Category Archives: Omicron variant

Coronavirus, Covid 19, Omicron variant

What to know about the new COVID variant before you go out this weekend

[Note from BenIndy Contributor Nathalie Christian: Between the Benicia Peddler’s Fair this weekend the start of school next week, we’re entering a period of high risk for COVID exposure. Please take a moment to read about the new, highly transmissible “Eris” variant below and make choices that match not just your risk level, but the risk level of those closest to you – especially the elderly and the immunocompromised. If you’re in a high-risk group, don’t hesitate to reach out to your healthcare provider if you are experiencing symptoms. Not only is Paxlovid plentiful, it is also very effective; in its initial trial involving unvaccinated, high-risk patients, Paxlovid reduced hospitalization or death by 86 percent. Stay vigilant, stay safe.]

What to know about ‘Eris,’ the new COVID-19 subvariant sweeping the US

Lu Foster receives a COVID-19 booster shot at the Lynne and Roy M. Frank Residences in San Francisco in October 2021. The FDA approved a second bivalent booster dose for older adults and people with compromised immune systems. | Brontë Wittpenn for The Chronicle.

Today, by Caroline Kee, August 10, 2023

The EG.5 “Eris” variant is now the dominant COVID-19 strain in the U.S. Here’s what to know about transmission and symptoms.

A new COVID-19 variant called EG.5 is sweeping across the United States as cases and hospitalizations rise. The fast-spreading new COVID subvariant, also referred to as Eris, is now the dominant strain circulating in the U.S., health officials say.

As of last week, EG.5 accounted for the largest proportion of COVID-19 infections in the country compared to any other variant, according to the latest data from the U.S. Centers for Disease Control and Prevention,

Eris is also on the rise in several other countries around the globe. On Wednesday, Aug. 9, the World Health Organization decided to classify EG.5 as a “variant of interest.”

The new subvariant, which experts nicknamed “Eris” on social media, started circulating in the U.S. earlier this spring. Last month, EG.5 quickly overtook the prevailing omicron XBB subvariants, which had been driving the largest share of cases in the country.

During a two-week period ending on Aug. 5, Eris accounted for an estimated 17.3% of new confirmed COVID-19 cases in the U.S., up from 12% two weeks prior, according to the latest CDC data.

Many are wondering if the EG.5 subvariant is more transmissible or severe, and whether it’s causing different symptoms.

What is EG.5 , aka Eris?

EG.5 is a descendant of the omicron XBB sublineage of the virus (specifically, XBB.1.9.2), but it has an extra mutation in its spike protein, according to a WHO risk evaluation report.

“When we look at its sequence, EG.5 is really similar to the other XBB variants that are circulating right now, with a couple of small changes,” Dr. Andrew Pekosz, a virologist at Johns Hopkins University, tells TODAY.com.

The WHO added EG. 5 to its list of variants under monitoring on July 19, 2023, but the variant was first detected in February 2023. “Scientists have known about this variant, and it’s been present in other countries, as well,” says Pekosz.

So far, EG.5 has been reported in 51 countries and there has been a steady increase in prevalence globally — the majority of sequences are from China, followed by the U.S., South Korea, Japan and Canada, per WHO.

XBB.1.16, also called the “Arcturus” variant, remains the most prevalent strain of COVID-19 worldwide.

WHO considers the public health risk posed by EG.5 to be “low” and similar to that of XBB.1.16 and other variants of interest.

Is EG. 5 more transmissible? 

The EG.5 variant is very similar to other omicron variants, which means it’s highly transmissible, Dr. Albert Ko, an infectious disease physician and professor at Yale School of Public Health, tells TODAY.com.

However, EG.5 is likely more transmissible than other XBB variants, Dr. Sharon Nachman, chief of the division of pediatric infectious diseases at Stony Brook Children’s Hospital, tells TODAY.com.

“If it was equally transmissible, then we wouldn’t see it gaining strength number-wise compared to some of the other variants,” says Nachman, adding that EG.5 quickly pushed out other XBB variants in the U.S., which were dominant over the summer.

Why exactly EG.5 is more transmissible is not yet known, Ko says.

“Whether it’s escaping population immunity or it has some intrinsic factor that makes it better able to transmit from one person to another … it’s hard to separate,” he adds.

According to WHO, EG.5 has increased immune escape properties compared to other variants. “EG.5 may cause a rise in case incidence and become dominant in some countries or even globally,” WHO said in a report.

However, Pekosz notes that the EG.5 variant may not be the sole reason for the U.S. summer uptick. “When you have a new variants, and cases creeping up, there’s always concern about whether that variant could be driving the increase,” says Pekosz.

“Right now, it doesn’t look like that variant alone is driving the case increases (in the U.S.) … there’s still a lot of other variants co-circulating,” he adds.

According to CDC estimates, EG.5 accounted for about 17% of COVID-19 cases in the U.S. during the two-week period ending on Aug. 3. — after EG.5, the next most common variants were XBB.1.16, XBB.2.3, and XBB.1.5, which accounted for 15%, 11% and 10% of cases, respectively.

“We’re keeping an eye on (EG.5) because of the uptick in cases, but it doesn’t look like there’s anything particularly concerning about this variant,” says Pekosz.

More data is needed to understand how EG.5’s transmissibility compares to other strains. However, decreased levels of testing and genomic sequencing are making it harder to accurately track new COVID-19 cases and which variants are driving them, Pekosz notes.

“Right now, there’s an awful lot of guesswork,” he says.

Is EG.5 more severe?

The data available do not indicate that EG.5 causes a more severe infection compared to other variants, the experts note.

In its risk assessment of EG.5, WHO said, “There have been no reported changes in disease severity to date.”

Although the U.S. recently saw the first increase in COVID-19 hospitalizations of the year, there isn’t evidence that EG.5 is causing this uptick or that it’s more likely to cause hospitalizations in general, Nachman notes.

“The people that are getting hospitalized often have lots of co-morbidities, and they’re at-risk no matter what COVID strain they get,” says Nachman.

However, it’s possible that hospitalizations could increase even more because of more people getting infected with EG.5, says Ko. “There’s no clear evidence of that at this point, but we have to keep on evaluating,” Ko adds

Population immunity from vaccination and prior infection should protect people from severe illness as EG.5 continues to circulate.

What are the symptoms?

There isn’t enough clinical data about the most common symptoms of EG.5 yet, NBC News previously reported.

“There’s no change in EG.5 symptoms right now,” says Pekosz. So far, the symptoms of EG.5 look very similar to the standard omicron symptoms, says Ko. These include:

    • Cough
    • Sore throat
    • Runny nose
    • Sneezing
    • Fatigue
    • Headache
    • Muscle aches
    • Altered sense of smell

“It may progress to some more significant feelings of difficulty in breathing as the infection spreads into your lungs,” says Pekosz.

Certain groups are at higher risk of developing severe illness or complications, including people over 65 and those who are immunocompromised or have underlying medical conditions.

Can COVID-19 tests detect EG.5? 

All COVID-19 tests — including PCR tests performed by a medical provider and rapid at-home antigen tests sold over-the-counter — should be detecting EG.5, says Pekosz.

The experts emphasize the importance of getting tested as COVID-19 cases increase, and especially during the fall when viruses that cause similar symptoms (such as flu and RSV) are circulating.

“If you’re in one of the high-risk groups for getting severe COVID, you really shouldn’t hesitate to get a test,” says Pekosz, adding that early detection and treatment is key. COVID-19 antivirals such as Paxlovid are effective against EG.5 and other variants, but they work best when taken early, he adds.

Whether your insurance covers COVID-19 testing may have changed since the end of the U.S. federal public health emergency in May, TODAY.com previously reported, so check with your insurer if you have questions about testing costs.

It’s also important to check the expiration date of at-home tests. The shelf life of rapid tests ranges from four to 24 months, according to the U.S. Food and Drug Administration, but the expiration dates of some tests have been extended.

Will I need a COVID-19 booster this fall?

The experts encourage everyone to stay up to date on COVID-19 vaccines, which may include a new booster dose in the coming months. In June 2023, the FDA advised vaccine manufacturers to update their boosters to target omicron XBB.1.5, which was the dominant strain at the time.

These shots haven’t been approved yet, but the FDA could authorize Pfizer’s booster shot by the end of August, NBC News reported.

Although the new boosters will not include the EG.5 strain, they may still provide protection, the experts note. “If I vaccinate you with the vaccine that contains XBB, you will make antibodies that are specific to XBB and pretty close to EG.5,” says Nachman.

“Right now, EG.5 looks like it’s very closely matched to the vaccine that’s going to be available this fall,” says Pekosz.

However, the CDC has not yet released any firm guidance or recommendations around booster doses for the fall.

“The message is to pay attention to the COVID vaccine program that’s going to come out in the fall. … It’s a vaccine that many people (especially high-risk individuals) should consider taking,” says Pekosz.

How to protect yourself from EG.5:

In addition to staying up to date on COVID-19 vaccinations, the experts emphasize taking precautions to protect yourself and curb transmission of COVID-19, including:

    • Washing your hands with soap and water frequently
    • Staying home when sick
    • Avoiding contact with sick people
    • Improving ventilation
    • Wearing a mask in crowded, indoor spaces
    • Covering coughs and sneezes

Coronavirus, Covid 19, Omicron variant

A recent uptick in COVID numbers proves it is alive and well in California

COVID numbers are ticking up in California. Here’s what to know

Lu Foster receives a COVID-19 booster shot at the Lynne and Roy M. Frank Residences in San Francisco in October 2021. The FDA approved a second bivalent booster dose for older adults and people with compromised immune systems. | Brontë Wittpenn for The Chronicle.

San Francisco Chronicle, by Aidin Vaziri, July 28, 2023

As people crowd movie theaters for “Barbie,” flock to stadiums to see sold-out Taylor Swift concerts and resume their annual trips to Europe, in what largely feels like a summer in the days before the pandemic, highly transmissible variants of the coronavirus have found ideal conditions to reemerge and infect people.

That’s why health officials say a subtle but sustained increase in key COVID-19 indicators is not unexpected. Emergency department visits, test positivity rates and wastewater virus levels in some areas signal a slight rise in infections, according to the latest figures from the California Department of Public Health and the U.S. Centers for Disease Control and Prevention. Meanwhile, hospital admissions across the United States are up by more than 10% from the previous week.

Kathleen Conley, a spokesperson for the CDC, said that the nation is still in a good place despite this increase.

“U.S. COVID-19 rates are still near historic lows after seven months of steady declines,” she said in a statement. “The U.S. has experienced increases in COVID-19 during the past three summers, so it’s not surprising to see an uptick.”

While the 7,109 hospital admissions nationwide reported for the week of July 15 marks the highest level since December, it remains significantly lower than the peak observed during the omicron surge last July, when weekly U.S. hospitalizations reached more than 44,000.

According to the state’s health department, as of Thursday, California reported an average of 858 COVID-related hospitalizations per day over 14 days, up by 7.4% since the beginning of the month, with an average of nine deaths per day over seven days, compared with five on July 1.

To date, nearly 1.14 million people in the United States have died because of COVID-19 since the onset of the pandemic. But the combination of vaccination and immunity from previous infections has driven down community transmission, while treatments such as the antiviral medication Paxlovid have helped significantly reduce the likelihood of severe illness and death due to COVID.

That progress led to the U.S. reaching a pandemic milestone last week as the rate of excess deaths — the number of Americans dying from any cause compared with statistical averages — fell to below 1% after growing to as high as 30% during previous virus surges, according to the CDC.

“The death rates are no longer different from the usual death rates at this time of year,” Dr. Bob Wachter, the chair of medicine at UCSF, said this week in a podcast interview for Medscape. “That is a remarkable achievement and says something about the state of the pandemic and the state of immunity, either from vaccines or from infection or both. And it’s worth celebrating. It’s worth going back to something that feels a little bit closer to normal than we’ve lived for the last three or four years. But you have to do it with your eyes open.”

In California, the coronavirus test positivity rate has jumped to 7.6% this week, compared with 4.1% a month ago. That figure is more indicative of trends than community penetration because so few people now get laboratory tests. Most now rely on home test kits whose results are rarely reported to authorities. Others have discontinued testing altogether.

“In the same way people stop wearing masks and throw caution to the wind, once they’ve run out of their home tests, are they going to go to Walgreens and spend $30 to buy some more?” said Wachter, who himself recently got COVID-19 after avoiding it for more than three years. “I’m guessing they’re not.”

There is no single variant driving the current increase in infections, as XBB.1.15 and XBB.1.16 have declined in circulation over the past two weeks, while newer omicron offshoots like EG.5, XBB.1.16.6 and XBB.2.3 are uniformly gaining traction. No individual variant accounts for more than 15% of the measured proportion.

The upturn is not limited to the U.S. Japan has experienced a rise in COVID-19 hospitalizations and emergency department visits for nine consecutive weeks, indicating the country may be entering its ninth waveof infections. But Europe is reporting flat numbers.

The World Health Organization continues to underscore that COVID-19 “remains a major threat,” as several countries grapple with high disease burdens. In its latest weekly update, the agency urged government leaders not to dismantle their pandemic response infrastructure.

The WHO noted that EG.5, a descendant of the XBB.1.9.2 variant, has an additional mutation that could aid its rapid global spread. However, it said there is “no evidence of rising cases and deaths or a change in disease severity associated with EG.5.”

Updated COVID-19 vaccines targeting the XBB.1.5 variant, which has been dominant in the United States throughout 2023, are expected to be available in late September, alongside this year’s flu shot.

“This is the new normal, and COVID will now be baked into the list of day-to-day risks that we all have,” Wachter said. “And all of us have to come to some sense of clarity of how we are going to live our lives in a way that’s fulfilling and maximizes joy.”

Coronavirus, Covid 19, Omicron variant, Vaccine booster

FDA authorizes 2nd COVID booster for older adults

UPDATE: Second COVID bivalent booster shots set to roll out. Here’s what you need to know

Lu Foster receives a COVID-19 booster shot at the Lynne and Roy M. Frank Residences in San Francisco in October 2021. The FDA approved a second bivalent booster dose for older adults and people with compromised immune systems. Brontë Wittpenn/The Chronicle 2021

San Francisco Chronicle, by Aidin Vaziri, April 18, 2023 [See also, this article updated: April 19, 2023]

On Tuesday, the U.S. Food and Drug Administration authorized a second COVID-19 booster dose for older Americans and individuals with weakened immune systems to enhance their protection this spring.

Coronavirus map: How many COVID cases are in Bay Area and California

The move comes amid concerns over newer variants of the virus causing the number of COVID-19 cases and deaths to tick back up in the United States, particularly among vulnerable populations.

Individuals age 65 or older may opt for a second shot of the bivalent vaccine targeting the omicron strains of the coronavirus at least four months after their initial dose. For those who are immunocompromised, a second booster shot may be received at least two months later, with additional doses at the discretion of their physician.

The FDA also announced that the original versions of the Pfizer and Moderna vaccines are outdated and will no longer be used. Instead, individuals receiving these shots will be administered the newer omicron-targeted version. For those receiving their first-ever vaccine, a single combo dose will suffice.

A Jackson, Miss., resident receives a Pfizer booster shot from a nurse at a vaccination site. The FDA approved a second bivalent booster dose for older adults and people with compromised immune systems. Rogelio V. Solis/Associated Press 2022

According to Dr. Peter Marks, the FDA vaccine chief, “At this stage of the pandemic, data support simplifying the use of Pfizer and Moderna vaccines. The agency believes this approach will help encourage future vaccination.”

Although Britain and Canada have already recommended an additional spring booster for vulnerable populations, high-risk Americans who last received a dose in the fall have been eagerly anticipating another dose.

Booster doses continue to stave off severe disease and death, even as more contagious variants have emerged, while protection against mild infections is short-lived.

At least 250 people in the U.S. still die from COVID-19 each day, many of them older and at higher risk for the worst outcomes of the disease.

Yvonne Maldonado, an infectious disease expert at Stanford, said, “If you look at who’s dying or getting sick now, it’s people who are unvaccinated or unboosted.”

The Centers for Disease Control and Prevention must approve the latest round of boosters, and its advisers are scheduled to meet on Wednesday.

The Pfizer and Moderna boosters contain protection against both the original coronavirus strain and omicron variants known as BA.4 and BA.5. Recent studies show that the bivalent shots are still effective, even as newer omicron cousins circulate.

The FDA’s simplification also means changes for unvaccinated children. Children under 5 may receive two doses of the bivalent Moderna vaccine or three doses of the Pfizer-BioNTech bivalent vaccine.

People 5 and older may get a single bivalent Pfizer shot or two Moderna doses. Children already fully or partially vaccinated with the original Pfizer or Moderna shots may get a bivalent vaccine, but the number of doses will depend on their vaccination history, the FDA said.

While over 95% of the U.S. population aged 65 and older received at least one vaccine dose, only 42.1% of those eligible have received the latest boosters, which were authorized in August, according to the CDC.

The offering of a second bivalent booster will not interfere with the Biden administration’s previously stated plan of moving the nation toward an annual COVID vaccine similar to the flu shot.

But for eligible high-risk groups, a second booster in the spring is a reasonable choice, said Dr. Matthew Laurens of the University of Maryland School of Medicine.

“We do have vaccines that are available to protect against these severe consequences, so why not use them?” he said. “They don’t do any good just sitting on a shelf. So let’s give them to individuals who are at the highest risk and who can benefit the most.”

The Associated Press contributed to this report.

Coronavirus, Coronavirus subvariant, Coronavirus variant, Covid 19, Delta variant, Omicron variant, SARS-CoV-2, Virus mutation

Virus mutations aren’t slowing down. New omicron subvariant proves it.

Coronavirus testing sites remain in business more than two years after the pathogen emerged. A medical worker administers tests April 18 in New York. (Spencer Platt/Getty Images)
Washington Post, By Joel Achenbach, May 1, 2022

During those terrifying early days of the pandemic, scientists offered one piece of reassuring news about the novel coronavirus: It mutated slowly. The earliest mutations did not appear to be consequential. A vaccine, if and when it was invented, might not need regular updating over time.

This proved overly optimistic.

The coronavirus, SARS-CoV-2, has had billions of chances to reconfigure itself as it has spread across the planet, and it continues to evolve, generating new variants and subvariants at a clip that has kept scientists on their toes. Two-and-a-half years after it first spilled into humans, the virus has repeatedly changed its structure and chemistry in ways that confound efforts to bring it fully under control.

And it’s not showing signs of settling down into a drowsy old age. Even with all the changes so far, it still has abundant evolutionary space to explore, according to virologists who are tracking it closely. What that means in practical terms is that a virus that’s already extremely contagious could become even more so.

“This virus has probably got tricks we haven’t seen yet,” virologist Robert F. Garry of Tulane University said. “We know it’s probably not quite as infectious as measles yet, but it’s creeping up there, for sure.”

The latest member of the rogue’s gallery of variants and subvariants is the ungainly named BA.2.12.1, part of the omicron gang. Preliminary research suggests it is about 25 percent more transmissible than the BA.2 subvariant that is currently dominant nationally, according to the Centers for Disease Control and Prevention. The CDC said the subvariant has rapidly spread in the Northeast in particular, where it accounts for the majority of new infections.

“We have a very, very contagious variant out there. It is going to be hard to ensure that no one gets covid in America. That’s not even a policy goal,” President Biden’s new covid-19 coordinator, Ashish Jha, said in his inaugural news briefing Tuesday.

He was answering a question about Vice President Harris, who recently tested positive for the virus and went into isolation. Harris had recently been boosted for the second time — her fourth shot of vaccine.

Her case highlights what has become painfully obvious in recent months: No amount of vaccination or boosting can create a perfect shield against infection from SARS-CoV-2. What the vaccines do very well, however, is greatly reduce the risk of severe illness. That is hugely consequential as a matter of public health, as is the wider use of therapeutics, such as the antiviral Paxlovid.

The vaccines currently deployed were all based on the genomic sequence of the original strain of the virus that spread in late 2019 in Wuhan, China. They essentially mimic the spike protein of that version of the virus and trigger an immune response that is protective when the real virus shows up.

But the variants that have emerged can evade many of the neutralizing antibodies that are the immune system’s front line of defense.

“It’s evolving at a fairly rapid rate,” said Jesse Bloom, a computational biologist at the Fred Hutchinson Cancer Research Center in Seattle. “I do think we need to aggressively consider whether we should update vaccines, and do it soon.”

Vaccines have reduced the virus’s worst effects. Community of Hope clinical nurse manager Imani Mark injects Ezekiel Akinyeni with a shot July 31, 2021, in D.C. (Craig Hudson/For the Washington Post)

BA.2.12.1 brings the novel coronavirus up another step on the contagiousness scale. Its close relative, BA.2, was already more transmissible than the first omicron strain that hit the country in late 2021.

And omicron was more transmissible than delta, and delta was more transmissible than alpha, and alpha was more transmissible than earlier variants that did not have the glory of a Greek alphabet name.

Most mutations are not advantageous to the virus. But when a mutation offers some advantage, the process of natural selection will favor it.

There are two fundamental ways that the virus can improve its fitness through mutation. The first could be described as mechanical: It can become innately better at infecting a host. Perhaps it improves its ability to bind to a receptor cell. Or perhaps the mutation allows the virus to replicate in greater numbers once an infection has begun — increasing the viral load in the person and, commensurately, the amount of virus that is shed, potentially infecting other people.

The other strategy involves the workaround of immunity. The human immune system, when primed by vaccines or previous infection to be alert for a specific virus, will deploy antibodies that recognize and neutralize it. But mutations make the virus less familiar to the immune system’s front-line defense.

The omicron subvariants keep coming: Scientists in South Africa have identified BA.4 and BA.5, which have mutations that were seen in earlier variants and are associated with immune evasion. Caseloads there are rising. New laboratory research, posted online Sunday but not yet peer-reviewed, indicated that the emerging subvariants are adept at eluding the neutralizing antibodies seen in people who recovered from infections with the original omicron variant. The authors of the study concluded that BA.4 and BA.5 have the “potential to result in a new infection wave.”

“The evolution is much more rapid and expansive than we initially estimated,” said Michael T. Osterholm, a University of Minnesota infectious-disease expert. “Every day I wake up, I fear there will be a new subvariant that we will have to consider. … We’re seeing subvariants of subvariants.”

Garry, the Tulane scientist, points out that mutations in the virus do not change its appearance dramatically. In fact, he said, even the heavily mutated variants don’t look much different from the original Wuhan strain, or different from other coronaviruses that cause common colds. These are subtle changes.

Garry has a software program that allows him to create a graphic image of the virus, and even rotate it, to observe the locations of mutations and draw inferences for why they matter. On Friday, asked about BA.2.12.1, and why it is spreading, he noted it has a mutation, named S704L, that probably destabilizes a portion of the spike protein on the virus’s surface. That essentially loosens up part of the spike in a way that facilitates infection.

This S704L mutation distinguishes this subvariant from BA.2.

The “704” refers to the 704th position for an amino acid on a chain of roughly 1,100 amino acids that form the protein. The S is one type of amino acid (“serine”) seen in the original strain of the virus, and the L (“leucine”) is what is there after the mutation. (The mutation is caused by a change in one nucleotide, or “letter,” in the genetic code of the virus; three nucleotides encode for an amino acid.)

The virus is spreading today in the United States on an immunological landscape much different from the one it first encountered in early 2020. Between vaccinations and infections, there aren’t many people entirely naive to the virus. The latest CDC data suggest the virus has managed to infect nearly 200 million people in the nation, which has a population of about 330 million. Among children and teenagers, about three out of four have been infected, the CDC estimates.

For the new CDC study, researchers looked at blood samples from thousands of people and searched for an antibody that is found after a natural infection, but not found after vaccination. The CDC concluded that the omicron variant managed to plow through the United States population during the winter almost as if it were an entirely new virus. The country by then was largely vaccinated. And yet 80 million people, approximately, became infected for the first time in that omicron wave.

On the family tree of this coronavirus, omicron is a distant cousin of delta, alpha and the other variants that had spread earlier — it came out of virologic left field. No one is sure of the origin of omicron, but many disease experts assume it came from an immunocompromised patient with a very lengthy illness, and the virus continued to use mutations to evade the immune system’s efforts to clear it.

Technicians inside a high-security coronavirus research lab in Durban, South Africa, on Dec. 15, 2021. (Waldo Swiegers/Bloomberg)

Omicron was mercifully less likely to kill a person than previous variants. But infectious-disease experts are clear on this point: Future variants could be more pathogenic.

As if mutation wasn’t enough of a problem, the virus has another trick up its sleeve: recombination. It happens when two distinct strains infect a single host simultaneously and their genes becoming entangled. The recombination process is the origin of what’s known as omicron XE. That recombinant probably emerged from a person co-infected with the original omicron variant and the BA.2 subvariant.

It was always possible in theory, but the identification of actual recombinants provides “proof of concept,” as Jeremy Luban, a virologist at the University of Massachusetts Medical School, puts it.

The worst-case scenario would be the emergence of a variant or recombinant that renders current vaccines largely ineffective at blocking severe disease. But so far, that hasn’t happened. And no “recombinant” has spread like omicron or other recent variants and subvariants.

This is the first catastrophic pandemic to occur in the age of modern genomic sequencing. A century ago, no one knew what a coronavirus was, and even a “virus” was a relatively new concept. But today, with millions of samples of the virus analyzed at the genetic level, scientists can track mutations virtually in real time and watch the virus evolve. Scientists across the planet have uploaded millions of sequences to the database known as GISAID.

Genomic sequencing has a major limitation in that, although scientists can track changes in the genome, they don’t automatically know what each of those changes is doing to the virus. Which mutations matter most is a question that can be discerned through laboratory experiments, modeling or epidemiological surveillance, but it’s not always simple or obvious.

Erica Saphire, president of the La Jolla Institute for Immunology, speculates that omicron has mutations that have changed the virus in ways not yet understood but which make it more resistant to antibody-mediated neutralization.

“It may have acquired some new trick that we haven’t uncovered yet,” Saphire said. “It’s harder to neutralize than I would have expected, based on the number of mutations alone.”

A reality check comes from Jeremy Kamil, associate professor of microbiology and immunology at Louisiana State University Health Shreveport: “These are all SARS-CoV-2.”

What he means is that these are all variations of the same virus, despite what seems like a tremendous amount of mutation. Correspondingly, someone who gets infected with one of these new variants has the same disease as people who got infected previously.

“They got covid,” he said.

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