New Coronavirus News from 2 Nov 2022

From Centaurus to XBB: your handy guide to the latest COVID subvariants (and why some are more worrying than others) [The Conversation, 2 Nov 2022]

By Ash Porter & Sebastian Duchene

The Omicron variant of concern has splintered into multiple subvariants. So we’ve had to get our heads around these mutated forms of SARS-CoV-2, the virus that causes COVID-19, includingBA.1 and the more recent BA.5.

We’ve also seen recombinant forms of the virus, such as XE, arising by genetic material swapping between subvariants.

More recently, XBB and BQ.1 have been in the news.

No wonder it’s hard to keep up.

The World Health Organization (WHO) has had to rethink how it describes all these subvariants, now labelling ones we need to be monitoring more closely.

What’s the big deal with all these subvariants?
Omicron and its subvariants are still causing the vast majority of COVID cases globally, including in Australia.

Omicron subvariants have their own specific mutations that might make them more transmissible, cause more severe disease, or evade our immune response.

Omicron and its subvariants have pushed aside previous variants of concern, the ones that led to waves of Alpha and Delta earlier in the pandemic.

Now, in Australia, the main Omicron subvariants circulating are BA.2.75, and certain versions of BA.5. More on these later.

We still don’t fully understand the driving forces behind the emergence and spread of certain SARS-CoV-2 subvariants.

We can, however, assume the virus will keep evolving, and new variants (and subvariants) will continue to emerge and spread in this wave-like pattern.
How do we keep track of this all?
To monitor these subvariants, the WHO has defined a new category, known as “Omicron subvariants under monitoring”.

These are ones that have specific combinations of mutations known to confer some type of advantage, such as being more transmissible than others currently circulating.

Researchers and health authorities keep track of circulating subvariants by sequencing the genetic material from viral samples (for instance, from PCR testing or from wastewater sampling). They then upload the results to global databases (such as GISAID) or national ones (such as AusTrakka).

These are the Omicron subvariants authorities are keeping a closer eye on for any increased risk to public health.

Newer versions of BA.5
The BA.5 subvariant that arose in early February 2022 is still accumulating more mutations.
The WHO is monitoring BA.5 versions that carry at least one of five additional mutations (known as S:R346X, S:K444X, S:V445X, S:N450D and S:N460X) in the spike gene.

The spike gene codes for the part of the virus that recognises and fuses with human cells. We are particularly concerned about mutations in this gene as they might increase the virus’ ability to bind with human cells.

Throughout recent months, BA.5 has been the dominant subvariant in Australia. However, BA.2.75 has now established a foothold.

BA.2.75 or Centaurus
The BA.2.75 subvariant, sometimes called Centaurus, was first documented in December 2021. It possibly emerged in India, but has been detected around the globe.

This includes in Australia, where more than 400 sequences have been uploaded to the GISAID database since June 2022.

This subvariant has up to 12 mutations in its spike gene. It seems to spread more effectively than BA.5. This is probably due to being better able to infect our cells, and avoiding the immune response driven by previous infection with other variants.

BJ.1
This was first detected in early September 2022 and has a set of 14 spike gene mutations.

It has mostly been detected in India or in infections coming from this area.

We know very little about the impact of its mutations and at the time of writing, there was only one Australian sequence reported.

BA.4.6 or Aeterna
BA.4.6, sometimes called Aeterna, was detected in January 2022 and has been spreading rapidly in the United States and the United Kingdom.

There have been more than 800 sequences uploaded to the GISAID database in Australia since May 2022.

It may be more easily transmitted from one person to the next due to its spike gene mutations.
Early data suggests it is better able to resist cocktails of therapeutic antibodies compared with BA.5. This makes antibody therapies, such as Evusheld, less effective against it.

BA.2.3.20
This was first detected in the US in August 2022. It has a set of nine mutations in the spike gene, including a rare double mutation (A484R).

Like BA.2.75, this subvariant is probably better able to infect our cells and avoid the immune response driven by previous infection.

There are more than 100 Australian genomic sequences reported in the GISAID database, all from August 2022.

XBB
This recombinant version of the virus was detected in August 2022. It is a result of the swapping of genetic material between BA.2.10.1 and BA.2.75. It has 14 extra mutations in its spike gene compared with BA.2.

Although there have only been 50 Australian genomic sequences reported in GISAID since September, we anticipate cases will rise. Lab studies indicate therapeutic antibodies don’t work so well against it, with XBB showing strong resistance.

Although XBB appears to be able to spread faster than BA.5, there’s no evidence so far it causes more severe disease.
How about BQ.1?
Although it is not on the WHO list of subvariants under monitoring, cases of the BQ.1 subvariant are rising in Australia. BQ.1 contains mutations that help the virus evade existing immunity. This means infection with other subvariants, including BA.5, may not protect you against BQ.1.

In the meantime, your best protection against severe COVID, whichever subvariant is circulating, is to make sure your booster shots are up-to-date. Other ways to prevent SARS-CoV-2 infection include wearing a fitted mask, avoiding crowded spaces with poor ventilation, and washing your hands regularly.

China is caught in a zero-Covid trap of its own making [CNN, 2 Nov 2022]

by Nectar Gan

Hong KongCNN —

It’s been little more than a week since Chinese leader Xi Jinping began his norm-breaking third term in power with a ringing endorsement of his relentless zero-Covid policy.

But the commitment to stick with it is already fueling scenes of chaos and misery across the country.

In the northwestern city of Xining, residents spent last week pleading desperately for food as they suffered through the late

It’s been little more than a week since Chinese leader Xi Jinping began his norm-breaking third term in power with a ringing endorsement of his relentless zero-Covid policy.

But the commitment to stick with it is already fueling scenes of chaos and misery across the country.

In the northwestern city of Xining, residents spent last week pleading desperately for food as they suffered through the latest of the country’s stringent lockdowns; to the west, in Lhasa, the regional capital of Tibet, angry crowds have been protesting in the streets after more than 70 days of stay-home orders.

In the central province of Henan, migrant workers have abandoned a locked-down Foxconn factory en masse, walking for miles to escape an outbreak at China’s largest iPhone assembling site. And, in the eastern financial hub of Shanghai, things are gloomy even at Disneyland – the park abruptly shut its gates on Monday to comply with Covid prevention measures, trapping visitors inside for compulsory testing.

In many other parts of the country, lockdowns, mandatory quarantines, incessant mass testing edicts and travel restrictions continue to cripple businesses and daily life, even as the rest of the world moves on from the pandemic.

Renewed zeal
Rather than relax Covid restrictions – as some had hoped for in the lead-up to the Communist Party’s five-yearly leadership reshuffle, Chinese authorities have ramped them up after Xi’ssweeping endorsement of the strategy.

“The 20th Party Congress didn’t provide a timetable for moving away from zero-Covid. Instead it highlighted the importance of sticking to the existing approach,” said Yanzhong Huang, a senior fellow for global health at the Council on Foreign Relations in New York.

Workers flee China's biggest iPhone factory over Covid outbreak
The congress reinforced Xi as an unrivaled supreme leader, and saw him stack the Communist Party’s top ranks with staunch allies – including those who had loyally carried out his Covid policies.

“The new political ecology also provided more incentive for local governments to impose more draconian Covid control measures,” Huang said.

A renewed zeal for the policy can be seen most clearly in smaller cities. While metropolises like Beijing and Shanghai can draw on their experiences of major flareups to implement more targeted lockdown measures, smaller cities with no such know-how tend to pursue zero-Covid goals in a more aggressive and extensive manner, Huang said.

‘It’s simply not working’
The repeating cycle of lockdowns, quarantines and mass testing is taking a heavy toll on the economy and society. Public patience is wearing thin, and frustrations are building.

On Monday in Baoding city, Hebei province, a father wielding a knife drove through a Covid checkpoint in a desperate bid to buy milk powder for his son. Video footage of the scene and his subsequent arrest sparked uproar online; the following day local police tried to soothe tempers by saying the man had been fined only 100 yuan ($13.75) and that his child’s “milk powder problem” had been “properly resolved.”

On Tuesday, the death of a 3-year-old in Lanzhou, Gansu province, sparked another outcry, after the child’s family said lockdown measures had delayed emergency responders. Police said later the child had stopped breathing by the time officers arrived, but did not address the family’s accusations that an ambulance had been delayed. CNN has reached out to Lanzhou authorities for comment.

In another sign of how sensitive the issue has become, Chinese stocks rallied on Wednesday following unverified social media rumors that China was forming a committee to prepare an exit from the zero-Covid policy.

Those rumors were quashed, however, when the Foreign Ministry said it was “unaware” of any such plan.

Chinese artist speaks out against zero-Covid policy by wearing 27 hazmat suits in Times Square

Meanwhile, experts say they see no signs of the Chinese government taking steps that would suggest it is rethinking its approach.

Chinese health officials maintain that changing tack now would risk a huge surge in infections and deaths that could overwhelm the country’s fragile health care system.

Beijing has so far refused to approve for use the mRNA vaccines developed in Western countries, which have been shown to be more potent than those made and used in China.

Experts say China also lacks an emergency response plan to cope with surging infections.

But Jin Dongyan, a virologist at the University of Hong Kong, said such catastrophic scenarios could be avoided with proper preparation.

Instead of spending vast amounts of time and resources on testing, contact tracing, quarantining and imposing lockdowns, authorities should introduce more effective vaccines and antiviral therapies and boost the vaccination rate among the elderly, Jin said.

With boosted immunity, asymptomatic or mild cases could be allowed to recover at home – freeing up space at hospitals to treat more severe cases, he said.

“Using lockdown and containment measures to deal with an infectious disease with such a low mortality rate and high transmissibility is no longer appropriate. The whole world has abandoned this approach – nobody can stand the cost, it’s simply not working,” he said.

Fear of the virus
Another hurdle to pivoting from zero-Covid is a pervasive fear of the virus among large swaths of the public, instilled by the Chinese government to justify its harsh control measures, experts say.

“Authorities have demonized Covid, exaggerating its severity and mortality rate and talking up long-Covid symptoms. Many ordinary people are still very afraid of the virus, with recovered Covid patients suffering from severe discrimination and stigmatization,” Jin said.

It was partly such fears that drove thousands of migrant workers to flee in panic from the Foxconn factory in Zhengzhou, he said.

Under Xi Jinping, zero-Covid is accelerating China's surveillance state

Videos of people traveling on foot, dragging their luggage on roads and across fields, went viral on Chinese social media over the weekend. Zhengzhou, a city of 12 million, imposed sweeping lockdown measures last month after identifying dozens of Covid-19 cases.

The Foxconn facility has been racing to control an outbreak since mid-October, though the company has not disclosed the number of infections among its workers. On Wednesday, the Zhengzhou Airport Economy Zone, where the Foxconn plant is located, announced new lockdown measures.

As the Foxconn exodus thrust the Zhengzhou outbreak into the spotlight, the city’s health authorities have tried to allay public fears. On Monday, the Zhengzhou municipal health commission published a WeChat article with the headline: “Covid is not that horrible, but preventable and treatable.”

Huang, the expert at the Council on Foreign Relations, said misconceptions about the virus would complicate matters if China did at some point decide to move away from zero Covid.
“Even if in the future, China wants to change the narrative and play down the seriousness of the disease, some people might not buy into the new narrative,” he said.

As the winter approaches, experts warn that China could be hit by a new wave of infections – and a new cycle of draconian lockdowns.

China reported 2,755 local infections for Tuesday, the highest daily tally since August.

“Judging from the situation in China, there will be a major outbreak sooner or later. China has deployed tremendous efforts and paid a heavy cost to prevent that from happening, but in the end, it won’t be able to stop such a highly infectious disease from spreading,” Jin said.

New Coronavirus News from 1 Nov 2022

Supreme Court Allows TSA To Issue Mask Mandates [Forbes, 1 Nov 2022]

On Monday the Supreme Court left in place a ruling that allows the Transportation Security Administration (TSA) to issue mask mandates on planes, trains and other forms of transport, as it had for more than a year during the peak of the Covid-19 pandemic.

The Supreme Court denied a California attorney’s request to overturn a U.S. Court of Appeals ruling in the D.C. Circuit from December, which found no merit in his claim and affirmed that the TSA does have the authority to maintain security and safety within the transportation system, including imposing the masking requirement.

California attorney Jonathan Corbett had claimed that the TSA did not have the authority to mandate masks on airlines and other types of transportation during the Covid-19 pandemic. The Court of Appeals had disagreed, ruling that the agency “plainly has the authority” to address transportation safety and security.

“Because we find no merit in Corbett’s claim, we deny the petition for review,” the Court wrote. “The Covid-19 global pandemic poses one of the greatest threats to the operational viability of the transportation system and the lives of those on it seen in decades.”

The TSA stopped enforcing the mask mandate in April, hours after a federal judge struck down the federal mask mandate for public transportation, which had been due to expire weeks later.
The mask mandate had been a bone of contention between the government and airlines. In March of this year, the chief executives of the seven U.S. airlines — Alaska, American, Delta, Hawaiian, JetBlue, United and Southwest — asked President Biden to end the mask mandate and drop the pre-departure testing requirement for international travelers coming to the U.S.

The U.S. tourism industry had long claimed that frictions like mask mandates and testing were bad for their business. “The current decision to halt enforcement of the federal mask mandate effectively returns the choice of mask usage on planes and other forms of public transportation to travelers and travel industry workers, a further step toward endemic management of Covid,” said Tori Emerson Barnes, executive vice president of public affairs and policy at the U.S. Travel Association, when the mandate was scrapped. “We also continue to urge the administration to immediately end pre-departure testing for vaccinated inbound international passengers, which discourages travel and provides limited public health benefits.”

Since the mandate was dropped, some travelers have chosen to keep their masks on. In April, when the mandate was dropped, six out of 10 Americans (60%) supported extending the mask mandate, according to The Harris Poll Covid-19 tracking survey. The next month, a survey by the Pew Research Center found a similar pre-mask majority.

The Centers for Disease Control and Prevention continues to recommend that people wear masks in indoor public transportation settings such as airports.

New Omicron Variants Are Here—What We Know So Far [Scientific American, 1 Nov 2022]

By Shannon Hall

The variants appear to sneak past the immune system, but vaccines will likely continue to hold strong

The Omicron family of SARS-CoV-2, the virus that causes COVID, has some new menacing members. At the end of the week ending October 29, data from the U.S. Centers for Disease Control and Prevention showed that two variants—BQ.1 and BQ.1.1—account for nearly 17 percent of viral samples genetically sequenced in the country. That was a huge increase over a month earlier when the variants were practically invisible in the data and suggests they will soon outcompete BA.5 and BA.4.6, the dominant strains in the United States. Meanwhile, a variant called XBB has been causing a substantial infection wave in Southeast Asia.

The three new variants are likely spreading so quickly because they sneak past some of the immune defenses acquired through previous infections and vaccinations. They also threaten to render monoclonal antibody treatments ineffective. These features warrant attention—especially as the country heads into the fall and winter—but not panic. Scientists suspect that the COVID vaccines will continue to protect against hospitalization and death. And Paxlovid, an oral antiviral pill, is also expected to remain effective. The mixed news means that the variants “have the ability to create a wave, but it’s not going to be a tsunami,” says Katelyn Jetelina, an epidemiologist at UTHealth and publisher of the “Your Local Epidemiologist” newsletter.

Omicron first emerged near the end of last year. The initial version known as BA.1 (previously known as B.1.1.539) overtook the Delta variant and caused more than 800,000 U.S. cases per day during its January peak. But BA.1 was just the first in a long line of Omicron subvariants. BA.2 took over from BA.1 and caused a surge in the spring. BA.5 edged out BA.2 and caused a surge in the summer. And now it looks like BQ.1, BQ.1.1, XBB—or some combination—will cause a surge this fall and winter. For the record: BQ.1.1 is the same as BQ.1 but with an additional mutation. So many scientists think the race will occur between BQ.1 or BQ.1.1 and XBB. But just how that race plays out—and whether it will cause a surge—depends on three essential metrics: how quickly these variants spread; if they cause more severe disease; and if they can circumvent our immune protection or evade immune-focused treatments.

There is no question these variants are increasing at a rapid rate. BQ.1.1, for example, currently accounts for 7,000 cases per day and appears to be doubling every nine days, says Trevor Bedford, a virologist at the Fred Hutchinson Cancer Center who models COVID evolution. It is outpacing BA.5—the current leading variant in the U.S. That’s because every person sick with BQ.1.1 is infecting an average of 1.4 other people, while those sick with BA.5 are averaging an infection of less than one other person. This so-called reproduction number can be telling. When BA.1 first arose, for example, it had a whopping reproduction number of 3. And when BA.5 first arose, it had a reproduction number of 1.6—roughly akin to that for BQ.1.1 and XBB. Barring the appearance of a totally new variant, the U.S. will likely see a wave similar to BA.5’s surge earlier this summer, but nothing on the scale of the Omicron surge last winter, Bedford says. And while it is too soon to tell whether BQ.1.1 or XBB will drive a larger fraction of infections, he predicts two likely scenarios: either BQ.1.1 hits first and suppresses the circulation of XBB (which has already been detected in the U.S. but is not yet widely circulating), or they cause two simultaneous waves. Depending on what comes into play, Bedford predicts the U.S. will see 100,000 to 200,000 COVID cases per day—much higher than today’s average of fewer than 40,000 cases per day.

But how the number of cases will translate to hospitalizations and deaths is a big question. BQ.1, BQ.1.1 and XBB all carry mutations in the spike protein—the studs on the pathogen’s surface that it uses to recognize and infect cells. These mutations make it harder for the immune system to recognize the virus and kick into action early. Indeed, a few preliminarystudies (neither of which have been peer-reviewed) have shown that antibodies from vaccination and earlier infections are less able to block infection from these new variants in a lab dish. That sounds scary, but our immune response includes additional levels of defense beyond antibodies, such as T cells and B cells. “These laboratory tests give us a really powerful and important data point—but they don't tell the whole story,” says Justin Lessler, an epidemiologist at the University of North Carolina Gillings School of Global Public Health. So while the likelihood of reinfections will increase with the new subvariants, it will not necessarily drive more severe disease.

To answer that question, scientists marry lab data with real-world data. Hospitalizations appear to be increasing in Germany, but scientists cannot say if that is a result of BQ.1.1 or behavioral changes since Oktoberfest just occurred. The same is true in New York, which has the highest proportion of BQ.1.1 and an uptick in hospitalizations. But again, that could be driven by behavioral changes as the weather cools and children are back in school. And scientists are hopeful that the vaccines will continue to work well against the new variants. The reason scientists chose a bivalent booster, which targets both the original strain and the currently circulating strains BA.4 and BA.5, is that it would provide a broader immune response to current and future variants. “The whole theory behind the bivalent booster is to protect against exactly this situation here, which is the rapid evolution of SARS-Cov-2,” says Sam Scarpino, a viral surveillance expert at the Rockefeller Foundation’s Pandemic Prevention Initiative.

Another tool used to combat infection is a greater cause for concern. These new variants threaten to disarm monoclonal antibody treatments, such as Evusheld, which have played an important role in protecting immunocompromised people and others at high risk of serious disease. But they work by targeting a specific shape on the virus and that shape has simply mutated. “Unfortunately, that means a lot of our tools to protect the most vulnerable in our population continue to be stripped away,” Jetelina says. Luckily, Paxlovid—which has proved effective at preventing serious cases of the disease, particularly in older populations—does not target a specific shape on the virus, and should continue to work well, Jetelina says.

All of this means that the new variants will likely exacerbate the expected fall and winter surge. That’s particularly worrisome when pediatric hospitals are overflowing with respiratory syncytial virus (RSV), influenza is ticking up and there are very few mitigation measures in place. And while the booster vaccine is expected to still do a good job of keeping people safe from severe infection, hospitalization and death, enthusiasm for it is low. As of late October, only about 20 million people in the U.S. had received the updated bivalent shot—roughly 8 percent of the eligible population. “The time for people to take action both for flu vaccines and for the bivalent booster is now,” Scarpino says. “I wouldn't wait.”

Scientists are also recommending dusting off those N95 or other high-quality masks, opening the windows at large gatherings and taking advantage of rapid tests—especially if you are going to see someone who is at high risk of severe disease. “I think everyone really needs to be laser focused this winter on protecting the vulnerable,” Jetelina says. If we can do that, she says, it will save lives and immensely reduce the pressure on our fragile health care system.