Understanding Nextstrain

Global Health

Tracking a Pandemic

As COVID-19 has spread across the globe, an international team of high-tech detectives has been close behind.

The scientists behind Nextstrain.org, which was co-created by researchers at Fred Hutch and the University of Basel, track small changes in the virus’s genetic code as it spreads from person to person. The changes act like fingerprints, helping researchers chart its global movements in near real time.

Here is how the Nextstrain researchers find, interpret and visualize those genetic clues.

How a Fred Hutch Lab is Chasing COVID-19

An animated map illustrating the spread of COVID-19

From a single dot in Wuhan, China, lines start to shoot out. They stretch into Thailand, Malaysia, Nepal. New colors crop up in distant lands. Soon, a multicolored web has spun across the globe.

The pulsating map found at Nextstrain.org tells the tale of a virus on the march. And that story is written in the genetic code of the virus itself.

When a virus infects a host, it churns out copies of itself. That process can be messy, and some of those copies have tiny mutations. The errors are then passed along to its “descendants” when the virus infects other people. Because those mutations occur at a regular rate, they act like a ticking molecular clock. Scientists use that clock to figure out how and when all those changes arose as viruses descended from a common ancestor in Wuhan.

Scientists around the world use powerful technologies to quickly find mutations in samples from COVID-19 patients. The Nextstrain team uses that data to build viral “family trees,” which let them trace the virus’s travels around the globe.

Presenting a Genetic Jigsaw Puzzle

A chart illustrating evolution of COVID-19
Map of COVID-19 spread

 

A Virus’s Family Tree

Next to the Nextstrain map is a phylogenetic tree. It is a snapshot of the evolutionary relationships among virus samples from around the world.

The tiny dots on each line represent a single genome sequence taken from a COVID-19 patient. The site’s default view (shown here) clusters these sequences by their genetic similarity and their sample date.

The leftmost vertical line is the tree’s “root.” At each branch point, or node, lies the most recent common ancestor of all the branches splitting off to the right. The different colors represent the country or region where its ancestor originated.

Map of COVID-19 spread

 

Mapping the Virus’s March

The family trees created by the Nextstrain team let them map how the outbreak has unfolded. The same mutations that identify evolutionary relationships also serve as genetic breadcrumbs. Scientists can follow them backwards to find out where the virus has been. Visitors at Nextstrain can follow them forward on the site’s animated map.

The circles indicate the number of samples sequenced in a particular country or region, and the colored lines indicate from where the virus traveled.

Following COVID-19 as it Spreads

Early Spread

January 2020

On Jan. 10, scientists in China publish the first genome sequence taken from a COVID-19 patient in Wuhan. The “ticking clock” used by the Nextstrain team has now started.

Expansion

February/March 2020

Using genetic clues, Nextstrain’s Dr. Trevor Bedford announces that COVID-19 has been spreading silently in Washington state for weeks. Clusters of cases soon begin to spread across the U.S.

Global Exposure

April 2020

Scientists around the world continue to sequence viral samples from COVID-19 patients. The additional data helps the Nextstrain team flesh out its family trees and gain deeper understanding of how the virus has spread.

Map of COVID-19 spread


The Nextstrain team relies on a worldwide network of scientists sharing open data through GISAID and other sources during the pandemic. Researchers continue to sequence viral samples that help fill in the branches of the novel coronavirus’s evolutionary tree. And that work will continue to give Nextstrain visitors a colorful look at the past, present and — perhaps — future of the COVID-19 pandemic. Learn more on Nextstrain.org