The new omicron variant is “more of a Frankenstein” than previous virus coronavirus variants, according to one virologist, and vaccine experts are at odds over how well current vaccines will provide protection against it.
A ‘Frankenstein’ variant
According to Alex Sigal, a virologist heading a team of researchers at the Africa Health Research Institute, the new variant is “probably the most mutated virus we’d ever seen.” However, Sigal added that he believes existing Covid-19 vaccines will continue to protect people against severe disease and hospitalization.
Similarly, Ugur Sahin, BioNTech co-founder, said that the Pfizer-BioNTechvaccine not only creates antibodies that prevent infection from occurring, but also creates T lymphocytes that attack cells after the body has been infected. Sahin argued that, even if omicron can evade antibodies, it would likely be vulnerable to T lymphocytes.
“Our message is: Don’t freak out, the plan remains the same: Speed up the administration of a third booster shot,” Sahin said.
Luke O’Neill, an immunologist and chair of biochemistry at Trinity College Dublin, said Sahin’s assumption makes sense from an immunological perspective. “There is optimism that the T-cells will hold the line—they are very good at stopping severe disease,” O’Neill said.
However, Stanley Plotkin, a scientist who has developed many vaccines, said Sahin’s assumptions were “gratuitous and without any proof.” Plotkin said so far there’s little evidence to suggest T-cells could fully protect against severe symptoms if a virus evades antibodies.
Further, Stéphane Bancel, CEO of Moderna, said, “There is no world, I think, where [the effectiveness] is the same level … we had with [the] Delta [variant] … I think it’s going to be a material drop. I just don’t know how much because we need to wait for the data. But all the scientists I’ve talked to … are like, ‘This is not going to be good.'”
However, former FDA commissioner Scott Gottlieb on Monday said, “There’s a reasonable degree of confidence in vaccine circles that [with] at least three doses … the patient is going to have fairly good protection against this variant.”
Angelique Coetzee, national chair of the South African Medical Association, said that so far, vaccinated patients who have tested positive for omicron “have no complication.” She noted that the nation’s hospitals were not overwhelmed by omicron patients, and most of those hospitalized were not fully vaccinated. Additionally, most patients she had seen did not lose their sense of taste and smell, and had only a slight cough, the New York Times reports.
“I have seen vaccinated people and not really very sick,” Coetzee said. “That might change going forward, as we say, this is early days. And this is maybe what makes us hopeful.”
Could omicron ‘outcompete’ delta?
Separately, Adrian Puren, acting executive director of South Africa’s National Institute for Communicable Diseases, said he believes omicron could become more pervasive than the delta variant. “We thought what will outcompete delta? That has always been the question, in terms of transmissibility at least … perhaps this particular variant is the variant,” Puren said.
William Schaffner, a professor of preventive medicine at Vanderbilt University School of Medicine, said that while nothing is certain yet, “it looks as though [omicron] will be as infectious as delta.”
As for how long it will take to answer questions about omicron, including its transmissibility and virulence, Tara Smith, an epidemiologist at Kent State University, said at minimum “it will take a month to get some preliminary data, and quite possibly longer to really know the fuller picture. We also won’t know about real-world experience in vaccine breakthroughs until that time.”
Here’s how the world as a whole is currently trending:
More than 570.6 million doses of the COVID-19 vaccine have been shipped to various U.S. states as of yesterday afternoon, of which more than 459.2 million doses have been administered, according to TIME’s vaccine tracker. About 59.3% of Americans have been completely vaccinated.
Nearly 263 million people around the world had been diagnosed with COVID-19 as of 12 a.m. E.T. today, and more than 5.2 million people have died. On Nov. 30, there were 615,787 new cases and 7,704 new deaths confirmed globally.
Here’s how the world as a whole is currently trending:
Here’s where daily cases have risen or fallen over the last 14 days, shown in confirmed cases per 100,000 residents:
And here’s every country that has reported over 5 million cases:
The U.S. had recorded more than 48.5 million coronavirus cases as of 12 a.m. E.T. today. More than 780,000 people have died. On Nov. 30, there were 116,588 new cases and 1,539 new deaths confirmed in the U.S.
Here’s how the country as a whole is currently trending:
The recent dip and rise in daily cases is likely due to reduced reporting during the holiday weekend; historically, the U.S. has seen similar short-term, apparent drop offs that were later shown to be outliers.
That said, here’s where daily cases have risen or fallen over the last 14 days, shown in confirmed cases per 100,000 residents:
All numbers unless otherwise specified are from the Johns Hopkins University Center for Systems Science and Engineering, and are accurate as of Dec. 1, 12 a.m. E.T. To see larger, interactive versions of these maps and charts, click here.
While no cases of the new coronavirus variant, Omicron, have been reported in the U.S. yet, it’s only a matter of time. In fact, Dr. Anthony Fauci, chief medical advisor on COVID-19 to President Biden, says it’s likely the virus is already in the country, given how much travel is occurring between countries as pandemic restrictions have started to lift in recent months.
Even if the variant were here, could existing tests tell if someone were infected by it? Testing experts say yes and no. The majority of tests used by commercial and public health labs can detect SARS-CoV-2, but they can’t confirm which version of the virus is present. That’s because the tests intentionally target parts of the virus that don’t change much. Variants are designated based on differences in mutations—in Omicron’s case, especially those in spike protein, a part of the virus that changes frequently to bypass drugs and immune cells, and thus are difficult to test for. So the majority of the tests available will show if a person is carrying the virus—but there’s no way to tell whether that virus is Omicron.
For that, a doctor would have to send your sample to a lab that can then sequence genetically to look for the genetic signatures unique to Omicron.
There is one commercial test, from Thermo Fisher Scientific, that can perform the two-fer: both detect the presence of the virus and give testers an inkling that what they’re dealing with might be the Omicron variant. The company’s test targets three different parts of SARS-CoV-2: two relatively stable regions, and the more variable spike protein. It turns out that Omicron will show positive matches on the two more stable regions, a pattern similar to the one from the Alpha variant, but will show a mismatch on the spike protein portion.
The Delta variant, which is now responsible for nearly 99% of new cases around the world, does not share this omission, and produces a three-for-three match on all three regions targeted by Thermo Fisher’s PCR test. That means, given Delta’s dominance, if a sample produces all three matches, it’s likely Delta; if it results in only two positive matches, it’s likely to be Omicron. To confirm, researchers can then send those samples in for sequencing to definitively look for Omicron’s genetic profile.
“This happens to be good fortune that this pattern can flag the presence of Omicron,” says Mark Stevenson, executive vice president and chief operating officer at Thermo Fisher. “It’s a good early warning system.” Clients using the company’s test in South Africa alerted Thermo Fisher last Wednesday that they were seeing those unusual patterns, even before the country’s health officials announced the spurt of new cases. Stevenson expects public health labs in Europe and the U.S. are now also using the test to look for the first cases of the Omicron variant.
At Qiagen, a global testing company that makes assays for both diagnostic testing and research purposes, the team immediately evaluated their test against the samples of genetic sequences of Omicron uploaded by public health experts into the public GISAID database. “We’ve seen no drop in performance in our products,” says Dr. Davide Manissero, chief medical officer at Qiagen.
Similarly, the research team at diagnostic testing company BD ran tests of its COVID-19 assays using the Omicron sequences in GISAID. “We are confident that our rapid antigen and PCR tests for COVID-19 will detect the novel variant,” Dave Hickey, president of BD Life Sciences, said in a statement.
If you prefer to rely on the at-home tests available over-the-counter at pharmacies that can provide results in a few minutes, those are also still useful, at least for letting you know if you might be positive. Like most PCR tests, the at-home kits cannot determine if someone is infected with the Omicron variant specifically, but they will turn positive for anyone infected with any version of the virus.
The first known U.S. case of the Omicron variant was detected in California, the Centers for Disease Control and Prevention confirmed Wednesday.
Driving the news: The confirmed case was detected in a traveler returning from South Africa who was fully vaccinated and has mild symptoms, according to the CDC.
Anthony Fauci, the director of the National Institute of Allergy and Infectious Diseases, had previously cautioned that the Omicron would “inevitably” be found in the U.S.
What they’re saying: “The recent emergence of the Omicron variant … further emphasizes the importance of vaccination, boosters and general prevention strategies,” the CDC said in a statement.
“We know what we need to do to protect people,” Fauci said following the announcement. “Get vaccinated if you’re not already vaccinated.”
Hospitals saw operating margins continue to erode in October, declining 12% from September under the weight of rising labor costs, according to a national median of more than 900 health systems calculated by Kaufman Hall. It was the second consecutive monthly drop and comes as facilities are preparing for the fast-spreading omicron variant of the coronavirus.
Although expenses remained highly elevated, patient days and average length of stay fell for the first time in months in October, likely reflecting lower hospitalization rates as the pressure of treating large numbers of COVID cases began to ease, Kaufman Hall said in its latest report.
At the same time, operating room minutes rose 6.8% from September, pointing to renewed patient interest in elective procedures.
Dive Insight:
Doctors and nurses have barely caught a breath from the most recent surge in inpatient volumes driven by the delta variant. Now, hospitals face the possibility of a fresh wave of cases led by omicron.
“Performance could continue to suffer in the coming months as hospitals face sustained labor increases and the uncertainties of the emerging omicron variant,” according to the Kaufman Hall report.
The new variant has not been detected in the U.S. as of Wednesday morning, but Canada is amongthe 20 countries that have confirmed cases.
Scientists are scrambling to understand the characteristics of the omicron variant. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, told a White House press briefing Tuesday that omicron’s mutation profile points to “increased transmissibility and immune evasion.” But it is too soon to tell whether omicron will cause more severe disease than other COVID-19 variants, or how well current vaccines and treatments work against it, Fauci said.
Moderna CEO Stéphane Bancel told the Financial Times he thought existing vaccines would be less effective against omicron than earlier variants. Moderna, Pfizer, Johnson & Johnson and other manufacturers are already working to adapt their vaccines to combat the new threat, first reported by South African scientists on Nov. 24.
Regeneron also said its COVID-19 antibody drug, the top-selling treatment in the U.S., might be less effective against omicron. The company said it is now conducting tests to determine how the variant affects its drug.
The median hospital operating margin, not including federal Coronavirus Aid, Relief, and Economic Security Act funding, was down 31.5% in October, compared to pre-pandemic levels in the same month of 2019, according to Kaufman Hall’s snapshot. Hospitals in the West, South and Midwest that were hardest hit by the delta variant saw year-over-year margin declines.
Total labor expenses rose nearly 3% from September to October, 12.6% compared to October 2020 and 14.8% compared to October 2019, Kaufman Hall said. Full-time equivalents per adjusted occupied bed decreased 4.5% versus 2020 and 4% versus 2019, suggesting higher salaries due to nationwide labor shortages, rather than increased staffing levels, are driving up labor expenses.
Total non-labor expenses, however, decreased 1% in October from September for supplies, drugs and purchased services, following months of increases.
“Broader economic trends such as U.S. labor shortages are adding to the extreme pressures of the pandemic. Hospitals face greater uncertainties in the coming months as a result, as COVID-19 cases and hospitalizations appear to once again be on the upswing before many have even had a chance to recover from the last surge,” Erik Swanson, a senior vice president of data and analytics at Kaufman Hall said.
There’s a lot of talk about “natural immunity” to Covid-19, and some people are refusing vaccination onthe grounds that they’ve got this natural immunity thanks to a previous Covid-19 infection. In this episode we take a look at how infection and vaccination compare in terms of immunity, reinfection, and overall health risks and benefits.
The healthcare industry’s staffing shortage crisis has had clear consequences for care delivery and efficiency, forcing some health systems to pause nonemergency surgeries or temporarily close facilities. Less understood is how these shortages are affecting care quality and patient safety.
A mix of high COVID-19 patient volume and staff departures amid the pandemic has put hospitals at the heart of a national staffing shortage, but there is little national data available to quantify the shortages’ effects on patient care.
The first hint came last month from a CDC report that found healthcare-associated infections increased significantly in 2020 after years of steady decline. Researchers attributed the increase to challenges related to the pandemic, including staffing shortages and high patient volumes, which limited hospitals’ ability to follow standard infection control practices.
“That’s probably one of the first real pieces of data — from a large scale dataset — that we’ve seen that gives us some sense of direction of where we’ve been headed with the impact of patient outcomes as a result of the pandemic,” Patricia McGaffigan, RN, vice president of safety programs for the Institute for Healthcare Improvement, told Becker’s. “I think we’re still trying to absorb much of what’s really happening with the impact on patients and families.”
An opaque view into national safety trends
Because of lags in data reporting and analysis, the healthcare industry lacks clear insights into the pandemic’s effect on national safety trends.
National data on safety and quality — such as surveys of patient safety culture from the Agency for Healthcare Research and Quality — can often lag by several quarters to a year, according to Ms. McGaffigan.
“There [have been] some declines in some of those scores more recently, but it does take a little while to be able to capture those changes and be able to put those changes in perspective,” she said. “One number higher or lower doesn’t necessarily indicate a trend, but it is worth really evaluating really closely.”
For example, 569 sentinel events were reported to the Joint Commission in the first six months of 2021, compared to 437 for the first six months of 2020. However, meaningful conclusions about the events’ frequency and long-term trends cannot be drawn from the dataset, as fewer than 2 percent of all sentinel events are reported to the Joint Commission, the organization estimates.
“We may never have as much data as we want,” said Leah Binder, president and CEO of the Leapfrog Group. She said a main area of concern is CMS withholding certain data amid the pandemic. Previously, the agency has suppressed data for individual hospitals during local crises, but never on such a wide scale, according to Ms. Binder.
CMS collects and publishes quality data for more than 4,000 hospitals nationwide. The data is refreshed quarterly, with the next update scheduled for October. This update will include additional data for the fourth quarter of 2020.
“It is important to note that CMS provided a blanket extraordinary circumstances exception for Q1 and Q2 2020 data due to the COVID-19 pandemic where data was not required nor reported,” a CMS spokesperson told Becker’s. “In addition, some current hospital data will not be publicly available until about July 2022, while other data will not be available until January 2023 due to data exceptions, different measure reporting periods and the way in which CMS posts data.”
Hospitals that closely monitor their own datasets in more near-term windows may have a better grasp of patient safety trends at a local level. However, their ability to monitor, analyze and interpret that data largely depends on the resources available, Ms. McGaffigan said. The pandemic may have sidelined some of that work for hospitals, as clinical or safety leaders had to shift their priorities and day-to-day activities.
“There are many other things besides COVID-19 that can harm patients,” Ms. Binder told Becker’s. “Health systems know this well, but given the pandemic, have taken their attention off these issues. Infection control and quality issues are not attended to at the level of seriousness we need them to be.”
What health systems should keep an eye on
While the industry is still waiting for definitive answers on how staffing shortages have affected patient safety, Ms. Binder and Ms. McGaffigan highlighted a few areas of concern they are watching closely.
The first is the effect limited visitation policies have had on families — and more than just the emotional toll. Family members and caregivers are a critical player missing in healthcare safety, according to Ms. Binder.
When hospitals don’t allow visitors, loved ones aren’t able to contribute to care, such as ensuring proper medication administration or communication. Many nurses have said they previously relied a lot on family support and vigilance. The lack of extra monitoring may contribute to the increasing stress healthcare providers are facing and open the door for more medical errors.
Which leads Ms. Binder to her second concern — a culture that doesn’t always respect and prioritize nurses. The pandemic has underscored how vital nurses are, as they are present at every step of the care journey, she continued.
To promote optimal care, hospitals “need a vibrant, engaged and safe nurse workforce,” Ms. Binder said. “We don’t have that. We don’t have a culture that respects nurses.”
Diagnostic accuracy is another important area to watch, Ms. McGaffigan said. Diagnostic errors — such as missed or delayed diagnoses, or diagnoses that are not effectively communicated to the patient — were already one of the most sizable care quality challenges hospitals were facing prior to the pandemic.
“It’s a little bit hard to play out what that crystal ball is going to show, but it is in particular an area that I think would be very, very important to watch,” she said.
Another area to monitor closely is delayed care and its potential consequences for patient outcomes, according to Ms. McGaffigan. Many Americans haven’t kept up with preventive care or have had delays in accessing care. Such delays could not only worsen patients’ health conditions, but also disengage them and prevent them from seeking care when it is available.
Reinvigorating safety work: Where to start
Ms. McGaffigan suggests healthcare organizations looking to reinvigorate their safety work go back to the basics. Leaders should ensure they have a clear understanding of what their organization’s baseline safety metrics are and how their safety reports have been trending over the past year and a half.
“Look at the foundational aspects of what makes care safe and high-quality,” she said. “Those are very much linked to a lot of the systems, behaviors and practices that need to be prioritized by leaders and effectively translated within and across organizations and care teams.”
She recommended healthcare organizations take a total systems approach to their safety work, by focusing on the following four, interconnected pillars:
Culture, leadership and governance
Patient and family engagement
Learning systems
Workforce safety
For example, evidence shows workforce safety is an integral part of patient safety, but it’s not an area that’s systematically measured or evaluated, according to Ms. McGaffigan. Leaders should be aware of this connection and consider whether their patient safety reporting systems address workforce safety concerns or, instead, add on extra work and stress for their staff.
Safety performance can slip when team members get busy or burdensome work is added to their plates, according to Ms. McGaffigan. She said leaders should be able to identify and prioritize the essential value-added work that must go on at an organization to ensure patients and families will have safe passage through the healthcare system and that care teams are able to operate in the safest and healthiest work environments.
In short, leaders should ask themselves: “What is the burdensome work people are being asked to absorb and what are the essential elements that are associated with safety that you want and need people to be able to stay on top of,” she said.
To improve both staffing shortages and quality of care, health systems must bring nurses higher up in leadership and into C-suite roles, Ms. Binder said. Giving nurses more authority in hospital decisions will make everything safer. Seattle-based Virginia Mason Hospital recently redesigned its operations around nurse priorities and subsequently saw its quality and safety scores go up, according to Ms. Binder.
“If it’s a good place for a nurse to go, it’s a good place for a patient to go,” Ms. Binder said, noting that the national nursing shortage isn’t just a numbers game; it requires a large culture shift.
Hospitals need to double down on quality improvement efforts, Ms. Binder said. “Many have done the opposite, for good reason, because they are so focused on COVID-19. Because of that, quality improvement efforts have been reduced.”
Ms. Binder urged hospitals not to cut quality improvement staff, noting that this is an extraordinarily dangerous time for patients, and hospitals need all the help they can get monitoring safety. Hospitals shouldn’t start to believe the notion that somehow withdrawing focus on quality will save money or effort.
“It’s important that the American public knows that we are fighting for healthcare quality and safety — and we have to fight for it, we all do,” Ms. Binder concluded. “We all have to be vigilant.”
Conclusion
The true consequences of healthcare’s labor shortage on patient safety and care quality will become clear once more national data is available. If the CDC’s report on rising HAI rates is any harbinger of what’s to come, it’s clear that health systems must place renewed focus and energy on safety work — even during something as unprecedented as a pandemic.
The irony isn’t lost on Ms. Binder: Amid a crisis driven by infectious disease, U.S. hospitals are seeing higher rates of other infections.
“A patient dies once,” she concluded. “They can die from COVID-19 or C. diff. It isn’t enough to prevent one.”
National Institutes of Health (NIH) Director Francis Collins offered caution about the new omicron variant of the coronavirus in a Sunday interview, saying it will take weeks to understand whether it can evade COVID-19 vaccines.
Appearing on “Fox News Sunday,” Collins explained that omicron has more than 30 mutations on its spike protein, which raises the question of how effective the antibodies created by vaccines are against the variant.
“If you’ve raised antibodies against [COVID-19] from previously being infected or from being vaccinated, the question is, will those antibodies still stick to this version of the spike protein, or will they evade that protection? We need to find that out, to be honest, though that’s gonna take two, three weeks in both laboratory and field studies to figure out the answer. And that’s what all of us as scientists want to know,” said Collins.
Collins stressed that the COVID-19 vaccines available in the U.S. have been shown to be effective against previous variants, such as delta, saying that was a good indication they also will work against omicron.
“Given that history, we expect that most likely the current vaccines will be sufficient to provide protection. And especially the boosters will give that additional layer of protection because there’s something about the booster that causes your immune system to really expand its capacity against all kinds of different spike proteins, even ones it hasn’t seen before,” he said.
“Please, Americans, if you’re one of those folks who are sort of waiting to see, this would be a great time to sign up get your booster. Or if you haven’t been vaccinated already, get started. Omicron is one more reason to do this,” he added.
National Institutes of Health (NIH) director Francis Collins said the emergence of a new variant of the coronavirus presents a “great reason” for people in the United States to seek a booster shot.
“There’s no reason to panic, but it’s a great reason to get boosted,” Collins said Sunday during an appearance on CNN.
The World Health Organization over the weekend held an emergency meeting regarding the new coronavirus strain first identified in South Africa, and classified it as being “of concern,” due to the variant’s large number of mutations and an increased risk of re-infection.
Several nations around the world, including the United States, have limited travel to several south African countries in recent days in an attempt to keep the variant from spreading more rapidly.
During an earlier appearance on Fox News Sunday, Collins said it may take weeks before world health officials can determine how effective vaccines being used in the United States are against the new variant, which has been dubbed “omicron.”
“Given that history, we expect that most likely the current vaccines will be sufficient to provide protection,” he said. “And especially the boosters will give that additional layer of protection because there’s something about the booster that causes your immune system to really expand its capacity against all kinds of different spike proteins, even ones it hasn’t seen before.”
Collins said on CNN that the emergence of the new variant is “another reason” for people who have not received a coronavirus booster shot to do so once they are eligible.
“The booster basically enlarges the capacity of your immune system to recognize all kinds of spike proteins its never seen,” Collins explained. “This is a great day to go and get boosted or find out how to do so.”
President Biden’s chief medical adviser, Anthony Fauci, on Sunday called the newly discovered omicron variant of COVID-19 “troublesome” and raised concerns that it “might evade immune protection.”
“Right now, what we have is we have the window into the mutations that are in this new variant. And they are troublesome in the fact that there are about 32 or more variants in that very important spike protein of the virus, which is the business end of the virus,” Fauci said during an interview on NBC’s “Meet the Press.”
“And there are about 10 or more of these mutations that are on that part of the virus — we call it the receptor binding domain — that actually binds to the cells in your nasopharynx and in your lung,” Fauci continued. “In other words, the profile of the mutations strongly suggest that it’s going to have an advantage in transmissibility and that it might evade immune protection that you would get, for example, from a monoclonal antibody or from the convalescent serum after a person’s been infected and possibly even against some of the vaccine-induced antibodies.”
Though Fauci confirmed that the omicron strain has not yet been detected in the U.S., he said on ABC’s “This Week” that it was “inevitable” that it would hit the country.
Fauci’s comments come as scientists are racing to learn more about the variant, which was first found in South Africa.
The director of the National Institutes of Health, Francis Collins, said during an interview on “Fox News Sunday” that it would take several weeks for scientists to better understand whether omicron could evade the protection of the COVID-19 vaccines.
However, Collins said that because the COVID-19 vaccines have been effective against other variants such as delta, there was reason to believe that it also be effective against omicron.
“Given that history, we expect that most likely the current vaccines will be sufficient to provide protection. And especially the boosters will give that additional layer of protection because there’s something about the booster that causes your immune system to really expand its capacity against all kinds of different spike proteins, even ones it hasn’t seen before,” Collins said.
HENRY KOTULA 