Remember Sharpiegate?

It turns out that the National Oceanic and Atmospheric Administration (NOAA) may still be reeling from that episode, when President Trump’s refusal to admit he was wrong ballooned into an actual scandal at one of the nation’s premier scientific institutions.

The New York Times reported this week that NOAA’s acting chief scientist, Craig McLean, who called out political interference during the ordeal, was removed from his post this month when he asked a new political appointee to acknowledge the agency’s scientific integrity guidelines. The guidelines prohibit manipulating scientific research for political ends.

The appointee, Erik Noble, a former White House adviser, was not pleased, according to the Times:

The request prompted a sharp response from Dr. Noble. “Respectfully, by what authority are you sending this to me?” he wrote, according to a person who received a copy of the exchange after it was circulated within NOAA.

Mr. McLean answered that his role as acting chief scientist made him responsible for ensuring that the agency’s rules on scientific integrity were followed.

The following morning, Dr. Noble responded. “You no longer serve as the acting chief scientist for NOAA,” he informed Mr. McLean, adding that a new chief scientist had already been appointed. “Thank you for your service.”

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McLean is still at NOAA, but he’s been replaced as chief scientist by Ryan Maue, a former research meteorologist at the Cato Institute.

It makes sense that scientific integrity was front of mind for McLean when dealing with a political appointee. NOAA in general and McLean in particular have been forced to police the line between science and politics ever since Hurricane Dorian in 2019 galloped toward the Gulf Coast. Trump tweeted at the time that Alabama was one of several states “most likely” to be struck. The National Weather Service’s Birmingham, Alabama, office quickly responded that the state was emphatically not in the path of the storm.

A few days later, McLean defended NOAA’s scientists, including researchers at the National Weather Service, and openly decried the interference from the White House in a statement.

It’s rare for a career employee at a government agency to publicly challenge political staff, which may be why a White House appointee at NOAA was so keen to remove him. And while the whole affair may seem silly, it has consequences beyond bruising the president’s ego.

Political interference, or even the appearance thereof, undermines the credibility of an agency like NOAA whose research is used to make life-or-death decisions, like who needs to get out of the path of a dangerous storm.

Now, even before an election, just as Hurricane Zeta, the 27th named storm of the Atlantic hurricane season, has left 2 million without power along the Gulf Coast, political staff are sidelining scientists at an agency tasked with staying ahead of natural disasters. And it’s likely more manipulation of science is in store if Trump wins a second term in office.

The Trump administration’s repeated attacks on scientific agencies weaken public trust

When his words didn’t match reality, President Trump tried to make reality match his words.

He responded with multiple tweets defending his statement that Alabama was in the path of Hurricane Dorian. He pressured his Homeland Security adviser to release a statement validating him. NOAA, the parent agency of the National Weather Service, issued a curt statement downplaying comments from its Birmingham station. Then, in the Oval Office, President Trump infamously presented a map of Hurricane Dorian’s path, but the forecast was doctored with a black line to include Alabama.

Altering an official weather forecast is actually illegal for a government employee, though it’s not clear who actually drew the black line on the map (it’s not clear whether it was drawn with a Sharpie, either).

In a September 10, 2019, statement, McLean criticized the decision to use NOAA’s press office to echo Trump and undercut the National Weather Service. “My understanding is that this intervention to contradict the forecaster was not based on science but on external factors including reputation and appearance, or simply put, political,” he wrote. “If the public cannot trust our information, or we debase our forecaster’s warnings and products, that specific danger arises.”

The inspector general of the US Department of Commerce, which oversees NOAA, agreed. A report from the inspector general this summer found that NOAA’s credibility “took a serious hit” when top officials at the agency contradicted the National Weather Service’s Birmingham office:

The Statement undercut the NWS’s forecasts and potentially undercut public trust in NOAA’s and the NWS’s science and the apolitical nature of that science. By requiring NOAA to issue an unattributed statement related to a then-5-day-old tweet, while an active hurricane continued to exist off the east coast of the United States, the Department displayed poor judgment in exercising its authority over NOAA.

But the political pressure on NOAA was mounting before Sharpiegate and has been aimed at influencing the science that drives policy, particularly around climate change.

Since Trump took office, NOAA has not had a Senate-confirmed leader. Currently, Neil Jacobs, the acting Under Secretary of Commerce for Oceans and Atmosphere, is serving as NOAA’s interim administrator. Meanwhile, Trump has repeatedly made his disdain for climate change science clear. Shortly after taking office, federal agencies began removing references to climate change from their websites.

For the most part, scientists at NOAA continued doing their jobs but have collided with the White House at times. NOAA is one of the contributing agencies to the National Climate Assessment, a report mandated by Congress to assess the impacts of climate change on the United States. After the last installment highlighted the economic costs of climate change, Trump said he didn’t believe the findings — likely because they undermined his administration’s policies to boost fossil fuels and relax greenhouse gas restrictions.

Since the report is foundational to how the government plans for the future, the Trump administration is aiming to alter it during a second term by “removing longtime authors of the climate assessment and adding new ones who challenge the degree to which warming is occurring, the extent to which it is caused by human activities and the danger it poses to human health, national security and the economy,” according to the New York Times.

The Trump administration has already pursued a similar tack at the Environmental Protection Agency. The EPA ousted numerous independent scientific advisers and instead brought in researchers from the industries it’s supposed to regulate. The agency also placed additional restrictions on what kinds of research could be used to develop environmental regulations, making it easier to roll back restrictions and harder to come up with new rules to govern hazards to air, water, and soil.

And now we’re also seeing this manipulation play out in the Covid-19 pandemic. The White House has repeatedly interfered with and undermined guidance from public health agencies like the Centers for Disease Control and Prevention. Because Trump talked them up, the FDA granted emergency use authorizations to therapies like hydroxychloroquine and convalescent plasma despite weak evidence for their effectiveness.

The net result of all this manipulation is a loss of public trust, making it less likely that people will adhere to guidelines to protect them from disease or environmental dangers. And with the science itself being twisted to meet political ends, dirtier air and water due to weaker regulations, communities left more vulnerable in a disaster, as well as unready and risky approaches being deployed to deal with the Covid-19 pandemic may result.

Most people who get the coronavirus will fully recover and go right back to their lives. But the latest research suggests that at least 10 percent have long-term symptoms, even after their body has apparently cleared the virus.

The condition, known as “long Covid,” has emerged as a scary feature of the pandemic — a reminder that even as hospitalizations and deaths come down, millions of people will continue to suffer from the aftermath of infection.

And, as it turns out, “this isn’t unique to Covid,” Akiko Iwasaki, an immunologist at the Yale School of Medicine, told Vox.

Instead, Covid-19 appears to be one of many infections, from Ebola to strep throat, that can give rise to stubborn symptoms in an unlucky subset of patients. “It is more typical than not that a virus infection leads to long-lasting symptoms in some fraction of individuals,” Iwasaki said.

The difference now is that, with 137 million Covid-19 cases worldwide and counting, long-haulers are more visible: Their suffering has come on in unprecedented numbers. It’s also possible the coronavirus causes long-term symptoms even more frequently than other infections.

In this week’s episode of Unexplainable, we dive into what we know about long Covid and what other viruses can teach us about the condition, including the leading hypotheses for what might be driving symptoms in Covid long-haulers.

We also look at what we can learn from patients who have been grappling with medically unexplained symptoms — the kind that don’t correspond to problematic diagnostic test results or imaging — for years before the pandemic hit. Here’s a rundown of what scientists think could explain the mysterious symptoms, and why even the vaccine might not help.

1) The virus and “viral ghosts” didn’t actually leave the body

The first explanation for what might cause persistent symptoms in people who’ve been infected with Covid-19 is the simplest: The virus or its components might still be lurking in the body somewhere, long after a person starts testing negative.

We’ve learned from other long-term viral illnesses that, in some cases, pathogens do not fully clear the body. “It’s out of the blood but gets into tissue in a low level — the gut, even maybe the brain in some people who are really sick — and you have a reservoir of the virus that remains,” PolyBio Research Foundation microbiologist Amy Proal told Vox. “And that drives a lot of inflammation and symptoms.”

These viral reservoirs have been documented following infections with many other pathogens. During the 2014-2016 Ebola epidemic, studies emerged showing the Ebola virus could linger in the eye and semen. There were similar findings during the 2015-2016 Zika epidemic when health officials warned about the possibility that Zika could be sexually transmitted. (Viral reservoirs are also why the moniker “post-viral” can be problematic, Proal added.)

A related explanation for what might be happening with long-Covid patients is what Iwasaki calls “viral ghosts.” While the intact virus may have left the body, “there may be RNA and protein from the virus that’s lingering and continuing to stimulate the immune system,” Iwasaki said. “It’s almost like having a chronic viral infection — it keeps stimulating the immune system because the virus or viral components are still there, and the body doesn’t know how to shut it off.”

Recent studies in Nature and The Lancet documented coronavirus RNA and protein in a variety of body systems, including the gastrointestinal tract and brain.

In autopsies of people with chronic fatigue syndrome, researchers also found enterovirus RNA and proteins in patients’ brains, including, in one case, in the brain stem region. The brain stem controls sleep cycles, autonomic function (the largely unconscious system driving bodily functions, such as digestion, blood pressure, and heart rate), and the flu-like symptoms we develop in response to inflammation and injury.

“If that area of the brain signaling becomes dysregulated [by viruses],” Proal said, “[that] can result in sets of symptoms that meet a diagnostic criteria for [chronic fatigue syndrome], or even for long Covid.”

2) Other pathogens lurking in the body reawaken

Other pathogens already lurking in the body prior to a coronavirus infection might also exacerbate symptoms. For example, viruses in the herpes family — such as Epstein-Barr (the cause of mono) or varicella zoster (the cause of chickenpox and shingles) — stay dormant in the body forever. Under normal conditions, the immune system can keep them in check.

“So, for example, 90 percent of people in the world already have herpes viruses,” said Proal. “But in those patients, the immune system keeps them in a place where they can’t replicate, where they can’t express proteins. They’re kind of controlled.”

But then Covid-19 comes along, and all of a sudden these other viruses get a chance to gain a foothold again. With the immune system tied up fighting Covid-19, the other viruses may reawaken. And they — not the coronavirus — drive symptoms.

3) The immune system turns on the body

Another key hypothesis: Long-Covid patients have developed an autoimmune disorder. The virus interrupts normal immune function, causing it to misfire, so that molecules that normally target foreign invaders — like viruses — turn on the body.

These “rogue antibodies,” known as autoantibodies, “attack either elements of the body’s immune defences or specific proteins in organs such as the heart,” according to Nature. The assault is thought to be distinct from cytokine storm, an acute immune system disorder that appeared as a potential threat early in the pandemic.

“Under that scenario, we talk about molecular mimicry,” Proal said. “Basically, the virus creates proteins that look like human proteins or tissue, and that kind of tricks the immune system.” Here, the the immune system tries to target the virus, which “if it has a similar size and shape to a human tissue or protein, it fires on the human tissue or protein as well,” she added.

4) The microbiome gets thrown out of whack

It’s also possible the coronavirus might deplete important microorganisms in the gut microbiome — the trillions of bacteria, viruses, and fungi that live in and on the body.

In one study, researchers tracked blood and stool samples from 100 patients hospitalized with SARS-CoV-2 infection, testing some up to 30 days after they cleared the virus. (They also collected samples from a control group for comparison.) And they found Covid-19 infection was linked to a “dysbiotic gut microbiome,” even after the virus cleared the respiratory tract; they also hypothesized that it might contribute to the persistent health problems some patients are experiencing.

“Under conditions of health, those communities are in a state of balance. It’s like a forest, like different organisms are doing different things, but it’s in a harmonious state,” Proal said. But Covid-19 could lead to an imbalance in the microbiome. “And a huge number of symptoms are tied to microbiome dysbiosis. Irritable bowel syndrome or even neuro-inflammatory symptoms can be driven by these ecosystems when they go out of balance, too.”

5) The body is injured

The virus might have cleared the body but left injuries in its wake — scars in the lungs or damage to the heart, for example — and these injuries might give rise to symptoms.

According to a recent preprint involving 201 patients, 70 percent had impairments in one or more organs four months after their initial Covid-19 symptoms set in. In other unpublished research, radiologists at the University of Southern California tracked hospitalized patients’ lung recovery using CT scans. They found one-third had scars caused by tissue death more than a month later. Other patients may have brain damage that causes neurological symptoms.

There’s also growing evidence of widespread cardiac injury, even in patients who aren’t hospitalized. In a JAMA Cardiology study, researchers performed cardiac MRIs on 100 patients in Germany who had recovered from Covid-19 within the past two to three months. An astounding 78 percent still had heart abnormalities.