New Covid Variant Leading Surge in Respiratory Illness

By Julie Appleby, KFF Health News

It’s winter, that cozy season that brings crackling fireplaces, indoor gatherings — and a wave of respiratory illness. Nearly four years since the pandemic emerged, people are growing weary of dealing with it, but the virus is not done with us.

Nationally, a sharp uptick in emergency room visits and hospitalizations for covid-19, influenza, and respiratory syncytial virus, or RSV, began in mid-December and appears to be gaining momentum.

Here are a few things to know this time around:

What’s Circulating Now?

The covid virus is continually changing, and a recent version is rapidly climbing the charts. Even though it appeared only in September, the variant known as JN.1, a descendant of omicron, is rapidly spreading, representing between 39% to half of the cases, according to pre-holiday stats from the Centers for Disease Control and Prevention.

Lab data indicates that the updated vaccines, as well as existing covid rapid tests and medical treatments, are effective with this latest iteration. More good news is that it “does not appear to pose additional risks to public health beyond that of other recent variants,” according to the CDC.

Even so, new covid hospitalizations — 34,798 for the week that ended Dec. 30 — are trending upward, although rates are still substantially lower than last December’s tally. It’s early in the season, though. Levels of virus in wastewater — one indicator of how infections are spreading — are “very high,” exceeding the levels seen this time last year.

And don’t forget, other nasty bugs are going around. More than 20,000 people were hospitalized for influenza the week ending Dec. 30, and the CDC reports that RSV remains elevated in many areas.

“The numbers so far are definitely going in the not-so-good direction,” said Ziyad Al-Aly, the chief of the research and development service at the Veterans Affairs St. Louis Healthcare System and a clinical epidemiologist at Washington University in St. Louis. “We’re likely to see a big uptick in January now that everyone is back home from the holidays.”

Milder Cases and Fewer Deaths

Certainly, compared with the first covid winter, things are better now. Far fewer people are dying or becoming seriously ill, with vaccines and prior infections providing some immunity and reducing severity of illness.

Even compared with last winter, when omicron was surging, the situation is better. New hospitalizations, for example, are about one-third of what they were around the 2022 holidays. Weekly deaths dropped slightly the last week of December to 839 and are also substantially below levels from a year ago.

“The ratio of mild disease to serious clearly has changed,” said William Schaffner, a professor of medicine in the division of infectious diseases at Vanderbilt University School of Medicine in Nashville, Tennessee.

Even so, the definition of “mild” is broad, basically referring to anything short of being sick enough to be hospitalized.

While some patients may have no more than the sniffles, others experiencing “mild” covid can be “miserable for three to five days,” Schaffner said.

How Will This Affect My Day-to-Day Life?

“Am I going to be really sick? Do I have to mask up again?” It is important to know the basics.

For starters, symptoms of the covid variants currently circulating will likely be familiar — such as a runny nose, sore throat, cough, fatigue, fever, and muscle aches.

So if you feel ill, stay home, said Marcus Plescia, chief medical officer of the Association of State and Territorial Health Officials. “It can make a big difference.”

Dust off those at-home covid test kits, check the extended expiration dates on the FDA website, and throw away the ones that have aged out. Tests can be bought at most pharmacies and, if you haven’t ordered yours yet, free test kits are still available through a federal program at covid.gov.

Test more than once, especially if your symptoms are mild. The at-home rapid tests may not detect covid infection in the first couple of days, according to the FDA, which recommends using “multiple tests over a certain time period, such as two to three days.”

With all three viruses, those most at risk include the very young, older adults, pregnant people, and those with compromised immune systems or underlying diseases, including cancer or heart problems. But those without high-risk factors can also be adversely affected.

While mask-wearing has dropped in most places, you may start to see more people wearing them in public spaces, including stores, public transit or entertainment venues.

Although a federal mask mandate is unlikely, health officials and hospitals in at least four states — California, Illinois, Massachusetts, and New York — have again told staff and patients to don masks. Such requirements were loosened last year when the public health emergency officially ended.

Such policies are advanced through county-level directives. The CDC data indicates that, nationally, about 46.7% of counties are seeing moderate to high hospital admission rates of covid.

“We are not going to see widespread mask mandates as our population will not find that acceptable,” Schaffner noted. “That said, on an individual basis, mask-wearing is a very intelligent and reasonable thing to do as an additional layer of protection.”

The N95, KN95, and KF94 masks are the most protective. Cloth and paper are not as effective.

And, finally, if you haven’t yet been vaccinated with an updated covid vaccine or gotten a flu shot, it’s not too late. There are also new vaccines and monoclonal antibodies to protect against RSV recommended for certain populations, which include older adults, pregnant people, and young children.

Generally, flu peaks in midwinter and runs into spring. Covid, while not technically seasonal, has higher rates in winter as people crowd together indoors.

“If you haven’t received vaccines,” Schaffner said, “we urge you to get them and don’t linger.”

Repeat Infections

People who have dodged covid entirely are in the minority.

At the same time, repeat infections are common. Fifteen percent of respondents to a recent Yahoo News/YouGov poll said they’d had covid two or three times. A Canadian survey released in December found 1 in 5 residents said they had gotten covid more than once as of last June.

Aside from the drag of being sick and missing work or school for days, debate continues over whether repeat infections pose smaller or larger risks of serious health effects. There are no definitive answers, although experts continue to study the issue.

Two research efforts suggest repeat infections may increase a person’s chances of developing serious illness or even long covid — which is defined various ways but generally means having one or more effects lingering for a month or more following infection. The precise percentage of cases — and underlying factors — of long covid and why people get it are among the many unanswered questions about the condition. However, there is a growing consensus among researchers that vaccination is protective.

Still, the VA’s Al-Aly said a study he co-authored that was published in November 2022 found that getting covid more than once raises an “additional risk of problems in the acute phase, be it hospitalization or even dying,” and makes a person two times as likely to experience long covid symptoms.

The Canadian survey also found a higher risk of long covid among those who self-reported two or more infections. Both studies have their limitations: Most of the 6 million in the VA database were male and older, and the data studied came from the first two years of the pandemic, so some of it reflected illnesses from before vaccines became available. The Canadian survey, although more recent, relied on self-reporting of infections and conditions, which may not be accurate.

Still, Al-Aly and other experts say taking preventive steps, such as getting vaccinated and wearing a mask in higher-risk situations, can hedge your bets.

“Even if in a prior infection you dodged the bullet of long covid,” Al-Aly said, “it doesn’t’ mean you will dodge the bullet every single time.”

KFF Health News is a national newsroom that produces in-depth journalism about health issues.

Spread of Delta Variant ‘Going to Get Worse’

By Liz Szabo, Kaiser Health News

Upon first inspection, the mutations in the highly contagious delta covid variant don’t look that worrisome.

For starters, delta has fewer genetic changes than earlier versions of the coronavirus.

“When people saw that the epidemic in India was driven by delta, they did not suspect it would be so bad or overtake other variants,” said Trevor Bedford, an evolutionary biologist at the Fred Hutchinson Cancer Research Center.

But those expectations were wrong.

Delta has kept some of the most successful mutations found in earlier variants, but also contains new genetic changes that enable it to spread twice as fast.

Delta is more dangerous in many ways. It has an incubation period of four days, rather than six, making people contagious sooner. When the pandemic began, people spread the original coronavirus to an average of two or three people. Today, people infected with delta infect six people, on average.

As of this week, the delta variant had caused at least 92% of the new infections in the United States, according to covariants.org, a research firm in Bern, Switzerland.

Although delta isn’t necessarily any more lethal than other variants, it can kill huge numbers of people simply because it infects so many more, said Dr. Eric Topol, founder and director of the Scripps Research Translational Institute.

Scientists have sequenced delta’s mutations but are still trying to understand their significance, said Angela Rasmussen, a virologist at the University of Saskatchewan’s Vaccine and Infectious Disease Organization. “When we see the same mutations appearing repeatedly and independently, that suggests they’re important,” Rasmussen said.

Scientists have the best understanding of mutations on the so-called spike protein — which sticks out from the surface of the virus like a club — and which have been studied the most intensely because of its serious ramifications, Rasmussen said. The coronavirus uses the spike protein to enter human cells, and changes in the spike can help the virus evade antibodies.

Scientists believe one of the most important areas of the spike is the receptor-binding domain, the specific part of the protein that allows the virus to latch onto a receptor on the surface of our cells, said Vaughn Cooper, a professor of microbiology and molecular genetics at the University of Pittsburgh. Receptors are like sockets or docking stations that allow proteins to interact with the cell. Once the virus gains entry to the cell, it can cause havoc, hijacking the cell’s genetic machinery and turning it into a virus-making factory.

Delta’s Worrisome Mix

Delta’s rapid spread is particularly surprising given it lacks two mutations that made earlier variants so scary.

Delta doesn’t have the N501Y spike mutation found in the alpha, beta and gamma variants, which enabled them to invade cells more successfully than the original virus. That mutation changed one amino acid — a building block of proteins — in the receptor-binding domain.

Delta also lacks the E484K mutation, which has made the gamma variant so worrisome. This genetic change, sometimes called “Eek,” allows the virus to spread even among vaccinated people.

Scientists use the Greek alphabet to name variants of concern. “The ‘D’ in delta stands for ‘different’ and a ‘detour’ to a different genomic mutation path,” Topol said. “But it doesn’t mean ‘doom,’” he said, noting that existing covid vaccines remain mostly effective against the delta variant.

Vaccines protect people from covid by providing them with antibodies that attach themselves to the spike protein, preventing the virus from entering cells. By dramatically reducing the number of viruses that enter cells, vaccines can prevent people from developing severe disease and make them less infectious to others.

Delta does share mutations with other successful variants. Like all the identified variants in circulation, delta contains a spike mutation called D614G, sometimes known as “Doug,” which became ubiquitous last year.

Scientists think Doug increases the density of spike protein on the surface of viral particles and makes it easier for the virus to enter cells.

Delta also has a spike mutation called P681R, which closely resembles a mutation in the alpha variant that appears to produce higher viral loads in patients, Cooper said. People infected with delta have 1,000 times more virus in their respiratory tract, making them more likely to spread the virus when they sneeze, cough or talk.

The P681R mutation, also found in the kappa variant, is located at the beginning of a part of the genome called the furin cleavage site, Cooper said.

Furin is a naturally occurring human enzyme that gets hijacked by the coronavirus, which uses it to slice the spike protein into the optimal shape for entering the cell, Rasmussen said. The new mutation makes that sculpting more efficient, Rasmussen said.

Another delta mutation — also found in kappa and epsilon — is called L452R. Experiments suggest this mutation, which also affects the receptor-binding domain, acts to prevent antibodies from neutralizing the virus, Cooper said.

These mutations appear to be more formidable as a team than alone.

The genetic changes “are certainly doing something, but why that combination makes the delta variant more fit is not entirely obvious,” Bedford said. “Putting them together seems to matter.”

Delta also has developed genetic changes not seen in other variants.

One such spike mutation is called D950N. “This might be unique,” Cooper said. “We don’t see that anywhere else.”

The D950N mutation is different than other mutations because it’s located outside the receptor-binding domain in an area of the coronavirus genome that helps the virus fuse with human cells, Cooper said. Fusing with human cells allows the coronavirus to dump its genetic material into those cells.

This mutation could affect which types of cells the virus infects, potentially allowing it to harm different organs and tissues. Mutations in this region are also associated with higher viral loads, Cooper said.

Delta also contains mutations in a part of the spike protein called the N-terminal domain, which provides a “supersite” for antibodies to latch onto the virus and prevent it from entering cells, said Dr. Hana Akselrod, an infectious diseases specialist at the George Washington University School of Medicine & Health Sciences.

Mutations in this region make monoclonal antibodies less effective in treating covid and increases the delta variant’s ability to escape vaccine-generated antibodies, Akselrod said. That may explain why vaccinated people are slightly more likely to become infected with delta, causing mostly mild illness but allowing them to transmit the virus.

Delta’s Future Course

Scientists say it’s impossible to predict exactly how delta will behave in the future, although Topol said, “It’s going to get worse.”

Topol noted that delta outbreaks tend to last 10 to 12 weeks, as the virus “burns through” susceptible populations.

If the United States continues to follow a pattern seen in the United Kingdom and the Netherlands, infections could rise from the current seven-day moving average of 42,000 cases to 250,000 a day. Yet Topol said the United States is unlikely to suffer the high death rates seen in India, Tunisia and Indonesia because nearly half the population here is fully vaccinated.

While some studies have concluded that the Johnson & Johnson vaccine stimulates strong and persistent antibodies against delta, a new report found that antibodies elicited by one shot may not be enough to neutralize delta. Authors of that study, from the New York University Grossman School of Medicine, suggested a second dose may be needed.

Two doses of the Pfizer-BioNTech vaccine protect 94% of people from any symptomatic infection by the alpha variant, compared with 88% against the delta variant, according to a new study in the New England Journal of Medicine. Two doses of the AstraZeneca vaccine protect 75% of people from alpha and 67% from delta.

Cooper said covid vaccines offer remarkably good protection. “I will always celebrate these vaccines as the scientific achievements of my lifetime,” he said.

The best way to slow down the evolution of variants is to share vaccines with the world, vaccinating as many people as possible, Bedford said. Because viruses undergo genetic changes only when they spread from one host to another, stopping transmission denies them a chance to mutate.

Whether the coronavirus evolves more deadly variants “is totally in our hands,” Cooper said. “If the number of infections remains high, it’s going to continue to evolve.”

By failing to contain the virus through vaccination, wearing masks and avoiding crowds, people are allowing the coronavirus to morph into increasingly dangerous forms, said Dr. William Haseltine, a former Harvard Medical School professor who helped design treatments for HIV/AIDS.

“It’s getting better, and we’re making it better,” he said. “Having half the population vaccinated and half unvaccinated and unprotected — that is the exact experiment I would design if I were a devil and trying to design a vaccine-busting virus.”

Kaiser Health News is a national health policy news service. It is an editorially independent program of the Kaiser Family Foundation, which is not affiliated with Kaiser Permanente.