Coronavirus Files: Testing shortage and bungled messaging complicate omicron surge

Coronavirus
January 10, 2022

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COVID cases shatter records and fill understaffed hospitals

Nearly two years into the pandemic, case rates are far higher than ever, with an average of over 600,000 new diagnoses reported in the U.S. every day. That’s most likely an undercount, since people who test at home might not be counted and people without symptoms might not test at all.

Case numbers mean less than they used to as infections in vaccinated people, though not uncommon, usually pose less of a burden on the health care system. But high case rates still mean many people will get very ill, making hospitalization rates a metric to watch — and those numbers, too, are rising to levels last seen during the deadly surge a year ago.

Moreover, those in need of hospital care must rely on an exhausted and decimated health care workforce. Nearly one in five health care workers has quit since the pandemic began, according to one survey. Add in those who’ve left work due to long COVID or other reasons, and the health workforce is down nearly 500 million.

“I’m actually worried that we don’t have enough staff to take care of the patients,” UC San Diego Health CEO Patricia Maysent told the San Diego Union-Tribune’s Paul Sisson.

At least one person, an Iowa man, has died waiting for a hospital bed in recent weeks.

The doctors who remain say there won’t be enough of the recently authorized antiviral pills in time to assuage the disaster, notes Katie Shepherd at The Washington Post.

Many experts predict the current surge will be sharp but swift, with the U.S. hitting peak omicron within days or weeks.

Even so, winter 2022 could easily become the “most devastating” surge to date, writes Megan Molteni at STAT.

Spike endangers well-vaccinated Puerto Rico

Puerto Rico, with 73% of people fully vaccinated — a rate higher than most states — was looking like a success story until mid-December, when cases went up by 4,600%, reports Frances Robles at The New York Times.

As daily case counts in the island of 3.2 million rocketed from 96 to 7,200 to 11,000, one statistician thought there must be some glitch in the database. There wasn’t.

“While the omicron variant has besieged the entire country,” writes Robles,” it is especially worrisome in Puerto Rico, a U.S. territory already overwhelmed by government bankruptcy, an exodus of health professionals and a fragile health system.”

Many young professionals left for the continental U.S. in recent years, including thousands of health workers. As a result, Puerto Rico’s population includes a high proportion of older adults who have diabetes, obesity or other COVID risk factors, and not enough doctors to help them.

The territory’s governor and health officials ordered a host of social distancing measures, including cancellation of New Year’s events and the Miss World pageant, as well as a requirement that air passengers arriving from the U.S. have a negative COVID test, and a booster mandate for restaurant workers and public safety employees.

Evidence builds that omicron is milder, but not mild

More than a half-dozen scientific studies now indicate that omicron is somewhat lower in virulence than the variants that came before. Researchers working with cells in dishes, mice and hamsters report the variant is less likely to infect the lungs.

That’s important because the lungs are where the virus performs much of its most damaging work, scarring the organ, blocking oxygen from entering the bloodstream, and setting off dangerous levels of inflammation, writes Max Kozlov at Nature.

“It’s clear that this one is different for hamsters,” Michael Diamond, a virologist at Washington University in St. Louis, told Kozlov. Diamond was shocked when the omicron-infected animals did not even lose much weight, as happened with previous variants.

The lungs’ relative immunity may have to do with a key viral entry protein called TMPRSS2. Lung cells have lots of this protein, but omicron uses it less than other variants.

A virus that hangs out in the upper airway, though, is likely very contagious, as omicron has proved to be in people.

Real-world data from infected people also supports the relative mildness of omicron. A U.K. study suggests it’s less likely to put people in the hospital.

And even where hospital beds are full, fewer people require intensive care, report Emily Anthes and Azeen Ghorayshi at The New York Times.

“We’re not sending as many patients to the ICU, we’re not intubating as many patients,” said emergency physician Dr. Rahul Sharma of New York-Presbyterian Hospital. “Most of our patients that are coming to the emergency department that do test positive are actually being discharged.”

Anthes and Ghorayshi do note that the number of ICU patients may rise in coming weeks, as may death rates.

Despite this silver lining in disease severity, reporters should take care in describing omicron, admonishes Al Tompkins at the Poynter Institute: “We are doing a disservice when we emphasize the ‘mild’ nature of the omicron variant.”

After all, more than 115,000 people are being hospitalized every day, and more than 1,000 are dying — rates last seen in winter 2021.

“Because so many people are being infected, it is not percentages but raw numbers that matter now,” writes Tompkins. “We are going backward.”

CDC bungles communications over isolation and quarantine

The Centers for Disease Control and Prevention baffled experts in late December when it shortened the required isolation time for infected individuals from 10 days to just five.

Unvaccinated people who are exposed to an infected person must quarantine for five days instead of 14, and people who are vaccinated and boosted need not quarantine at all.

“Some (experts) view the policy shift as a nod to reality,” writes Charlotte Klein at Vanity Fair. “Others see it as confusing and even irresponsible.”

The new regulations proved so convoluted that Maine’s public health agency crafted flow charts for who can leave isolation or quarantine when.

Notably, the agency did not require infected or exposed people to take any sort of COVID test to venture back into the world, though it did request they stay masked until 10 days had passed.

Harvard epidemiologist Michael Mina called the lack of a testing requirement “reckless,” noting some people stay infectious for the better part of two weeks. “What the heck are we doing here?” he asked on Twitter.

The American Medical Association said the lack of a test-to-exit policy risks “further spread of the virus.”

CDC director Dr. Rochelle Walensky defended the change, saying that up to 90% of COVID transmission happens in the first five days. Shortly after releasing the new policy, the CDC posted a bit of data from an omicron cluster in Nebraska. The study suggested the median time from infection to symptoms was three days for omicron, compared to five or more for the original strain of the coronavirus.

A spokesperson for the American Nurses Association said it’s too soon to change policies for omicron, and noted that delta is still prevalent.

“A major concern voiced by scientists is that the isolation policy fails to distinguish between vaccinated and unvaccinated people, who recover at different rates,” writes Julie Steenhuysen at Reuters. Dr. Eric Topol of Scripps Research told her that unvaccinated people take longer to clear the virus and called the policy a “new low” for the beleaguered public health agency.

The state of Michigan has so little trust in the CDC it announced it would delay adopting the new guidelines until it conducted its own review of the data, though the state has since said it is now on board with the change.

California also issued stricter guidelines, recommending people exit isolation only after a negative test.

Of courses, test kits and appointments have become hard to come by, despite President Joe Biden’s promise of 500 million more at-home kits (enough for every person in the U.S. to have one or two) and the recent authorization of two more rapid test brands. Mina suggested the current shortage of rapid tests is why the CDC left testing out of the new guidelines.

According to The Washington Post, the worry that too many isolated and quarantining Americans would cause essential services to break down drove the policy change. 

After a deluge of criticism and further consideration, the CDC doubled down on its policy last week. Walensky said that rapid tests aren’t reliable enough to determine if someone is no longer contagious.

This messaging boondoggle is the latest entry in a recurring pattern with the CDC during the pandemic, notes The New York Times. Despite Walensky’s efforts to clue in top health officials before the change this time around, both Fauci and surgeon general Dr. Vivek Murthy took issue with the lack of a testing requirement to leave quarantine on national TV.

One CNN reporter asked Walensky, “How do you expect people to keep track of what they can and can’t do?”

The science on the virus is rapidly evolving, so some change is to be expected. “But Dr. Walensky’s critics say the CDC’s recommendations are sometimes so confusing or abruptly modified that they seem more like drafts than fully vetted proclamations,” write Sharon LaFraniere, Sharyl Gay Stolberg, and Noah Weiland in The Times.

Or as late-night comedian Stephen Colbert tweeted: “We're 2 days from the next CDC guideline: ‘Hey, man. You do you.’”

Return to school complicated by test shortage

More than 5,000 schools shuttered for at least one day in the week after New Year’s, according to the tracker Burbio.

Some closed in anticipation of the omicron wave, others due to rising transmission in schools or delays in testing results. Testing requirements sent parents scrambling in what one epidemiologist called the “COVID Test Hunger Games,” reports Katie Reilly at Time.

Meanwhile, teachers feel unsafe. Chicago schools closed late last week when the teachers union deadlocked with the district over protective measures. Nearly nine hundred teachers in San Francisco, concerned about safety measures they considered inadequate, staged a sickout last Thursday.

In an effort to stay open in the coming months, many schools have begun to embrace a ‘test-to-stay’ policy, allowing students who test negative to remain in the classroom instead of automatically quarantining everyone who was in contact with an infected person. U.S. Education Secretary Migual Cardona has promised more tests for schools are forthcoming.

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What we're reading

  • “Omicron is our past pandemic mistakes on fast-forward,” by Katherine J. Wu, Ed Yong, and Sarah Zhang, The Atlantic
  • “The Biden administration rejected an October proposal for ‘Free rapid tests for the holidays,’” by Katherine Eban, Vanity Fair
  • “The stakes in the Supreme Court’s vaccine case are even bigger than they seem,” by Ian Millhiser, Vox
  • “What happened to the Novavax vaccine?” by Jennifer Henderson, MedPage Today
  • “Parents grapple with how long to wait for their children’s second shots,” by Cassandra Willyard, The New York Times
  • “The first Christmas as a layperson: Burned out by the pandemic, many clergy quit in the last year,” by Michelle Boorstein, The Washington Post
  • “Native American tribes have made progress against COVID-19. Omicron has them ‘back in crisis mode.’” By Bill Keveney and Trevor Hughes, USA Today
  • “To learn how COVID affects the ear, scientists turn to cadavers,” by Elizabeth Landau, Undark
  • “Desperate patients are shelling out thousands for a long COVID cure. Is it for real?” by Kiera Butler, Mother Jones
  • “How the pandemic made hotel housekeeping more difficult—and disgusting,” by Hugo Martín, Los Angeles Times
  • “COVID is rampant among deer, research shows,” by Evan Bush, NBC News

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