New variant appears to evade immunity and shows signs of being more transmissible
7 DEC 2021
SCIENCE
SCIENCE
The departure terminal at Cape Town International Airport on 3 December. Many countries have halted travel from southern Africa in a bid to slow Omicron’s spread.
DWAYNE SENIOR/BLOOMBERG VIA GETTY
Testing stations and hospital wards in Gauteng, South Africa’s most populous province. A company’s Christmas party in Oslo, Norway, that became a superspreading event. Infection patterns in the United Kingdom.
Scientists are scouring patchy evidence from around the world to better understand Omicron, the new SARS-CoV-2 variant, and what it might mean for the next phase of the pandemic. Three weeks after Omicron was discovered, there are still mostly questions, but a few hints have emerged—some worrisome, others more encouraging.
Researchers are focusing on three key questions: Can Omicron evade immunity from vaccines or previous infections? How transmissible is it? And how much severe disease will it cause?
The most solid clues so far pertain to the first question—and they are not reassuring. The genome alone—with more than 30 mutations in the all-important spike protein—suggested the variant might well be the best yet at dodging our immune defenses. And early data from South Africa seem to confirm that worry: A study published last week that analyzed 35,670 reinfections among nearly 2.8 million positive tests carried out through late November suggested an earlier infection with COVID-19 only offers half as much protection against the new variant as it does against Delta. That’s a sign Omicron is able to escape at least some of the immune system’s defenses, and it suggests COVID-19 vaccines may be less effective against the new variant as well. How big a problem that will become depends on whether vaccinations and previous infections still protect against severe disease, says Justin Lessler, an epidemiologist at the University of North Carolina. Chapel Hill.
Whether Omicron is more transmissible than its predecessors—as both Alpha and Delta were—is harder to judge. Omicron cases in South Africa have risen steeply in the past few weeks, but that could be explained in part by chance or the variant’s ability to infect those who are vaccinated or had a previous infection.
But Jeremy Farrar, head of the Wellcome Trust, sees cause for concern. “The evidence that this is more transmissible is getting stronger every day,” he says. In the United Kingdom, the number of positive polymerase chain reaction tests in which the gene encoding the spike protein cannot be detected (a sign of a likely Omicron infection) is increasing rapidly. In Oslo, a company Christmas party at a restaurant became a superspreading event, with at least 120 people testing positive; 19 cases so far have been confirmed as Omicron. (All attendees were vaccinated and had tested negative before the event.) In Denmark, 53 of 150 high school students who attended a party went on to test positive for Omicron.
“None of this alone tells us that this is more transmissible,” says Kristian Andersen, an infectious disease researcher at Scripps Research. Superspreading events, for instance, have been a hallmark of SARS-CoV-2 from the start. “But Omicron is really rare still, so the fact that we see early cases being associated with superspreading events is quite concerning,” Andersen says.
Early signs that Omicron causes less severe symptoms than previous variants offer some reassurance. Doctors in South Africa are reportedly seeing a larger proportion of mild COVID-19 cases in the hospital than at the start of earlier waves. The number of hospital patients infected with SARS-CoV-2 has been rising rapidly, but that includes “incidental” cases—patients seeking care for other reasons who test positive for the virus as well. Data through 6 December indicate the number who needed oxygen support was lower than in previous waves, suggesting fewer patients are suffering the serious lung damage from COVID-19 that has put so many in the hospital during the pandemic.
But it’s too early to tell whether Omicron is really more benign. Many early cases in South Africa have been linked to a university outbreak and occurred in young people, who are less susceptible to severe disease. Previous infections could also be providing some protection, as could the steadily climbing vaccination rate in South Africa. Or it might simply be too early to see many serious cases, which can take weeks to develop and always make up a small proportion of the total number. “I haven’t seen anything yet that tells me whether this is as severe or less severe, or more severe,” Farrar says. “At the moment, my working assumption is that the clinical syndrome of illness is the same as previous variants.”
If that assumption holds, but the virus spreads more rapidly than Delta, more people would get severely sick in a short time period, which could mean a huge extra burden on health care systems that are already stretched thin—especially in places with low vaccine uptake and low levels of infection-induced immunity.
Even if Omicron causes milder disease, rapid spread could still quickly overwhelm hospitals in many places. “A small percentage of a large number is still a large number,” says genomicist Mads Albertsen of Aalborg University, who serves on a panel advising the Danish government on SARS-CoV-2 variants. And it’s not just about deaths and hospitalizations, says Mary Bushman, an epidemiologist at Harvard. “Part of what we need to think about is whether it’s causing Long Covid,” Bushman says.
More data from countries with different vaccination patterns will soon give a better picture of the threat Omicron poses. Scientists are particularly interested to see whether people who have had a booster shot are better protected.
In the meantime countries are scrambling to slow the variant’s spread, with few signs of success. Bans against travelers from southern Africa are quickly losing their justification now that the virus seems entrenched in dozens of countries. Denmark, which has identified 183 Omicron cases so far, is trying to contain spread by broadening quarantine rules—asking not just people infected with the new variant and their close contacts to isolate, but also the close contacts of close contacts. But the rapid spread already makes that strategy impractical, Albertsen says.
That means it’s down to the standard defenses such as wearing masks, social distancing, vaccination, testing, and isolation for those who test positive. “It’s doing the basics well that matters, whatever the variant is called,” Farrar says. Maria Van Kerkhove, an epidemiologist at the World Health Organization, says countries should pay extra attention to getting all of their vulnerable people fully vaccinated, including the elderly and those with conditions that can worsen COVID-19. “These are the people that governments should be targeting right now,” she says.
Van Kerkhove is exasperated that with Omicron on their doorstep, many countries in the Northern Hemisphere haven’t done enough to control big winter outbreaks of Delta. “We’re not even out of the middle of this pandemic yet,” she says, “and we’re moving in the wrong direction.”
Testing stations and hospital wards in Gauteng, South Africa’s most populous province. A company’s Christmas party in Oslo, Norway, that became a superspreading event. Infection patterns in the United Kingdom.
Scientists are scouring patchy evidence from around the world to better understand Omicron, the new SARS-CoV-2 variant, and what it might mean for the next phase of the pandemic. Three weeks after Omicron was discovered, there are still mostly questions, but a few hints have emerged—some worrisome, others more encouraging.
Researchers are focusing on three key questions: Can Omicron evade immunity from vaccines or previous infections? How transmissible is it? And how much severe disease will it cause?
The most solid clues so far pertain to the first question—and they are not reassuring. The genome alone—with more than 30 mutations in the all-important spike protein—suggested the variant might well be the best yet at dodging our immune defenses. And early data from South Africa seem to confirm that worry: A study published last week that analyzed 35,670 reinfections among nearly 2.8 million positive tests carried out through late November suggested an earlier infection with COVID-19 only offers half as much protection against the new variant as it does against Delta. That’s a sign Omicron is able to escape at least some of the immune system’s defenses, and it suggests COVID-19 vaccines may be less effective against the new variant as well. How big a problem that will become depends on whether vaccinations and previous infections still protect against severe disease, says Justin Lessler, an epidemiologist at the University of North Carolina. Chapel Hill.
Whether Omicron is more transmissible than its predecessors—as both Alpha and Delta were—is harder to judge. Omicron cases in South Africa have risen steeply in the past few weeks, but that could be explained in part by chance or the variant’s ability to infect those who are vaccinated or had a previous infection.
But Jeremy Farrar, head of the Wellcome Trust, sees cause for concern. “The evidence that this is more transmissible is getting stronger every day,” he says. In the United Kingdom, the number of positive polymerase chain reaction tests in which the gene encoding the spike protein cannot be detected (a sign of a likely Omicron infection) is increasing rapidly. In Oslo, a company Christmas party at a restaurant became a superspreading event, with at least 120 people testing positive; 19 cases so far have been confirmed as Omicron. (All attendees were vaccinated and had tested negative before the event.) In Denmark, 53 of 150 high school students who attended a party went on to test positive for Omicron.
“None of this alone tells us that this is more transmissible,” says Kristian Andersen, an infectious disease researcher at Scripps Research. Superspreading events, for instance, have been a hallmark of SARS-CoV-2 from the start. “But Omicron is really rare still, so the fact that we see early cases being associated with superspreading events is quite concerning,” Andersen says.
Early signs that Omicron causes less severe symptoms than previous variants offer some reassurance. Doctors in South Africa are reportedly seeing a larger proportion of mild COVID-19 cases in the hospital than at the start of earlier waves. The number of hospital patients infected with SARS-CoV-2 has been rising rapidly, but that includes “incidental” cases—patients seeking care for other reasons who test positive for the virus as well. Data through 6 December indicate the number who needed oxygen support was lower than in previous waves, suggesting fewer patients are suffering the serious lung damage from COVID-19 that has put so many in the hospital during the pandemic.
But it’s too early to tell whether Omicron is really more benign. Many early cases in South Africa have been linked to a university outbreak and occurred in young people, who are less susceptible to severe disease. Previous infections could also be providing some protection, as could the steadily climbing vaccination rate in South Africa. Or it might simply be too early to see many serious cases, which can take weeks to develop and always make up a small proportion of the total number. “I haven’t seen anything yet that tells me whether this is as severe or less severe, or more severe,” Farrar says. “At the moment, my working assumption is that the clinical syndrome of illness is the same as previous variants.”
If that assumption holds, but the virus spreads more rapidly than Delta, more people would get severely sick in a short time period, which could mean a huge extra burden on health care systems that are already stretched thin—especially in places with low vaccine uptake and low levels of infection-induced immunity.
Even if Omicron causes milder disease, rapid spread could still quickly overwhelm hospitals in many places. “A small percentage of a large number is still a large number,” says genomicist Mads Albertsen of Aalborg University, who serves on a panel advising the Danish government on SARS-CoV-2 variants. And it’s not just about deaths and hospitalizations, says Mary Bushman, an epidemiologist at Harvard. “Part of what we need to think about is whether it’s causing Long Covid,” Bushman says.
More data from countries with different vaccination patterns will soon give a better picture of the threat Omicron poses. Scientists are particularly interested to see whether people who have had a booster shot are better protected.
In the meantime countries are scrambling to slow the variant’s spread, with few signs of success. Bans against travelers from southern Africa are quickly losing their justification now that the virus seems entrenched in dozens of countries. Denmark, which has identified 183 Omicron cases so far, is trying to contain spread by broadening quarantine rules—asking not just people infected with the new variant and their close contacts to isolate, but also the close contacts of close contacts. But the rapid spread already makes that strategy impractical, Albertsen says.
That means it’s down to the standard defenses such as wearing masks, social distancing, vaccination, testing, and isolation for those who test positive. “It’s doing the basics well that matters, whatever the variant is called,” Farrar says. Maria Van Kerkhove, an epidemiologist at the World Health Organization, says countries should pay extra attention to getting all of their vulnerable people fully vaccinated, including the elderly and those with conditions that can worsen COVID-19. “These are the people that governments should be targeting right now,” she says.
Van Kerkhove is exasperated that with Omicron on their doorstep, many countries in the Northern Hemisphere haven’t done enough to control big winter outbreaks of Delta. “We’re not even out of the middle of this pandemic yet,” she says, “and we’re moving in the wrong direction.”
ABOUT THE AUTHORS
Kai Kupferschmidt
Author
Kai is a contributing correspondent for Science magazine based in Berlin, Germany. He is the author of a book about the color blue, published in 2019.
Gretchen Vogel
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Author
Gretchen Vogel is a contributing correspondent for Science magazine based in Berlin, Germany.
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