Category Archives: Coronavirus variant

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.

Why experts are ‘not concerned’ San Francisco Bay Area’s COVID rate is highest in California

Solano is only Bay Area County not among highest rates in the state

SFGATE, By Amy Graff, April 6, 2022
San Francisco has the highest COVID-19 case rate of any other county in California, but experts aren’t concerned as cases and hospitalizations are still extremely low compared to what they were amid the winter surge. In this file photo, people wearing masks walk along at path in front of the “Painted Ladies,” a row of historical Victorian homes, and the San Francisco skyline at Alamo Square Park during the coronavirus pandemic in San Francisco. | Jeff Chiu/Associated Press

San Francisco County has the highest COVID-19 case rate of any other county in California with a seven-day average of 13 cases per 100,000 residents, state data showed on Tuesday. By comparison, Los Angeles is reporting 5 cases per 100,000 residents. And San Francisco isn’t the only Bay Area spot sitting at the top of the list. All counties in the region except Solano have among the highest rates in the state.

But multiple experts say this news isn’t alarming, and does not warrant any policy changes. Despite the region’s ranking, cases are extremely low compared to what they were amid the winter surge when the city’s seven-day average soared above 250 cases per 100,000 at the peak.

“No I’m not concerned,” said Dr. George Rutherford, director of UCSF’s Prevention and Public Health Group. “I don’t think it’s any reason to go back to putting the brakes on and our masks back on. We have lots of hospital capacity.”

“I am not too concerned as our hospitals remain eerily quiet — only 2 patients with COVID hospitalized today at the main UCSF Health hospital on Parnassus, compared to close to a 100 in this hospital on January 25,” UCSF infectious diseases expert Dr. Peter Chin-Hong wrote in an email.

“I don’t anticipate any lockdowns, and I am not even sure any restrictions will be re-implemented as long as our hospitals remain protected.” Chin-Hong continued. “There may be disruptions in the community in the workplace and schools as people need to be taken out to isolate for at least 5 days if infected. Is it interesting that countries like the UK, Denmark and South Africa have removed the mandate for a compulsory isolation when infected and this softens the potential disruptions to life in this way.”

While San Francisco’s case rate may not be concerning, you may still be wondering why it’s higher than other places. UCSF’s Dr. Monica Gandhi believes a primary reason is the city’s robust testing apparatus.

“We do a lot of testing in San Francisco with mass community testing sites established via a collaboration between UCSF and the San Francisco Department of Public Health,” Gandhi said. “This allows us to detect slight increases in cases better than other counties in the setting of BA.2 (now 72% of strains in the U.S.) and with increased movement of the population.”

Rutherford agreed that testing is playing into the city’s higher rate and added that the city is a medical hub and people are coming to the city for care that requires testing. “Theoretically, positive tests should be reported back to the county of residence, but that might not always be happening,” he said.

The highly transmissible BA.2 variant — that’s spreading at a time when more people are traveling and society is reopening — is another likely factor, said Chin-Hong.

“A combination of spring break travel, visitors from lots of other parts of the country and world (Asia, Europe), reopening and the resumption of large indoor events like sports and concerts,” Chin-Hong wrote in an email. “This is all fueled by BA.2, which is more transmissible in a city that is compact. There may be more susceptible people to infection in San Francisco and the Bay Area (compared to other parts of the state) who haven’t gotten breakthrough infection with BA.1 and whose immunity to infection has waned. Strategies that have been used in the past to avoid infection may not work quite as well with COVID.”

Could the Bay Area be at the start of a BA.2-driven surge?

The experts that SFGATE talked to all said they don’t expect cases to skyrocket.

“There’s going to be some sort of a sawtooth pattern and it’s not surprising that things are going to be up and down,” said Rutherford. “We’ll see some clusters and bumps from BA2, but I think the overall pattern is it’s going to broaden the base of that curve as it comes down.”

Chin-Hong emphasized that the region has high vaccination rates and this combined with immunity people infected with COVID gained during the original omicron surge “will provide enough immunity ammunition to protect people from getting seriously ill and so protect our hospital resources so we can continue to take care of the spectrum of non-COVID illnesses without interruption.”

You, me and Omicron, oh my!

By Roger Straw, November 28, 2021

You think YOU’RE tired of this…  I’ve about had it!

Roger Straw, The Benicia Independent

I’m a news junkie.  Every morning since I don’t know when, I’ve gotten up in the morning and sat in front of the newspaper and tv news over 3 cups of coffee.

With cream – well, it can’t be all work and no play.

But waking this morning, I almost couldn’t bring myself to do it.  I didn’t want to see the daily news shows.  I’d heard the early reports yesterday about the outbreak of the new COVID variant – Omicron – in Southern Africa and its early spread to Europe.  And I actually dreaded learning more.

But, no!  I’m the one PUSHING COVID news here in Benicia / Solano County, right?  Almost daily, since April, 2020, I’ve monitored the local and regional COVID news and let you know.  I’ve spent over a year and a half immersed in the daily toll: numbers with faces behind each one, totals that belie pain and loss and grief, words and spreadsheets and blog postings that failed, really, at every turn, to tell the heart-rending stories of friends and families.

I was actually tired of it long ago.  And now this.

You know that I’m not among those saying we are almost out of the danger zone.  I’ve never let up on the alarm bells.  But when Omicron surfaced, it seemed too much even for me.  Please, not again, not more, not more….

How many of you out there have long ago turned off the tv reports on COVID, or at least diverted your attention?  We keep on with the masking and social distancing, but increasingly, we need to plug our ears.  I know my readership is down on the BenIndy.  People are really, really tired of hearing about COVID.

Brian Stelter, of CNN’s Reliable Sources outlines the difficulty we all are facing – early warnings about Omicron with no certainty as to what is coming.  I’ll leave it to him to sum up what we know and don’t know, and to help clarify our anxiety-ridden responses to Omicron.  This is really good, and well-written – read on…


Covid news “purgatory”

Friday’s satirical headline by The Onion said it best: “Nation Nearly Strings Together 3 Good Days In Row.”

The blessing of Thanksgiving on Thursday was followed by a curse on Friday: Urgent news about the new Covid variant named Omicron. “We know almost nothing about the Omicron variant,” as this headline on The Atlantic‘s website helpfully states. But the abrupt reactions to the news — stock selloffs, travel restrictions, endless Twitter threads — made Omicron the top story of the weekend across all sorts of news websites and networks.

Now the world is in a sort of information holding pattern, as reflected by this banner on CNN Sunday afternoon: “QUESTIONS & CONCERNS BUT STILL SPARSE DATA ON NEW COVID VARIANT.” Zeynep Tufekci put it this way: “South Africa has gifted us an early warning with Omicron. But earlier the warning, the less we know.”

Author and podcaster Derek Thompson, one of the smartest voices out there about the media and society, said Sunday that “the gap between information and meaning at this moment in the Omicron story is immense. It’s deeply impressive but also discombobulating to have access to so much genetic and virological data with the big-picture takeaway being ‘we don’t really know what any of this means yet.'” He added“there’s something uncanny about these sort of news purgatories where information is abundant but meaning is scarce, and the only reasonable thing is to *not* draw conclusions from an abundance of factoids.”

True — but that’s hard to do when the information sounds alarming and is repeated ad nauseam all across the media…

A two-week wait

“Wait two weeks” seems to be the consensus. Dr. Paul Burton, the chief medical officer for Moderna, told CNN’s Paula Reid on Sunday, “We have to go through a couple of weeks here of uncertainty.” The White House’s readout of President Biden’s meeting with Dr. Anthony Fauci and members of his Covid Response Team made the same point: “Dr. Fauci informed the President that while it will take approximately two more weeks to have more definitive information on the transmissibility, severity, and other characteristics of the variant, he continues to believe that existing vaccines are likely to provide a degree of protection against severe cases of Covid.” So in the meantime, get boosted if you haven’t already. “There’s no reason to panic, but it’s a great reason to get boosted,” NIH Director Dr. Francis Collins told Dana Bash on “State of the Union…”

Biden admin is in “a messaging bind”

WaPo’s Dan Diamond observed that “in interviews, officials keep admitting that Omicron (and the current lack of data) presents a messaging bind. No one wants to sound alarm unnecessarily — but failing to warn about potential risks is a bigger sin in public health, especially if actions now could protect people.”

Politico’s Alex Thompson said on CNN’s “Inside Politics” that he spoke with a WH official late Saturday “and the phrase they kept using over and over is ‘We’re not going to get caught flat-footed.’” That’s why Fauci and Collins blanketed the Sunday AM shows, Thompson said. But what’s left unsaid, he added, is that “they did get caught flat-footed by Delta” last summer. But the risk now, Thompson added on Twitter, is “that they are overcorrecting…”

Let’s inform, not speculate

Oliver Darcy writes: “When there are information vacuums — coupled with the need to fill cable news air time, get eyeballs reading news stories, and satisfy the SEO gods — it can be tempting to delve into the arena of speculation. That’s been quite clear over the past few days. Actual data has been more scarce than speculation on what the variant might mean for the world moving forward. But journalists, particularly newsroom leaders who set the tone of coverage, should resist the temptation to hype conjecture. We still have very little knowledge on what the new variant could mean for the world. Unnerving the public by playing out the worst-case scenarios in stories and amplifying the worst fears of the scientific community in chyrons and headlines isn’t the way to go. Audiences deserve better.”

>> Dr. Jonathan Reiner‘s reaction when I asked him if Omicron should be the lead story right now: No, “because it’s a story that is based entirely on speculation. We will have data from really hard-working scientists over the next few weeks that will help inform how we can put this new variant into context…”


 — Biden will deliver an update on the new variant sometime Monday…

— Over the weekend I noticed a corollary to the “choose your own news” phenomenon: “Choose your own Twitter thread.” Some threads have ominous warnings about Omicron while others are much more optimistic…

— Johns Hopkins epidemiologist David Dowdy criticizing his colleagues: “In this situation – where data are early & societal implications are large – scientists have a duty not to oversell. And we are doing exactly that. Shame on us…” (Twitter)

— Dr. Peter Hotez, a regular doc across cable news, said “my biggest concern” is not Omicron, it’s that “we’re about to undergo another big winter Delta wave…” (MSNBC)

— “I have come to the conclusion that people love to panic,” science journalist Erin Biba remarked. She called it “completely and utterly exhausting that doomsday headlines and uninformed reporters create mass hysteria before we even have any details or information. Always wait! Before you panic, wait! Wait until you have more info…” (Twitter)

— Juliette Kayyem wrote this on Wednesday, pre-Omicron, and reaffirmed it on Sunday: “Even though the threat still exists,” the US “needs to be nudged into the recovery phase — and only elected leaders can provide that nudge…” (The Atlantic)

“Two years into this horror show…”

NYT reporter Stephanie Nolen left South Africa on Thursday after spending time with scientists there – and wound up reporting live from an airplane quarantined on the tarmac in Amsterdam. She wrote that “Europe apparently panicked” about the variant news “while I was somewhere over the Sahara; by the time we landed, we were told we would not be permitted off the plane.” She eventually tested negative and was allowed to continue onward to Canada.

On Sunday afternoon, Nolen finished her multi-day Twitter thread by saying she is “opting to self-quarantine, in an AirBnB, and keep testing, after the airport exposure I had courtesy of the Dutch authorities.” She expressed frustration with Dutch and British officials, plus the people on her flight who failed to wear masks, “even when I pleaded and we KNEW people were already testing positive.” She wrote, “Two years into this horror show, we’ve just got to be smarter and better at managing. I don’t know how you make people care about each other.”


“Covid is everything”

On Sunday’s “Reliable,” I talked with Chris Arnade, the banker turned photographer who now walks the streets of American towns and writes about what he hears and learns. He remarked about Covid being the primary drag on voters’ perceptions of Biden: “Covid is everything.” Those three words apply to more than Biden’s approval rating, obviously. Covid continues to be the throughline of every story, every struggle.

And folks who feel forgotten, who feel exploited by “elites,” feel like Covid-era policies benefited the Zoom class and punished them, Arnade said. There’s a huge cynicism towards institutions,” he added, “and Covid has made that cynicism worse.” We’re already seeing some incredibly cynical reactions to the news about Omicron…

KTVU News coverage – Benicia City Council to Consider Renewing Mask Mandate on Tues. Aug. 24

Benicia considering indoor mask mandate

KTVU News, By Greg Liggins, August 22, 2021

BENICIA, Calif. – A city in Solano County will soon decide whether to bring back its indoor mask mandate.

Solano County has been an outlier throughout much of the pandemic and recently decided not to join other Bay Area counties in requiring masks indoors for everyone.

Without such county guidance, cities are forced to make up their own rules, and that’s what the City Council of Benicia will be considering next week.

The council may bring back the indoor mask mandate that ended in June.

And if it does so, it will be taking action the County Health Director is against.

Lots of people are currently donning masks voluntarily in Benicia.

Masks are not currently required, even indoors, because the county health director has gone on the record saying the data doesn’t support it, and it could be bad for business.

But Benicia may go ahead and make it a requirement anyway.

“I think the majority of the council, I guess we’ll see, but I think the majority of the community is of the opinion that the direction the county is taking is not necessarily in the long-term health and safety interest of our community,” said Benicia Mayor, Steve Young.

Benicia dropped its indoor mask mandate in June when the state opened up and Covid appeared to be on its way out.

The Delta variant, however, is prompting a potential pivot.

The council will decide Tuesday whether to be the first city in its county to reprise an indoor mask mandate in public spaces, like retail and restaurant, a move already made at the county level in most of the Bay Area.

A business owner says a uniform policy in Benicia would make things easier on establishments that can only put up recommendation signs they really can’t enforce.

“It is what it is. I mean, you really can’t. We just have to trust people. That’s really all we can do,” said Cecilia Climaco, owner of Succulents and More.

A recent cancer survivor says she’s onboard with her city joining the majority of the Bay Area.

“I think since most of the Bay Area is requiring it we ought to too,” said Margaret Linderman.

Another resident also supports the city mandating masks, but doesn’t take issue with different places doing their own thing.

“I think because different areas have different problems with Covid, so I think it should be up to each city to make their own rules,” said Alicia Gallagher.

The Mayor says it’s potentially unsafe to have unmasked, unvaccinated people interacting closely indoors with workers that really don’t have a choice.

It’s also unfortunate, he says, that cities and counties are again having to consider requiring behaviors people could well do on their own.

It’s personally frustrating because if everybody had been vaccinated, if everybody was wearing a mask, we wouldn’t be here, but that’s clearly not the case,” said Mayor Young.

The City Council will vote on the ordinance at their meeting Tuesday and need just three of five members to approve.

The Mayor says the Health Director will be phoning-in to argue against approval.

If passed, the mandate would be temporary, perhaps 90 days, but could also be extended or rescinded sooner, all depending on what the Delta variant is doing.

For safe and healthy communities…