Why Are So Many People Getting COVID a Second and Third Time?

Doctors say if you got infected with the Omicron BA.1 or BA.2 variants, your antibodies might not fully protect you against the newer BA.4 and BA.5 subvariants now spreading through Southern California

Authors: Joel Grover and Josh Davis  June 16, 2022 NBC News

A sign encouraging mask use hangs on a fence before the local school council and the Chicago Teachers Union held a press conference Tuesday, Sept. 28, 2021 outside Jensen Elementary School in Chicago’s North Lawndale neighborhood. (Brian Cassella/Chicago Tribune/Tribune News Service via Getty Images)

Just days after Congresswoman Maxine Waters attended the Summit of the Americas in downtown LA last week, she tested positive for COVID-19. It was the second time in less than two months Waters has tested positive.

Until recently, many people who got COVID-19 thought they had months or years of protection from getting it again. But researchers tell the NBC4 I-Team that’s not the case.

“I’m not surprised to see people testing positive a second and third time,” says Dr. Saahir Khan, an infectious disease expert at USC’s Keck School of Medicine.

“The virus is mutating very quickly,” Dr. Khan told NBC4.

Doctors like Khan say if you got infected with the Omicron BA.1 or BA.2 variants, your antibodies might not fully protect you against the newer BA.4 and BA.5 subvariants now spreading through Southern California.

“As the virus mutates more and more, the antibodies to the prior variants give less and less protection over time,” Dr. Khan says.

But public health experts say second and third infections are often very “manageable.”

“The thing about these reinfections, is they get increasingly milder. Much less likely to even cause you to call your doctor,” says Dr. Amesh Adalja of Johns Hopkins Bloomberg School of Public Health.

So how soon can you get COVID for a second or third time, after a previous infection?

U.S. Health and Human Services Secretary Xavier Becerra tested positive this past Monday, less than a month after his first positive test.

“I wouldn’t say there’s a hard and fast timeline when you can get reinfected. It’s just that your protection wanes over time, over the course of a few months,” says Dr. Khan at USC.

Public health experts say the vaccines that are now available might not prevent reinfection by newer variants, but a new class of vaccines that could be out by this fall could provide wider protection.

“COVID is spread through the air, particularly in indoor spaces where people share the same air. And so what you can do to prevent reinfection is wear a mask indoors, particularly in a high risk situation where a lot of people congregate, like airports and grocery stores, Dr. Khan told the I-Team.

Omicron sub-variants BA.4 and BA.5 account for up to 13% of COVID variants in U.S. – CDC

Authors: Mrinalika Roy Reuters

The BA.4 and BA.5 sub-variants of Omicron are estimated to make up nearly 5% and 8% of the coronavirus variants in the United States as of June 4, the U.S. Centers for Disease Control and Prevention (CDC) said on Tuesday.

The two sublineages, which were added to the World Health Organization’s monitoring list in March and designated as variants of concern by the European Centre for Disease Prevention and Control (ECDC), were present in all U.S. regions.

Last month, South African scientists found that the sublineages of the Omicron coronavirus variant can dodge antibodies from earlier infection well enough to trigger a new wave.

BA.4 made up 5.4% of the variants in the country for the week ending June 4, according to CDC estimates, while BA.5 made up 7.6% of the variants during the same time.

The seven-day moving average of U.S. COVID-19 cases stood at 98,010 as of June 4.

Overlapping, highly contagious COVID subvariants are spreading fast in Florida

Authors: David Schutz, Cindy Krischer Goodman June 4, 2022 Sun Sentinel

Overlapping waves of omicron are sweeping through the state, leading more people to get infected with COVID.

The more transmissible BA.2.12.1 omicron subvariant became officially dominant in the U.S. last week, yet it already is being pushed out nationally by newcomers BA.4 and BA.5, both of which have arrived in Florida.

While BA.2.12.1 has gained an advantage by being more contagious than the omicron subvariant BA.2 before it, the newcomers (4 and 5) are particularly good at evading antibodies and infecting those who are vaccinated or previously infected.

Some epidemiologists are describing what’s happening as the “battle of omicron.”

Helix, a private lab that identifies COVID strains circulating in states, found BA.4 and BA.5 crept into Florida in May, and represent about 5% of samples. The majority of cases in Florida — about 58% — are still BA.2.12.1.

The omicron subvariant BA.4 was first identified in January in cases sequenced in South Africa, and BA.5 surfaced a month later. The omicron strain, BA.2.12.1, accounted for nearly all of South Africa’s daily cases at the end of February. By the end of April, however, BA.4 and BA.5 were found in 90% of all positive test samples analyzed in that nation, exemplifying the infectiousness of the newcomers.

Health officials say evidence seems to point to increasingly rapid, overlapping waves of new variants, which likely means more infections in Florida in the summer months ahead.

“My theory is we may see more variants, and they may be more contagious, but they will continue to get less problematic with fewer harmful outcomes,” said Dr. Mona Amin with Pediatric Associates in Fort Lauderdale.

In Florida, much like other states, COVID reporting has become spotty with many learning of the diagnosis through at-home tests. So far, wastewater has proven useful in learning the prevalence of the virus.

An analysis of wastewater in South Florida counties by Biobot Analytics, shows COVID cases are rising to levels last seen during the winter omicron wave in early 2022. Delta no longer is a factor in the state, Biobot’s analysis shows. The samples taken in Miami-Dade and Palm Beach counties show omicron and its subvariants are circulating at increasingly high levels.

With a seven-day daily average of more than 10,200 cases on Friday, Florida is a state classified by the Centers for Disease Control and Prevention as having a “high level” of transmission. Broward and Miami-Dade counties are reporting a test positivity rate of more than 20%. Palm Beach County’s positivity rate is 18.9%. Health officials consider transmission levels under control when the rate is less than 5%.

Jason Salemi, an epidemiologist at the University of South Florida, points out, “We might actually (finally) be seeing some improvement in the Northeast, but in Florida — 3 in 4 people live in a high-risk county, based on the hospitalization-based measure.”

On Friday, 2,834 people were in Florida hospitals with COVID, representing nearly 5% of all beds, according to U.S. Health and Human Services data. That’s a significant increase from about 1,000 COVID patients in early April, but nowhere near the more than 17,000 people hospitalized during the delta wave in August 2021.

Why boosted Americans seem to be getting more COVID-19 infections

BAuthors: ALEXANDER TIN JUNE 2, 2022

As COVID-19 cases began to accelerate again this spring, federal data suggests the rate of breakthrough COVID infections in April was worse in boosted Americans compared to unboosted Americans — though rates of deaths and hospitalizations remained the lowest among the boosted.

The new data do not mean booster shots are somehow increasing the risk. Ongoing studies continue to provide strong evidence of additional protection offered by booster shots against infection, severe disease, and death.

Instead, the shift underscores the growing complexity of measuring vaccine effectiveness at this stage of the pandemic. It comes as officials are weighing key decisions on booster shots and pandemic surveillance, including whether to continue using the “crude case rates” at all.

It also serves to illustrate a tricky reality facing health authorities amid the latest COVID-19 wave: even many boosted Americans are vulnerable to catching and spreading the virus, at a time when officials are wary of reimposing pandemic measures like mask requirements.

“During this Omicron wave, we’re seeing an increased number of mild infections — at-home type of infections, the inconvenient, having a cold, being off work, not great but not the end of the world. And that’s because these Omicron variants are able to break through antibody protection and cause these mild infections,” John Moore, a professor of microbiology and immunology at Weill Cornell Medical College, told CBS News.

“So, one of the dynamics here is that people feel, after vaccination and boosting, that they’re more protected than they actually are, so they increase their risks,” he said. “That, I think, is the major driver of these statistics.”

On the CDC’s dashboard, which is updated monthly, the agency acknowledges several “factors likely affect crude case rates by vaccination and booster dose status, making interpretation of recent trends difficult.”

The CDC had rolled out the page several months ago, amid demands for better federal tracking of breakthrough cases. It has now grown to encompass data from immunization records and positive COVID-19 tests from 30 health departments across the country

For the week of April 23, it said the rate of COVID-19 infections among boosted Americans was 119 cases per 100,000 people. That was more than double the rate of infections in those who were vaccinated but unboosted, but a fraction of the levels among unvaccinated Americans.

That could be because there is a “higher prevalence of previous infection” right now among those who are unvaccinated and unboosted, the CDC said. More boosted Americans may now have abandoned “prevention behaviors” like wearing masks, leading to an uptick.

Some boosted Americans might be more likely to seek out a lab test for COVID-19, as opposed to relying on over-the-counter rapid tests that go largely unreported to health authorities.

“Home testing has become, I think, the single biggest concern in developed countries that can interfere with our measurements,” CDC’s Ruth Link-Gelles told a conference hosted by the National Foundation for Infectious Diseases last month. 

Some federal officials have floated the possibility of adopting a survey — similar to those relied on by authorities in the United Kingdom — as an alternative way to track a “ground truth” in COVID-19 cases, though plans to stand up such a system do not appear imminent.

“Moving beyond this crisis, I do think the future is in random sampling. And that’s an area that we’re looking at closely,” Caitlin Rivers, a top official on the agency’s disease forecasting team, told an event hosted by the National Academies last week. 

Meanwhile, federal officials are also preparing for key decisions on future COVID-19 vaccine shots, which might up the odds that additional shots might be able to fend off infections from the latest variants. 

In the short term, CDC Director Dr. Rochelle Walensky recently told reporters that her agency was in talks with the Food and Drug Administration about extending the option for second boosters to more adults. 

Right now, only adults 50 and over and some immunocompromised Americans are eligible to receive a fourth dose

Next generation of vaccines and boosters

Further down the road, a panel of the Food and Drug Administration’s outside vaccine advisers is scheduled to meet later this month to weigh data from new booster candidates produced by Pfizer and BioNTech as well as Moderna. 

BioNTech executives told investors last month that regulators had asked to see data for both shots specifically adapted for the Omicron variant in addition to “bivalent vaccines,” which target a blend of mutations. 

Those new vaccines would take about three months to manufacture, the White House’s top COVID-19 official Dr. Ashish Jha told reporters.

“It’s a little bit of a challenge here because we don’t know how much further the virus will evolve over the next few months, but we have no choice because if we want to produce the hundreds of millions of doses that need to be available for a booster campaign, we have to start at risk in the early July timeframe or even somewhat sooner,” Dr. Peter Marks, the FDA’s top vaccines official, said at a recent webinar hosted by the American Medical Association. 

Marks said that bivalent shots seemed likely to be favored, given the “wiggle room” it could offer for unforeseen variants beyond Omicron. 

Vaccines that might offer even better “mucosal immunity” – actually fighting off the virus where it first infects the respiratory system – are still a ways off, Marks cautioned. 

“I think that we are in a transition time and I, again, will speak openly to the fact that 2022 to 2023 is a year where we have to plan for trying to minimize the effect of COVID-19 with the tools that we have in hand,” Marks said at a recent event with the National Foundation for Infectious Diseases. 

“I do believe that, potentially by the 2023-2024 season, we’ll start to see second generation SARS-CoV-2 vaccines,” he added later.

Some people test positive for Covid-19 for weeks. Are they still infectious?

Authors: Advisory Board June 1, 2022

After contracting Covid-19, some people may continue to test positive on rapid tests for 10 days or longer—and experts are split about whether these individuals should continue to isolate past 10 days or just employ safety precautions until they test negative.

How long can people test positive with omicron?

According to the New York Times, the omicron variant of the coronavirus moves quickly, with viral levels typically peaking less than five days after the virus is first detectable. However, some people will continue to test positive for the virus even up to 14 days later.

For example, a new analysis, which has not yet been peer-reviewed, found that roughly 20% people who were repeatedly tested during the omicron wave still tested positive on rapid tests 11 days after they first became symptomatic or initially tested positive.

“For some people, they’re seeing fairly prolonged courses of being antigen-positive,” said Yonatan Grad, an immunologist and infectious disease expert at the Harvard T.H. Chan School of Public Health. “I think we chalk it up to some variation in people’s immune system and ability to respond to infection and clear this virus.”

However, a positive test may not always mean that an individual is still infectious. “Some people may not be infectious at the end of their course even if still antigen-positive, whereas others may be infectious even if antigen-negative,” Grad said.

According to research from Amy Barczak, an infectious disease expert at Massachusetts General Hospital, and her team, some people have tested positive even though they did not have positive viral cultures, which indicate infectious virus. This suggests that tests are detecting lingering viral remnants rather than any infectious virus.

What should you do if you keep testing positive?

According to CDC‘s current Covid-19 isolation guidance, people can end their isolation after five days if they no longer have a fever and their other symptoms have improved. However, if symptoms continue, it recommended that people isolate until their symptoms subside and wear a mask through day 10.

Currently, CDC does not require people to test negative before they end their isolation. For people who do choose to test themselves, the agency recommends people who test positive to isolate until day 10, while those who test negative can end their isolation but should wear a mask until day 10.

However, there is no clear consensus about whether people should continue to isolate past 10 days if they are still testing positive.

Michael Mina, an epidemiologist and chief science officer at eMed, said people who test positive should assume they are infectious, which will allow them to adjust their behavior and be more careful around others to avoid spreading the virus.

Separately, Aubree Gordon, an infectious disease epidemiologist at the University of Michigan School of Public Health, agreed with Mina’s assessment. “They’re probably less contagious than they were in the first few days,” she said. “But I would still certainly advise some caution.”

While some health experts recommend people isolate until they test negative, others argue that it doesn’t make sense to ask people who are otherwise healthy to isolate or test past 10 days.

“Nobody’s saying that there aren’t some people, maybe statistically speaking at the end of the tail, who might transmit after Day 10,” said Peter Chin-Hong, an infectious disease specialist at the University of California, San Francisco. However, people at this stage are not likely to play a large role in viral transmission, and continued testing could keep many people out of school or work.

“And also you raise an equity issue,” Chin-Hong added, “like ‘Who on Earth can have enough tests?'”

In addition, Mina noted that there are other ways to reduce viral spread than just isolating, including choosing not to visit vulnerable family members or attend crowded public areas, including churches and bar, until you test negative. 

“It’s not just isolating, and never has been,” Mina said. “It’s all the little things you can do to prevent infecting someone else, even without isolating.”

During COVID’s omicron wave in U.S., death rates soared for older people

Authors: BENJAMIN MUELLER and Eleanor LutzThe New York Times May 31, 2022 

Despite strong levels of vaccination among older people, COVID killed them at vastly higher rates during this winter’s omicron wave than it did last year, preying on long delays since their last shots and the variant’s ability to skirt immune defenses.

This winter’s wave of deaths in older people belied the omicron variant’s relative mildness. Almost as many Americans 65 and older died in four months of the omicron surge as they did in six months of the delta wave, even though the delta variant, for any one person, tended to cause more severe illness.

While overall per capita COVID death rates have fallen, older people still account for an overwhelming share of them.

“This is not simply a pandemic of the unvaccinated,” said Andrew Stokes, an assistant professor in global health at Boston University who studies age patterns of COVID deaths. “There’s still exceptionally high risk among older adults, even those with primary vaccine series.”

COVID deaths, though always concentrated in older people, have in 2022 skewed toward older people more than they did at any point since vaccines became widely available.

That swing in the pandemic has intensified pressure on the Biden administration to protect older Americans, with health officials in recent weeks encouraging everyone 50 and older to get a second booster and introducing new models of distributing antiviral pills.

In much of the country, though, the booster campaign remains listless and disorganized, older people and their doctors said. Patients, many of whom struggle to drive or get online, have to maneuver through an often labyrinthine health care system to receive potentially lifesaving antivirals.

Nationwide COVID deaths in recent weeks have been near the lowest levels of the pandemic, below an average of 400 a day. But the mortality gap between older and younger people has grown: Middle-aged Americans, who suffered a large share of pandemic deaths last summer and fall, are now benefiting from new stores of immune protection in the population as COVID deaths once again cluster around older people.

And the new wave of omicron subvariants may create additional threats: While hospitalizations in younger age groups have remained relatively low, admission rates among people 70 and older in the Northeast have climbed to one-third of the winter omicron wave’s towering peak.

“I think we are going to see the death rates rising,” said Dr. Sharon Inouye, a geriatrician and a professor of medicine at Harvard Medical School. “It is going to become more and more risky for older adults as their immunity wanes.”

Harold Thomas Jr., 70, of Knoxville, Tennessee, is one of many older Americans whose immunity may be waning because he has not received a booster shot. The COVID States Project, an academic group, recently estimated that among people 65 and older, 13% are unvaccinated, 3% have a single Moderna or Pfizer shot, and another 14% are vaccinated but not boosted.

When vaccines first arrived, Thomas said, the state health department made getting them “convenient” by administering shots at his apartment community for older people. But he did not know of any such effort for booster doses.

On the contrary, he remembered a state official publicly casting doubt on boosters as they became available.

“The government wasn’t sure about the booster shot,” he said. “If they weren’t sure about it, and they’re the ones who put it out, why would I take it?”

Thomas said COVID recently killed a former boss of his and hospitalized an older family friend.

Deaths have fallen from the heights of the winter wave in part because of growing levels of immunity from past infections, experts said. For older people, there is also a grimmer reason: So many of the most fragile Americans were killed by COVID over the winter that the virus now has fewer targets in that age group.

But scientists warned that many older Americans remained susceptible. To protect them, geriatricians called on nursing homes to organize in-home vaccinations or mandate additional shots.

In the longer term, scientists said that policymakers needed to address the economic and medical ills that have affected especially nonwhite older Americans, lest COVID continue cutting so many of their lives short.

“I don’t think we should treat the premature death of older adults as a means of ending the pandemic,” Stokes said. “There are still plenty of susceptible older adults — living with comorbid conditions or living in multigenerational households — who are highly vulnerable.”

The pattern of COVID deaths this year has re-created the dynamics from 2020 — before vaccines were introduced, when the virus killed older Americans at markedly higher rates. Early in the pandemic, mortality rates steadily climbed with each extra year of age, Stokes and his collaborators found in a recent study.

That changed last summer and fall, during the delta surge. Older people were getting vaccinated more quickly than other groups: By November, the vaccination rate in Americans 65 and older was roughly 20 percentage points higher than that of those in their 40s. And critically, those older Americans had received vaccines relatively recently, leaving them with strong levels of residual protection.

As a result, older people suffered from COVID at lower rates than they had been before vaccines became available. Among people 85 and older, the death rate last fall was roughly 75% lower than it had been in the winter of 2020, Stokes’ recent study found.

At the same time, the virus walloped younger and less vaccinated Americans, many of whom were also returning to in-person work. Death rates for white people in their late 30s more than tripled last fall compared to the previous winter. Death rates for Black people in the same age group more than doubled.

The rebalancing of COVID deaths was so pronounced that, among Americans 80 and older, overall deaths returned to pre-pandemic levels in 2021, according to a study posted online in February. The opposite was true for middle-aged Americans: Life expectancy in that group, which had already dropped more than it had among the same age range in Europe, fell even further in 2021.

“In 2021, you see the mortality impact of the pandemic shift younger,” said Ridhi Kashyap, a lead author of that study and a demographer at the University of Oxford.

By the time the highly contagious omicron variant took over, researchers said, more older Americans had gone a long time since their last COVID vaccination, weakening their immune defenses.

As of mid-May, more than one-quarter of Americans 65 and older had not had their most recent vaccine dose within a year. And more than half of people in that age group had not been given a shot in the past six months.

The omicron variant was better than previous versions of the virus at evading those already weakening immune defenses, reducing the effectiveness of vaccines against infection and more serious illness. That was especially true for older people, whose immune systems respond less aggressively to vaccines in the first place.

For some people, even three vaccine doses appear to become less protective over time against omicron-related hospital admissions. A study published recently in The Lancet Respiratory Medicine found that trend held for people with weakened immune systems, a category that older Americans were likelier to fall into. Sara Tartof, the study’s lead author and a public health researcher at Kaiser Permanente in Southern California, said that roughly 9% of people 65 and older in the study were immunocompromised, compared with 2.5% of adults younger than 50.

During the omicron wave, COVID death rates were once again dramatically higher for older Americans than younger ones, Stokes said. Older people also made up an overwhelming share of the excess deaths — the difference between the number of people who actually died and the number who would have been expected to die if the pandemic had never happened.

Dr. Jeremy Faust, an emergency physician at Brigham and Women’s Hospital in Boston, found in a recent study that excess deaths were more heavily concentrated in people 65 and older during the omicron wave than the delta surge. Overall, the study found, there were more excess deaths in Massachusetts during the first eight weeks of omicron than during the 23-week period when delta dominated.

As older people began dying at higher rates, COVID deaths also came to include higher proportions of vaccinated people. In March, about 40% of the people who died from COVID were vaccinated, according to an analysis of figures from the Centers for Disease Control and Prevention.

Fewer older Americans have also been infected during the pandemic than younger people, leading to lower levels of natural immunity. As of February, roughly one-third of people 65 and older showed evidence of prior infections, compared with about two-thirds of adults younger than 50.

Long-ago COVID cases do not prevent future infections, but reinfected people are less likely to become seriously ill.

A drop-off in COVID precautions this winter, combined with the high transmissibility of omicron, left older people more exposed, scientists said. It is unclear how their own behavior may have changed. An earlier study, from scientists at Marquette University, suggested that while older people in Wisconsin had once been wearing masks at rates higher than those of younger people, that gap had effectively disappeared by mid-2021.

Antiviral pills are now being administered in greater numbers, but it is difficult to know who is benefiting from them. Scientists said that the wintertime spike in COVID death rates among older Americans demanded a more urgent policy response.

Inouye, of Harvard Medical School, said she had waited for a notice from her mother’s assisted living facility about the rollout of second booster shots even as reports started arriving of staff members becoming infected. But still, the facility’s director said that a second booster shot drive was impossible without state guidance.

Eventually, her family had to arrange a trip to a pharmacy on their own for a second booster.

“It just seems that now the onus is put completely on the individual,” she said. “It’s not like it’s made easy for you.”

COVID-19: Omicron variant did not wipe out Delta, it could return

While the Delta virus wiped out the variants that preceded it, Omicron has not eliminated Delta, according to a new study from Israel’s Ben-Gurion University of the Negev.

Authors:  JUDY SIEGEL-ITZKOVICH Published: MAY 2, 2022 

Don’t throw away your unused face masks yet. COVID-19’s Omicron variants may burn themselves out in the next couple of months, and the Delta variant might re-emerge, researchers at Beersheba’s Ben-Gurion University of the Negev (BGU) suggest in a new scientific paper.

Their findings were just published in the peer-reviewed journal Science of the Total Environment under the title “Managing an evolving pandemic: Cryptic circulation of the Delta variant during the Omicron rise.”

The first new coronavirus to appear at the end of 2019 was Alpha, followed by Beta (first detected in South Africa); Gamma (first detected in Brazil); Delta (that revealed itself in India); and the more-infectious but milder Omicron, which has developed a variety of sub-variants and spread all over the world.

While the Delta variant wiped out the variants that preceded it, Omicron has not eliminated Delta, according to Prof. Ariel Kushmaro and Dr. Karin Yaniv, who just received her doctorate in the field.

The lab team has developed sensitive arrays that can differentiate variants from each other in wastewater, which continues to give indications of where the coronavirus is active, even when PCR and rapid testing of people declines.

Kushmaro, who earned his advance degrees in molecular microbiology and biotechnology at Tel Aviv University, trained as postdoctoral fellow at the Hebrew University and at Harvard. He arrived at BGU 21 years ago and established a lab at the School of Sustainability and Climate Change and the Goldstein-Goren Department of Biotechnology Engineering.

The lab specializes in wastewater microbiology, marine microbial ecology and antimicrobial activity of varies microorganisms as well as biological treatment of industrial wastewater.

His team monitored Beersheba’s sewage from December 2021 to January 2022 and noticed this disturbing interaction between the Omicron and Delta variants.

They also built a model with Granek that predicts that Omicron is burning itself out while Delta is just waiting to pounce on the population again.

“SARS-CoV-2 continued circulation results in mutations and the emergence of various variants. Until now, whenever a new, dominant, variant appeared, it overpowered its predecessor after a short parallel period,” they wrote.

“Despite vaccination efforts in Israel, with a large portion of the population being vaccinated between the first to fourth dose of vaccine and despite high infection rates by previous variants, the Omicron variant had now rooted itself in Israel.”

The latest variant of concern, Omicron, is spreading swiftly around the world with record morbidity reports, wrote the authors. “Unlike the Delta variant, previously considered to be the main variant of concern in most countries, including Israel, the dynamics of the Omicron variant showed different characteristics.”

If their prediction comes to pass, its circulation may result in the reemergence of a Delta morbidity wave or in the possible generation of a new threatening variant, they wrote.

With the expected significant decline in morbidity from all the recovered Omicron cases, the Israeli government and the Health Ministry have eliminated most restrictions. “In the meantime, the Delta, which is still circulating in a population with waning immunity and under fewer restrictions, may re-emerge in larger numbers or even produce a new, different variant to generate infections in Israel.”

In any case, the team recommended wastewater-based epidemiology as a “convenient and representative tool for pandemic containment.

“Of course, there are a lot of factors involved, but our model indicates there could be another outbreak of Delta or another coronavirus variant this summer,” warned Kushmaro, who was assisted by Dr. Eden Ozer and Marilou Shagan at BGU and Dr. Yossi Paitan from Ilex Labs. 

New Mutant “XE” Omicron Variant May Be The Most Transmissible Version Of Covid Yet, According To WHO

Authors:  Tom Tapp March 31, 2022 4:46pm Deadline Breaking News Alerts

The CDC announced this week that the BA.2 Omicron variant, which is reportedly 30% more transmissible than the original BA.1 Omicron strain — has become dominant among new cases sequenced in the United States. That’s a startling rise for a variant that was less than 1% of all sequences as recently as January. But, just as Americans are hearing about BA.2, there’s already a newer, even more transmissible variant on the rise.

There are actually three new variants that have been given designations. According to a recently-released report from the UK Health Services Agency, the two being called XD and XF are combinations of Delta and BA.1, or so-called “Deltacron” strains, which have been talked about for months but made no significant inroads in any country.

XD is present in several European countries, but has not been detected in the UK, according to the report. XF caused a small cluster in the UK but has not been detected there since February 15. The variant of greater concern, it seems, is the one dubbed XE.

Like the other two new arrivals, XE is a recombinant strain, meaning it is made up of two previously-distinct variants. But it is not a Deltacron mix. XE is actually made up of the original Omicron (BA.1) and the newer Omicron (BA.2) which has taken over in the U.S.

Omicron BA.2 Variant Now Dominant In U.S.; Hitting Northeast Hard

The World Health Organization issued a report yesterday with some preliminary findings about XE.

“The XE recombinant was first detected in the United Kingdom on 19 January and >600 sequences have been reported and confirmed since,” reads the WHO document. “Early-day estimates indicate a community growth rate advantage of ~10% as compared to BA.2, however this finding requires further confirmation.”

Further confirmation is getting more difficult by the day, according to WHO, which registered concern this week at what it calls “the recent significant reduction in SARS-CoV-2 testing by several Member States. Data are becoming progressively less representative, less timely, and less robust. This inhibits our collective ability to track where the virus is, how it is spreading and how it is evolving: information and analyses that remain critical to effectively end the acute phase of the pandemic.”

Covid BA.2 Omicron Variant Likely Now Accounts For Majority Of New Cases In Los Angeles

Last week’s briefing from the UK Health Services Agency reinforces some of the WHO report’s assertions and urges caution about jumping to conclusions. One difference between the two documents is that the WHO data and analysis seems to be more recent.

From the UK HSA briefing:

XE shows evidence of community transmission within England, although it is currently less >1% of total sequenced cases. Early growth rates for XE were not significantly different from BA.2, but using the most recent data up to 16 March 2022, XE has a growth rate 9.8% above that of BA.2. As this estimate has not remained consistent as new data have been added, it cannot yet be interpreted as an estimate of growth advantage for the recombinant. Numbers were too small for the XE recombinant to be analysed by region.

To be clear, XE only accounts for a tiny fraction of cases worldwide. That may change, given that XE is thought to be about 10% more transmissible than the already more-transmissible BA.2. That means it may be roughly 43% more transmissible than the original Omicron that savaged the globe last winter.

But a new wave of infections from the now-dominant BA.2 has not materialized, even as restrictions have been eased. So hopefully the trend with XE, should it out-compete BA.2, will be similar. Only time — and good surveillance — will tell.

The Omicron subvariant BA.2: Birth of a new challenge during the COVID-19 pandemic

Authors: Farid Rahimia and Amin Talebi Bezmin Abadib,∗

Int J Surg. 2022 Mar; 99: 106261.Published online 2022 Feb12. doi: 10.1016/j.ijsu.2022.106261 PMCID: PMC8837492PMID: 35167986

In November 2021, many patients presented with the atypical pneumonia due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in South Africa [1]. Subsequently, the WHO Technical Advisory Group called Omicron the variant B.1.1.529 which caused the rise in the COVID-19 cases in South Africa; WHO classified Omicron as a variant of concern (VOC) [2]. Omicron, which is the fifth SARS-CoV-2 VOC, was detected among individuals who were partially immunized either by natural infection or vaccination. Omicron shares many mutations with the Delta and Alpha VOCs [3]. According to the WHO classification, Omicron has three subvariants, BA.1, BA.2, and BA.3 [4]. All the three subvariants were detected in South Africa, indicating fast evolutionary divergence of the subvariants. The Omicron subvariants share 39 mutations (mostly in the Spike protein); however, BA.1, BA.2, and BA.3 carry 20, 27, and 13 additional mutations, respectively. BA.1, BA.2, and BA.3 contain 13, 10, and 1 unique mutations, respectively. BA.1 has caused a considerable rise in the number of COVID-19 patients so far; however, BA.2 seems to surpass BA.1 and become the dominant Omicron subvariant in many European countries. Scientists have been puzzled by the rapid spread of the new subvariant BA.2. BA.2 has been skyrocketing in more than 57 countries, indicating that it is more highly contagious than its precursor (See https://outbreak.info/situation-reports?pango=BA.2&selected=ZAF).

BA.2 has informally been called the “stealth” variant because its PCR identification has been difficult. To differentiate between Delta and Omicron variants, a specific PCR was used to target a region known as “S gene target failure” (SGTF). Unfortunately, BA.2 lacks this signature deletion at 69–70, making its rapid identification difficult in clinical samples. Furthermore, the subvariants contain a combination of mutations. Thus, only sequencing technology can confirm BA.2.

To date, BA.2 is known to have a substantial growth rate, indicating a massive threat for individuals with naïve immune systems. The Omicron variants have three unusual biologic properties compared with previously emerged SARS-CoV-2 variants. First, the high transmissibility has enabled the subvariants to infect many individuals efficiently. Second, weaker virulence has mostly caused less severe disease. Third, the subvariants can subvert the neutralizing antibodies in immune individuals. In January 2022, the Omicron BA.2 increased the case numbers in the United states, Denmark, and France [5,6]. A similar rate of new cases of BA.2 was documented in the United Kingdom [4]. Because not all of the suspected samples could be sequenced, the true numbers and the real prevalence of the circulating subvariant remain unknown.

Birth of new challenge?

The high transmissibility of BA.2 causes another major public-health problem, threatening unvaccinated individuals. This high transmissibility rate explains the high number of positive cases in Europe and other continents. Initial assessments by Denmark’s Statens Serum Institut (SSI) suggest that BA.2 is 1.5-fold more contagious than BA.1. In Denmark, the number of positive cases doubled over a week, signifying the high transmissibility of BA.2 [5]. So far, the risk of high hospitalization rates remains the same.

Evidence shows that both vaccinated and unvaccinated individuals can be infected with the highly transmissible subvariant. Some hypothesize that Omicron is the preferred variant to catch, and the pandemic will be ending soon. However, the best SARS-CoV-2 (sub)variant will be the one that is inactive.

In conclusion, emergence of new SARS-CoV-2 (sub)variants should be monitored by gene sequencing in those countries where an active surveillance program does not exist. The recommended countermeasures including vaccination, physical distancing, correctly donning the recommended types of facemasks, and avoidance of mass-gathering events must continue. Considering nation-wide lockdowns to fight the subvariants could still be pertinent.

Provenance and peer review

Not commissioned, internally peer-reviewed.

Ethical approval

This study received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.

Author contribution

Amin Talebi Bezmin Abadi: Conceptualization, Data Curation, Writing – Original Draft, Writing – review & editing. Farid Rahimi: Writing – Review & editing. All authors critically reviewed and approved the final version of the manuscript before submitting.

Research registration Unique Identifying number (UIN)

  • 1.Name of the registry: Not applicable.
  • 2.Unique Identifying number or registration ID: Not applicable.
  • 3.Hyperlink to your specific registration (must be publicly accessible and will be checked): Not applicable.


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Data statement

Data not available/not applicable.Go to:


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Here are all the mutations in the Omicron variant and why they are scaring scientists

Authors: Marianne Guenot December 1, 2021

Here are all the mutations in the Omicron variant and why they are scaring scientists

Omicron was named a “variant of concern” in part because of its peculiar set of mutations.

It is not yet clear whether this variant spreads faster or causes more severe infections.

It’s not yet clear whether the Omicron coronavirus variant is more transmissible, deadlier, or can evade existing vaccines.

But the constellation of mutations it carries is concerning, partly because many of them are completely new to science, experts told Insider.

Here are all the mutations of the Omicron variant, and why they’re scaring scientists.

Mutations in potentially dangerous places

The Omicron variant has more than 30 mutations on the spike protein.

The spike protein acts as a grappling hook to bind the coronavirus to cells in the human body and is the main target for the COVID-19 vaccine.

What’s concerning about Omicron is that the changes to the protein are clustering in areas that could help the coronavirus evade antibodies or become more infectious.

This can be seen in the graphic below of the Omicron spike protein, where changes to the protein are shown as colored dots. Mutations are in blue, while insertions or deletions are in red.

The changes tend to cluster in three areas of the protein, circled below. Two of them are antibody-binding sites, where antibodies from vaccines or natural immunity block the virus.

  • The receptor-binding domain (RBD), the part of the spike protein that binds the cell.
  • The furin cleavage site (FCS), a region that undergoes a chemical reaction before the virus can infect the cells.
  • The N-terminal domain (NTD), another part of the protein.
A schematic shows mutations on the spike protein of the Omicron variant, and arrows indicate where these mutations could be clustering to have a potential biological effect.
An annotated schematic of the Omicron Spike protein.Ulrich Elling, Institute of Molecular Biotechnology/Insider

“There are two regions that are known to bind neutralizing antibodies … the NTD and the RBD domain,” Dr. Ulrich Elling, group leader at the Institute of Molecular Biotechnology in Austria, told Insider.

“Worryingly, the mutations of Omicron cluster exactly in these two domains.”

Some of the mutations could also increase the virus’ ability to infect human cells.

Mutations to the FCS have been shown to potentially increase the transmissibility of the virus, per CoVariants.org, a website that tracks coronavirus variants and mutations.

Mutations in the RBD can also make the virus more “sticky,” making it more likely to infect — which is what happened with the Delta variant, as Martin Hibberd, professor of emerging infectious diseases at the London School of Hygiene and Tropical Medicine, told Insider.

Many mutations are completely new to science

The Omicron also carries many mutations that haven’t been seen before.

This color-coded list, as shared by Jeffrey Barrett, a geneticist at the Wellcome Sanger Institute, sheds some light on the types of mutations scientists are looking at.


Each row is a different mutation. Here’s what the colors mean, according to Barrett:

  • Red: These nine mutations are already shared with other variants of concern, meaning Omicron could have the same worrying characteristics as those other variants. (Delta, for instance, is believed to be able to escape immune responses from vaccination or prior infections.)
  • Yellow: These three mutations haven’t been seen in other variants of concern, and could make the virus fitter, meaning more transmissible or better at escaping immunity. (For instance, a mutation around the 484 amino acid on the protein — “E484A” — could enhance the ability of the virus to infect the cells, Elling said.)
  • Green: Another mutation that has been shared by many variants since early 2020.
  • Purple: These are completely new mutations for a variant of concern, but lab data suggests they could increase the virus’ ability to escape immunity or infect a person.
  • Blue: These are 11 mutations that have been seen “rarely or never before,” Barrett said. Scientists don’t know what the mutations could do.

One scientist is hopeful that existing vaccines work

Hibberd said it’s too early to know the effect of the new mutations because of the way the Omicron likely arose.

Viruses evolve as they move through the population. Immune reactions put fierce selection pressure on the virus, so any mutation that is left probably makes the virus fitter.

But that’s likely not what happened with the Omicron variant, Hibberd said.

“It’s not a direct descendant of Delta or Alpha,” he said. Instead, it is similar to the Beta variant, which is “quite a long way back in the evolutionary route,” he said.

What likely happened was that an immunocompromised person caught a Beta-like variant, carried it for a long time, and the coronavirus evolved inside them, Hibberd said. Because their immune system would have been weaker, it would have put less selection pressure on the virus.

This wouldn’t be unprecedented: A case study previously showed an immunocompromised woman carried the coronavirus for at least 216 days in a row, accumulating over 30 mutations.

While it’s too early to tell if existing vaccines can work against Omicron, Hibberd said he’s confident they will.

“What was reassuring for me is that [Omicron] actually had quite a few of the mutations that we have seen before. And that makes me think that the vaccines will work against it.”