President Trump’s illness from coronavirus infection last month was the most significant health crisis for a seated president in nearly 40 years. Little is known, however, about how the virus arrived at the White House and how it spread.
The administration has not taken basic steps to track the outbreak, limit contact tracing, keep cases secret, and shut down the Centers for Disease Control and Prevention. The origin of the infections, said a spokesmanwas “not recognizable”.
However, a standard public health technique can shed some light: tracking the cluster’s genetic fingerprints.
To better understand the outbreak, The Times worked with prominent geneticists to determine the genetic sequence of viruses that infected two Times journalists believed to have been exposed to the coronavirus as part of their work on the White House .
The study reveals, for the first time, the genetic sequence of the virus that could have infected President Trump and dozens of others, researchers said. This genome is a critical clue that researchers can use to determine where the outbreak came from and whether it is infecting others across the country.
The White House has not announced any efforts to conduct similar genetic testing, but the study’s results show that weeks of positive testing can still do so. Additional sequencing could help pinpoint the virus’ path through the White House, the role of a possible high-prevalence event for Judge Amy Coney Barrett, and the origin of an outbreak among Vice President Mike Pence’s staff last week.
Journalists Michael D. Shear and Al Drago were both exposed to significant, separate exposures to White House officials in late September, days before they developed symptoms. They didn’t spend time around each other in the weeks leading up to their positive tests.
Mr. Shear was traveling with Mr. Trump and other Air Force One staff on Sept. 26 when Mr. Trump approached within five or six feet without a mask. Mr Drago covered Judge Barrett’s event that day and a press conference the next day near officers who were not wearing masks and who later tested positive.
The two journalists’ viral genomes shared the same different mutation pattern. Together with their exposure history, the results suggest they were infected as part of the White House outbreak, said Trevor Bedford, a geneticist at the Fred Hutchinson Cancer Research Center and the University of Washington who led the research team.
“These mutations that these viruses have are quite rare in the United States,” said Dr. Bedford. “I strongly believe that because of their genome, these viruses come from the same outbreak or cluster.”
The study that has been put online but not yet peer-reviewed or published in a science journal, academic protocols followed that require genetic samples to be anonymous. Mr. Shear and Mr. Drago have chosen to disclose their identities for this article.
Viruses are constantly mutating and making tiny, random changes to their genetic material as they reproduce. Few mutations change the way a virus works. By comparing mutation patterns across many genetic sequences, scientists can construct Family trees a virus that sheds light on how it spreads.
The genomes these researchers believe may be related to the White House outbreak do not identify a current geographic source, partly because they are unusual. The ancestors of these viruses spread from Europe to the United States and spread across the country in April and May, but according to Dr. Bedford gets cold the track after that.
Geneticists said the genomes were a key piece of the puzzle that could spark future research to determine where the White House outbreak originated and where it could lead next. Scientists collect and publish tens of thousands of new sequences of the coronavirus every month, and additional tests can fill in the picture.
The results show that even weeks after its identification, the White House outbreak can be better understood when samples from more infected people are sequenced. Swabs used in positive tests are often stored in laboratories for months after an initial infection, and genetic material for the coronavirus is stable when properly stored.
The C.D.C. routinely relies on genetic testing to understand Covid-19 outbreaks in other parts of the country. In one study published Thursday the C.D.C. cited genetic sequencing and intense contact tracing which documented a widespread occurrence at a Wisconsin high school retreat.
However, the Trump administration is not known to have carried out its own genetic analysis on those infected in the outbreak. The White House declined to answer questions about genetic sequencing from Mr Trump and the group of aides and officials who tested positive or fell ill.
There’s still a distant possibility, said Dr. Bedford reported that a previously invisible version of the virus was spread undetected in Washington or Northern Virginia, infecting both journalists independently of the White House cluster. Further testing of the outbreak could completely rule out that possibility, he said.
Scientists who were not involved in the research and reviewed the results agreed with the conclusion that the two samples that had rare mutations strongly suggested they are part of the same outbreak.
“These genomes will likely be identical or nearly identical to the genome that infected the president,” said Michael Worobey, director of the Department of Ecology and Evolutionary Biology at the University of Arizona.
Mr Worobey denied the White House’s characterization that the source of the outbreak could not be known.
“Many things are undetectable if you don’t make an effort to know about them, and that falls into that category,” said Dr. Worobey. “All of these things can actually be seen when you try hard and have the transparency that scientists are desperate to promote when we sequence hundreds of thousands of these genomes around the world.”
For months, the White House minimized the virus threat and avoided basic safety precautions at official events such as wearing a mask or being two meters away.
At least 11 people who attended a rose garden party for Judge Amy Coney Barrett on September 26, which included an indoor no-mask event, were infected with the coronavirus, including President Trump. Additional genetic testing could help determine the role of this event more clearly.
Dr. Bedford and his colleagues were able to obtain a complete genetic sequence for the virus that infected Mr. Shear and a partial sequence for the virus that infected Mr. Drago. Several unusual mutations matched in the two samples, sufficient evidence to have a very high probability that they were essentially the same genome, said Dr. Bedford.
The work was carried out by a multidisciplinary Research team at the University of Washington Medical School, the Hutchinson Center, and the Brotman Baty Institute for Precision Medicine in Seattle.
The work is compelling and the best way to sum up the progression of such an outbreak, said David Engelthaler, director of the infectious diseases division at the Translational Genomics Research Institute in Arizona, where he and his colleagues have sequenced thousands of genomes to track the spread of the coronavirus , including devastating outbreaks on Native American reservations in the state.
“It matters wherever we are supposed to sequence this virus,” said Dr. Angel thaler. “Not just in the White House, but on the White Mountain Apache Reservation here in Arizona.”
Carl Zimmer contributed to the reporting.