New Coronavirus News from 11 Apr 2022

The latest Covid-19 subvariant: XE [The Daily Briefing, 11 Apr 2022]

A new coronavirus subvariant, called XE, contains a combination of the omicron variant BA.1 and the BA.2 subvariant, known as "stealth" omicron. And while it has infected around 600 people in the United Kingdom, experts say "there's still a lot we don't know about XE."

What we got right (and wrong) in our Covid-19 predictions

What is XE?

The XE subvariant contains a combination of the omicron variant BA.1, which first surfaced in late 2021, and the BA.2 subvariant, known as "stealth" omicron—currently the dominant variant around the world.

XE is a "recombinant" virus—a type of variant that can occur when an individual has a coinfection of two or more variants at the same time, mixing the variants' genetic features within a patient's body. Notably, XE is the fifth recombinant virus that has stemmed from omicron, USA Today reports.

Although data on XE's severity and ability to evade immunity is not yet clear, early estimates suggest it could be more contagious than earlier strains, CNBC reports.

According to data from the UK Health Security Agency (UKHSA), XE has a growth rate that is 9.8% higher than BA.2—a figure the World Health Organization estimates to be 10%.

"This particular recombinant, XE, has shown a variable growth rate and we cannot yet confirm whether it has a true growth advantage. So far there is not enough evidence to draw conclusions about transmissibility, severity or vaccine effectiveness," said UKHSA chief medical advisor Susan Hopkins.

Where has XE been detected?

In the U.K., the earliest confirmed case of XE has a specimen date of Jan. 19, which means it could have been circulating in the population for several months, CNBC reports. In total, UKHSA has confirmed 637 cases of XE. It has since also been identified in Thailand.

The U.K. is currently facing a Covid-19 surge, largely driven by the BA.2 subvariant, and the XE variant currently accounts for less than 1% of total cases that have gone through genomic sequencing in the UK.

Are experts worried about XE?

Jeremy Luban, an infectious disease specialist at the University of Massachusetts Medical School, said he is monitoring XE but is not concerned yet.

"XE has a powerful combination of all these variants of coronavirus. Should it spread rapidly through the U.S. at some point, we would be concerned," Luban said.

Separately, William Schaffner, an infectious disease specialist at the Vanderbilt University School of Medicine, said there is no reason to panic.

"There's still a lot we don't know about XE," Schaffner said. "XE could surprise us, so we have to wait to see how severe it will be."

Notably, Schaffner said he is more concerned about BA.2, which currently accounts for 72% of Covid-19 cases in the United States and remains the dominant variant around the world.

On Tuesday, CDC Director Rochelle Walensky noted that even though BA.2 has sparked several outbreaks around the world, it has not caused a significant increase in cases in the United States. In fact, Walensky said cases dropped 4% from the previous week, and hospitalizations and deaths both declined by over 16%.

According to Schaffner, variants will continue to pose a risk to the world's "return to normalcy" because of their unpredictability. "This is our new reality, variants popping up everywhere because fortunately, we are detecting them," he said. "The more we can find, the more we can study and contain."

New Coronavirus News from 12 Apr 2022

Peter Hotez: What omicron XE COVID variant means for summer 2022 [Houston Chronicle, 12 Apr 2022]

by Andrew Dansby

Dr. Peter Hotez is celebrating a few milestones: Corbevax, a COVID-19 vaccine developed by a team he and Dr. Maria Elena Bottazzi led, has reached 20 million children in India. Indonesia and Botswana also approved the protein-based vaccine last week.

Hotez —dean of the National School of Tropical Medicine at Baylor College of Medicine and co-director of the Center for Vaccine Development at Texas Children’s Hospital — made the announcements in his typically understated way, via Twitter.

The Houston-based Hotez continues to track the pandemic near and far, charting infection rates in the U.S. as well as Texas, while reminding people that global vaccination is crucial to stopping the variants that have marched through the States.

Hotez took time to field questions about Corbevax, the BA.2 variant and what two years of COVID-19 may mean for summer 2022.

Q: I feel like we always start with Texas. But for a change of pace, could you talk about how the Corbevax rollout is going in India?

A: Corbevax is going to have multifacted uses. It can be used both as a pediatric vaccine, an adult vaccine and also as a booster vaccine for both populations. That’s the way I break it down. But we’ve worked with Biological E in India and got emergency authorization last year.
The first population it is going into as of March was kids 12 to 14. And so far the Ministry of Health estimates about 20 million kids in India age 12 to 14 across the country have gotten their first dose of Corbevax. So that’s exciting.

There are other things happening. As those numbers start to climb, there are clinical studies confirming safety and efficacy in five to 11 year olds that are rolling out. So we hope that happens in the next few weeks as well. So we should see kids in India from 5 to 14 vaccinated.

You might ask why it’s not going to adults there. The reason is because so many adults in India have gotten the AstraZeneca or the Chinese inactivated virus vaccines. Those have been used for adults, and our vaccine could be used as a booster to improve protection because the effectiveness of those vaccines against the variants has not been very strong. … All of this has relevance globally. It should feed into other global approvals. In the meantime the government in Botswana approved Corbevax as a vialed vaccine or in bulk. They’re looking at 100 million doses. You might ask why a country with 2 million people, which is what Botswana is, needs that many doses. That’s because they want to be purveyors and providers of the COVID vaccine for that part of the continent. Not only Botswana, but also Namibia, Zambia, Zimbabwe, the list goes on.

Q: You’ve long maintained Asia and Africa need the vaccines to halt variants that keep reaching here. How do you feel about future variants with these rollouts?

A: I think when I look at the new variants that are a threat to the United States, I break them into two components. Component 1 are brand new variants totally unrelated to things we’ve seen before. We have a track record of this with alpha and then delta and then omicron. I still worry about more of those emerging in lower- and middle-class countries. We may see something like that this summer in Texas and Southern states. We saw big epidemics in the summer in Texas in 2020 and 2021 into the fall. So I worry about that.

The other side of this is the fact that BA.2 arose out of the same town where omicron arose.
So I’m concerned we may see down the road some spinoffs of BA.2. And BA.2 has been partially successful infecting some individuals with omicron previously. So we may see new fronts. But the first is brand new variants unrelated to previous ones. The others are those that might step out of the initial omicron wave: from omicron to BA.2 to BA.X or some type of combination. My colleague Trevor Bedford at the University of Washington does modeling on this front. And he wrote about sub-subvariants of BA.2 that we may have to think about as well.

Q: That said, mask mandates are going away, events are taking place again. If you look at those maps of the U.S., the states in crimson are gone. How do you feel about that going forward with BA.2?

A: So a few things about BA.2: BA.2 is not necessarily behaving in the same way the other variants of concern did. We saw the alpha variant and the delta variant go up as a percentage of total virus isolates in the U.K. followed immediately by a wave. Then the wave subsequently hit the U.S. BA.2 in western European countries, it’s not as straightforward. In some countries BA.2 is becoming a dominant variant and cases are up. In others it’s not dominant and cases are not going up. Or cases are going up, but it’s not BA.2. It’s a messier picture. But there’s no question BA.2 — if you look at wastewater or virus isolates — there’s no question it’s becoming the dominant variant in the U.S. How much that could translate into another big wave is the big unknown. It does look now like it’s translating into case numbers going up in New York state and New York City; Washington, D.C. Nancy Pelosi just got infected. Whether that’s a consequence of BA.2 going up or becoming a full-blown wave, we don’t know. Maybe it’s more a bump that goes up and then down. That’s unknown. How it could reach different part of the country is unknown. For example the alpha variant, we saw it hang up there in Michigan for a while. And it had less impact in other places. We could see something along those lines.

Q: School is winding down and travel and camps are about to start back up. What do you think about summer? Two years ago we heard the suggestion that summer would kill this thing. And here we are.

A: The thinking was that upper respiratory coronaviruses pre-pandemic showed winter spikes, but they weren’t big players in the summer. But summer 2020 was a rude wake-up call for Texans, who were devastated. The vaccine wasn’t out yet. So it was devastating for Hispanic populations, essential workers and some low-income communities that got hit hard. Essential workers didn’t have the option of staying home and doing things through Zoom. But in multi-generational households, a 22-year-old construction worker could come home and infect parents and grandparents. The following summer was a different scenario altogether. In 2021, Texas had another huge wave, but it was different after the vaccine became widely available.
Those going into hospitals and ICUs were largely those defying the vaccine. The demographics were quite different, with a lot of groups in Texas being hesitant and defying the vaccine because of political allegiance, as self-defeating as that was.

Q: I’ve had several parents and parents-to-be asking about the vaccine for kids 5 and under.
Do you think that’ll be here soon? And what do you expect it do do?

A: Well, I think even for a pediatric vaccine, what we saw with both Pfizer and Moderna was that the dose of the vaccine was greatly reduced, the dose of the mRNA component. As a consequence, the immune responses were not as strong. We may have underdosed a bit too much. Whether it meets the immunological criteria to say the immune response is adequate to release them for emergency use is the big question. So they may wait for a third dose before they go and greenlight it. I think that’s what we’re waiting for.

Q: This is anecdotal based on friends, family and colleagues, but I feel like I’m hearing about more breakthrough cases among those who have received three doses. Am I reading too much into this?

A: Well a few things: We thought once you got that third immunization — based on what the data from alpha and delta looked like — once you got that booster, that third dose, we thought you were done. You had a big bump in virus-neutralizing antibodies, and it looked like the protection was holding up well. It wasn’t one-and-done or two-and-done. But we thought three, you’re done. We’ve had this conversation.

But clearly with omicron and BA.2, something else is happening. That protection is neither as durable nor as strong as we’d thought. Against the third dose vs. omicron, four months after you got it, protection against hospitalization went down to 78 percent. And protection against ER visits went to 66 percent. Still pretty good, but not as good as it was. Even against infection, you were still 3.6 times less likely to get omicron if you were fully vaccinated and boosted compared to an unvaccinated individual. So there were more breakthrough infections, but not as many and certainly with less severity. But those declines were sufficient to make people concerned about maybe needing a second booster, a fourth immunization. I’m a big proponent of that. I think it will help a lot — data from Israel suggests that.

The big unknown now with omicron and BA.2 is the durability of protection not holding up as well. That means what? They started those conversations at the FDA advisory committee meetings yesterday, but I was a bit disappointed that they didn’t come up with much in the way of conclusions. I think the situation is this: the mRNA vaccine … every vaccine has its strengths and weaknesses, including ours, and including the mRNA vaccines. It may be with mRNA vaccines, until we fix the technology, that the durability won’t be as strong as we’d like.
Therefore, what’s the plan? Let’s say for now, we try to convince a lot of American people to get a second booster. I got my second booster. Four or five months from now, will we need a fifth booster? Or do we try to think outside the box and bring in another vaccine technology that might give you longer lasting and more enduring protection?

Q: What might that look like?

A: I think it could be a protein-based vaccine like ours. The problem is that we’re not seeing that higher-ordered thinking coming from the federal government right now. In public statements, we’re not seeing any movement toward trying to convene experts to say, “Hey, maybe giving mRNA vaccines in perpetuity may not be the best strategy. Maybe it’s the only choice, but we’re not seeing that discussion yet. That’s the next big thing I’m looking for: convening experts, which isn’t something that’s happening in the FDA advisory meetings to inform us what else we need to do assuming this pandemic continues.

Q: I feel like each time we talk, we’d have better information if we waited two weeks. But I guess that’s the nature of this.

A: And the answer is we do, actually. But it’s still not complete. The omicron variant and BA.2 are disappointing. We thought we had this thing figured out with a third dose lasting, giving five- or six-year protection; we thought that would buy us more time to think about this. Now now we’re already thinking about what happens this fall. Do you ask the American people to get a fifth dose? Do you ask immunocompromised people to get a fifth dose? Will they accept that? If you look at the numbers, fewer than half of Americans eligible for the first booster got it. For a second booster, there’ll probably be further drop off. You’re going start seeing people getting more fed up.

Q: Have you observed that sort of fatigue elsewhere in the world?

A: Israel seems to have buy-in. But again, one problem is that a country doesn’t speak with one voice. There’s one part of our country that is very much in tune with what the CDC says. And there’s a part of the country that completely tuned out and wants no part of it — people who won’t get a booster or who aren’t even vaccinated at all. This is part of the problem I see coming from the White House. And that’s a challenge for the new coordinator, Ashish Jha, will have. Because trying to speak to the whole country with one voice is really problematic. It has been in the past. It comes out as babytalk. If you try to reach all parts of the country with one message, you wind up serving nobody.

Q: What are your thoughts on the “XE” variant?

A: By XE, I think you mean the sort of hybrid. I think we’re going to see recombination hybrid variants coming along. That’s what I mean when I talk about the next generation BA.2. I call it BA.X. Which … then the question is going to be do we finally get around to making an omicron booster? I don’t know the answer to that. There’s some evidence that there are these recombinant variants like XE, so should we make an omicron-specific booster?

On the other hand, there was an important paper in the medical journal “Cell” that suggested if you’re getting vaccinated and boosted with a vaccine connected to the original lineage, you may not respond robustly to a booster made up of the variant. There’s a phenomenon in our field called “original antigenic sin,” which means whatever you started with, that’s basically driven the immune system in one direction. And it’s hard to bring it back to a new variant through boosting. There’s both data for and against that. And that could be a bigger problem. In the past I’ve said — even in the recent past — there’s no point in making an omicron-specific booster. But if we continue to see bumps if not waves of omicron — things like BA.2 and XE — there may be logic to that.

New omicron XE Covid variant first detected in the UK spreads to Japan as cases rise [CNBC, 12 Apr 2022]

by Karen Gilchrist

Japan has reported its first case of omicron XE — a new Covid-19 strain first detected in the U.K. — just as British cases of the subvariant rise.

The XE variant was found in a woman in her 30s who arrived at Narita International Airport from the U.S. on March 26. The woman, whose nationality was not immediately disclosed, was asymptomatic, Japan’s health ministry said Monday.

It comes as cases of the new strain have almost doubled in Britain, according to the latest statistics from the U.K. Health Security Agency.

As of April 5, 1,125 cases of XE had been identified in the U.K., up from 637 on March 25. The earliest confirmed case has a specimen date of Jan. 19 of this year, suggesting it could have been in circulation in the population for several months.

XE has since been detected in Thailand, India and Israel. It is suspected that the latter Israeli cases may have developed independently. The U.S. has not yet reported any XE cases.

What is omicron XE?
XE is what’s known as a “recombinant,” a type of variant that can occur when an individual becomes infected with two or more variants at the same time, resulting in a mixing of their genetic material within a patient’s body.

In the case of XE, it contains a mix of the previously highly infectious omicron BA.1 strain, which emerged in late 2021, and the newer “stealth” BA.2 variant, currently the U.K.’s dominant variant.

Such recombinants are not uncommon, having occurred several times during the course of the coronavirus pandemic. However, health experts say it is too soon to draw conclusions on the new subvariant’s severity or ability to evade vaccines.

“We continue to monitor cases of the recombinant XE variant in the U.K., which currently represents a very small proportion of cases,” Meera Chand, director of clinical and emerging infections at UKHSA, said in a statement.

On Sunday, the U.K. reported 41,469 new Covid cases, with a seven-day average of 59,578 cases. As such, XE likely accounts for only a small percentage of total Covid cases currently.

How worried should we be?
Early estimates suggest XE may be more transmissible than earlier strains, having so far demonstrated a slightly higher growth rate than its predecessor.

UKHSA data shows XE has a growth rate of 9.8% above that of BA.2, while the World Health Organization has so far put that figure at 10%.

However, experts say they expect it to wane in severity even as it spreads more easily. XE has so far not been declared a variant of concern.

“XE seems to be moving in the same direction as BA.2, having an increased transmissibility to BA.1 but being less severe,” Jennifer Horney, professor of epidemiology at the University of Delaware, told CNBC.

“It is the devil we know, so to speak. [It is] essentially a reshuffling of the same deck of cards,” added Mark Cameron, associate professor in the School of Medicine at Case Western Reserve University.

XE contains spike and structural proteins from the same virus family, i.e. omicron, meaning that it should, theoretically at least, behave as omicron has done before. Existing vaccines and immunity should, therefore, provide some level of protection against infection.

“Recombinants that contain the spike and structural proteins from a single virus (like XE or XF) are fairly likely to act similarly to [their] parental virus,” Tom Peacock, virologist at Imperial College London’s Department of Infectious Disease, wrote in a thread of tweets in mid-March.
XF refers to another recombinant previously detected in the U.K. in February.

However, other recombinants containing spike and structural proteins from different virus families continue to emerge. That includes the XD subvariant, recently discovered in Germany, the Netherlands and Denmark, which contains delta structural proteins and omicron spike proteins and which Peacock described as “a little more concerning.”

As such, all new emergences need to be closely monitored, especially in their early phases, to ensure they don’t evolve into something more serious.

“The virus is still capable of evolving, recombining and developing a new branch of its family tree,” Cameron said.

“The key takeaway is that for each of these variants and subvariants, risk of hospitalization and death appears to be, on average, lower where vaccination rates are higher, indicating that vaccination, including a third dose, should be effective in reducing risk for severe disease,” added Stephanie Silvera, professor of public health at Montclair State University.

Shanghai tweaks lockdown rules amid COVID-19 surge [Al Jazeera English, 12 Apr 2022]

City will be divided into three tiers depending on recent cases amid rising anger over food shortages and lack of necessities.

Shanghai has eased a punishing citywide lockdown that it imposed to break a surge in cases that is the biggest test of China’s two-year strategy to stamp out the disease wherever it appears.

Authorities in Shanghai introduced the three-tier disease control system on Monday, allowing residents in areas where no cases have been reported for 14 days to leave their homes so long as they follow health protocols and remain in their sub-district.

Those living in areas where no cases have been confirmed for seven days are allowed to collect food deliveries or take a walk at a designated time and location.

City health official Wu Qianyu emphasised the need for continued controls at a press briefing.

“After a long period of lockdown, it is understandable that people want to go out and get some air, and they need to go shopping for food and medicine and go for medical treatment,” she said. “But if lots of people gather in a disorderly way, it will cause hidden dangers to our epidemic prevention work.”

Of the city’s 17,600 communities, however, some 7,624 remain in the strictest lockdown designation and people there are required to stay at home.

Gu Honghui, deputy secretary-general of the Shanghai municipal government, said the zoning would be updated regularly based on the situation in each community.

“Our principle, as always, is to strive to minimise the impact of the epidemic on residents’ daily lives,” Gu told the daily briefing on the city’s epidemic control situation.

The Shanghai outbreak is the most severe since the initial surge in cases in Wuhan that triggered the global pandemic, and is proving to be a considerable test of China’s ‘zero COVID’ strategy, which relies on mass testing, quarantine and draconian lockdowns to stamp out the virus.

Anger over restrictions
But the Shanghai lockdown, which was initially supposed to be just a few days long, has fuelled anger among residents who have complained about food shortages and a lack of basic necessities.

On Tuesday, the United States said it had ordered all non-essential consulate staff to leave the city, citing the COVID response. The US earlier advised its consulate staff to leave and also urged Americans to reconsider travel to China due to “arbitrary enforcement” of local laws and COVID-19 restrictions, particularly in Hong Kong, Jilin province and Shanghai in an announcement that drew anger from Beijing.

China was “strongly dissatisfied with and firmly opposed to the US side’s groundless accusation against China’s epidemic response,” Foreign Ministry Spokesperson Zhao Lijian said on Sunday.

Guangzhou, a sprawling metropolis of 18 million people on China’s southern coast, is also battling an outbreak of the disease and is conducting a mass testing campaign.

Residents have been advised not to travel unless absolutely necessary and the city has been closed to arrivals from outside.

Guangzhou’s health commission said it had found 27 new confirmed local cases and 11 asymptomatic cases as of Monday evening. A total of 61 infections have been reported in the current outbreak since Friday.

China is still mainly closed to international travel, even as most of the world has sought ways to live with the virus.

Mainland China reported a total of 24,659 confirmed cases on April 11, most of them people without symptoms, the national health authority said on Tuesday. More than 23,000 cases were in Shanghai.

Shanghai COVID lockdown lifted for some, but millions remain trapped as China sticks to strict "zero-COVID" policy [CBS News, 12 Apr 2022]

Tokyo — The U.S. State Department has ordered all non-emergency consular staff to leave China's largest city, Shanghai, as the global business hub enters its third week of lockdown in response to a surge in COVID-19 cases. The U.S. Embassy in Beijing said it was ordering the departure because of the outbreak in Shanghai and as American diplomats had raised "concerns about the safety and welfare of U.S. citizens" in the city.

"It is best for our employees and their families to be reduced in number and our operations to be scaled down as we deal with the changing circumstances on the ground," a statement from the embassy said, according to The Associated Press.

Shanghai officials reported more than 23,000 new coronavirus cases on Tuesday. The vast majority of them are asymptomatic, but despite that, and some limited easing of the restrictions, the government has largely stuck to its strict lockdown and isolation measures — even as it battles public anger, food shortages and a major impact on business.

China's central government has bristled at criticism of its tactics from the U.S. and Europe, insisting over the weekend that its draconian "zero-COVID" policy was "effective and scientific."
Analysts at the global financial services firm Nomura estimated that as many as 45 cities in China were implementing either full or partial lockdowns as of Tuesday, impacting more than a quarter of the country's overall population, according to the Reuters news agency.

As CBS News senior foreign correspondent Elizabeth Palmer reports, Shanghai is under the single biggest COVID lockdown in the world. For more than two weeks, the megacity of more than 25 million people has been eerily quiet.

The only bustle is at food depots, where there's a daily race to deliver groceries to millions of people who haven't been allowed out to shop.

Amid an outcry from residents, city authorities on Tuesday did allow people in some COVID-free neighborhoods to leave their homes, and officials said some pharmacies and grocery stores would reopen, too.

A local news outlet said fewer than 7 million Shanghai residents were being liberated, however, and details on who would be freed and when remained murky.

American Billy Stockton, who lives and works in Shanghai, is among the millions who have been confined to their apartments since late March.

"No one knows where to get stuff," he told Palmer. "No one knows where to get medical help… and it's creating panic, fear and, just, instability."

There have been angry protests — rare anywhere in China — in areas where food ran out. Videos posted to social media show crowds of frustrated residents shouting, "we're starving!"
Last week, a man vented his fury in a video recorded on his phone, and then uploaded online.

"What am I supposed to buy," he shouted. "What do I eat? You're driving us to our deaths!"
Small groups of residents have now been allowed out over the past couple weeks, but only briefly, for COVID testing. Anyone who tests positive has no choice: As one patient showed on TikTok, they had to board a special bus and then check into a government-run mass-isolation center.

The authorities are clearly ready to quarantine an onslaught of new cases, even as they release old ones who are now testing negative.

But for the recently released, it's a false sense of freedom. The roughly 6,000 people who were let out of isolation centers on Monday headed straight back into lockdown at home.

Looking out of Billy Stockton's window, however, there was no sign of that. He was busy taking stock of his dwindling food supply.

"I have sausages and then they supplied a bag of rice yesterday, so simple stuff like that," he said of his meal plan.

"It's like a movie," he told Palmer, saying he felt like he was trapped in a nightmare. "I just can't believe I'm in this. It's beyond surreal. You kind of have to pull yourself out of it to get through it."

Like millions of other Shanghai residents, Stockton has no choice but to just get through it.

That could take another couple of weeks, however, and the question is whether there will be lasting fallout among Shanghai's massive population, who have rarely, if ever, felt so mistreated and abused by their government.