US tracking of virus variants has improved after slow start - WXIX

(AP) – After a slow start, the United States has improved its surveillance system for tracking new coronavirus variants such as omicron, boosting its capacity by tens of thousands of samples per week since early this year.

Viruses mutate constantly. To find and track new versions of the coronavirus, scientists analyze the genetic makeup of a portion of samples that test positive.

They’re looking at the chemical letters of the virus’s genetic code to find new worrisome mutants, such as omicron, and to follow the spread of known variants, such as delta.

It’s a global effort, but until recently the U.S. was contributing very little. With uncoordinated and scattershot testing, the U.S. was sequencing fewer than 1% of positive specimens earlier this year. Now, it is running those tests on 5% to 10% of samples.

“Genomic surveillance is strong,” said Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories.

Contributing to the effort are nearly 70 state and local public health labs, which are sequencing 15,000 to 20,000 specimens each week. Other labs, including those run by the Centers for Disease Control and Prevention and its contractors, bring the total to 40,000 to 80,000 weekly.

Nine months ago, about 12,000 samples each week were being analyzed in this way.

“We’re in a much, much better place than a year ago or even six or nine months ago,” said Kenny Beckman of the University of Minnesota, who credited federal dollars distributed to public and private labs. He directs the university’s genomics laboratory, which now sequences about 1,000 samples a week from Minnesota, Arkansas and South Dakota. A year ago, the lab did no sequencing.

Relying on $1.7 billion in President Joe Biden’s coronavirus relief bill, the U.S. has been setting up a national network to better track coronavirus mutations.

Still, about two dozen countries are sequencing a larger proportion of positive samples than the U.S., said Dr. William Moss of the Johns Hopkins Bloomberg School of Public Health. Omicron’s emergence could “stimulate the United States to do this better.”

“I think we still have a long way to go,” Moss said.

Adding to surveillance efforts, standard PCR tests that use nasal swabs sent to laboratories can detect a sign that someone probably has the omicron variant. If a PCR test is positive for only two of the three target genes — a so-called S-dropout test result — it’s a marker for omicron even before the extra step of genetic sequencing to prove it.

“It’s fortuitous,” said Trevor Bedford, a biologist and genetics expert at Fred Hutchinson Cancer Research Center. “If you need to do sequencing to identify the variant you’re always going to be lagged a bit and it’s going to be more expensive. If you just rely on this S-dropout as identification then it’s easier.”

He said other variants also have sparked this quirk in PCR test results, but not the delta variant. With delta so dominant in the U.S. right now, an S-dropout result will get noticed, Bedford said. (Bedford receives funding from the Howard Hughes Medical Institute, which also supports The Associated Press Health and Science Department.)

Dr. Anthony Fauci, the nation’s top infectious disease expert, said it is “inevitable” that omicron will make its way into the United States.

Many experts said it’s probably already here and will be picked up by the surveillance system soon. But the question is, then what?

University of Wisconsin AIDS researcher David O’Connor noted: “We don’t have the sorts of interstate travel restrictions that would make it possible to contain the virus in any one place.”

Instead, genomic surveillance will tell officials if omicron is spreading unusually fast somewhere and whether more resources should be sent to those places, he said.

When omicron does surface, public health authorities will have to consider other variables in their triage efforts, such as the level of infection already present in that community and the vaccination rate. Serious outbreaks in highly vaccinated areas would be particularly concerning.

Still, the University of Minnesota’s Beckman sees little upside in vastly ramping up sequencing.

“You don’t need to sequence more than a few percent of positive cases to get a feel for how quickly it’s growing,” he said.

Unlike in some other countries, U.S. government officials haven’t exercised the authority to force people to quarantine if they test positive for worrisome variants. Given that, sequencing is mainly a surveillance tool for tracking mutations’ spread.

“I think it’s important to track variants, but I don’t think it’s practical to think that we’re going to be able to sequence quickly and broadly enough to stop a variant in its tracks,” Beckman said.

___

AP writers Lauran Neergaard, Matthew Perrone and Ricardo Alonso-Zaldivar contributed.

___

The Associated Press Health and Science Department receives support from the Howard Hughes Medical Institute’s Department of Science Education. The AP is solely responsible for all content.

Copyright 2021 The Associated Press. All rights reserved.

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Distortion: Researchers discover new strategy for antibodies to disable viruses - Phys.Org

The same type of antibody can neutralize Zika and dengue viruses in two different ways — one where it binds to the virus and deactivates it (left), which is the traditional way we think about antibody activity, and the other where it burrows in and distorts the virus (right). Credit: Ganesh Anand, Penn State

It is widely understood that antibodies neutralize viruses by latching onto their surfaces and blocking them from infecting host cells. But new research reveals that this barrier method isn't the only way that antibodies disable viruses. An international team of researchers led by Penn State has discovered that antibodies also distort viruses, thereby preventing them from properly attaching to and entering cells.

"Everybody thinks of antibodies as binding to viruses and blocking them from entering cells—essentially locking them down," said Ganesh Anand, associate professor of chemistry, Penn State. "But our research reveals for the first time that antibodies may also physically distort viruses, so they are unable to properly attach to and infect host cells."

In their study, which published online today in the journal Cell, Anand and his colleagues investigated the interactions between human monoclonal antibody (HMAb) C10 and two disease-causing viruses: Zika and dengue. The HMAb C10 antibodies they used had previously been isolated from patients infected with dengue virus and had also been shown to neutralize Zika virus.

The researchers used a combination of techniques, including cryogenic electron microscopy (cryo-EM) to visualize the viruses and hydrogen/deuterium exchange mass spectrometry (HDXMS) to understand their movement.

"Cryo-EM involves flash-freezing a solution containing molecules of interest and then targeting them with electrons to generate numerous images of individual molecules in different orientations," explained Anand. "These images are then integrated into one snapshot of what the molecule looks like. The technique provides much more accurate pictures of molecules than other forms of microscopy."

To document the effects of antibodies on Zika and dengue viruses, the team collected cryo-EM snapshots of the viruses under conditions of increasing concentrations of antibodies.

In parallel, the team applied HDXMS, a technique in which molecules of interest—in this case Zika and dengue virus, along with HMAb C10 antibodies—are submerged in heavy water. Heavy water, Anand explained, has had its hydrogen atoms replaced with deuterium, hydrogen's heavier isotopic cousin.

"When you submerge a virus in heavy water, the hydrogen atoms on the surface of the virus exchange with deuterium," he said. "You can then use mass spectrometry to measure the heaviness of the virus as a function of this deuterium exchange. By doing this, we observed that dengue virus, but not Zika virus, became heavier with deuterium as more antibodies were added to the solution. This suggests that for dengue virus, the antibodies are distorting the virus and allowing more deuterium to get in. It's as if the virus is getting squished and more surface area becomes exposed where hydrogen can be exchanged for deuterium."

In contrast, Zika virus did not become heavier when placed in heavy water, suggesting that its surface, while fully occupied by antibodies, is not distorted by the antibodies.

Anand explained that by combining cryo-EM and HDXMS, the team was able to get a comprehensive picture of what happens when antibodies attach to Zika and dengue viruses.

"It's like those cartoon flipbooks, where each page has a slightly different image, and when you flip through the book, you see a short movie," he said. "Imagine a flipbook with drawings of a racehorse. Cryo-EM shows you what the racehorse looks like and HDXMS shows you how fast the racehorse is moving. You need both techniques to be able to describe a racehorse in motion. This complementary set of tools enabled us to understand how one type of antibody differentially affects two types of viruses."

He noted that the fact that the more antibodies they added, the more distorted the dengue virus particles became, suggests that stoichiometry—the relationship between the quantities of the reactants and the products before, during and after a chemical reaction—matters.

"It's not enough to just have antibodies present," he said. "How much antibody you add determines the extent of neutralization."

In fact, the team found that at saturating conditions, in which antibodies were added at high enough concentrations to fill all the available binding locations on the dengue viruses, 60% of the virus' surfaces became distorted. This distortion was enough to protect the cells from infection.

"If you have enough antibodies, they will distort the virus particle enough so that it's preemptively destabilized before it even reaches its target cells," Anand said.

Indeed, when the scientists incubated the antibody-bound dengue viruses with BHK-21 cells, a cell line from the kidneys of baby hamsters that is often used in viral infection research, they found that 50-70% fewer cells were infected.

Anand explained that with some viruses, including Zika, antibodies work by jamming the exits so the passenger cannot get out of the car. We have found a new mechanism in dengue virus whereby antibodies basically total the car so it cannot even travel to a cell."

How are the antibodies distorting the dengue virus particles?

Anand explained that contrary to the now-familiar SARS-CoV-2, which has spike proteins protruding in all directions, the surfaces of both Zika and dengue is a smoother surface with peaks and valleys.

Anand noted that for dengue virus, antibodies especially prefer binding the 'peaks' known as 5-fold vertices. Once all the proteins on the 5-fold vertices have been bound, antibodies will turn to their second-favorite peaks—the 3-fold vertices. Finally, they are left with only the 2-fold vertices.

"Antibodies do not like two-fold vertices because they are very mobile and difficult to bind to," said Anand. "We found that once the 5- and 3-fold vertices have been fully bound with antibodies, if we add more antibodies to the solution, the virus starts to shudder. There's this competition taking place between antibodies trying to get in and the virus trying to shake them off. As a result, these antibodies end up burrowing into the virus rather than binding onto the 2-fold vertices, and we think it's this digging into the virus particle that causes the virus to shake and distort and ultimately become non-functional."

What is the difference between Zika and dengue?

Anand explained that Zika is a much more stable, less dynamic virus than dengue, which has a lot of moving parts.

"Dengue and Zika look similar but each one has a different give. Dengue may have evolved as a more mobile virus as a way of avoiding being caught by antibodies. Its moving parts confuse and throw off the immune system. Unfortunately for dengue, antibodies have evolved a way around this by burrowing into the virus and distorting it."

It appears, he said, that the same type of antibody can neutralize Zika and dengue in two different ways—one where it binds to the virus and deactivates it, which is the traditional way we think about antibody activity, and the other where it burrows in and distorts the virus.

What about other viruses?

Anand said the distortion strategy his team discovered may be used by antibodies when they are confronted with other types of viruses as well.

"Dengue is just a model virus that we used in our experiments, but we think this preemptive destabilization strategy may be broadly applicable to any virus," he said. "It may be that the antibodies first attempt to neutralize viruses through the barrier method and if they are unsuccessful, they resort to the distortion method."

Are there any potential applications of the findings?

The findings could be useful in designing therapeutic antibodies, Anand said.

"HMAb C10 antibodies are specific to dengue and Zika viruses, and happen to be capable of neutralizing Zika and dengue viruses in two different ways," he said. "But you could potentially design therapeutics with the same capabilities for treating other diseases, such as COVID-19. By creating a therapeutic with antibodies that can both block and distort viruses, we can possibly achieve greater neutralization."

He added, "You don't want to wait for a virus to reach its target tissue, so if you can introduce such a therapeutic cocktail as a nasal spray where the virus first enters the body, you can prevent it from even entering the system. By doing this, you may even be able to use less antibody since our research shows that it takes less antibody to neutralize a virus through the distortion method. You can get better bang for the buck."

Overall, Anand stressed that the importance of the study is that it reveals an entirely new strategy that some antibodies use to disable some viruses.

"Previously, all we knew about antibodies was that they bind and neutralize viruses," he said. "Now we know that antibodies can neutralize viruses in at least two different ways, and perhaps even more. This research opens the door to a whole new avenue of exploration."

Other authors on the paper include Xin-Xiang Lim, graduate student; Jian Shi, manager, Cryo-EM Facility; and Shee-Mei Lok, professor, National University of Singapore. Co-authors also include Bo Shu, research fellow; Shuijun Zhang, assistant professor; Aaron W.K. Tan, graduate student; Thiam-Seng Ng, graduate student; Xin-Ni Lim, graduate student; and Valerie Chew, assistant professor, Duke-National University of Singapore Medical School. Gavin R. Screaton, head of the Medical Sciences Division, Oxford University, also is an author.

---

Explore further

Secrets of antibodies: When it comes to dengue and Zika, dengue antibodies can knock out Zika—and vice versa

---

Journal information: Cell

Provided by Pennsylvania State University

Citation: Distortion: Researchers discover new strategy for antibodies to disable viruses (2021, November 30) retrieved 30 November 2021 from https://ift.tt/32LXszI

This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.

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Omicron vs. Delta: More mutations don't necessarily make a meaner Covid-19 virus - CNN

(CNN)The new Omicron variant of coronavirus, with its many mutations and seemingly quick spread in South Africa, is worrying scientists and government officials.

But doctors want to remind Americans that they're already facing a pretty formidable coronavirus variant, and that's Delta.

Delta managed to take over the entire United States in a matter of weeks in early summer, changing the outlook for a country that was rolling out vaccines and hope with equal speed.

"In late June, the seven-day moving average of reported cases was around 12,000. On July 27, the seven-day moving average of cases reached over 60,000. This case rate looked more like the rate of cases we had seen before the vaccine was widely available," the US Centers for Disease Control and Prevention says on its website. "The Delta variant is highly contagious, more than 2x as contagious as previous variants."

Delta currently accounts for more than 99% of cases of coronavirus that are genetically sequenced in the US, according to CDC.

It remains to be seen whether Omicron will outcompete Delta, but it will be tough.

"We still have, of course, in the US, a serious surge of the Delta variant. We should be thinking about that," National Institutes of Health Director Dr. Francis Collins told CNN on Monday.

The US is now averaging 70,094 new Covid-19 cases and 730 deaths each day, according to Johns Hopkins University. And JHU says 75% of intensive care unit beds in the US are occupied, 15% of them by Covid-19 patients.

Comparing Omicron and Delta

Much is being made of the 50 mutations that mark the Omicron variant -- 32 of them on the spike protein, which is the club-shaped structure that covers the surface of the virus and is used to attach to human cells so the virus may infect them.

But Delta has its own constellation of scary mutations, and they've made it the worst version of the virus yet seen. It races through populations, replacing more worrying variants that have mutations that should allow them to evade the effects of vaccines, like the Beta variant, for instance.

Robert Garry, a virologist at Tulane University, has done a head-to-head comparison of the mutations seen in Delta and Omicron.

Omicron does have "a chunk of them at once," Garry told CNN. "But we've kind of seen that kind of leap in evolution before," he added.

"There are definitely hotspots where this virus likes to mutate now," he said. But just because there are many mutations doesn't necessarily mean they'll add up to a meaner virus.

"What all those changes in the aggregate are going to do for the things that matter for this virus, we don't really know yet," Garry said.

But he does not see many important mutations that might make the Omicron version more contagious than Delta.

"The ones that might affect transmissibility, I mean, I'm just not seeing a whole lot that would give it a real strong advantage over Delta," he said.

"That's really the big question. You know, when it gets into a population that has Delta, is it going to out-compete or not out-compete?"

Other genetics experts also note Omicron does not carry some of the changes that helped make Delta so very contagious.

"Given that Omicron lacks so many of the non-spike mutations that have seemed to contribute to Delta's increased fitness I wouldn't be surprised if its intrinsic transmissibility is similar to Gamma," Trevor Bedford, a genome scientist and epidemiologist at the University of Washington and Fred Hutchinson Cancer Center in Seattle, said on Twitter. He referenced a study in September from researchers at the Broad Institute who found at least three mutations on the Delta variant that they said appeared to help make it more transmissible.

Some of the mutations that increase transmissibility are also seen in variants that died out, such as one called Kappa.

Protecting against Covid-19

Garry does see mutations that might help Omicron to evade the body's immune response -- especially from previous infections.

"It's likely immune evasive. So is Delta, and before that Alpha and Beta. Should we be working on a specific vaccine? Yes," he said.

The immune response prompted by vaccination is broader than the response produced by a natural infection, so vaccinated people may still be protected from severe disease, doctors said.

"Your best protection against Delta is to get vaccinated, and if you've already been vaccinated and six months have passed since you got Pfizer or Moderna, get your booster, two months since J&J, get your booster," Collins told CNN.

"That was a reason already, but now add Omicron to the mix," he said. "And we do believe that this new variant, which will probably come to our shores, will also be something vaccines and boosters can help you with."

The CDC strengthened its guidance on boosters Monday, saying all adults should get booster shots six months after finishing the first two doses of Moderna's or Pfizer/BioNTech's vaccine and two months after getting Johnson & Johnson's single-dose vaccine.

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And there's no known mutation that can make a virus evade precautions such as face masks, handwashing and physical distancing. Even if a mutation helps a virus become more viable as an airborne pathogen, better ventilation can help prevent transmission.

CNN's Naomi Thomas and Deidre McPhillips contributed to this story

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Judge blocks U.S. COVID-19 vaccine rule for health workers in 10 states - Reuters

Nov 29 (Reuters) - A federal judge on Monday blocked in 10 states a Biden administration vaccine requirement, finding the agency that issued the rule mandating healthcare workers get vaccinated against the coronavirus likely exceeded its authority.

The ruling by U.S. District Judge Matthew Schelp in St. Louis prevents the U.S. Centers for Medicare and Medicaid Services (CMS) from enforcing its vaccine mandate for healthcare workers until the court can hear legal challenges brought by the 10 states.

CMS in a statement said it was reviewing the ruling, adding that unvaccinated healthcare staff pose a threat to patient safety.

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The ruling is the second legal setback for President Joe Biden, who has focused on vaccines to halt the COVID-19 pandemic, a point he emphasized on Monday amid concerns about the spread of the new COVID-19 Omicron variant. read more

A federal appeals court in New Orleans earlier this month blocked a sweeping workplace mandate that requires businesses with at least 100 employees to get their staff vaccinated or tested weekly. read more

Republican state attorneys general sued the administration in early November over the CMS rule, seeking to block the requirement because they alleged it would worsen healthcare staffing shortages.

Schelp, who was appointed by President Donald Trump, said CMS had understated the "overwhelming" cost of its mandate and by declining to submit the rule to public comment the agency had fed the vaccine hesitancy the rule is meant to counter.

Schelp also said the CMS rule altered the balance of power between the federal and state governments.

"Congress did not clearly authorize CMS to enact this politically and economically vast, federalism-altering, and boundary-pushing mandate, which Supreme Court precedent requires," he wrote.

Schelp's ruling applied in the 10 states that brought the case: Missouri, Nebraska, Arkansas, Kansas, Iowa, Wyoming, Alaska, South Dakota, North Dakota and New Hampshire.

On Nov. 4, CMS issued the interim final rule it said covers over 10 million people and applies to around 76,000 healthcare providers including hospitals, nursing homes and dialysis centers.

The rule requires health facilities to mandate all employees, volunteers and contractors have a first vaccine dose by Dec. 6 and to be fully vaccinated by Jan. 4. Providers that fail to comply could lose access to Medicare and Medicaid funds.

Medicare serves people 65 and older and the disabled. Medicaid serves the poor.

In addition to the CMS rule and the workplace vaccine requirement, the Biden administration imposed coronavirus vaccine rules on government contractors, military personnel and federal employees, which are all being challenged in court.

Courts have upheld mandates by private employers and state governments, which have helped to increase the rate of COVID-19 vaccination in the United States.

On Wednesday, the Biden administration said a total of 92% of U.S. federal workers have received at least one dose of a COVID-19 vaccine.

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Reporting by Tom Hals in Wilmington, Delaware; additional reporting by Ahmed Aboulenein in Washington; Editing by Bill Berkrot

Our Standards: The Thomson Reuters Trust Principles.

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WHO warns that new virus variant poses ‘very high’ risk - The Times Herald

By JAMEY KEATEN, RAF CASERT and MARI YAMAGUCHI

GENEVA (AP) — The World Health Organization warned Monday that the global risk from the omicron variant is “very high” based on the early evidence, saying the mutated coronavirus could lead to surges with “severe consequences.”

The assessment from the U.N. health agency, contained in a technical paper issued to member states, amounted to WHO’s strongest, most explicit warning yet about the new version that was first identified days ago by researchers in South Africa.

It came as a widening circle of countries around the world reported cases of the variant and moved to slam their doors in an act-now-ask-questions-later approach while scientists race to figure out just how dangerous the mutant version might be.

Japan announced it is barring entry to all foreign visitors, joining Israel in doing so. Morocco banned all incoming flights. Other countries, including the U.S. and members of the European Union, have moved to prohibit travelers arriving from southern Africa.

WHO said there are “considerable uncertainties” about the omicron variant. But it said preliminary evidence raises the possibility that the variant has mutations that could help it both evade an immune-system response and boost its ability to spread from one person to another.

“Depending on these characteristics, there could be future surges of COVID-19, which could have severe consequences, depending on a number of factors, including where surges may take place,” it added. “The overall global risk … is assessed as very high.”

The WHO stressed that while scientists are hunting evidence to better understand this variant, countries should accelerate vaccinations as quickly as possible.

While no deaths linked to omicron have been reported so far, little is known for certain about the variant, including whether it is more contagious, more likely to cause serious illness or more able to evade vaccines. Last week, a WHO advisory panel said it might be more likely to re-infect people who have already had a bout with COVID-19.

Scientists have long warned that the virus will keep finding new ways to exploit weaknesses in the world’s vaccination drive, and its discovery in Africa occurred in a continent where under 7% of the population is vaccinated.

“The emergence of the omicron variant has fulfilled, in a precise way, the predictions of the scientists who warned that the elevated transmission of the virus in areas with limited access to vaccine would speed its evolution,” said Dr. Richard Hatchett, head of CEPI, one of the founders of the U.N.-backed global vaccine sharing initiative COVAX.

Spain on Monday became one of the latest countries to report its first confirmed omicron case, detected in a traveler who returned Sunday from South Africa after making a stopover in Amsterdam.

While the majority of omicron infections recorded around the world have been in travelers arriving from abroad, cases in Portugal and Scotland have raised fears that the variant may already be spreading locally.

“Many of us might think we are done with COVID-19. It’s not done with us,” warned Tedros Adhanom Ghebreyesus, WHO’s director-general.

Days after the variant sent a shudder through the financial world nearly two years into the pandemic that has killed over 5 million people, markets had a mixed reaction Monday. European stocks rebounded and Wall Street steadied itself, while Asian markets fell further.

U.S. President Joe Biden called the omicron variant a cause for concern but “not a cause for panic.” He said he is not considering any widespread U.S. lockdown and instead urged mask-wearing and vaccinations, even as a federal judge blocked his administration from enforcing a requirement that thousands of health care workers in 10 states get the shot.

Dr. Rochelle Walensky, director of the U.S. Centers for Disease Control and Prevention, reacted to the potential threat by urging everyone 18 and older to get booster shots, because “strong immunity will likely prevent serious illness.” Earlier this month, the U.S. opened boosters to all adults but recommended them only for those 50 and older or people in long-term care.

The omicron infections have underscored the difficulty in keeping the virus in check in a globalized world of jet travel and open borders. Yet many countries are trying to do just that, against the urging of the WHO, which noted that border closings often have limited effect and can wreak havoc on lives and livelihoods.

Some have argued that such restrictions can buy valuable time to analyze the new variant.

While the initial global response to COVID-19 was criticized as slow and haphazard, the reaction to the omicron variant came quickly.

“This time the world showed it is learning,” said EU Commission President Ursula von der Leyen, singling out South African President Cyril Ramaphosa for praise. “South Africa’s analytic work and transparency and sharing its results was indispensable in allowing a swift global response.”

Late last week, von der Leyen successfully pushed the 27-nation EU to agree to ban flights from seven southern African nations, similar to what many other countries are doing.

Cases have been reported in such places as Canada, Germany, Britain, Belgium, Denmark, the Netherlands and Portugal, where authorities identified 13 omicron infections among members of the Belenenses professional soccer team.

Taking no chances, Japan, which has yet to detect any omicron cases, reimposed border controls that it had eased earlier this month.

“We are taking the step as an emergency precaution to prevent a worst-case scenario in Japan,” Prime Minister Fumio Kishida said.

Israel likewise decided to bar entry to foreigners, and Morocco said it would suspend all incoming flights for two weeks.

Britain reacted by expanding its COVID-19 booster program to everyone 18 and older, making millions more people eligible. Up until now, booster shots were available only to those 40 and over and people particularly vulnerable to the virus. The U.K. has reported about a dozen omicron cases.

Despite the global worry, doctors in South Africa are reporting patients are suffering mostly mild symptoms so far. But they warn that it is early. Also, most of the new cases are in people in their 20s and 30s, who generally do not get as sick from COVID-19 as older patients.

___

Yamaguchi reported from Tokyo, Casert from Brussels. Associated Press journalists from around the world contributed to this report.

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LIVE MARKETS Three virus scenarios for airlines - Reuters

• European shares hit 7-week low, volatility spikes
• Moderna CEO raises vaccine efficacy doubts
• Travel stocks eye worst month since March 2020
• U.S. stock index futures tumble

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THREE VIRUS SCENARIOS FOR AIRLINES (1110 GMT)

Omicron has thrown travel plans up in the air as governments tighten curbs just ahead of the key Christmas shopping season.

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Clearly the whole travel and leisure sector has been hardly hit with the European index < .SXTP> down more than 20% so far in November and set for its biggest monthly drop since March 2020, when COVID-19 fears reached their peak market impact.

Airlines, too, have been hammered with a Refintiv Global Airline index (.TRXFLDGLPUARLI) down over 10% month-to-date, and also on course for its worst month since March last year.

HSBC has tried to put some order around what are the risks for airlines in the coming months, setting out three scenarios for European carriers.

"The current outlook for aviation stocks will likely be shaped by the effectiveness of vaccines against the new Omicron variant. Pending clarity on this, aviation is being impacted by a swathe of travel restrictions, which will weaken trading to Christmas," they say.

Its base case assumes vaccine effectiveness is not materially weaker, which means "only a one-quarter delay to a travel recovery" and a 5% cut to price targets.

Its middle scenario of a "somewhat degraded effectiveness" envisages a six-month delay to recovery, while in a third unfavourable case it sees a full-year delay to recovery.

snapshot

(Danilo Masoni)

*****

EUROPE SET FOR NOVEMBER LOSSES ON OMICRON WORRIES BITE (0810 GMT)

The pan-European STOXX 600 is on course for losses of about 3% in November as the warning from Moderna's CEO that COVID-19 vaccines may be less effective against the Omicron variant rocks the last day of trading of the month.

Remarks by President Joe Biden that the United States would not reinstate lockdowns had helped soothe markets as did upbeat Chinese factory activity but the comments from the Moderna CEO were a total game changer.

"As a result of these rather frank comments, markets in Asia dropped sharply and the gains made yesterday in European trading look set to disappear as we look to a sharply lower open later this morning, while US futures have also rolled over", CMC Markets analyst Michael Hewson wrote ahead of the open.

"As we look ahead to the rest of the week, this morning’s drop in markets shows that sentiment is set to remain extremely fickle until we get a clearer idea of what comes next when it comes to the new variant", he added.

European stocks opened down 1% at 462 points, that's 4% below the close on last Thursday, when the word Omicron meant little or nothing to most of the world.

As one would expect, oil and gas stocks are losing badly, down 1.6% with oil prices sliding down again. Most cyclical stocks are in a bad place too: banks, car makers and retail are down about 1.5%.

stoxx

(Julien Ponthus)

*****

LONG COVID (0801 GMT)

World stocks' 0.6% rise on Monday came nowhere close to recouping Friday's 2.2% loss, but even that is under threat after Moderna CEO Stephane Bancel predicted existing vaccines would struggle with the Omicron variant.

Fed Chairman Jerome Powell will also tell U.S. lawmakers later in the day the variant could imperil economic recovery, prepared remarks show read more . Those comments have already sent 10-year Treasury yields down 7 basis points this morning .

So a loss-making Asian session has given way to red ink in Europe, where German markets appear headed 2% lower. Futures point to hefty Wall Street losses, the yen and Swiss franc are again catching a bid and oil prices have slid more than $1.

COVID headlines overshadowed a pickup in official Chinese PMIs, which showed factory activity cranking up in November and services coming in steady from the previous month.

And for those still in data watching mode, euro zone inflation data could show a big number, accelerating from October's 4.1%. Remember, Monday brought German November CPI of 5.2% year-on-year, the highest since 1992. The picture is one of economic growth under threat, even as a possible COVID comeback risks exacerbating supply chain glitches.

What happens next is anyone's guess. Citi analysts write that Friday's selloff wiped out investors' bullish bias on the S&P 500, while European positioning had already turned neutral in Europe.

There is room for more position unwinding, but also scope for a bounce.

Key developments that should provide more direction to markets on Tuesday:

- ECB likely to keep buying bonds through 2022; could resume PEPP - ECB Vice President Luis de Guindos read more

-South Korea, global trade bellwether, saw October factory output shrink at the sharpest pace in nearly 1-1/2 years read more

-Airline easyJet sees softening in demand as COVID clouds outlook read more

-Macau gambling group Suncity's shares plunge after CEO arrested read more

- Twitter CEO Jack Dorsey hands reins to technology chief Agrawal read more

-NATO Foreign Ministers meeting in Latvia

-France flash CPI; Euro zone flash inflation

-Fed speakers: Jerome Powell testifies before a Senate Banking Committee; New York President John Williams

-Emerging markets: Hungary central bank meets: Turkey Q3 GDP, India Q3 GDP

-Monthly US house prices/Chicago PMI

-Europe earnings; EasyJet, Wise,

-US earnings: Salesforce

Euro zone inflation

(Sujata Rao)

*****

FASTEN YOUR SEATBELT: EUROPE SET TO DROP ON MODERNA WARNING(0710 GMT)

European stocks are set to open sharply lower this morning after Moderna's CEO warned that COVID-19 vaccines are likely to be less effective against the Omicron variant.

MSCI's broadest index of Asia-Pacific shares outside Japan is currently down 0.75% and futures for European indexes are falling about 1.5%.

The direction of travel is pretty much the same for Wall Street.

(Julien Ponthus)

*****

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Moderna CEO warns COVID-19 shots less effective against Omicron, spooks markets - Reuters

• Moderna CEO comments on Omicron jolt markets
• Hong Kong bans non-resident arrivals from more countries
• Singapore: 2 travellers to Sydney with Omicron transited Changi
• Biden says variant is 'cause for concern, not a cause for panic'

HONG KONG/SYDNEY, Nov 30 (Reuters) - Drugmaker Moderna's CEO (MRNA.O) set off fresh alarm bells in financial markets on Tuesday after he warned that COVID-19 vaccines were unlikely to be as effective against the Omicron variant as they have been against the Delta version.

Crude oil futures shed more than a dollar, the Australian currency hit a year low, and Nikkei gave up gains as Stéphane Bancel's comments spurred fears that vaccine resistance could lead to more sickness and hospitalisations, prolonging the pandemic.

"There is no world, I think, where (the effectiveness) is the same level . . . we had with Delta," Moderna CEO Bancel told the Financial Times in an interview.

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"I think it's going to be a material drop. I just don't know how much because we need to wait for the data. But all the scientists I've talked to . . . are like 'this is not going to be good'," Bancel said. read more

Moderna did not reply to a Reuters' request for comment on the interview and on when it expects to have data on the effectiveness of its vaccine against Omicron, which the World Health Organization (WHO) says carries a "very high" risk of infection surges.

Bancel had earlier said on CNBC that there should be more clarity on the efficacy of COVID-19 vaccines against Omicron in about two weeks, and that it could take months to begin shipping a vaccine that work against the new variant.

The WHO and scientists have also said it could take days to several weeks to understand the level of severity of the variant and its potential to escape protection against immunity induced by vaccines. read more

"Vaccination will likely still keep you out of the hospital," said John Wherry, director of the Penn Institute for Immunology in Philadelphia.

The uncertainty about the new variant has triggered global alarm, with border closures casting a shadow over a nascent economic recovery from a two-year pandemic. read more

News of its emergence wiped roughly $2 trillion off the value of global stocks on Friday, but some calm was restored this week as investors waited for more data on Omicron.

Remarks by President Joe Biden that the United States would not reinstate lockdowns had also helped soothe markets before comments from the Moderna CEO spooked investors.

Biden has called for wider vaccination, while the U.S. Centers for Disease Control and Prevention has urged everyone aged 18 years and older to get a booster shot. Britain too has expanded its COVID-19 booster programme amid Omicron fears.

First reported on Nov. 24 from South Africa, Omicron has since spread to over a dozen countries. Japan, the world's third-largest economy, has confirmed its first case. read more

"The World Health Organization classified Omicron as a "variant of concern," due to the number of mutations that might help it spread or evade antibodies from prior infection or vaccination.

HONG KONG EXPANDS CURBS

Countries around the world have moved quickly to tighten border controls to prevent a recurrence of last year's strict lockdowns and steep economic downturns. read more

Hong Kong has expanded a ban on entry for non-residents from several countries. It said non-residents from Angola, Ethiopia, Nigeria and Zambia would not be allowed to enter as of Nov. 30.

Additionally, it said non-residents who have been to Austria, Australia, Belgium, Canada, the Czech Republic, Denmark, Germany, Israel and Italy in the past 21 days would not be allowed to enter the city from Dec. 2. read more

The global financial hub, among the last places pursuing a zero-COVID strategy, has already banned non-residents arriving from South Africa, Botswana, Eswatini, Lesotho, Malawi, Mozambique, Namibia and Zimbabwe.

In Australia, five travellers tested positive for Omicron.

Singapore's health ministry said two travellers from Johannesburg who tested positive for the variant in Sydney had transited through its Changi airport. read more

Australian authorities have also identified a sixth traveller who was most likely infected with the variant and had spent time in the community. read more

Canberra delayed on Monday the reopening of the nation's borders for international students and skilled migrants, less than 36 hours before they were due to be allowed back in.

"We're doing this out of an abundance of caution but our overwhelming view is that whilst (Omicron) is an emerging variant, it is a manageable variant," Federal Health Minister Greg Hunt said. read more

An upsurge in new coronavirus variants and poor access to vaccines in developing countries threaten a full recovery from the COVID-19 pandemic.

The global curbs on travellers from southern Africa also raised concerns about vaccine inequality.

"The people of Africa cannot be blamed for the immorally low level of vaccinations available in Africa – and they should not be penalized for identifying and sharing crucial science and health information with the world," U.N. Secretary-General Antonio Guterres said in a statement. read more

India, home to the world's largest vaccine maker, has approved supplies of COVID-19 vaccines to many African countries and said it stands ready to "expeditiously" send more. China too has pledged 1 billion doses to the continent. read more

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Reporting by Marius Zaharia in Hong Kong, Renju Jose in Sydney, Tom Westbrook in Singapore and Reuters bureaus; Writing by Himani Sarkar; Editing by Shri Navratnam

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