Date: March 30, 2020

How HPC research is helping to fight the Corona virus

Camila Pontes received a Eurolab4HPC Short Term Collaboration Grant to stay 3 months (from January to March) in Alfonso Valencia's lab at the Barcelona Supercomputing Center. Due to the Corona virus, she had to go back home. It triggered her to adapt her research project to a coronavirus-related research project, since she got a grant, called Excalate4CoV, to work on this topic. Now she is involved in a coronavirus project, doing sequence and structural analysis of viral proteins of SARS-CoV-2.

The coronavirus responsible for the current Covid-19 pandemic, SARS-CoV-2, has on it’s surface a protein, called spike protein, that is responsible for the attachment to host cell receptors. This protein is also present in other types of coronaviruses, like SARS-CoV and MERS-CoV, which were responsible for epidemics in the past. In the context of the current Covid-19 pandemic, BSC’s Computational Biology Group is applying computational approaches to better understand what specific regions on the spike protein are important for host specificity, i.e. why some coronaviruses infect human and other coronaviruses infect other kinds of animals. As a part of the Exscalate4CoV project, our group identified important amino acid residues on the SARS-CoV-2 spike protein using a computational analysis based on a multiple sequence alignment. The identified residues were validated using available theoretical/experimental data and will be very important for guiding other types of computational research, like Molecular Dynamics simulations, as well as experimental assays for the development of treatments and vaccines.

The BSC-CNS is collaborating in the fight against the coronavirus in different fronts: 1) Investigating about the virus and possible treatments, by analyzing mutations on the coronavirus genome, and searching for possible drugs and immunologic therapies (antibodies and vaccines); 2) Employing artificial intelligence and natural language processing to analyze data about the propagation and impact of the epidemic in the society, generating data to help decision making; 3) Using the supercomputer MareNostrum 4 to internal research and giving access to external investigators working on the epidemic.