How to track the variants of the pandemic faster

Emma Hodcroft, PhD © Oliver Hochstrasser - A global group of researchers is calling for better integration of viral genetics, bioinformatics, and public health to enable better pandemic response now and better pandemic preparedness in the future. In a comment piece , an international collaboration of specialists in viral and genetic analysis lay out the 'bioinformatics bottlenecks' that are hindering response to the SARS-CoV-2 pandemic, and propose ways to 'clear the road' for better tools and approaches. "What scientists have achieved in a year since the discovery of a brand-new virus is truly remarkable,' says Emma Hodcroft from the Institute of Social and Preventive Medicine (ISPM) of the University of Bern, first author on the piece, "but the tools scientists are using to study how SARS-CoV-2 is transmitting and changing were never designed for the unique pressures - or volumes of data - of this pandemic.' SARS-CoV-2 is now one of the most sequenced pathogens of all time, with over 600,000 full-genome sequences having been generated since the pandemic began, and over 5,000 new sequences coming in from around the world every day. However, the analysis and visualization tools used today (including Nextstrain, co-developed by Prof. Richard Neher's group at the SIB and the University of Basel) were never designed to handle the volume and speed of sequences being generated today, or the scale of the involvement with public health response. "Across the world, genomic surveillance rests on the initiative of academic researchers to find essential answers.