SARS-CoV-2 Through the Lens of Computational Biology:How bioinformatics is playing a key role in the study of the virus and its origins

In December 2019, the Chinese Center for Disease Control reported several cases of severe pneumonia that resisted usual treatments inthe city of Wuhan. This announcement marked the beginning of the COVID19 pandemic, which caused more than 80 million infection casesand 1.7 million deaths worldwide in 2020 alone and is still raging. The pandemic has given rise to global public health responses and international research efforts of unprecedented scope and speed. This scientific mobilization has yielded remarkable results, enabling a great deal of knowledge accumulation in just a few months: from the identification of the virus and its main proteins to the analysis of its origin and mechanisms. This basic biological knowledge is mandatory for medical advances.In this document, one year after the beginning of the spread of the disease, we wish to shed particular light on the contribution of bioinformatics in all this work. This discipline, at the crossroads of computer sciences, mathematics, biology, and physics, has taken oninestimable importance in modern biology and medicine. It provides computational models, algorithms, software, and guidelines to help thescientific community handle biological data and accelerate research. The discovery and study of the SARS-CoV-2 coronavirus is an emblematicexample of these contributions. Bioinformatics methods have been at the heart of several essential milestones: sequencing the virus genome, analyzing its origin and evolutionary dynamics, modeling interacting biological entities at the structural and network scales, and studying host genetic susceptibility. For several of these topics, research on SARS-CoV-2 could benefit from a wide range of off-the-shelf software packages that rely on well-established algorithms developed by the bioinformatics community over the years. For other topics, the analysis of SARS-CoV-2 pushes the limits of knowledge and invites the community to develop new computational models and methods. This work, as a whole, has made it possible to elucidate the nature and the functioning of the novel pathogen. It has contributed to the fight against COVID19, even if much remains to be done to fully understand the disease and control the epidemic