genomes an important source of information for reconstructing their evolutionary history and spread.

That we can work with this in epidemiology, has been known for some time. To handle this molecular information, we need powerful computational methods and statistical models based on principles from evolutionary biology. Using such bioinformatic analyses, we have been able to figure out, for example, how the human immunodeficiency virus, the cause of the AIDS pandemic, made the leap from ape to man around the beginning of the 20th century, spread further in Central Africa before finally being introduced to the United States via the Caribbean, where it was only discovered decades later as the AIDS virus. Such research is fertile ground for multi-disciplinarity; indeed, I have been fortunate to work on such projects with medics, historians and anthropologists.

Technological advances have generated a huge increase in the volume of genetic data. How we can process and transform this data into useful knowledge has taken on crucial importance. For COVID-19, over 15 million genomes have already been obtained. During the largest epidemic that preceded it – the Ebola outbreak in West Africa during the years 2014 to 2016 – it was still just 1,500 genomes. But it was then that the foundations were laid for making molecular epidemiology a key element in epidemic response. New sequencing technologies were implemented to rapidly generate viral genomes. It became clear that viral genome analysis could contribute to contact tracing. And when colleagues and I were able to integrate all the data from the various independent efforts, it was possible to piece together a detailed picture of the spread of the virus. It became clear to many of us that we could take this research in a new direction – one that wasn’t so much about historical reconstructions, but which could provide important information during the spread of an epidemic.

With molecular epidemiology, we do not cure patients, but we can get insights to develop intervention strategies to curb infection rates. That is the translational aspect of our discipline. A concrete example was when in 2018 the incidence of Lassa virus, which like Ebola can cause severe hemorrhagic fever, increased dramatically in Nigeria where it is endemic. The fear was that a new variant could be more easily transmitted from person to person. With colleagues, we were then able to very quickly characterize the viruses responsible for this outbreak. We were able to show that this was a major transmission of rodent viruses to humans and this was important information for the local health authorities; instead of focusing on human-to-human transmission, there was a need for sanitation and pest control.

The fight against infectious diseases requires the efforts of a whole community of researchers, and involves different players from health authorities and various fields of research. I’m delighted that this prize is highlighting computational work. Bioinformatics has long been regarded as a discipline supporting other fields of research, and this is still the case. But it is increasingly playing a central role and building bridges between research fields. The methods we have developed to study viruses are also used in bacteriology, in evolutionary biology in the broadest sense, and even beyond, as in historical linguistics. That knowledge of evolutionary biology can have a major impact on the medical sciences was also demonstrated by the Nobel Prize for Medicine awarded last year to Svante Pääbo for his discoveries on human evolution.

Isaac Newton once said « If I have been able to see a little farther, it is because I stand on the shoulders of giants.« . This principle applies generally in science. We build on the insights and developments of others and it is important to recognize this. I can name many names from epidemiology, statistics and evolutionary biology who have all made crucial contributions to the insights and possibilities we have at hand today. But today I want to thank especially those who have supported me and given me the opportunity to contribute to science in turn. First and foremost, I thank Annemie Vandamme and Marc Van Ranst who allowed me to take my first steps in science and to whom I can still turn for advice. I would also like to thank colleagues in our branch, our department and far beyond. I am also thinking of international colleagues, some of whom have become close friends. I am grateful to Erik De Clercq and Piet Herdewijn, both professors emeriti, from the Rega Institute for supporting my candidacy for this award. Erik, my respect for what you have meant to the Rega and antiviral research is enormous. I am grateful to the current and former members from my research group – they are the ones who make the concrete efforts on the ground, and nothing creates more pleasure in this job than seeing them grow into independent researchers themselves. It is also important to thank the funding agencies, in my case the Fund for Scientific Research Flanders and the European Research Council. I hope that, like the Francqui Foundation, they can remain committed to basic and translational research of an innovative nature.

I am grateful to friends and family, and to my parents in particular. I think of my late father from whom I inherited the love of both science and computer science. And finally, also my own family. Lieve, you have yourself a demanding job and you make your own strides in science. Yet you continue to set the example of how to put our family, Hanne and Margot, at the center of our lives. For this, we also get a lot of support from our parents.

It is a great honor to receive this award for clinical and translational research from you. It is an enormous motivation to pursue this research with heart and soul in the years to come. In this way, I also hope to inspire the next generation of young researchers.

I thank you from the bottom of my heart.