We have a new COVID-19 variant—BA.2.86—turning heads even among the calm, cool, and collected scientists. This is what we know, what we don’t know, and what’s likely next. What is happening? SARS-CoV-2 continues to mutate. This is expected, as this is what viruses do to survive. There was ~20% possibility of another “Omicron-like event” in 2023. Since Omicron arrived on the scene in November 2021, we’ve only seen incremental changes, which have created a ladder-like pattern (see panel A below). This is a good thing—we
Like others who have already commented, the thing that strikes me most about this post is how marvelous you are, Katelyn. The work you do to stay on top of the scientific information and then present it to the rest of us in clear, straightforward prose is unexcelled in its skill and its value. Thank you!
1. Why not a spillover from any of the many animal reservoirs? Seems more than possible, as does the immuno-comp option. Not sure the origin is even knowable—and it’s somewhat academic.
2. Where does/did the 20% chance of a major set of mutations come from? Seems pretty arbitrary. How can anyone possibly know the future evolutionary morphospace of this virus?
One comment: evolutionary rates are not guaranteed to be slow and additive. We have erected a permanent global selective pressure to escape immunity.
3. “This is because SARS-CoV-2 has historically evolved to escape antibodies (first line of defense) rather than T-cells (second line of defense) that primarily protect us from severe disease.”
That’s no guarantee that it won’t ever start eating into the second line of defense. Is there something about its structural biology (or our immune systems, etc) that constrains such a move? Because “it hasn’t happened yet” is a thin reed.
Close cousins of this virus have much higher death rates. Like, 15% for Sars and ~40% for Mers. If this virus can jack up its death rate while maintaining sufficient infectivity—and we are obviously going to let it “figure it out” as we are doing nothing—then we are screwed.
Any biophysical, genetic, or any other reason(s) to think this is impossible?
4. Sure, there has to be a ceiling to infectivity but how do we know what it is?
We’ll of course find out, and if this is bad, we’ll be hit hard, with less excuse than we had in 2020, which was already pretty close to zero.
5. If the upcoming vax formula doesn’t help, will companies provide a new one? Will the govt pay? Will we simply have to have more mass death before anyone takes advantage of the much hyped miracle of fast mRNA production and distribution?
Flying nearly blind, as you said; didn’t ventilate buildings; and all the rest. We had the chance; we blew it off.
At least here, we might luck out (sooner or later, we won’t, of course, whatever the epidemic pathogen).
Carbon? Nukes? Entirely and literally guaranteed to crush us—and we are doing net-nothing. Less than net-nothing.
2. This was estimated (and he continues to update us) by Trevor Bedford, who specializes in viral evolution. I’ll find the slide deck for you.
3. This is correct, but at this point we are making educated guesses.
4. Agree
5. It’s very unlikely that the companies could turn around and update vaccine. I think we will just take XBB vaccine and focus on preventing severe disease
Nukes haven't destroyed humanity in the last 78 years. Big Bangs are understood by even politicians.
Carbon? Scientific capitalism is hard at work: atmospheric and oceanic carbon capture is rapidly approaching scale and profitability. But timelines and politics are serious issues.
And just to tickle your thoughts - 9 billion (9,000,000,000) of us on the globe produce 95 metric tons of carbon, just by breathing. Unprecedented. Every day.
Spillover from animal reservoir - yes, how can scientists be so sure the new variant with a staggering 36 mutations came from an immunocompromised human?
There are also worse possibilities - rogue scientist?
Relatively large jumps come from recombination, as I understand it—perhaps “hybridization” is a better term—of multiple forms of the virus. That has to happen in some animal, whether us, deer, whatever.
Rogue scientist is pretty unlikely. Things are potentially bad enough (potentially) without bringing in such possibilities.
I kind of wonder whether covid's ability to infect a wide range of animals could actually be useful for surveillance. For instance, if I did ever develop a very highly infectious bout of covid in my 1 BR apartment, I'd almost certainly pass it to my cat.
Good one! Whenever a few possible explanations exist, and Science is certain only one explanation is valid and the others don't merit investigation, I become skeptical.
My question for YLE: is Long COVID something we shoule be worried about? That's a rhetorical question. We know it is. That makes we wonder why it is not mentioned in this post.
I'm sorry if this is something that you're dealing with, but I think it's OK for our heroine to discuss one subject at a time. She's got lots of other entries that discuss Long Covid and its ramifications and generally avoids loaded terms like "worry" in favor of conveying information.
I appreciate your understanding, but I disagree with you re: Long COVID being a different subject. Anything related to C19 infections warrants consideration of risks from Long COVID. There's even a section of this post on "What we don't know." A reference to the uncertainty re: Long COVID risks would be very appropriate there. With any C19 infection, there's more to worry about than "severe illness."
I'm not saying it's not part of the larger subject of Covid. I just think it's OK to focus on one subtopic at a time in what's basically a short form medium.
I think our disagreement is on how narrow that focus can be. I think that when the topic is C19 infections, Long COVID is by definition relevant. But, I also see a larger issue. There are many in our society who very deliberately discount or ignore Long COVID, and some who dismiss it outright as nonexistent. That's why I get concerned when forums like this one seem comfortable with ignoring it, because it feeds those other narratives.
Thank you. If I understand correctly, it sounds as if the jury is out about whether the OTC swab tests will detect a positive case of this. I hope I misunderstood.
We’ve been considering investing in one of the 3 FDA-approved at-home molecular tests, specifically for our elderly relatives. The XBB strains don’t seem to pop up positive on antigen tests until just at (or after) the window for starting Paxlovid. If the molecular tests pick up infections data faster, we can get our loved ones on Paxlovid faster. We will be hoping someone somewhere confirms that this new variant is detected quickly by the at home molecular tests, so if you see that information in the coming weeks, could you please link to it?
Thank you (understatement)! Is it likely the home "PCR" (molecular, *not* antigen based) tests will detect the new variant? (Unfortunately Lucira no longer makes these tests but there are others - none of them are cheap though)
I missed it if she talked about any change to antigen tests detecting it. If they don't, that certainly would explain the lack of cases given it shows up in wastewater samples. She did say that PCR tests could differentiate it from the other circulating variants (don't need to do a genetic sequence to differentiate it).
Drive thru testing at Walgreen’s and urgent care/doctor where I live. But, when my son had Covid in March, urgent care would not test him because “it’s not a big deal anymore.”
Very hard to get one. My kids used to get one every time they came to visit for a while - long weekends etc. Virtually the day after the Emergency was lifted in May, they couldn't find a location in all of Boston. Finally found a couple, but of course the cost was huge. "It's all over" so no "gold standard" testing is necessary.
Here are a couple of options for finding testing. No guarantee on what *types* of test will be available there, but my hope is that PCR should be available at many if not most:
TL; DR: They should still work, but we don't know for certain until we see how things go in the real world.
Long version:
All of the tests, (to my knowledge) target at least one gene that is NOT involved with the spike protein, so changes there should not change the ability of any test to detect the virus. This includes OTC tests both antigen and molecular (PCR and LAMP), as well as non-OTC tests.
However, if changes happen in the area that most tests DO look at (much less likely, because that gene deals with the virus's coating), that would be a much bigger problem.
The sensitivity of the tests is a different issue. We won't know what that is until we see the tests in action.
Thank you for this timely and informative post. Why, do you think, is public health “searching in the dark”? One would think that governments would strengthen sentinel points, not dismantle or weaken them. Are the reasons political, fiscal, denial...all of the above? It’s hard to make sense of it since COVID is here to stay, as is its ongoing mutation. Shouldn’t those entrusted with safeguarding public health have all the tools needed to, well, safeguard us? Seems like the preparedness lessons our governments should have learned have not stuck.
Thank you again for keeping the public updated and informed. I am so grateful. I also wanted to know whether the typical home test will be sensitive and specific in detecting this new version of Covid. And I was curious to see maps, as they emerge, of the geographical spread of BA 2.86.
Thank you for being a model for science reporting, Dr. Jetelina! Calm balanced, curiously skeptical when appropriate (which is a lot of the time with science - if only the media and public agencies did that). Question: What are some examples of viruses that have followed Path B (the non-ladder)? Also - are there (or should there be) vaccines that target (or incite our making antibodies to) parts of the virus other than spike, and which 'evolve' much less than the spike component? With natural infection, do we make antibodies to both spike and other parts of SARS-Cov2?
Good question. Flu and other coronaviruses mutate like Panel A. This is why we expect C19 to eventually follow this pattern.
Measles represents Panel B, for example. While measles mutates, it does not mutate to escape immunity. It has a more balanced evolutionary tree. There is no immune pressure that constantly pushes one mutation to outcompete another. So there is no ladder-like pattern. And, thankfully, our vaccines from the mid-1960s still work today.
I'll join the "thank you's", for your calm, objective, interpretation of the latest in the Covid evolution. On my personal level, of course, this information is frightening, maybe not as much as when this pandemic began, but still...back to "shields up and good luck!"
Yes, but if the other currently circulating variants light up 3 channels, then only those that light up 2 channels would need to be sequenced to confirm BA.2.86.
If this means what I think it does (Dr. J, please correct me if I'm wrong):
TL;DR: Right now the only circulating variant that only "lights up two channels" is BA.2.86. The others that are in circulation right now light up all three. The "channels" refer to the three genes that are targeted by ThermoFisher's TaqPath PCR test, which a lot of labs use.
Long version:
Oddly (and luckily) enough, ever since the Alpha variant arrived, each succeeding wave of COVID in the US either has lit up all three channels or has lit up only two, as follows:
Alpha: two → Delta: three → original Omicron: two → XBB.1.5: three → BA.2.86: two
What that means in practice: If you're using the TaqPath test and a sample tests positive, you can tell which variant is in the sample. If it lights up three channels, it's XBB.1.5 (or maybe EG.5? not sure about that one). If it only lights up two channels, it's BA.2.86.
Thank you. You are a highly trustworthy source of information on this evolving saga. I was planning on getting another booster in October, but I wonder if the available mixture will include the new variant by then.
Thank you, again, for calm and comprehensive comment on what's happening. You are making a difference.
Thank you. This is unwelcome but extremely valuable news. Appreciate your comprehensive and well organized presentation of it.
Second all of this. Very grateful to Dr. Jetelina for this clear, timely information.
Like others who have already commented, the thing that strikes me most about this post is how marvelous you are, Katelyn. The work you do to stay on top of the scientific information and then present it to the rest of us in clear, straightforward prose is unexcelled in its skill and its value. Thank you!
Some questions:
1. Why not a spillover from any of the many animal reservoirs? Seems more than possible, as does the immuno-comp option. Not sure the origin is even knowable—and it’s somewhat academic.
2. Where does/did the 20% chance of a major set of mutations come from? Seems pretty arbitrary. How can anyone possibly know the future evolutionary morphospace of this virus?
One comment: evolutionary rates are not guaranteed to be slow and additive. We have erected a permanent global selective pressure to escape immunity.
3. “This is because SARS-CoV-2 has historically evolved to escape antibodies (first line of defense) rather than T-cells (second line of defense) that primarily protect us from severe disease.”
That’s no guarantee that it won’t ever start eating into the second line of defense. Is there something about its structural biology (or our immune systems, etc) that constrains such a move? Because “it hasn’t happened yet” is a thin reed.
Close cousins of this virus have much higher death rates. Like, 15% for Sars and ~40% for Mers. If this virus can jack up its death rate while maintaining sufficient infectivity—and we are obviously going to let it “figure it out” as we are doing nothing—then we are screwed.
Any biophysical, genetic, or any other reason(s) to think this is impossible?
4. Sure, there has to be a ceiling to infectivity but how do we know what it is?
We’ll of course find out, and if this is bad, we’ll be hit hard, with less excuse than we had in 2020, which was already pretty close to zero.
5. If the upcoming vax formula doesn’t help, will companies provide a new one? Will the govt pay? Will we simply have to have more mass death before anyone takes advantage of the much hyped miracle of fast mRNA production and distribution?
Flying nearly blind, as you said; didn’t ventilate buildings; and all the rest. We had the chance; we blew it off.
At least here, we might luck out (sooner or later, we won’t, of course, whatever the epidemic pathogen).
Carbon? Nukes? Entirely and literally guaranteed to crush us—and we are doing net-nothing. Less than net-nothing.
Gosh these are good questions. Going to take it one at a time.
1. Yes could be reverse zoonosis. In fact, there was evidence presented today (after post) that it may be. See here: https://x.com/solidevidence/status/1693998034617778435?s=46&t=EHMZfYCqU3td2UlR84uRhw We still have a lot to learn
2. This was estimated (and he continues to update us) by Trevor Bedford, who specializes in viral evolution. I’ll find the slide deck for you.
3. This is correct, but at this point we are making educated guesses.
4. Agree
5. It’s very unlikely that the companies could turn around and update vaccine. I think we will just take XBB vaccine and focus on preventing severe disease
Thanks!
Yo, Doug -
Nukes haven't destroyed humanity in the last 78 years. Big Bangs are understood by even politicians.
Carbon? Scientific capitalism is hard at work: atmospheric and oceanic carbon capture is rapidly approaching scale and profitability. But timelines and politics are serious issues.
And just to tickle your thoughts - 9 billion (9,000,000,000) of us on the globe produce 95 metric tons of carbon, just by breathing. Unprecedented. Every day.
Spillover from animal reservoir - yes, how can scientists be so sure the new variant with a staggering 36 mutations came from an immunocompromised human?
There are also worse possibilities - rogue scientist?
Relatively large jumps come from recombination, as I understand it—perhaps “hybridization” is a better term—of multiple forms of the virus. That has to happen in some animal, whether us, deer, whatever.
Rogue scientist is pretty unlikely. Things are potentially bad enough (potentially) without bringing in such possibilities.
I kind of wonder whether covid's ability to infect a wide range of animals could actually be useful for surveillance. For instance, if I did ever develop a very highly infectious bout of covid in my 1 BR apartment, I'd almost certainly pass it to my cat.
Or...wait for it...an immunocompromised animal! Like a cat with untreated FIV
Good one! Whenever a few possible explanations exist, and Science is certain only one explanation is valid and the others don't merit investigation, I become skeptical.
We need a chalkboard
Thank you. Wondering if it would be timely to re-up vaccination? Last shot was October 2022.
It would be, watch for news next month regarding availability of new vaccines.
We are so stinking grateful for your calm, comprehensive reporting. Thank you!
My question for YLE: is Long COVID something we shoule be worried about? That's a rhetorical question. We know it is. That makes we wonder why it is not mentioned in this post.
I'm sorry if this is something that you're dealing with, but I think it's OK for our heroine to discuss one subject at a time. She's got lots of other entries that discuss Long Covid and its ramifications and generally avoids loaded terms like "worry" in favor of conveying information.
I appreciate your understanding, but I disagree with you re: Long COVID being a different subject. Anything related to C19 infections warrants consideration of risks from Long COVID. There's even a section of this post on "What we don't know." A reference to the uncertainty re: Long COVID risks would be very appropriate there. With any C19 infection, there's more to worry about than "severe illness."
I'm not saying it's not part of the larger subject of Covid. I just think it's OK to focus on one subtopic at a time in what's basically a short form medium.
I think our disagreement is on how narrow that focus can be. I think that when the topic is C19 infections, Long COVID is by definition relevant. But, I also see a larger issue. There are many in our society who very deliberately discount or ignore Long COVID, and some who dismiss it outright as nonexistent. That's why I get concerned when forums like this one seem comfortable with ignoring it, because it feeds those other narratives.
That's quite unnecessary. And somewhat insulting. So, let's call this thread closed.
Thank you. If I understand correctly, it sounds as if the jury is out about whether the OTC swab tests will detect a positive case of this. I hope I misunderstood.
Jury is still out, but we are hopeful that they will. TBD.
We’ve been considering investing in one of the 3 FDA-approved at-home molecular tests, specifically for our elderly relatives. The XBB strains don’t seem to pop up positive on antigen tests until just at (or after) the window for starting Paxlovid. If the molecular tests pick up infections data faster, we can get our loved ones on Paxlovid faster. We will be hoping someone somewhere confirms that this new variant is detected quickly by the at home molecular tests, so if you see that information in the coming weeks, could you please link to it?
Thank you (understatement)! Is it likely the home "PCR" (molecular, *not* antigen based) tests will detect the new variant? (Unfortunately Lucira no longer makes these tests but there are others - none of them are cheap though)
I missed it if she talked about any change to antigen tests detecting it. If they don't, that certainly would explain the lack of cases given it shows up in wastewater samples. She did say that PCR tests could differentiate it from the other circulating variants (don't need to do a genetic sequence to differentiate it).
Where can a person get a PCR test these days? Most of the centers have been shut, because “covid is over.”
Drive thru testing at Walgreen’s and urgent care/doctor where I live. But, when my son had Covid in March, urgent care would not test him because “it’s not a big deal anymore.”
Very hard to get one. My kids used to get one every time they came to visit for a while - long weekends etc. Virtually the day after the Emergency was lifted in May, they couldn't find a location in all of Boston. Finally found a couple, but of course the cost was huge. "It's all over" so no "gold standard" testing is necessary.
I wouldn't necessarily call PCR the "gold standard":
https://www.nytimes.com/2020/08/29/health/coronavirus-testing.html
Here are a couple of options for finding testing. No guarantee on what *types* of test will be available there, but my hope is that PCR should be available at many if not most:
https://www.hhs.gov/coronavirus/community-based-testing-sites/index.html
https://testinglocator.cdc.gov/
At this point I'm interpreting "get a PCR test" as "see my doctor if I have covid-like symptoms and get tested if he thinks it's warranted."
TL; DR: They should still work, but we don't know for certain until we see how things go in the real world.
Long version:
All of the tests, (to my knowledge) target at least one gene that is NOT involved with the spike protein, so changes there should not change the ability of any test to detect the virus. This includes OTC tests both antigen and molecular (PCR and LAMP), as well as non-OTC tests.
However, if changes happen in the area that most tests DO look at (much less likely, because that gene deals with the virus's coating), that would be a much bigger problem.
The sensitivity of the tests is a different issue. We won't know what that is until we see the tests in action.
Thank you for this timely and informative post. Why, do you think, is public health “searching in the dark”? One would think that governments would strengthen sentinel points, not dismantle or weaken them. Are the reasons political, fiscal, denial...all of the above? It’s hard to make sense of it since COVID is here to stay, as is its ongoing mutation. Shouldn’t those entrusted with safeguarding public health have all the tools needed to, well, safeguard us? Seems like the preparedness lessons our governments should have learned have not stuck.
Thank you again for keeping the public updated and informed. I am so grateful. I also wanted to know whether the typical home test will be sensitive and specific in detecting this new version of Covid. And I was curious to see maps, as they emerge, of the geographical spread of BA 2.86.
Thank you for being a model for science reporting, Dr. Jetelina! Calm balanced, curiously skeptical when appropriate (which is a lot of the time with science - if only the media and public agencies did that). Question: What are some examples of viruses that have followed Path B (the non-ladder)? Also - are there (or should there be) vaccines that target (or incite our making antibodies to) parts of the virus other than spike, and which 'evolve' much less than the spike component? With natural infection, do we make antibodies to both spike and other parts of SARS-Cov2?
Good question. Flu and other coronaviruses mutate like Panel A. This is why we expect C19 to eventually follow this pattern.
Measles represents Panel B, for example. While measles mutates, it does not mutate to escape immunity. It has a more balanced evolutionary tree. There is no immune pressure that constantly pushes one mutation to outcompete another. So there is no ladder-like pattern. And, thankfully, our vaccines from the mid-1960s still work today.
Where has it shown up in wastewater testing?
Thank you for all you do! I can't imagine trying to navigate this pandemic without your wonderful info! Stay the course.
I'll join the "thank you's", for your calm, objective, interpretation of the latest in the Covid evolution. On my personal level, of course, this information is frightening, maybe not as much as when this pandemic began, but still...back to "shields up and good luck!"
Thank you. You are amazing.
“It lights up 2 channels instead of 3.” Isn’t it possible that other variants could exist or develop that only light up 2 channels?
-family physician, mom of twin girls, scientist, admirer
Yes, but if the other currently circulating variants light up 3 channels, then only those that light up 2 channels would need to be sequenced to confirm BA.2.86.
(I love your signature line)
If this means what I think it does (Dr. J, please correct me if I'm wrong):
TL;DR: Right now the only circulating variant that only "lights up two channels" is BA.2.86. The others that are in circulation right now light up all three. The "channels" refer to the three genes that are targeted by ThermoFisher's TaqPath PCR test, which a lot of labs use.
Long version:
Oddly (and luckily) enough, ever since the Alpha variant arrived, each succeeding wave of COVID in the US either has lit up all three channels or has lit up only two, as follows:
Alpha: two → Delta: three → original Omicron: two → XBB.1.5: three → BA.2.86: two
What that means in practice: If you're using the TaqPath test and a sample tests positive, you can tell which variant is in the sample. If it lights up three channels, it's XBB.1.5 (or maybe EG.5? not sure about that one). If it only lights up two channels, it's BA.2.86.
As a non-doctor I don’t understand what it means to light up 2 vs 3 channels. What does that mean for at home testing (antigen or mooecular)?
Thank you. You are a highly trustworthy source of information on this evolving saga. I was planning on getting another booster in October, but I wonder if the available mixture will include the new variant by then.
Sure seems unlikely in two months, especially given how long it has taken to go from the bivalent to the monovalent.