1. Epidemiology and Global Health
  2. Evolutionary Biology

Evolutionary analysis shows SARS-CoV-2 variants converging

A web-based computer platform is helping scientists use massive datasets to track the evolution of SARS-CoV-2 and other viruses.
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An analysis of massive amounts of genetic data on the SARS-CoV-2 virus suggests that COVID-19 variants worldwide are repeatedly evolving the same mutations, according to a study published today in eLife and carried out by researchers at the Francis Crick Institute.

The analysis was made possible by a new web-based tool called Taxonium that allows the analysis of reams of data collected by scientists around the globe to monitor the genetic trajectory of the virus. Taxonium can be used by scientists to monitor the evolution of SARS-CoV-2 and other viruses or organisms.

Scientists have long tracked the evolution of viruses. But the urgent situation created by the COVID-19 pandemic launched a massive global collaboration that collected and sequenced the genomes of 13 million SARS-CoV-2 samples – far more genetic data than had ever been generated before. However, most existing tools designed to trace viral evolution cannot handle that much data.

"We needed a new tool that would allow us to explore the family tree represented by these millions of SARS-CoV-2 genome sequences," says the study's author Theo Sanderson, a Sir Henry Wellcome Fellow at the Francis Crick Institute in London, UK.

To help, Sanderson built Taxonium – a free, web-based interface that allows scientists to analyse the genetic relationships between tens of millions of virus samples. Scientists can access and analyse the data through a website or a desktop app. Taxonium can help them search for viruses with specific genetic mutations, or in a particular location, and zoom in on large viral family trees to find the information they need.

Sanderson teamed up with scientists at the University of California, Santa Cruz, to build a SARS-CoV-2-specific version of Taxonium called Cov2Tree, which organises publicly available data on more than six million SARS-CoV-2 sequences into evolutionary trees. Using the tool, the team tracked the recent evolution of the SARS-CoV-2 virus and found that many separate regions of the tree showed the acquisition of similar changes in the Spike protein. The analysis suggests that the same mutations are occurring again and again in different individuals around the world and are persisting.

"Scientists worldwide have used Cov2Tree to track the SARS-CoV-2 virus's evolution," says Sanderson. "But this application is probably just the start. Taxonium could be used to study the evolutionary tree of countless other viruses and bacteria."

Sanderson notes that Taxonium is just one part of a growing ecosystem of freely available online tools to help scientists manage what he calls the "avalanche of sequencing data". Scientists can use many of the tools together, and some of them have distinct features from Taxonium that may be better suited for specific tasks.

"With sequencing getting cheaper and cheaper, genetic sequence datasets as large as those created for SARS-CoV-2 are likely to become more common in the future," concludes Sanderson. "New tools to manage those datasets, like Taxonium, will be crucial to managing this new scale of data."

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About eLife

eLife transforms research communication to create a future where a diverse, global community of scientists and researchers produces open and trusted results for the benefit of all. Independent, not-for-profit and supported by funders, we improve the way science is practised and shared. From the research we publish, to the tools we build, to the people we work with, we’ve earned a reputation for quality, integrity and the flexibility to bring about real change. eLife receives financial support and strategic guidance from the Howard Hughes Medical Institute, Knut and Alice Wallenberg Foundation, the Max Planck Society and Wellcome. Learn more at https://elifesciences.org/about.

To read the latest Epidemiology and Global Health research published in eLife, visit https://elifesciences.org/subjects/epidemiology-global-health.

And for the latest in Evolutionary Biology, see https://elifesciences.org/subjects/evolutionary-biology.

About the Francis Crick Institute

The Francis Crick Institute is a biomedical discovery institute dedicated to understanding the fundamental biology underlying health and disease. Its work is helping to understand why disease develops and to translate discoveries into new ways to prevent, diagnose and treat illnesses such as cancer, heart disease, stroke, infections, and neurodegenerative diseases.

An independent organisation, its founding partners are the Medical Research Council (MRC), Cancer Research UK, Wellcome, UCL (University College London), Imperial College London and King’s College London.

The Crick was formed in 2015, and in 2016 it moved into a brand new state-of-the-art building in central London which brings together 1500 scientists and support staff working collaboratively across disciplines, making it the biggest biomedical research facility under a single roof in Europe.

http://crick.ac.uk/