Covid-19: in a race against the clock

Posted on: March 25, 2020 by Natalia Jiménez Lozano

We are in uncharted territory: the effects of the Covid-19 pandemic are unfolding rapidly, with profound effects on bereaved families and on people's health and prosperity around the world. Yet while today’s events are unprecedented, so too are the capabilities of advanced computing to help human beings combat the disease.

Time is now of the essence as agencies everywhere work hard to contain the outbreak while scientists continue their search for a cure. Artificial intelligence (AI), in combination with high performance, edge and quantum computing, all increase and accelerate humans’ ability to understand the virus itself and the mechanism of the disease, and then develop a vaccine.

Modelling the structure of the virus

Researchers at the Biocomputing Unit of the Spanish National Center for Biotechnology (CNB-CSIC) and the Instruct Image Processing Center (CSIC and Spanish Ministry of Research), headed by Prof. Carazo and Dr Sorzano, as many other groups all over the world, use a range of scientific techniques, supported by computing power and complex algorithms, to unlock the mysteries of macromolecules. 3D cryoelectron microscopy (3D cryo-EM) stands out among these techniques because it enables scientists to create 3D models of molecular structures, the very building blocks of life. Having a 3D model of target molecules is key for research institutes and pharmaceutical companies to find a vaccine. Yet without large storage servers and a whole complement of GPUs and CPUs clusters, these approaches would be unthinkable.

In the context of 2019-nCoV global emergency, Prof. McLellan and his team from the University of Texas at Austin, have been using 3D cryo-EM and applying a whole variety of computational techniques. As a result, the team has been able to decipher the 3D structure of a key viral complex: the ‘spike’ that actually binds to the target cell, initiating infection.

A key step forward

This was a complex specimen to work with, and the resolution achieved made difficult in some cases to identify the molecular entities involved and their relative spatial positions. The use of the Instruct Center state-of-the-art methodologies, and in particular the approach known as ‘LocalDeblurr’, enabled the team to increase the informational content of some areas of the reconstructed map in order to better understand this macromolecule, which could perhaps be the real ‘key’ to unlocking the virus.

This is a step forward in the functional understanding of the viral infection mechanism, although there is still some way to go until this is of practical clinical use. There is no doubt that the combination of impeccable sample preparation methods, outstanding microscopy techniques, and cutting-edge algorithms running on powerful computers, has all been critical to this success.

Visualizing the mechanics of the infection

Understanding how the infection works in individual and populations is also ongoing. Research scientists and clinicians must carry out complex simulations of how the virus infects a cell and spreads to better understand the mechanics of the disease. Simulating the performance of drugs against the virus can also be very useful to speed up the production of new treatments. Once again, advanced computing and data are a vital part of the picture.

In addition to high performance computing, edge computing can transform what humans can achieve because data can be collected and analyzed in a distributed way, ‘at the edge’, rather than by a centralized computer. This can vastly increase and accelerate research scientists’ capabilities’ because the processes can be simulated in real time, using big data (in the form of biological data) close to where the data is generated. In addition, emergent quantum computing offers exponentially increased computing capability to enable almost unimaginably complex and fast simulations.

Toward a new antidote

As new diseases advance, so too do technologies as their digital antidote. In parallel with the research and drug discovery process, by collecting and analyzing data from various medical organizations, technology platforms enable agencies to predict how 2019nCoV is spreading in order to define the appropriate measures to contain the outbreak and shape the best-possible emergency response.

In the still-unknown territory of this new virus, it's clear that collaboration between the scientific community and leading digital providers is mission-critical. The combination of human intelligence with the world’s most advanced computing offers more power than ever before to win the fight against 2019nCoV.

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About Natalia Jiménez Lozano
Director, Atos HPC, AI & Quantum Life Sciences CoE, Distinguished Expert and member of the Scientific Community
Natalia has a MSc in Biochemistry and PhD in Molecular Biology. Working in life sciences and technology since 2012, following 14 years in bioinformatics research, Natalia’s contributions have already been profound and significant. Having pioneered the development and application of the Precision Medicine model and since seen her vision realised in frontline care, in 2020 she achieved her dream of opening the HPC, AI and Quantum Life Sciences Centre of Excellence in Cambridge. She has been instrumental in starting a new chapter for Atos, partners, and customers to accelerate innovation to improve health outcomes and wellbeing of people worldwide.  

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