Scientists are still unclear on how effective vaccines will be against the new variant flagged by a team in South Africa, which displays mutations that might resist neutralization. Only several dozen cases have been fully identified so far in South Africa, Botswana, Hong Kong and Israel.
The new variant, B.1.1.529, has a “very unusual constellation of mutations,” with more than 30 in the spike protein alone, according to Tulio de Oliveira, director of the KwaZulu-Natal Research and Innovation Sequencing Platform.
The variant shares similarities with the Lambda and Beta variants, which are associated with an innate evasion of immunity, said Richard Lessells, an infectious diseases specialist at the KwaZulu-Natal Research and Innovation Sequencing Platform.
“All these things are what give us some concern that this variant might have not just enhanced transmissibility, so spread more efficiently, but might also be able to get around parts of the immune system and the protection we have in our immune system,” Dr. Lessells said.
The new variant has largely been detected among young people, the cohort that also has the lowest vaccination rate in South Africa. Just over a quarter of those ages between 18 and 34 in South Africa are vaccinated, said Dr. Joe Phaahla, the country’s minister of health.
While cases of the variant are mainly concentrated in the country’s economic hub, particularly in the country’s administrative capital, Pretoria, it is “only a matter of time” before the virus spreads across the country as schools close and families prepare to travel for the holiday season, Dr. Phaahla said.
— Lynsey Chutel
https://www.nytimes.com/live/2021/11/26 ... rs-variant
What scientists know about the new variant, B.1.1.529.
Re: What scientists know about the new variant, B.1.1.529.
The Omicron variant has worrisome mutations, but scientists say vaccines seem likely to work against it.
Scientific experts at the World Health Organization warned on Friday that a new coronavirus variant discovered in southern Africa was a “variant of concern,” the most serious category the agency uses for such tracking.
The designation, announced after an emergency meeting of the health body, is reserved for dangerous variants that may spread quickly, cause severe disease or decrease the effectiveness of vaccines or treatments. The last coronavirus variant to receive this label was Delta, which took off this summer and now accounts for virtually all Covid cases in the United States.
The W.H.O. said the new version, named Omicron, carries a number of genetic mutations that may allow it to spread quickly, perhaps even among the vaccinated.
Independent scientists agreed that Omicron warranted urgent attention, but also pointed out that it would take more research to determine the extent of the threat. Although some variants of concern, like Delta, have lived up to initial worries, others have had a limited impact.
William Hanage, an epidemiologist at the Harvard T.H. Chan School of Public Health and other researchers said that vaccines will most likely protect against Omicron, but further studies are needed to determine how much of the shots’ effectiveness may be reduced.
Coronavirus Variants and Mutations
As the coronavirus replicates inside people, new mutations constantly arise. Most provide the virus with no new advantage. When worrisome mutations do emerge, the World Health Organization uses Greek letters to name the variants. The first “variant of concern,” Alpha, appeared in Britain in late 2020, soon followed by Beta in South Africa.
Omicron first came to light in Botswana, where researchers at the Botswana Harvard H.I.V. Reference Laboratory in Gaborone sequenced the genes of coronaviruses from positive test samples. They found some samples sharing about 50 mutations not found in such a combination before. So far, six people have tested positive for Omicron in Botswana, according to an international database of variants.
Around the same time, researchers in South Africa stumbled across Omicron in a cluster of cases in the province of Gauteng. As of Friday, they have listed 58 Omicron samples on the variant database. But at a news conference on Thursday, Tulio de Oliveira, the director of the Centre for Epidemic Response & Innovation in South Africa, said that “close to two or three hundred” genetic sequences of Omicron cases would be released in the next few days.
— Carl Zimmer
https://www.nytimes.com/live/2021/11/27 ... riant-news
Scientific experts at the World Health Organization warned on Friday that a new coronavirus variant discovered in southern Africa was a “variant of concern,” the most serious category the agency uses for such tracking.
The designation, announced after an emergency meeting of the health body, is reserved for dangerous variants that may spread quickly, cause severe disease or decrease the effectiveness of vaccines or treatments. The last coronavirus variant to receive this label was Delta, which took off this summer and now accounts for virtually all Covid cases in the United States.
The W.H.O. said the new version, named Omicron, carries a number of genetic mutations that may allow it to spread quickly, perhaps even among the vaccinated.
Independent scientists agreed that Omicron warranted urgent attention, but also pointed out that it would take more research to determine the extent of the threat. Although some variants of concern, like Delta, have lived up to initial worries, others have had a limited impact.
William Hanage, an epidemiologist at the Harvard T.H. Chan School of Public Health and other researchers said that vaccines will most likely protect against Omicron, but further studies are needed to determine how much of the shots’ effectiveness may be reduced.
Coronavirus Variants and Mutations
As the coronavirus replicates inside people, new mutations constantly arise. Most provide the virus with no new advantage. When worrisome mutations do emerge, the World Health Organization uses Greek letters to name the variants. The first “variant of concern,” Alpha, appeared in Britain in late 2020, soon followed by Beta in South Africa.
Omicron first came to light in Botswana, where researchers at the Botswana Harvard H.I.V. Reference Laboratory in Gaborone sequenced the genes of coronaviruses from positive test samples. They found some samples sharing about 50 mutations not found in such a combination before. So far, six people have tested positive for Omicron in Botswana, according to an international database of variants.
Around the same time, researchers in South Africa stumbled across Omicron in a cluster of cases in the province of Gauteng. As of Friday, they have listed 58 Omicron samples on the variant database. But at a news conference on Thursday, Tulio de Oliveira, the director of the Centre for Epidemic Response & Innovation in South Africa, said that “close to two or three hundred” genetic sequences of Omicron cases would be released in the next few days.
— Carl Zimmer
https://www.nytimes.com/live/2021/11/27 ... riant-news
Re: What scientists know about the new variant, B.1.1.529.
More proof why anti-vaxers and anti-maskers should be investigated by grand juries.
Re: What scientists know about the new variant, B.1.1.529.
3 Questions We Must Answer About the Omicron Variant
Nov. 27, 2021
By Ashish Jha
Dr. Jha is the dean of the Brown University School of Public Health.
Every few months, the world learns of a new variant of the coronavirus. While most of these variants turn out to be inconsequential, some, like the Delta variant, are immensely consequential. The latest, B.1.1.529, now known as the Omicron variant, bears very close watching because of concerns that it may spread more quickly than Delta, possibly even among the vaccinated. It is essential that world leaders respond quickly and aggressively even before all the data about this variant emerge.
In the days ahead, as information builds, it will be tempting to give in to fear or indifference. We cannot succumb to either. The global community must take each variant seriously. Acting early is far superior to waiting until all the facts are in. It may turn out that the variant is not more contagious or that it responds perfectly well to our current vaccines. In that latter fortuitous scenario, the current response may be seen as an overreaction. But if this variant, with all of its concerning features, turns out to be as contagious and immune-evasive as many experts worry it might be, waiting until all the facts are in will leave us hopelessly far behind.
How worrisome is Omicron? There are three key questions that help scientists understand how consequential any variant might be.
The first question is whether the variant is more transmissible than the current, prevalent Delta strain? Second, does it cause more severe disease? And third, will it render our immune defenses — from vaccines and prior infections — less effective (a phenomenon known as immune escape)?
On transmissibility, the data, while early, look worrisome. This new variant appears to have taken off very quickly in South Africa, with early national data suggesting the variant already makes up the majority of sequenced cases in the country. It’s possible that this early data will be revised as epidemiologists look closer at factors other than transmissibility, such as whether an early Omicron superspreader event led to the variant appearing more highly contagious than it really is. While this is possible, the more likely scenario is that Omicron does spread more easily than Delta.
Because the variant is so new, scientists simply do not have adequate data yet to assess whether the new variant causes more severe disease. Answering this question will require careful case tracking in hospitals along with expanded viral sequencing efforts, both in South Africa and elsewhere. A key part of this analysis is ensuring that countries are doing adequate testing of a broad sample of people. It will likely take weeks to sort this out.
Finally, the big concern with Omicron is immune escape. Let’s be clear: It is extremely unlikely that Omicron will render the Covid-19 vaccines completely ineffective. And right now, there’s not much data on how much the vaccines may be less effective against this variant, although there is reason for concern. Omicron has a large number of mutations, including in the spike protein — the part of the protein that the virus uses to bind to and enter human cells. These areas of the protein are critical for vaccine-induced (and infection-induced) antibodies to protect against the virus. Even small hits to vaccine efficacy will leave us more vulnerable to infection and illness and can make it harder to contain the virus.
The Biden administration just announced a travel ban against foreign nationals coming from eight African countries. This will slow the spread of the virus into the United States by a modest amount at best. And it sends a negative signal to South Africa, which has done an extraordinary job in first identifying the variant and then quickly sharing the information with the global community. Whether the travel ban will be worth it or not is far from clear.
But there are things the Biden administration can do to prepare the country.
The United States must support ongoing studies that help researchers answer the key questions about how transmissible the variant is, whether it causes more severe disease and whether it can evade immunity. This will give health authorities a more complete picture as quickly as possible.
Second, the United States must ramp up genomic surveillance — monitoring viral genes and how they evolve over time — to identify Omicron when it arrives and track it as it potentially spreads through the country. The United States has been a surprising laggard on genomic sequencing and must do better.
American leaders should also start talking with vaccine makers about the potential need to create Omicron-specific vaccines. It may not be needed, but if there is a large hit to vaccine efficacy then new vaccine shots will be critical.
Lastly, America must push for a global effort to get more people in Africa vaccinated. While global vaccinations have been rising quickly, much of the African continent has been left behind. In South Africa, just under a quarter of the population has been fully vaccinated.
It has been a long pandemic thus far, but let’s remember that this is not a reset to March of last year — the world has the means to manage this variant. Let’s use them.
https://www.nytimes.com/2021/11/27/opin ... virus.html
Nov. 27, 2021
By Ashish Jha
Dr. Jha is the dean of the Brown University School of Public Health.
Every few months, the world learns of a new variant of the coronavirus. While most of these variants turn out to be inconsequential, some, like the Delta variant, are immensely consequential. The latest, B.1.1.529, now known as the Omicron variant, bears very close watching because of concerns that it may spread more quickly than Delta, possibly even among the vaccinated. It is essential that world leaders respond quickly and aggressively even before all the data about this variant emerge.
In the days ahead, as information builds, it will be tempting to give in to fear or indifference. We cannot succumb to either. The global community must take each variant seriously. Acting early is far superior to waiting until all the facts are in. It may turn out that the variant is not more contagious or that it responds perfectly well to our current vaccines. In that latter fortuitous scenario, the current response may be seen as an overreaction. But if this variant, with all of its concerning features, turns out to be as contagious and immune-evasive as many experts worry it might be, waiting until all the facts are in will leave us hopelessly far behind.
How worrisome is Omicron? There are three key questions that help scientists understand how consequential any variant might be.
The first question is whether the variant is more transmissible than the current, prevalent Delta strain? Second, does it cause more severe disease? And third, will it render our immune defenses — from vaccines and prior infections — less effective (a phenomenon known as immune escape)?
On transmissibility, the data, while early, look worrisome. This new variant appears to have taken off very quickly in South Africa, with early national data suggesting the variant already makes up the majority of sequenced cases in the country. It’s possible that this early data will be revised as epidemiologists look closer at factors other than transmissibility, such as whether an early Omicron superspreader event led to the variant appearing more highly contagious than it really is. While this is possible, the more likely scenario is that Omicron does spread more easily than Delta.
Because the variant is so new, scientists simply do not have adequate data yet to assess whether the new variant causes more severe disease. Answering this question will require careful case tracking in hospitals along with expanded viral sequencing efforts, both in South Africa and elsewhere. A key part of this analysis is ensuring that countries are doing adequate testing of a broad sample of people. It will likely take weeks to sort this out.
Finally, the big concern with Omicron is immune escape. Let’s be clear: It is extremely unlikely that Omicron will render the Covid-19 vaccines completely ineffective. And right now, there’s not much data on how much the vaccines may be less effective against this variant, although there is reason for concern. Omicron has a large number of mutations, including in the spike protein — the part of the protein that the virus uses to bind to and enter human cells. These areas of the protein are critical for vaccine-induced (and infection-induced) antibodies to protect against the virus. Even small hits to vaccine efficacy will leave us more vulnerable to infection and illness and can make it harder to contain the virus.
The Biden administration just announced a travel ban against foreign nationals coming from eight African countries. This will slow the spread of the virus into the United States by a modest amount at best. And it sends a negative signal to South Africa, which has done an extraordinary job in first identifying the variant and then quickly sharing the information with the global community. Whether the travel ban will be worth it or not is far from clear.
But there are things the Biden administration can do to prepare the country.
The United States must support ongoing studies that help researchers answer the key questions about how transmissible the variant is, whether it causes more severe disease and whether it can evade immunity. This will give health authorities a more complete picture as quickly as possible.
Second, the United States must ramp up genomic surveillance — monitoring viral genes and how they evolve over time — to identify Omicron when it arrives and track it as it potentially spreads through the country. The United States has been a surprising laggard on genomic sequencing and must do better.
American leaders should also start talking with vaccine makers about the potential need to create Omicron-specific vaccines. It may not be needed, but if there is a large hit to vaccine efficacy then new vaccine shots will be critical.
Lastly, America must push for a global effort to get more people in Africa vaccinated. While global vaccinations have been rising quickly, much of the African continent has been left behind. In South Africa, just under a quarter of the population has been fully vaccinated.
It has been a long pandemic thus far, but let’s remember that this is not a reset to March of last year — the world has the means to manage this variant. Let’s use them.
https://www.nytimes.com/2021/11/27/opin ... virus.html
Re: What scientists know about the new variant, B.1.1.529.
Will the Vaccines Stop Omicron? Scientists Are Racing to Find Out.
A “Frankenstein mix” of mutations raises concerns, but the variant may remain vulnerable to current vaccines. If not, revisions will be necessary.
By Apoorva Mandavilli
Nov. 28, 2021
As nations severed air links from southern Africa amid fears of another global surge of the coronavirus, scientists scrambled on Sunday to gather data on the new Omicron variant, its capabilities and — perhaps most important — how effectively the current vaccines will protect against it.
The early findings are a mixed picture. The variant may be more transmissible and better able to evade the body’s immune responses, both to vaccination and to natural infection, than prior versions of the virus, experts said in interviews.
The vaccines may well continue to ward off severe illness and death, although booster doses may be needed to protect most people. Still, the makers of the two most effective vaccines, Pfizer-BioNTech and Moderna, are preparing to reformulate their shots if necessary.
“We really need to be vigilant about this new variant and preparing for it,” said Jesse Bloom, an evolutionary biologist at the Fred Hutchinson Cancer Research Center in Seattle.
“Probably in a few weeks, we’ll have a better sense of how much this variant is spreading and how necessary it might be to push forward with a variant vaccine,” Dr. Bloom said.
Even as scientists began vigorous scrutiny of the new variant, countries around the world curtailed travel to and from nations in southern Africa, where Omicron was first identified. Despite the restrictions, the virus has been found in a half-dozen European countries, including the United Kingdom, as well as Australia, Israel and Hong Kong.
Already, Omicron accounts for most of the 2,300 new daily cases in the province of Gauteng, South Africa, President Cyril Ramaphosa announced on Sunday. Nationally, new infections have more than tripled in the past week, and test positivity has increased to 9 percent from 2 percent.
Scientists have reacted more quickly to Omicron than to any other variant. In just 36 hours from the first signs of trouble in South Africa on Tuesday, researchers analyzed samples from 100 infected patients, collated the data and alerted the world, said Tulio de Oliveira, a geneticist at the Nelson R. Mandela School of Medicine in Durban.
Within an hour of the first alarm, scientists in South Africa also rushed to test coronavirus vaccines against the new variant. Now, dozens of teams worldwide — including researchers at Pfizer-BioNTech and Moderna — have joined the chase.
They won’t know the results for two weeks, at the earliest. But the mutations that Omicron carries suggest that the vaccines most likely will be less effective, to some unknown degree, than they were against any previous variant.
“Based on lots of work people have done on other variants and other mutations, we can be pretty confident these mutations are going to cause an appreciable drop in antibody neutralization,” Dr. Bloom said, referring to the body’s ability to attack an invading virus.
South African doctors are seeing an increase in reinfections in people who already had a bout of Covid-19, suggesting that the variant can overcome natural immunity, said Dr. Richard Lessells, an infectious diseases physician at the University of KwaZulu-Natal.
Omicron has about 50 mutations, including more than 30 in the spike, a viral protein on its surface that the vaccines train the body to recognize and attack.
Some of these mutations have been seen before. Some were thought to have powered the Beta variant’s ability to sidestep vaccines, while others most likely turbocharged Delta’s extreme contagiousness.
“My best guess is that this combines both of those elements,” Penny Moore, a virologist at the National Institute for Communicable Diseases in South Africa, said of the new variant.
But Omicron also has 26 unique spike mutations, compared with 10 in Delta and six in Beta. Many of them seem likely to render the variant more difficult for the immune system to recognize and thwart.
“There are many we’ve never studied before, but just looking at the location on the spike, they are in regions that we know are immuno-dominant,” Dr. Moore said, referring to parts of the spike protein that interact with the body’s immune defenses.
Dr. Moore’s team is perhaps the furthest along in testing how well the vaccines hold up against Omicron. She and her colleagues are preparing to test blood from fully immunized people against a synthetic version of the Omicron variant.
Creating such a “pseudovirus” — a viral stand-in that contains all of the mutations — takes time, but results may be available in about 10 days.
To more closely mimic what people are likely to encounter, another team led by Alex Sigal, a virologist at the Africa Health Research Institute, is growing live Omicron, which will be tested against the blood of fully immunized people, as well as those who were previously infected.
Those results may take longer but should provide a fuller picture of the vaccines’ performance, Dr. Sigal said.
If the vaccines prove to be much less potent against Omicron, they may need to be tweaked to enhance their effectiveness. Preparing for the worst, Moderna, Pfizer-BioNTech and Johnson & Johnson are planning to test an artificial version of Omicron against their vaccines.
The mRNA vaccines in particular — Moderna’s and Pfizer-BioNTech’s — were built with technology that should permit rapid modification. Pfizer’s scientists “can adapt the current vaccine within six weeks and ship initial batches within 100 days in the event of an escape variant” that eludes the immune system, said Jerica Pitts, a spokeswoman for Pfizer.
Moderna’s work began on Tuesday, immediately after its scientists learned of Omicron — the fastest the company has ever responded to a variant, said Dr. Stephen Hoge, Moderna’s president.
Even without data on Omicron’s spread, it was obvious the variant would be a formidable threat to vaccines, he said.
“This thing is a Frankenstein mix of all of the greatest hits,” Dr. Hoge said, referring to the variant’s many concerning mutations. “It just triggered every one of our alarm bells.”
Moderna could update its current vaccine in about two months and have clinical results in about three months if necessary, he said.
Both companies also plan to test whether booster shots will bolster the immune system enough to fend off the new variant. Boosters of the Pfizer-BioNTech and Moderna vaccines have been shown to raise antibody levels significantly.
But those antibodies may not be broadly effective against every iteration of the virus, and may not be enough to neutralize Omicron entirely, said Michel Nussenzweig, an immunologist at Rockefeller University in New York.
People who recover from Covid and then receive even one dose of a vaccine tend to produce a broader range of antibodies, capable of recognizing more versions of the virus, than do people who are only vaccinated.
“It’s clear that hybrid immunity, the kind that people get when they are both infected and vaccinated, is superior, and that is very, very likely to take care of this thing, too,” Dr. Nussenzweig said.
“After two doses of vaccine, we did not see that. But we’re hoping that after three doses, maybe there’ll be some catching up,” he said.
Dr. Nussenzweig and his colleagues are preparing to test Omicron against the mRNA vaccines, as well as the vaccines made by Johnson & Johnson and AstraZeneca. They hope to have results within a month.
Omicron-specific vaccines created in just weeks would be a miraculous feat. But the prospect of producing and distributing them raises daunting questions.
If new versions are required to protect people everywhere, companies should make them available to the African countries that most need them and can least afford them, Dr. de Oliveira said.
“South Africa at least has managed to procure their own vaccines,” he said. But poorer countries like Sudan, Mozambique, Eswatini and Lesotho will need low-cost options.
Pfizer did not respond to a question about low-cost vaccines for African nations. Dr. Hoge, of Moderna, said the company already had an agreement with the African Union to deliver 110 million doses at $3.50 per half dose of vaccine.
Dr. Hoge said he recognized that 110 million was less than 10 percent of Africa’s population. But, he noted, “we’re also the smallest of all manufacturers out there, and so 10 percent hopefully is useful.”
Despite the frustration that South African scientists have expressed about vaccine inequity and punishing travel restrictions, they have been inundated with requests for genetic sequences of Omicron from Italy, Germany, Australia and New Zealand, as well as labs in North America.
The more teams involved, the better, said Dr. Moore, who received about 50 requests just on Saturday. As the virus moves across the globe, it is likely to keep changing. “Getting the right combination of mutations in itself is a moving target,” she said.
Researchers everywhere want to avoid drawing conclusions prematurely, a mistake they made when the Beta variant surfaced. Preliminary tests of that variant took only one known mutation into account and underestimated its ability to evade the immune system, Dr. Moore recalled. (Fortunately, the variant also turned out to be less contagious.)
To get a full picture of the effectiveness of the vaccines against Omicron, scientists must look not just at antibody levels but also at immune cells that can recognize and destroy infected cells. Immune cells called T cells are crucial for preventing an infection from progressing to serious illness and death.
Some of Omicron’s mutations occur in parts of the virus targeted by T cells, meaning the variant may be more difficult for T cells to recognize.
Already, a computer simulation has predicted that those mutations may alter about six of the hundreds of regions that T cells can recognize, said Wendy Burgers, an immunologist at the University of Cape Town.
That may not seem like much. But people make varying sets of T cells, so depending on which targets the mutations knock out, some people may barely be affected by Omicron — and others may be left vulnerable.
Dr. Burgers is hoping to obtain blood from 50 people infected with the variant to gauge how the mutations will play out across a population. Once the samples are in hand, results will be available after “probably a week of very late nights and analysis,” she said.
Even if the vaccines hold up against Omicron, new versions will probably be needed at some point, and perhaps soon. The virus is acquiring mutations much faster than expected, Dr. Bloom said.
Seasonal influenza is the often cited example of a virus that mutates quickly, requiring regular updates to vaccines. But the coronavirus is “at least comparable and possibly even faster than that,” Dr. Bloom said. “There’s always going to be new variants arising.”
Lynsey Chutel contributed reporting from South Africa.
https://www.nytimes.com/2021/11/28/heal ... unity.html
A “Frankenstein mix” of mutations raises concerns, but the variant may remain vulnerable to current vaccines. If not, revisions will be necessary.
By Apoorva Mandavilli
Nov. 28, 2021
As nations severed air links from southern Africa amid fears of another global surge of the coronavirus, scientists scrambled on Sunday to gather data on the new Omicron variant, its capabilities and — perhaps most important — how effectively the current vaccines will protect against it.
The early findings are a mixed picture. The variant may be more transmissible and better able to evade the body’s immune responses, both to vaccination and to natural infection, than prior versions of the virus, experts said in interviews.
The vaccines may well continue to ward off severe illness and death, although booster doses may be needed to protect most people. Still, the makers of the two most effective vaccines, Pfizer-BioNTech and Moderna, are preparing to reformulate their shots if necessary.
“We really need to be vigilant about this new variant and preparing for it,” said Jesse Bloom, an evolutionary biologist at the Fred Hutchinson Cancer Research Center in Seattle.
“Probably in a few weeks, we’ll have a better sense of how much this variant is spreading and how necessary it might be to push forward with a variant vaccine,” Dr. Bloom said.
Even as scientists began vigorous scrutiny of the new variant, countries around the world curtailed travel to and from nations in southern Africa, where Omicron was first identified. Despite the restrictions, the virus has been found in a half-dozen European countries, including the United Kingdom, as well as Australia, Israel and Hong Kong.
Already, Omicron accounts for most of the 2,300 new daily cases in the province of Gauteng, South Africa, President Cyril Ramaphosa announced on Sunday. Nationally, new infections have more than tripled in the past week, and test positivity has increased to 9 percent from 2 percent.
Scientists have reacted more quickly to Omicron than to any other variant. In just 36 hours from the first signs of trouble in South Africa on Tuesday, researchers analyzed samples from 100 infected patients, collated the data and alerted the world, said Tulio de Oliveira, a geneticist at the Nelson R. Mandela School of Medicine in Durban.
Within an hour of the first alarm, scientists in South Africa also rushed to test coronavirus vaccines against the new variant. Now, dozens of teams worldwide — including researchers at Pfizer-BioNTech and Moderna — have joined the chase.
They won’t know the results for two weeks, at the earliest. But the mutations that Omicron carries suggest that the vaccines most likely will be less effective, to some unknown degree, than they were against any previous variant.
“Based on lots of work people have done on other variants and other mutations, we can be pretty confident these mutations are going to cause an appreciable drop in antibody neutralization,” Dr. Bloom said, referring to the body’s ability to attack an invading virus.
South African doctors are seeing an increase in reinfections in people who already had a bout of Covid-19, suggesting that the variant can overcome natural immunity, said Dr. Richard Lessells, an infectious diseases physician at the University of KwaZulu-Natal.
Omicron has about 50 mutations, including more than 30 in the spike, a viral protein on its surface that the vaccines train the body to recognize and attack.
Some of these mutations have been seen before. Some were thought to have powered the Beta variant’s ability to sidestep vaccines, while others most likely turbocharged Delta’s extreme contagiousness.
“My best guess is that this combines both of those elements,” Penny Moore, a virologist at the National Institute for Communicable Diseases in South Africa, said of the new variant.
But Omicron also has 26 unique spike mutations, compared with 10 in Delta and six in Beta. Many of them seem likely to render the variant more difficult for the immune system to recognize and thwart.
“There are many we’ve never studied before, but just looking at the location on the spike, they are in regions that we know are immuno-dominant,” Dr. Moore said, referring to parts of the spike protein that interact with the body’s immune defenses.
Dr. Moore’s team is perhaps the furthest along in testing how well the vaccines hold up against Omicron. She and her colleagues are preparing to test blood from fully immunized people against a synthetic version of the Omicron variant.
Creating such a “pseudovirus” — a viral stand-in that contains all of the mutations — takes time, but results may be available in about 10 days.
To more closely mimic what people are likely to encounter, another team led by Alex Sigal, a virologist at the Africa Health Research Institute, is growing live Omicron, which will be tested against the blood of fully immunized people, as well as those who were previously infected.
Those results may take longer but should provide a fuller picture of the vaccines’ performance, Dr. Sigal said.
If the vaccines prove to be much less potent against Omicron, they may need to be tweaked to enhance their effectiveness. Preparing for the worst, Moderna, Pfizer-BioNTech and Johnson & Johnson are planning to test an artificial version of Omicron against their vaccines.
The mRNA vaccines in particular — Moderna’s and Pfizer-BioNTech’s — were built with technology that should permit rapid modification. Pfizer’s scientists “can adapt the current vaccine within six weeks and ship initial batches within 100 days in the event of an escape variant” that eludes the immune system, said Jerica Pitts, a spokeswoman for Pfizer.
Moderna’s work began on Tuesday, immediately after its scientists learned of Omicron — the fastest the company has ever responded to a variant, said Dr. Stephen Hoge, Moderna’s president.
Even without data on Omicron’s spread, it was obvious the variant would be a formidable threat to vaccines, he said.
“This thing is a Frankenstein mix of all of the greatest hits,” Dr. Hoge said, referring to the variant’s many concerning mutations. “It just triggered every one of our alarm bells.”
Moderna could update its current vaccine in about two months and have clinical results in about three months if necessary, he said.
Both companies also plan to test whether booster shots will bolster the immune system enough to fend off the new variant. Boosters of the Pfizer-BioNTech and Moderna vaccines have been shown to raise antibody levels significantly.
But those antibodies may not be broadly effective against every iteration of the virus, and may not be enough to neutralize Omicron entirely, said Michel Nussenzweig, an immunologist at Rockefeller University in New York.
People who recover from Covid and then receive even one dose of a vaccine tend to produce a broader range of antibodies, capable of recognizing more versions of the virus, than do people who are only vaccinated.
“It’s clear that hybrid immunity, the kind that people get when they are both infected and vaccinated, is superior, and that is very, very likely to take care of this thing, too,” Dr. Nussenzweig said.
“After two doses of vaccine, we did not see that. But we’re hoping that after three doses, maybe there’ll be some catching up,” he said.
Dr. Nussenzweig and his colleagues are preparing to test Omicron against the mRNA vaccines, as well as the vaccines made by Johnson & Johnson and AstraZeneca. They hope to have results within a month.
Omicron-specific vaccines created in just weeks would be a miraculous feat. But the prospect of producing and distributing them raises daunting questions.
If new versions are required to protect people everywhere, companies should make them available to the African countries that most need them and can least afford them, Dr. de Oliveira said.
“South Africa at least has managed to procure their own vaccines,” he said. But poorer countries like Sudan, Mozambique, Eswatini and Lesotho will need low-cost options.
Pfizer did not respond to a question about low-cost vaccines for African nations. Dr. Hoge, of Moderna, said the company already had an agreement with the African Union to deliver 110 million doses at $3.50 per half dose of vaccine.
Dr. Hoge said he recognized that 110 million was less than 10 percent of Africa’s population. But, he noted, “we’re also the smallest of all manufacturers out there, and so 10 percent hopefully is useful.”
Despite the frustration that South African scientists have expressed about vaccine inequity and punishing travel restrictions, they have been inundated with requests for genetic sequences of Omicron from Italy, Germany, Australia and New Zealand, as well as labs in North America.
The more teams involved, the better, said Dr. Moore, who received about 50 requests just on Saturday. As the virus moves across the globe, it is likely to keep changing. “Getting the right combination of mutations in itself is a moving target,” she said.
Researchers everywhere want to avoid drawing conclusions prematurely, a mistake they made when the Beta variant surfaced. Preliminary tests of that variant took only one known mutation into account and underestimated its ability to evade the immune system, Dr. Moore recalled. (Fortunately, the variant also turned out to be less contagious.)
To get a full picture of the effectiveness of the vaccines against Omicron, scientists must look not just at antibody levels but also at immune cells that can recognize and destroy infected cells. Immune cells called T cells are crucial for preventing an infection from progressing to serious illness and death.
Some of Omicron’s mutations occur in parts of the virus targeted by T cells, meaning the variant may be more difficult for T cells to recognize.
Already, a computer simulation has predicted that those mutations may alter about six of the hundreds of regions that T cells can recognize, said Wendy Burgers, an immunologist at the University of Cape Town.
That may not seem like much. But people make varying sets of T cells, so depending on which targets the mutations knock out, some people may barely be affected by Omicron — and others may be left vulnerable.
Dr. Burgers is hoping to obtain blood from 50 people infected with the variant to gauge how the mutations will play out across a population. Once the samples are in hand, results will be available after “probably a week of very late nights and analysis,” she said.
Even if the vaccines hold up against Omicron, new versions will probably be needed at some point, and perhaps soon. The virus is acquiring mutations much faster than expected, Dr. Bloom said.
Seasonal influenza is the often cited example of a virus that mutates quickly, requiring regular updates to vaccines. But the coronavirus is “at least comparable and possibly even faster than that,” Dr. Bloom said. “There’s always going to be new variants arising.”
Lynsey Chutel contributed reporting from South Africa.
https://www.nytimes.com/2021/11/28/heal ... unity.html
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