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Tests show genetic signature of virus that may have infected President Trump

President Trump’s illness from a coronavirus infection last month was the biggest health crisis for a sitting president in nearly 40 years. Yet, little is known about how the virus got to the White House and how it spread.

The administration has failed to take basic steps to track the outbreak, limiting contact tracing, keeping cases secret and removing centers for disease control and prevention. The origin of the infections, said a spokesperson, was “unknowable”.

But a standard public health technique can still shed light: tracking the genetic fingerprints of the cluster.

To better understand the outbreak, The Times worked with prominent geneticists to determine the genetic sequence of viruses that infected two Times reporters suspected of having been exposed to the coronavirus as part of their work covering 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 crucial clue that can allow researchers to identify the origin of the outbreak and whether has infected others across the country.

The White has not revealed any efforts to perform similar genetic tests, but the study results show it is still possible, even weeks after positive tests. Additional sequencing could help establish the virus’s path through the White , the role of a possible super-spread event for Judge Amy Coney Barrett, and the origin of an outbreak among Vice President Mike’s staff Pence in the last week or so.

Journalists, Michael D. Shear and Al Drago, both had separate and significant exposure to White House officials in late September, several days before developing symptoms. They did not spend time close to each other in the weeks leading up to their positive tests.

Mr. Shear traveled with Mr. Trump and other Air Force One personnel on September 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 officials who were not wearing masks and who subsequently tested positive. Both journalists wore masks.

The viral genomes of the two reporters shared the same distinct pattern of mutations, according to the research. In addition to their history of exposure, the results suggest they were infected as part of the larger 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 are possessed by these viruses are quite rare in the United States,” said Dr. Bedford. “I strongly believe that these viruses originate from the same epidemic or the same cluster depending on their genomes.”

The study, which has been posted online but not yet peer-reviewed or published in a scientific journal, followed academic protocols 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, picking up accidental tiny changes in their genetic material as they reproduce. Few mutations change how a virus works. But by comparing the patterns of mutations across many genetic sequences, scientists can build family trees of a virus, shedding light on how it spreads.

The genomes these researchers believe are linked to the White House outbreak do not identify a recent geographic source, in part because they are unusual. The ancestors of these viruses spread to the United States from Europe and circulated widely across the country in April and May, but the trail cools off after that, according to Dr Bedford.

Geneticists have said genomes are a key piece of the puzzle that could stimulate future research to determine where the White House outbreak is coming from and where it could go next. Scientists collect and release tens of thousands of new coronavirus sequences each month, and additional testing may complete the picture.

The results show that even weeks after its identification, the White House outbreak would be better understood by sequencing samples from a larger number of infected people. Swabs used in positive tests are often stored in laboratories for months after initial infection, and the genetic material of the coronavirus is stable if stored properly.

The CDC regularly relies on genetic testing to help understand Covid-19 outbreaks elsewhere in the country. In a study released Thursday, the CDC cited genetic sequencing and intensive contact tracing that documented a super-spread event at a high school retreat in Wisconsin.

But the Trump administration is not known to have conducted its own DNA analysis of those infected with the epidemic. The White House declined to answer questions about DNA sequencing from Mr. Trump and the group of aides and officials who have tested positive or have fallen ill.

There is still a remote possibility, Dr Bedford said, that an unprecedented version of the virus circulated undetected in Washington or Northern Virginia and infected the two reporters regardless of the White House group. Further testing of the outbreak could rule out that possibility altogether, he said.

Scientists not involved in the research who reviewed the results agreed with the conclusion that the two samples sharing rare mutations strongly suggested that they were part of the same epidemic.

“These genomes will likely be identical or nearly identical to the genome that infected the president,” said Michael Worobey, head of the Department of Ecology and Evolutionary Biology at the University of Arizona.

Dr Worobey took issue with the White House statement that the source of the outbreak could not be known.

“A lot of things are unknowable if you don’t make an effort to find out anything about them, and that falls into that category,” Dr Worobey said. “All of these things can actually be known if you put in the effort and have the transparency that scientists are desperately trying to promote as we sequence hundreds of thousands of these genomes around the world.”

For months, the White House played down the threat of the virus and avoided basic safety precautions at official events, such as wearing a mask or being six feet apart from people.

At least 11 people who attended a Rose Garden celebration on September 26 for Judge Amy Coney Barrett, which included an indoor event without a mask, have been infected with the coronavirus, including President Trump. Further genetic testing could help more clearly establish the role of this event.

Dr. Bedford and his colleagues were able to obtain a complete genetic sequence of the virus that infected Mr. Shear and a partial sequence of the virus that infected Mr. Drago. Several unusual mutations matched in the two samples, enough evidence to determine with a very high probability that it was essentially the same genome, Dr Bedford said.

The work was carried out by a multidisciplinary team of researchers from the University of Washington School of Medicine, the Hutchinson Center and the Brotman Baty Institute for Precision Medicine in Seattle.

The work is compelling and it’s the best way to piece together the progress of such an epidemic, said David Engelthaler, head of the infectious diseases branch of the Translational Genomics Research Institute in Arizona, where he and his colleagues have sequenced thousands genomes to track the spread of the coronavirus, including the devastating epidemics on the state’s Native American reservations.

“Sequencing this virus is essential, no matter where we are,” said Dr Engelthaler. “Not just at the White House, but at the White Mountain Apache Reservation here in Arizona.”

Carl Zimmer contributed reporting.