Analyzing pathogen genomes from 160 patients, a team of U.K. geneticists has traced the early months of the novel coronavirus’ spread across Asia, Europe, and the Americas—and the trajectory is as complex as it is staggering.
The team, led by Cambridge University geneticist Peter Forster, drew a map of the pandemic’s spread between Dec. 24 and March 4.
“The viral network we have detailed is a snapshot of the early stages of an epidemic, before the evolutionary paths of COVID-19 become obscured by vast numbers of mutations,” Forster told Science Daily. “It’s like catching an incipient supernova in the act.”
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The team’s map confirms, and adds nuance to, virologists’ understanding of the pandemic. It all started when SARS-CoV-2 leaped from bats or pangolins to human beings, apparently at an illicit wildlife market in Wuhan, China.
The virus kicked around China a while before hitching rides to other countries via cruise ships and airlines.
The U.K. scientists’ “phylogenetic” approach to analyzing and visualizing the pandemic revealed three distinct strains of SARS-CoV-2. Each with its own unique behaviors.
They called the strains A, B, and C.
“The A and C types are found in significant proportions outside East Asia, that is, in Europeans and Americans,” Forster’s team explained in a March 30 article in Proceedings of the National Academy of Sciences of the United States of America.
“In contrast, the B type is the most common type in East Asia, and its ancestral genome appears not to have spread outside East Asia without first mutating into derived B types,” the team added.
In other words, China caught the coronavirus first. And it quickly passed along two different versions of the virus. China then got its own, fairly unique strain of the pathogen—one that people in other countries mostly appeared to be immune to until it mutated... a lot.
To make their map, Forster’s team first needed data. They tapped the GISAID dataset, a public collection of genetic sequences of influenza viruses and similar pathogens. Researchers from all over the world have been depositing SARS-CoV-2 genomes in GISAID as a way of assisting each other’s research.
In early March, the cutoff date for Forster’s team’s study, there were 253 novel-coronavirus sequences in the dataset, Forster told The Daily Beast. He said he eliminated any incomplete or low-quality sequences and ended up with 160 that could stand up to close scrutiny.
“Data confidence,” Forster said, “is in my view not a limiting factor.”
To draw connections between the virus samples, the U.K. researchers used special software that Forster and his brother Michael had developed.
The resulting map reads like a guide to a subway system, where the stations are countries, and the rail lines are particular strains of the virus mutating and spreading from person to person before landing in another station (that is, another country) in a new and unique form.
In an appendix to their journal article, the scientists highlighted several particular forms of the virus to help make sense of their journeys across the globe.
Take, for example, one Canadian with a highly mutated B-version of SARS-CoV-2 who got infected while traveling in Wuhan in the early weeks of the pandemic. The person fell ill after returning to Ontario. Doctors collected a sample of their virus and dropped it in the GISAID database.
Analyzing the sample’s genome, the U.K. team determined that this particular strain mutated twice before infecting the Ontario patient. One mutation later, a descendant of the Ontario strain showed up in California. Two mutations later, it popped up elsewhere in Canada.
These revelations are useful. In identifying hotspots and mutation pathways, scientists can help governments plan quarantines and other public-health measures.
“Phylogenetic network analysis has the potential to help identify undocumented COVID-19 infection sources, which can then be quarantined to contain further spread of the disease worldwide,” Forster told Science Daily.
Forster told The Daily Beast that a map like his can also help frontline doctors, provided they know the clinical outcomes for patients with particular strains of the virus: incubation time, recovery time, mortality, etc. If you know your city’s got a lot of, say, the A-strain and you also know that the A-strain makes people sick in certain ways, you can tailor your patient care accordingly.
What map-style visualization can’t do, however, is perfectly predict the future behavior of coronavirus or any other pathogen. Even after Chinese scientists first identified SARS-CoV-2 back in December, no one knew it would branch three ways, with two branches shooting out across the planet while one just wrapped around China before sending a few thin tendrils abroad.
Alice McHardy, a researcher in computational biology at the Helmholtz Centre for Infection Research in Germany, has used phylogenetic mapping technique to trace the spread of SAR-CoV-2 through air travel. “In my mind, it would uncover ongoing local outbreaks but not predict future ones,” McHardy told The Daily Beast.
David Morrison, a biologist at Uppsala University in Sweden, said he’s more comfortable using phylogenetic methods to anticipate where a virus might go next, but he urged caution. “We call it forecasting, just like the weather bureau does.”
Sometimes the weather forecast turns out to be wrong.
