Using computational models to predict the spread of coronavirus
Due to the increasing mobility of people on a global scale, infectious diseases now spread rapidly and frequently reach epidemic, and in the case of the current COVID-19 virus, even pandemic proportions. How can the spread of such epidemics be better predicted, anticipated and controlled?
Vittoria Colizza, ERC grantee, computational epidemiologist and research director at INSERM:
I work in computational epidemiology, a new scientific discipline that brings together mathematics, statistics, computational sciences and epidemiology. This novel combination of different scientific disciplines and methods enables us, among other things, to collect and integrate massive datasets on historical epidemics with which to develop computational models. Such models can then be used to provide reliable, detailed and accurate predictions of the spread of future epidemics.
As part of the ERC-funded EPIFOR project, which ran from 2008-2013, together with my team I have developed an array of computational tools that could provide accurate predictions of future viral outbreaks, enabling a timely and efficient response to the threat. The aim was to enhance our ability to control the transmission of a disease, to better target interventions and to understand more about its effects on large populations.
During the lifetime of the project, we faced two emerging epidemics – the 2009 H1N1 pandemic (or swine flu) and the MERS-CoV epidemic – so we were able to concretely test our innovative approaches in real-life situations. These experiments confirmed the significant capabilities of the computational models developed and provided useful patterns on the potential future spread of infectious diseases.
Today I am research director at INSERM (French National Institute for Health and Medical Research), where we are working around the clock as part of a multi-disciplinary team to help manage the health crisis caused by the COVID-19 outbreak. Our work is supported by several other H2020 projects; however, the computational models and other tools developed during the EPIFOR project laid the foundation for this work and are proving to be instrumental. Over the course of the last couple of months, we have produced several important papers, using computational models to predict the spread of the disease and the expected impact of mitigation measures being implemented all over Europe.
Fighting the disinformation pandemic
Covid-19 is keeping people indoors, forcing us to social distance to try and contain the virus SARS-CoV-2. But while we sit at home, another aspect of this diseaseis proving rather "viral".
The spread of fake news linked to its nature, propagation and cure seems as inevitable as it is damaging. Philip Howard, director of the the Oxford Internet Institute and ERC grantee talks to us about who stands to benefit from this different type of pandemic, why it occurs, and how we can behave to prevent untrustworthy information from circulating.
Developing SARS-CoV-2 antiviral drugs
Marcin Nowotny, Group Leader, International Institute of Molecular and Cell Biology in Warsaw, Poland, was awarded ERC Starting Grant in 2011.
'We are a molecular biology group at the International Institute of Molecular and Cell Biology in Warsaw. In our work, we predominantly use two methods: protein crystallography and recently also cryo-electron microscopy. The two methods allow us to visualise molecules which are the gears of each living cell at the level of single atoms. This in turn allows us to understand how these molecules function in health and disease.
To understand how molecules function in health and disease
The ERC grant was the main source of funding for our group for several years. It was thus instrumental in consolidating our research potential and also allowed us to explore medically relevant aspects of the atomic structures of proteins. For example, as a part of our ERC project we studied a protein that is in involved in the maintenance of the genetic information, which prevents mutations and cancer. Using protein crystallography we defined for the first time the atomic structure of this protein and its mechanism of action. Defects in this protein in humans lead to severe genetic diseases and we proposed the basis of these defects at the atomic level.
ERC grant was instrumental in consolidating our research potential
The information about the atomic structure of biological molecules is also instrumental in the design of new drugs. These are usually small molecules that specifically stick to a particular protein and block it. Over the last six years a subdivision of our group collaborated closely with the pharmaceutical industry on numerous projects in which we determined three-dimensional atomic structures of proteins with bound potential drugs. Such structures are invaluable in understanding how potential drugs work and in rational computational improvement of their properties.
Now we will contribute our research potential to the [coronavirus] project
We will now contribute our research potential to the project which aims at developing drugs for combating the new SARS-CoV-2 virus. We are part of large consortium EXSCALATE4CoV coordinated by an Italian company Dompe, which aims at developing substances that can be developed into antiviral drugs. The first step is a powerful computational search for candidate substances. The found chemicals will be next characterised experimentally and we will be involved in the determination of the atomic structures of viral proteins with bound candidate substances identified through the search. This information can be used to further optimise the initial compounds to develop them into antiviral drugs.'
The basic science of immunity
Aleksandra Walczak, Research Director, Centre national de la recherche scientifique, France, was awarded ERC Starting Grant in 2012 and Consolidator Grant in 2016. In 2018 she was awarded ERC Proof of Concept Grant.
'I’m a physicist and I study the adaptive immune system. This is the army of cells that protects us from attacks, for example from viruses. They have specialised receptors that can recognise and respond to different pathogens. We have around the same number of receptors as there are people on the planet, and the composition of the cells with different receptors changes throughout our life. It’s a dynamic, complex system that can only be understood statistically.
There are many things we don’t understand about [immunity]
We know this system works. We fight infections. But there are many things we don’t understand about it. For example, we’re hearing recently that different individuals show different reactions to COVID-19. Why is this? What makes a good immune system? What makes a bad immune system? Even if we are generally considered healthy, we’re not the same. This is clearer now more than ever.
In my ERC grant, my team and I study the co-evolution of viruses and the immune system. On the one hand, if we encounter a pathogen, the immune system will change to control it as best as it can. On the other hand, you can think of the spread of the virus as a pinball machine. We all put pressure on it by trying to fight it, so the virus evolves rapidly to try and find a way to move to a new host. They shape each other.
Basic science is important
think this is a moment when everyone is realising that basic science is important. My group’s research is not directly in the battlefield, we will not find the immediate solution in a day or a month. But perhaps we can help answer basic questions like why are we seeing so many different responses to the virus and can we help people in some way? And, as the situation evolves, how will the virus coevolve to stay in the population? At the moment we don’t have a framework to think about these problems, but this is what me and the people I work with are trying to achieve.'