New ways proposed to overcome barriers in COVID-19 response

An international research team is calling for better consolidation of bioinformatics, viral genetics, and public health to allow better pandemic response today and more improved pandemic preparedness in the future.

Emma Hodcroft, PhD. Image Credit: Oliver Hochstrasser.

In a comment piece published in the Nature journal, an international consortium of experts in viral and genetic analysis, headed by Swiss researchers Dr. Emma Hodcroft at the University of Bern and Professor Christophe Dessimoz at the University of Lausanne, both from the SIB Swiss Institute of Bioinformatics, together with Dr. Nick Goldman from EMBL-EBI in the United Kingdom, has explained the “bioinformatics bottlenecks” that are obstructing response to the SARS-CoV-2 pandemic and suggested ways to “clear the road” for improved techniques and tools. These are the main take-home messages and perspectives from the Swiss viewpoint.

What scientists have achieved in a year since the discovery of a brand-new virus is truly remarkable. 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.”

Emma Hodcroft, Study First Author, Institute of Social and Preventive Medicine, University of Bern

Currently, SARS-CoV-2 is one of the most sequenced pathogens of all time, with more than 600,000 full-genome sequences that were produced since the outbreak of the pandemic, and more than 5,000 new sequences emerging from around the world daily.

But the analysis and visualization equipment utilized today (such as Nextstrain, jointly developed by Professor Richard Neher’s team at the Swiss Institute of Bioinformatics (SIB) and the University of Basel) was never developed to manage the speed and volume of sequences being produced today, or the degree 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.”

Christophe Dessimoz, Study Last Author, Swiss Institute of Bioinformatics, University of Lausanne

What an improved sequencing would enable

The SARS-CoV-2 genetic sequences hold useful data to implement effective pandemic measures and stay ahead of the coronavirus. By comparing the number of mutations shared by various samples, for instance, researchers can track the viral transmission, helping to detect international transmission and super-spreading events.

But currently, it can be difficult to integrate this genetic data with other key variables—such as, who took part in an event, and when symptoms emerged—which could help make these techniques even more informative.

The “R-number” has moved from a scientific idea a household term in 2020—it calculates the average number of individuals an infected person will transmit to. In this case, sequences can also help by aiding to distinguish between local transmission and imported cases. This enables a more precise estimate of R-number but still requires complex analyses and high levels of sequencing, which are presently not extensively implemented.

Lastly, sequencing is the only means to detect and monitor the several mutations that emerge in SARS-CoV-2. Although mutations are a regular part of virus life, researchers need to find out which mutations are harmless variations and which ones could alter the transmissibility of the virus or clinical result.

Integrating sequences, computational predictions, and laboratory work could enable a better interpretation of mutational effects; however, there is a small framework to help such varied specialties work collectively.

The viral data - sequences and associated metadata- must be determined, gathered and harmonized thanks to stable infrastructures compatible with the principles of Open Data to facilitate peer-review by the community and their reuse.”

Christophe Dessimoz, Study Last Author, Swiss Institute of Bioinformatics, University of Lausanne

Benefits for Switzerland

Emma Hodcroft explained, “In Switzerland, the population could benefit from more systematic and representative sequencing, for example through better contract tracing, targeted isolation and quarantine of smaller regions, and guiding the closing and opening of schools based on the presence of certain variants.”

Harmonization of health data practices is also a crucial subject. Switzerland is already putting plenty of effort at the national level via the Swiss Personalized Health Network (SPHN).

The team is convinced that Switzerland’s capacity with respect to infrastructure and expertise is just waiting to be explored, to the benefit of public health.

“The tools to enable research are there, and researchers have self-organized and taken the first step: to scale up and sustain these efforts to bring research and public health closer together, we rely on sustainable public funding,” concluded Dessimoz.