Emergence of a Deadly Coronavirus

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Americans have transmitted COVID-19 to wild deer hundreds of times, an analysis of thousands of samples collected from the animals suggests, and people have also caught and spread mutated variants from deer at least three times.

The analysis published Monday stems from the first year of a multiyear federal effort to study the virus as it has spread into American wildlife, spearheaded by the U.S. Department of Agriculture's Animal and Plant Health Inspection Service, or APHIS.

Scientists analyzed 8,830 samples collected from wild white-tailed deer across 26 states and Washington, D.C., from November 2021 to April 2022, to study the COVID variants that had infected 282 of them.

By comparing sequences from the viruses in deer against other publicly reported samples from databases of human infections around the world, they were able to trace the likely spread of these variants between humans and animals.

A total of 109 "independent spillover events" were identified, matching viruses spotted in deer to predecessors it likely descended from in previously infected humans.

Several of these viruses appear to still be mutating and spreading between deer, including the Alpha, Gamma, and Delta variants of concern that drove an increase in deaths earlier in the pandemic, long after these lineages were subsumed by the wave of Omicron variants that continue to dominate nationwide.

Eighteen of the samples had no "genetically close human SARS-CoV-2 sequences within the same state" reported, foiling efforts to track down a precursor variant in humans.

"Overall, this study demonstrated that frequent introductions of new human viruses into free-ranging white-tailed deer continued to occur, and that SARS-CoV-2 VOCs were capable of persisting in white-tailed deer even after those variants became rare in the human population," the study's authors wrote.

Three had mutations that match a distinctive pattern of first spilling over from a human to deer, and then later another so-called "spillback" from deer back into humans. Two of these spillback variants were in North Carolina and one was in Massachusetts.

Scientists who wrote a paper dismissing the so-called “lab leak theory” of the origin of COVID-19 admitted they feared blaming China for accidentally releasing the virus, according to internal communications obtained by a House subcommittee.

A co-author of the March 2020 Nature Medicine article “The Proximal Origin of SARS-CoV-2” and other scientists who collaborated on the paper privately worried about the “s–tshow that would happen” if “China in particular” were deemed responsible for COVID escaping one of their research labs, the House Select Subcommittee on the Coronavirus Pandemic majority revealed in an interim report Tuesday.

“​​Given the s–tshow that would happen if anyone serious accused the Chinese of even accidental release, my feeling is we should say that given there is no evidence of a specifically engineered virus, we cannot possibly distinguish between natural evolution and escape so we are content with ascribing it to natural process,” Dr. Andrew Rambaut, a professor of evolutionary biology at the University of Edinburgh, wrote in a Feb. 2, 2020, Slack message to co-authors Dr. Kristian Andersen, Dr. Edward Holmes and Dr. Robert Garry.

Yup, I totally agree that that’s a very reasonable conclusion,” Andersen responded. “Although I hate when politics is injected into science — but its [sic] impossible not to, especially given the circumstances.”

Another scientist — who had joined the co-authors, then-National Institutes of Health Director Dr. Francis Collins and National Institute of Allergy and Infectious Diseases Director Dr. Anthony Fauci a day earlier on a conference call — also urged his colleagues to tamp down lab leak discussions that might imperil “science in China.”

“An accusation that nCoV-2019 might have been engineered and released into the environment by humans (accidental or intentional) would need to be supported by strong data, beyond reasonable doubt,” Dutch virologist Dr. Ron Fouchier wrote in a Feb. 2, 2020, email. “It is good that this possibility was discussed in detail with a team of experts. However, further debate about such accusations would unnecessarily distract top researchers from their active duties and do unnecessary harm to science in general and science in China in particular.”

The House COVID panel’s report combed through more than 8,000 pages of documents from the scientists and interviewed five of them about the paper that Fauci twice “suggested” and that Andersen said was ultimately written to “disprove” the COVID lab leak theory.

Fauci and Collins involved themselves so much in the effort that co-authors referred to them in email exchanges as the “Bethesda Boys,” the report shows, and Fauci later cited the paper in a televised White House briefing to discredit the lab leak hypothesis.

The House report also shows the article faced initial rejection from Nature Medicine for not sufficiently disproving non-natural origins of COVID-19.

In an email to one of the publication’s editors on Feb. 20, 2020, Andersen lamented not being able to “refute a lab origin” in an earlier draft.

“[T]he possibility must be considered as a serious scientific theory (which is what we do) and not dismissed out of hand as another ‘conspiracy’ theory,” he said. “We all really, really wish that we could do that (that’s how this got started), but unfortunately it’s just not possible given the data.”

Pandemic recovery has essentially stalled for most of the nation’s students, new data shows, and upper elementary and middle school students actually lost ground this year in reading and math.

On average, students need four more months in school to catch up to pre-pandemic levels, according to the results from NWEA, a K-12 assessment provider. This fall’s ninth graders need far more — roughly a full extra school year.

“There’s still a pretty big distance between the COVID and the pre-COVID trends,” said Karyn Lewis, director of NWEA’s Center for School and Student Progress. “We’re not doing anything to shrink that distance.”

Within the grim results, however, there was a spark of hope for the youngest students. First- through third-graders were the only students to make above-average gains. But that progress only returns them to “an already significantly inequitable state of academic achievement,” researchers said.

They described the data from 6.7 million students who took the organization’s MAP Growth tests last school year as “education’s long COVID.” The results come just weeks after the latest National Assessment of Educational Progress revealed sharp declines in reading and math for the nation’s 13-year-olds, continuing a downward trend that began a decade ago.

Students who experienced the greatest setbacks during the pandemic — the intended beneficiaries of billions of dollars in federal aid — have the most ground to make up. But time is running out to use the remaining relief funds for tutoring, expanded summer school programs and other recovery efforts. The extended emergency, Lewis said, has kept her up at night.

“I very much worry that these results will fan the flames of ‘Schools didn’t use these dollars wisely,’ and I don’t think that’s the case at all,” she said, noting that many are using proven teaching methods for students below grade level. “It’s just not enough. The dosage is not in line with the magnitude of the crisis.”

But Dan Goldhaber, director of the Center for Analysis of Longitudinal Data in Education Research at the American Institutes for Research, is more critical of efforts to reach students who have fallen the furthest behind. The data, he said, lines up with CALDER’s research on 12 districts showing low participation in optional interventions like tutoring and summer programs.

“You’d never know that there had been a pandemic,” he said. He acknowledged the views of those who argue there’s too much emphasis on test scores, but added that such assessments still predict the types of courses students take and whether they’re on track to go to college. “The education ecosystem is not healthy.”

The NWEA results show students who finished eighth grade this year need an additional 7.4 months of learning to reach pre-pandemic levels in reading and 9.1 months in math. Black and Hispanic students need even more extra instruction to get there, the data show.

Lewis compared pandemic learning loss to tornado damage. A hammer and nails, she said, might be sufficient to repair a lost shingle or a loose shutter. But if a garage is flattened or the roof is gone “a hammer and nail is not going to cut it,” she said.

The fact that the gap between pre- and post-pandemic achievement for fourth through eighth graders grew larger this year instead of smaller was a hard pill to swallow, said NWEA’s Lewis.

“There was a hope that a lot of lessons learned in 21-22 could be applied in 22-23,” she said. “We actually see the opposite. It was shocking to us.”

In a summary of the results, she and Megan Kuhfeld, an NWEA senior research scientist, said the backslide was likely due to ongoing “behavioral, academic and staffing challenges.” Many districts are still reporting high chronic absenteeism rates.

They attribute the encouraging signs in first- through third-grades to younger students’ tendency to learn faster.

In another thread on this site, I discussed the linkage between COVID and the small eruption by a nearby star called Betelgeuse.

Weekly COVID-19 hospitalizations have risen by more than 10% across the country, according to new data published by the Centers for Disease Control and Prevention, marking the largest percent increase in this key indicator of the virus since December.

At least 7,109 admissions of patients diagnosed with COVID-19 were reported for the week of July 15 nationwide, the CDC said late Monday, up from 6,444 during the week before.

Another important hospital metric has also been trending up in recent weeks: an average of 0.73% of the past week's emergency room visits had COVID-19 as of July 21, up from 0.49% through June 21.

The new figures come after months of largely slowing COVID-19 trends nationwide since the last wave of infections over the winter.

"U.S. COVID-19 rates are still near historic lows after 7 months of steady declines.  Early indicators of COVID-19 activity (emergency department visits, test positivity and wastewater levels) preceded an increase in hospitalizations seen this past week," CDC spokesperson Kathleen Conley said in a statement.

Conley said virtually all counties are at "low" COVID-19 hospital admission levels, below the thresholds at which the CDC recommends additional precautions to curb the virus.

Only one part of the country did not record more hospitalizations last week compared to the week prior: the Midwestern region spanning Illinois, Indiana, Michigan, Minnesota, Ohio and Wisconsin.

For now, hospitalizations remain far below the levels recorded at this time last year nationwide. July 2022 peaked at more than 44,000 weekly hospitalizations and 5% of emergency room visits with COVID-19 during a summer surge that strained many hospitals.

"The U.S. has experienced increases in COVID-19 during the past three summers, so it's not surprising to see an uptick," said Conley.

Projections have differed over what the coming months will hold.

Scientists estimate that over 20% of people who get infected with COVID never have any symptoms – and a portion of them never even know they were infected. Now a new study published in Nature on July 19 says their genetics might be why the virus didn't make them sick.

Some people have a version of a gene in their immune system called HLA-B that protects them from feeling the effects of the virus. The study found that people with this special HLA-B variant are 2 to 8 1/2 times more likely to be asymptomatic than those without the variant.

Goats and Soda covered an early version of this study last year. Since then, the scientists have found out how this genetically enhanced protection works – it's because of immune cells that remember infections from other seasonal coronaviruses, i.e. many common colds, and thus know how to attack COVID-19 too.

Bone marrow donors were key to the study
Jill Hollenbach, an immunologist at the University of California, San Francisco who led the research described in the new study, didn't have a mild COVID experience.

"I had COVID. I was sick for about a week. I didn't love it."

Hollenbach had a common kind of COVID experience, moderate symptoms and eventually a full recovery. But in her research, she says she's most interested in those with extreme cases.

"One extreme is very severe disease [leading to hospitalization or death]. And the other end of that spectrum is you didn't have any symptoms. We really haven't understood what's driving that," she says.

The new findings are thanks, in part, to the Good Samaritans who signed up to donate bone marrow through the Be The Match program. Some people who had provided a DNA sample to the program also signed up to participate in Hollenbach's COVID-19 Citizen Science Study.

"We simply asked people who were registered donors to track their COVID experience through a smartphone app and consented to let us look at their genetic data and link it to their answers," Hollenbach says.

Hollenbach thought that the same HLA genes used to find bone marrow matches could also be involved with COVID outcomes. "There's more diseases and conditions associated with variation in the HLA genomic region than any other genomic region. And that's by a wide margin," she says.

HLAs are a class of genes involved in the immune system that sit on the surface of our cells. When we're infected by a virus, HLAs will hold out a piece of that virus like a flag, telling the immune system to kill the infected cell.

There are hundreds of different HLA variants. Hollenbach found that one of them, HLA-B*15:01, was associated with asymptomatic COVID.

"To be fair, not everybody that has HLA-B*15:01 will be asymptomatic," Hollenbach says. "But it was a really clear, robust and replicable association."

They call it 'cross-reactive immunity'
So how does this protection work?

The research shows that people with HLA-B*15:01 have an enhanced protection against COVID after being exposed to closely related common cold viruses. That's the result of a process called cross-reactive immunity.

"The thinking is that your exposure to some seasonal cold viruses, that in some cases share a lot of similarities with parts of SARS-CoV-2, gave you some existing immunity," Hollenbach says.

This is similar to how many vaccines, including the COVID vaccine, work. If you show the immune system a piece of a virus, it can use that as a template to create "Memory T cells." which can recognize viruses in future infections that match the template and start an immune response.

So when people with HLA-B*15:01 are exposed to the common cold, they create Memory T cells from a template that's so similar to COVID. And this template gives them enough protection from the virus that if infected they might never show any symptoms.

Hollenbach and her team demonstrated this by turning to samples of T cells from people with HLA-B*15:01 that were taken before the pandemic and then exposing those cells to COVID. Lo and behold, the T cells could react to the COVID virus.

The study doesn't have all the answers but could hold clues to better COVID treatments
The scientific community is raving about the new study.

"Well, it's a breakthrough," says Dr. Eric Topol, a physician-scientist at the Scripps Research Institute who wasn't involved in the study. "I think it may wind up giving us a whole new map for what to do in terms of drugs and vaccines, which is really notable."

While Topol is overall very enthusiastic about this research, he does have some concerns. "The main limitation is [the study] has three cohorts that were almost all European ancestry," he says.

This type of limited ethnic pool is an unfortunately common problem in disease research and means that this research might not apply to broad swaths of people.

The other main limitation of the study, Topol says, is that symptoms were self-reported, meaning that some people who reported as asymptomatic might have had a late onset of symptoms or mild symptoms that they didn't record in the app. But he says that the research team "did a really good job to deal with that" by making sure no symptoms were reported both 2 weeks before and after a positive test.

And there's the caveat that this research doesn't fully explain the mystery of asymptomatic COVID infections. "The genetic association that we found in this study explains some but not all asymptomatic disease," Hollenbach says. "So surely there are other genetic and non-genetic factors that are important in asymptomatic infection."

The paper says that only one of every five people in the study who reported being asymptomatic for COVID had the HLA-B*15:01 variant.

I've just tested positive for COVID. I can't believe I managed to avoid it for so long.

I've got a horrible raw sore throat and a streaming nose. I ache all over and can hardly sleep. My skin feels weird and tingly. Drying my hands on a towel is a very strange sensation.

Get lotsa rest. Drink lots of water.

Thats a reminder to us all that we still cant let our guard down yet.

I've just tested positive for COVID. I can't believe I managed to avoid it for so long.

I've got a horrible raw sore throat and a streaming nose. I ache all over and can hardly sleep. My skin feels weird and tingly. Drying my hands on a towel is a very strange sensation.

Sorry. Take care.

As has been said a number of times in this thread our natural inclination when we get hurt or sick is to get back to normal as fast as possible. Normally that is a good idea because we have to rebuild our endurance and that can’t happen by sleeping all day. With COVID pushing the limit is often counterproductive.

COVID rates in the U.S. have risen for the fourth summer in a row, elevating hospitalization rates and adding more weight to the argument that the virus has found summer seasonality, in addition to winter.

Nationally, COVID wastewater levels are similar to that of every pandemic summer except for 2022, when the world saw a spike due to Omicron variant BA.5.

The U.S. Centers for Disease Control and Prevention’s data tracker shows a 10.3% rise in hospitalizations July 9 to 15, the most recent period for which data is available. Deaths, however, are holding steady.

COVID wastewater levels are on the rise in the Houston area, and positive tests in the community have been elevated since late June, Dr. Michael Chang, pediatric infectious disease specialist at Children’s Memorial Hermann Hospital and UTHealth, tells Fortune.

But so far, that hasn’t translated into a significant increase in kids admitted to his hospital for COVID, he said. Still, he adds, “our colleagues in the city have reported some increased pediatric hospitalizations.” And his system’s adult hospitals have seen an increase in COVID hospitalizations since the end of June.

Cases are trending steadily upward in the southern region of the U.S., of which Texas is a part, according to BioBot Analytics, which monitors COVID wastewater levels for the federal government. They’re also trending steadily upward in the Northeast, and more sharply upward in the West and Midwest, though levels in both still lag the rest of the country.

Reasons behind the rise in COVID cases
Chang attributes this summer’s elevated level of COVID cases to increased indoor activities driven by heat and people seeking air conditioning. Similarly, winter spikes are attributable to increased indoor activities driven by cold and people seeking heat. Summer travel is likely also contributing, he said.

Another factor: waning immunity. Antibody immunity from both infection and vaccination lasts roughly three to six months. Those who were infected last winter are likely more susceptible to the virus again.

While new XBB.1.5 COVID boosters are expected this fall, the variant is “on its way out,” Raj Rajnarayanan—assistant dean of research and associate professor at the New York Institute of Technology campus in Jonesboro, Ark., and a top COVID-variant tracker—told Fortune.

“By the time the booster hits the market, there won’t be any XBB.1.5 in circulation,” he said, referencing the strain known as Kraken that grew rapidly last winter. It made up an estimated 12% of U.S. cases last week.

The new jabs should still be useful, Rajnarayanan said, as the XBB.1.5 variant holds a good deal of similarities to top variants in circulation now.

But it’s hard to say how the booster will hold up to the new variants the world is seeing by the time it rolls out, he added.

Like other respiratory viruses, COVID seems to spike in the winter. As for whether the virus will become a summer trend we can count on, Chang said he doesn’t think we can definitively draw that conclusion—yet.

But people’s COVID-related behavior, or lack thereof, “has stabilized in the last two summers,” Chang said.

“This summer will give us the best answer to whether we see summer spikes every year, depending on how big this summer wave turns out to be.”

Thank you. I will be careful.