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.
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 in the journal Nature, an international collaboration of specialists in viral and genetic analysis, led by Swiss scientists Dr. Emma Hodcroft at the University of Bern and Prof. Christophe Dessimoz at University of Lausanne, both at the SIB Swiss institute of Bioinformatics, alongside Dr. Nick Goldman at EMBL-EBI in the UK, 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. Here are the key take home messages and perspective from the Swiss angle.
“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. Public health decision making would benefit from a more sustainalble collaboration framework,” says Christophe Dessimoz at SIB and University of Lausanne.
Read more at University of Bern
Image: Specialists in viral and genetic analysis, led by Swiss scientists Dr. Emma Hodcroft at the University of Bern and Prof. Christophe Dessimoz at University of Lausanne, alongside Dr. Nick Goldman at EMBL-EBI in the UK, 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. (Credit: © Oliver Hochstrasser)
