Covid News: Lack of Quick Test to Diagnose Omicron or Delta Complicates Treatments

Airlines, schools and businesses are curbing operations in the United States because they lack healthy workers. Members of Congress are urged to work remotely.

With no way to identify Omicron and Delta patients, treatment decisions are vexing doctors.

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Credit...Chandan Khanna/Agence France-Presse — Getty Images

Most U.S. doctors have no way to determine which variant of the coronavirus a patient is carrying, a distinction that could mean the difference between life and death.

High-risk patients carrying the Delta variant could benefit greatly from two particular monoclonal antibody treatments shown to reduce hospitalization and death. But those medications would most likely do nothing for patients with Omicron, who would only respond to a third antibody treatment that is in very short supply.

While U.S. officials have endorsed using a workaround test that can identify Omicron’s genetic signature, experts say it’s not feasible for large health systems facing a crush of patients to employ in each case.

That makes treating patients challenging in places like Maryland, where cases are spiking and Omicron accounts for roughly 58 percent of them. The Delta variant is also holding strong in the Great Plains and swaths of the West, including California.

While there is no approved test to determine each individual’s variant, a national network of state and other labs use genome-sequencing tests to track variants broadly in communities. Health systems then use those regional estimates or their own data to decide which antibody treatments to use in their clinics and hospitals.

Many of them concluded that a community of largely Delta patients would benefit most from the antibody drugs made by Regeneron and Eli Lilly, while communities where Omicron patients are predominant would benefit from antibodies from GlaxoSmithKline and Vir Biotechnology.

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Credit...Ted S. Warren/Associated Press

Federal officials have dabbled with making the decision for the nation. On Dec. 23, they stopped shipments of antibody treatments by Eli Lilly and Regeneron after the Centers for Disease Control and Prevention said 73 percent of U.S. Covid cases were Omicron.

An outcry followed from Republican political leaders, who argued that some people in their states were still infected with Delta. And on Tuesday, the C.D.C. slashed its estimate of national Omicron cases to 59 percent. On Dec. 31, federal officials resumed national shipping all of the antibody treatments.

For the next few weeks, as the country grapples with this uneven mix of both variants, tailoring treatments to each patient will be “extraordinarily difficult,” said Dr. Alex Greninger, assistant director of the clinical virology laboratories at the University of Washington Medical Center.

Dr. Greninger is credited with developing one of the first tests to detect the coronavirus in the United States. But he is pessimistic that health systems can pivot quickly to sort out which patients have Delta or Omicron. And although a shortcut test can detect Omicron, there’s no simple way to report the results in bulk, he said.

What’s more, the genome sequencing used by public health officials takes nearly a week — too long to target the early antibody treatments that have been found to reduce the need for hospitalizations. That makes patient care particularly difficult right now, said Dr. Mark Siedner, an infectious disease clinician and researcher at Massachusetts General Hospital.

In Massachusetts and nearby states, an estimated 44.5 percent of cases are Omicron. Dr. Siedner said his health system has stopped using the Regeneron and Eli Lilly antibodies that are not effective against Omicron and are “anxiously awaiting” more doses of the effective treatment by GlaxoSmithKline and Vir Biotechnology.

“We’re in a holding pattern and it’s a terrible time to be in that place,” he said.

The United States struggles to avoid widespread shutdowns as Omicron spreads.

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Credit...Nicole Craine for The New York Times

Officials across the United States, from President Biden on down, have been insisting that they are no longer in the shutdown business, and will not order any closures to contain the latest surge in coronavirus cases.

But Omicron may be taking the decision out of their hands. So many workers are testing positive or calling in sick that businesses, schools, government agencies and more are being crippled by staff shortages that may force them to close some operations anyway.

Coronavirus cases in the United States by region

This chart shows how reported cases per capita have changed in different parts of the country. The state with the highest recent cases per capita is shown.

Airlines began canceling flights in large numbers on Christmas Eve for lack of crews, and the problems have continued into the new year. Broadway shows have been canceled because of outbreaks backstage. Major companies have delayed or entirely jettisoned return-to-office plans. Many colleges are switching back to virtual classes to start the semester.

And public school leaders are struggling to respond to a situation that has changed greatly from when students went on holiday breaks before Christmas, barely a week ago. Four large city school systems — Cleveland, Detroit, Milwaukee, and Newark — have joined a growing list of public schools around the country that put off reopening on Monday, switched to remote instruction, or both. Covid-19 outbreaks and staffing shortages forced their hands.

Omicron has driven case numbers to staggering new heights: The United States is averaging more than 484,600 daily cases over the past week, a 238 percent increase from two weeks ago. Hospitalizations are up 41 percent in the past two weeks, while deaths are down by 3 percent.

In some cases, the very resources needed to cope with Omicron’s staffing disruptions are themselves being disrupted, from the call-center agents who rebook canceled flights to the frontline medical professionals who care for sick workers.

Infected police officers, firefighters, paramedics, and transit workers are leaving shifts unfilled. In New York City, subway lines have been delayed by staff shortages, and the Fire Department has asked residents not to call 911 except in a real emergency.

Many elected leaders of both parties have discarded their sharpest pandemic-curbing tools, like closing government offices, schools and businesses, which have come with staggering economic, social and political costs. Instead, elected officials have stressed the importance of vaccination, booster shots and mask-wearing.

“I am not prepared to shut down schools or the economy at this time,” Gov. Kathy Hochul of New York, a Democrat, said before New York suffered a string of new daily case records last week. “I will not overreact and send this economy spiraling out of control once again.”

Many leading public health experts aren’t seeking shutdowns, either. If anything, many appear to be taking an opposite tack.

The Centers for Disease Control and Prevention announced new guidelines to help schools stay open, by allowing children who are exposed to the coronavirus to “test to stay” instead of automatically having to quarantine at home. And it has said that some Americans who test positive can leave isolation after five days, half as long as previous recommendations.

Jin Yu Young contributed reporting.

Tracking the Coronavirus ›

A federal judge blocks the Defense Dept. from punishing Navy forces who refuse the vaccine.

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Credit...Kenny Holston for The New York Times

A federal judge granted a preliminary injunction on Monday blocking the Department of Defense from taking “any adverse action” against 35 Navy sailors who have refused to get vaccinated against the coronavirus, arguing that it violated their religious freedoms.

The service members — including Navy SEALs and members of the Naval Special Warfare Command — had filed suit against the Biden administration arguing that their “sincerely held religious beliefs forbid each of them from receiving the Covid-19 vaccine for a variety of reasons based upon their Christian faith.” The Pentagon had mandated that all active-duty troops receive the vaccine.

The judge, Reed O’Connor of the Northern District of Texas, effectively blocked the department from punishing those troops.

“Our nation asks the men and women in our military to serve, suffer, and sacrifice. But we do not ask them to lay aside their citizenry and give up the very rights they have sworn to protect,” Judge O’Connor wrote in his 26-page order. He added: “The Covid-19 pandemic provides the government no license to abrogate those freedoms. There is no Covid-19 exception to the First Amendment. There is no military exclusion from our Constitution.”

The group represents a small fraction of active-duty troops from the United States, and as of mid-December, most active-duty soldiers and members of the Navy had received at least one dose of the vaccine. Thousands have requested religious exemptions, and none have been granted so far, officials said in December.

The decision follows another injunction by a judge in November against President Biden’s national vaccine mandate for health care workers.

Judge O’Connor, who was appointed by President George W. Bush, has reliably tossed several Democratic policies that have been challenged on the federal bench. In response to the injunction on Monday, Senator Ted Cruz, Republican of Texas, wrote on Twitter, “This is a major win!”

A spokesperson for the Pentagon could not immediately be reached for comment. But on Monday evening, John Kirby, a Pentagon spokesman, said that defense officials were reviewing the injunction, according to The Washington Post.

The virus is spreading faster than ever, but new data offer hope.

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Credit...Calla Kessler for The New York Times

The coronavirus is spreading faster than ever at the start of 2022, but the last days of 2021 brought some encouraging news about the latest wave of infections.

With growing evidence that the Omicron variant produces less severe illness than in earlier waves, governments are redoubling their focus on vaccinations and boosters, which are increasingly seen as the world’s ticket to “living with Covid.”

Dr. Anthony S. Fauci, the U.S. government’s top infectious disease expert, said on Sunday that hospitalizations, which are not rising as fast, were a more important barometer than reported cases for the severity of the Omicron wave, a sharp distinction after nearly two years of tallying daily case counts.

“As you get further on and the infections become less severe, it is much more relevant to focus on the hospitalizations as opposed to the total number of cases,” Dr. Fauci said.

Still, the case numbers remain staggering. The world is recording an average of nearly 1.5 million new cases every day, twice as many per day as were recorded nearly a week ago, although the figures in many places may have been distorted by holiday reporting delays. In the United States, experts forecast that the Omicron wave could crest in mid-January, but not before millions were infected every week. Across Europe, caseloads have soared to new highs and ushered in another bitter winter of social restrictions, mask mandates and shifting travel rules.

The holidays made things worse as colder weather and festive gatherings drove people indoors, where the virus circulates more easily. Airports and mass transit hubs were snarled with travelers after many people stayed home last year. And with many government offices closed, testing and case data were not being compiled as regularly, leaving officials and experts, at least temporarily, with an incomplete picture of how bad things were getting.

As much of the world returns to work this week, however, several trends are becoming clearer:

  • Omicron seems milder: A large British study determined that people who contract Omicron are far less likely to be hospitalized than those infected with the Delta variant. Other studies found that Omicron may not spread as easily to the lungs, a possible explanation of why its effects appear less severe.

  • Vaccines, especially boosters, help: The British study also underlined that the risk of hospitalization was significantly lower for people who had received two or three vaccine doses, compared with unvaccinated people. Among Covid cases who developed symptoms, people who had three doses were 88 percent less likely to be hospitalized than those who had not had any shots.

  • Delta remains a threat: The earlier variant still accounts for a large share of new infections in many countries — including more than 41 percent in the United States, according to federal data from the week ending on Christmas Day — and is significantly more virulent.

Although many governments are loath to lock down again, officials are tweaking rules to account for Omicron’s blazing spread. Paris last week became the latest European city to reimpose an outdoor mask mandate. South Korea joined France and others in setting an expiry date for its vaccine passes, hoping to push more people to get boosters.

Here are some other trends to watch for:

  • Hospitalizations rising: Experts warn that with so many infections, the sheer number of patients needing care will strain health systems already frayed by two years of Covid. In Australia, hospitalizations from the virus have more than doubled over the past week, to nearly 2,000. Worldwide, more health workers are likely to be sidelined by infections, adding to the stress on hospitals.

  • Risks to older people: Much of the early data, including the British study, covers younger patients, leaving significant questions about how Omicron will affect older people. On Monday, Britain’s education secretary, Nadhim Zahawi, told BBC radio that Omicron cases were rising among those 50 and older, but added that they were well protected since more than 90 percent of such people in Britain had booster shots. In the United States, according to the Centers for Disease Control and Prevention, less than half of fully vaccinated people over 50 have received a booster dose.

  • More countries considering a fourth dose: As studies suggest that immunity from boosters wanes against Omicron, Israel said it would offer a fourth vaccine dose to people age 60 and older, even though there is so far little evidence about its effectiveness. On Monday, French officials said that they would decide as early as mid-February whether to offer a fourth dose.

  • Trouble for the less vaccinated: As wealthy nations rush to offer additional doses, experts fear that poorer nations will be left even farther behind, and ever more vulnerable to Omicron. Many of the countries with the fastest rising case counts — including Ivory Coast, Ghana and Angola — are in Africa, the continent with the lowest vaccination rates.

N.Y.C. schools are ‘staying open,’ Mayor Eric Adams says.

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‘We Are Staying Open,’ New York City Mayor Says of Schools

Mayor Eric Adams of New York City insisted schools would remain open despite surging Omicron cases in the city. He said remote learning has been too damaging, especially to children in low-income neighborhoods and homeless students.

We’re really excited about the opening of our schools, and we want to be extremely clear: The safest place for our children is in a school building. And we are going to keep our schools open, and ensure that our children are safe — in a safe environment. Our children were exposed to an environment of crime and of uncertainty. It really traumatized parents that did not have child care. The remote learning aspect of it was terrible for in poorer communities, particularly those children that lived in homeless shelters or that lived — were housing insecure. The food aspect — schools provide primary meals for many students in this city. And then the socialization. We saw an increase in suicide, attempted suicides. We’re not sending an unclear message of what is going to happen day to day. I’m going to tell you what’s going to happen day to day. We are staying open. We’re going to do everything that we have to do to keep our schools open. And I know there’s questions about staffing. I know this question about testing. There’s a lot of questions, but we’re going to turn those question marks into an exclamation point. We’re staying open.

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Mayor Eric Adams of New York City insisted schools would remain open despite surging Omicron cases in the city. He said remote learning has been too damaging, especially to children in low-income neighborhoods and homeless students.CreditCredit...Dave Sanders for The New York Times

Mayor Eric Adams insisted on Monday morning that New York City’s schools would stay open despite an extraordinary surge in Omicron cases. But about a third of city parents did not send their children back to classrooms on the first day after the holiday break. Attendance was just over 67 percent, slightly higher than the low point of 65 percent the system reached on the day before winter break.

Throughout the day on Monday, Adams was adamant that the system would remain open. He repeated the message in a series of television interviews and after his first official school visit since taking office on New Year’s Day.

“We’re really excited about the opening of our schools,” Mr. Adams said outside the school, Concourse Village Elementary School in the Bronx. “We want to be extremely clear: the safest place for our children is a school building.”

Mr. Adams said that remote learning had been disastrous for too many of the city’s nearly one million schoolchildren in the nation’s largest school district, and had been particularly harmful for children in low-income neighborhoods and homeless students.

But the calm that Mr. Adams sought to project was not shared by the many parents and educators who greeted Monday morning with profound trepidation. After roughly a year of remarkably low virus transmission in schools, Covid cases soared in the week before the winter break, prompting the closures of 11 schools and over 400 classrooms, and the contact tracing system for city schools effectively collapsed amid the surge.

New York City reported 35,650 new virus cases on Sunday, with a 7-day average test positivity rate of nearly 22 percent, according to state data.

Some families and elected officials have called on Mr. Adams to delay the start of school by a few days to allow every child and educator to get tested. And teachers have raised questions about how schools will be properly staffed with so many teachers sick with the virus or quarantining due to exposures.

“This is an all hands on deck moment,” Mr. Adams said, acknowledging that administrators who are not normally in the classroom would be used to address staff shortages if necessary.

Mr. Adams has endorsed a plan created by former Mayor Bill de Blasio that is designed to keep more classrooms open as the surge continues. The plan calls for distributing 1.5 million rapid at-home test kits to schools.

Starting Monday, the city is also doubling its random in-school testing program to give P.C.R. tests to 20 percent of consenting children in each school weekly. But most families have not opted in to allow their children to be tested, which has made the testing pool very small at some schools.

The mayor and the new schools chancellor, David C. Banks, are betting that their plan to increase testing will prevent major outbreaks.

“We’re going to turn those question marks into an exclamation point: we’re staying open,” Mr. Adams said.

Mr. Adams and Mr. Banks have so far resisted calls to mandate booster shots for educators or vaccines for children. The mayor has said a decision will be made this spring about mandating vaccines for students for the fall.

“We’re not at the point of mandate,” Mr. Adams said Monday, as he encouraged eligible New Yorkers to get vaccinated and boosted.

Michael Mulgrew, president of the city’s teachers’ union, said in an email to members that he had encouraged Mr. Adams to start the year remotely. But on Monday morning, Mr. Mulgrew said he was working closely with the new mayor and that schools had been some of the safest places in the city throughout the pandemic.

Later on Monday, Gov. Kathy Hochul reiterated her commitment to keeping New York’s children in schools.

“My view is that every child should be back in school unless they are testing positive,” she said.

The state has distributed 5.2 million at-home test kits to schools thus far, and another 3.8 million arrived yesterday and have yet to be distributed.

Under the current rule, test kits will only be provided to students for known exposures that occur in classrooms, although Ms. Hochul said that policy was under review.

She also cautioned against a return to remote learning. “The teachers did the best they could. The parents did the best they could,” she said. “But we ask too much.”

In particular, she spoke about the effects of remote learning on children in communities of color, those who lacked resources and those without high-speed internet access — an existing digital divide that she said had widened into a “digital canyon.”

“We cannot have that,” Ms. Hochul said. “That was an injustice. We cannot have that anymore.”

For millions of California students, school reopening hinges on testing.

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Credit...Andri Tambunan for The New York Times

SACRAMENTO — With the Omicron variant raging across California, millions of schoolchildren returned to classrooms on Monday, ending the holiday break as many had spent it — masked, distanced, apprehensive and in long lines with their parents, scrambling for coronavirus tests.

Few schools were closed in a state whose Covid-19 precautions have been among the most aggressive in the nation. California has managed to maintain comparatively low rates of virus-related deaths and hospitalizations.

But infections have soared recently because of the highly contagious variant, which appears to result in less severe cases. In hundreds of districts, in-person instruction was conditioned on heightened health requirements and fraught with the understanding that even those might not prevent a return to remote learning.

“Frankly, the disruption I’m worried about isn’t Day 1 — it’s Day 2, 3 or 4 if we get 30 or 40 or 50 positive cases,” said Alex Cherniss, the superintendent of the Palos Verdes Peninsula Unified School District, where, after days of impassioned community debate, some 10,000 students in coastal Los Angeles County returned to class on Monday.

“People are exhausted here,” he said.

California’s largest school district, Los Angeles Unified, was not scheduled to resume classes until next week. But on Monday, the district issued new rules requiring baseline testing as a condition of returning to campus, regardless of vaccination status. Previously, testing had been optional for vaccinated and asymptomatic students and employees.

New reported cases by day
Feb. 2020
Jul.
Dec.
May 2021
Oct.
Mar. 2022
10,000
20,000 hospitalized
7–day average
1,977
Source: U.S. Department of Health and Human Services. The seven-day average is the average of a day and the previous six days of data. Currently hospitalized is the most recent number of patients with Covid-19 reported by hospitals in the state for the four days prior. Dips and spikes could be due to inconsistent reporting by hospitals. Hospitalization numbers early in the pandemic are undercounts due to incomplete reporting by hospitals to the federal government.