A team of geneticists has mapped the sweep of coronavirus through the United States, revealing how the COVID-19 epidemic unfolded.
Much of California’s outbreak is fueled by an early introduction of a lineage from Asia – but the state also experienced later sparks of infection due to repeated introductions from New York and elsewhere in the U.S., according to the analysis, released Tuesday.
Like California, some states had a single early introduction that fueled the majority of cases in the epidemic’s first days — while in others, like Wisconsin, illness appears to be driven by a larger number of separate introductions.
Now infections are intermingling, according to Trevor Bedford and his team of researchers from the University of Washington and the Fred Hutchinson Cancer Research Center.
“Overall, we see substantial mixing of transmission chains across states. This mixing largely occurred during February and early March,” Bedford wrote on Twitter.
The analysis is based on a library of 23,000 full genetic sequences of the virus, donated by scientists and stored on an online public database called GISAID. Of these, at least 200 are from California.
Using advanced sequencing technologies, a team of virus evolution experts are tracing tiny genetic changes in the virus as it reproduces. About twice a month, on average, the virus changes one letter in its RNA strand of 29,903 nucleotides.
These viral genomes reveal the the origin of the virus, called SARS CoV-2, in Wuhan, China. Now, in a project called Nextstrain, scientists are building a family tree, linking cases and tracking its march across America.
California is interesting in that like WA, much of the outbreak is fueled by an early introduction of a lineage from Asia and then later cases derived from repeated introductions from elsewhere in the US. 7/14 pic.twitter.com/DvSbV9fDSO
— Trevor Bedford (@trvrb) May 12, 2020
In addition to California, the analysis included:
New York: Most infections appear to derive from an introduction from Europe in mid-February. This introduction rapidly grew to a substantial epidemic focused in New York City, but was frequently introduced to other locations.
Washington: One lineage from China dominated its early outbreak in January and February, but then multiple introductions from New York fueled further transmission chains in March.
Wisconsin: A large number of separate introductions from other states and Europe drove its outbreaks. There was no single early successful introduction, as seen in California, New York and Washington. While Wisconsin had a travel-related infection very early in the pandemic — Jan. 30, the nation’s 12th case – that resident went directly to a hospital emergency room. So the introduction was unsuccessful; the illness never spread.
Louisiana: The outbreak here is “remarkably focused,” with most cases deriving from a couple of closely related introduction events – apparently from New York.
Texas: Much of this state’s virus is genetically linked to a Louisiana virus. But there were also a large number of separate introductions from other states.
Now, with reduced travel, “I’d expect…more geographically focused transmission chains,” said Bedford. “I believe almost all states now have greater local transmission than outside introductions.”
As states lift their stay-at-home orders, do the findings warrant a candid discussion about domestic travel restrictions?
“I can imagine a future where some states — or groups of neighboring states — manage suppression, while other states do not,” said Bedford. “This would suggest travel restrictions, but (we’re) not there yet.”
