I hope everyone in the States had a fantastic Thanksgiving (even if you’re a Dallas Cowboys football fan). I hate to ruin the holiday, but… We have a new variant. I’ve not seen this much anxiety ridden chatter among scientists about a COVID19 variant before. Even among the calm, cool, and collected scientists.
Thank you so much for this rapid explanation of what's happening with this new variant. I also appreciated your discussion of travel bans, validating my impression of them as well.
travel bans are reactionary, meaning after the fact. By the time a government enacts a ban it is too late. The Nu variant was in the airplanes, airports, public transportation and hotel spread by the Hong Kong travelers.
This is what I am wondering as well. Many healthcare facilities lean heavily on antigen tests. Thankfully it is pretty easy now to get results from a PCR in under 24-36 hours(at least at the time I am writing this comment). But I really want to know if the current batch of rapid tests would be able to detect Omicron as readily as they have with prior variants given the differences in how the antigen tests work vs PCRs.
"The BinaxNOW™ COVID-19 Antigen Self Test is a lateral flow immunoassay intended for the qualitative detection of nucleocapsid protein antigen from SARS-CoV-2."
BinaxNOW rapid antigen tests detect the N protein. Mutations in the Spike protein don't affect them, so they should work equally well for Omicron as for Delta (etc.)
On the other hand, they also can't distinguish Delta from Omicron.
Hi Dr. Jetelina, if this variant has the ability to evade vaccines, therapies, and natural immunity as South African scientists suggest it may, could we not have both Delta and Omicron hitting us at the same time? Wouldn’t Delta not be able to stop Omicron because Omicron wouldn’t recognize Delta antibodies and be able to reinfect those people? Could people have both Delta and Omicron simultaneously?
Probably not, because antibodies are polyclonal and a constantly evolving population, even during a single infection. The antibodies you make on day 5 of an infection are better tuned to the virus than the antibodies you make on day 1. Also, there's more to the immune system than antibodies. T cells recognize a huge number of possible epitopes. What may happen is an increase in the number of breakthrough infections in vaccinated people, but most of them should still be protected from severe disease.
Reinfection of someone previously infected with Delta is a possibility. But the gold standard, hybrid immunity (previous infection/recovery followed by vaccination) seems to block a huge variety of variants. So get vaccinated, even if you were previously infected/recovered.
Do we know how this is going to affect the vaccine trials for under 5s? If that vaccine is eventually approved but we're dealing with Omicron now, will our kids have to wait even longer for no real reason again?
No, there's no systematic variant genotyping of breakthrough infections. A small percentage of positive PCR tests are sent for sequencing to track the emergence of new variants. One advantage for tracking Omicron is that it can be distinguished from Delta by PCR, because there's a deletion in the S gene that causes that channel to drop out on the qPCR. This potentially opens up the entire data set of PCR testing for variant tracking.
Is there any evidence to support you hypothesis that "So this likely means it mutated over time in one, likely immunocompromised, individual" What if we find that the mutations arose in a fully vaccinated individual? What if we find they occurred in an animal reservoir?
There are case studies tracking the diversity of variants in long-term infected, immunocompromised people, showing this kind of clonal evolution. In some cases it's happened over a period of months. In contrast, vaccinated people with breakthrough infections clear the virus *more* quickly than unvaccinated, so there's even less time for the virus to mutate and evolve in-host.
I find this concerning: "mRNA vaccines are really easy to alter. Once the minor change is made, only 2 dozen people need to enroll in a trial to make sure the updated vaccine works. Then it can be distributed to arms. Because the change is small, an updated vaccine doesn’t need Phase III trials and/or regularity approval. " Where is this codified? In what kind of "trial"? A challenge trial?
it would be a phase I trial. it would be like a flu vaccine every year. we don't have a new formula go through regulatory approval each year, that's because the formula is just changed a little for new variants.
@Katelyn, where are you getting your new variant info? I need an early source. Right now, for B.1.1.529, that was you. Thanks for the in-depth information. I'm now officially concerned.
honestly I just follow scientists (other epidemiologists and virologists) around the world on twitter. for example, Tom Peacock was the first to discover this variant and input it into GSAID
"The BinaxNOW™ COVID-19 Antigen Self Test is a lateral flow immunoassay intended for the qualitative detection of nucleocapsid protein antigen from SARS-CoV-2."
BinaxNOW rapid antigen tests detect the N protein. Mutations in the Spike protein don't affect them, so they should work equally well for Omicron as for Delta (etc.)
Read it'll be 100 days from now to shots in arm for reconfigured mRNA vaccine. Let's hope Omicron isn't much more transmissable than Delta so it'll take a long time to edge it out. Delta R0 is something like 6-7 - a beast of a respiratory virus. Hard to imagine something beating it by much...
That’s what I was coming to ask as well. My youngest gets her second dose of Pfizer tomorrow. I just want my life back. And convincing people to get another. Vaccine is going to be a nightmare.
I disagree -- speaking for my family (all vaccinated and boosted) we will roll up our sleeves for another vaccine, no problem. Those who've resisted thus far, will resist. I don't think anything has changed.
My husband has gotten all three willingly and will keep doing so because I can be a pain in the kiester but was wondering last week when we got our boosters at how many we are getting and how many times they will change their mind on what we need. He is pro-vaccine but people have their limits.
Yes, but for many families, even getting the two shot sequence was difficult, even with our County Department of Health scheduling at home visits. People have caregiving duties or no transportation or no broadband access or no primary care physician or an unpredictable work schedule. I know in my county, they are still working to get hard to reach people to get the original vaccine - these are mostly in urban and rural areas, for more similar reasons than you might think.
I completely understand that there are people who may have limits. I don't agree that "they" keep changing their minds as to what we need. I believe we'd ultimately have to give credit to the virus for that.
The tolerance for, and acceptance of, the fact that there will inevitably be new/more/ worse mutations/ viruses which will then lead to development of updated vaccines/ boosters in general as time goes on, has to be done on an individual level. If we all accept what is known at the moment, while understanding it can- and likely will-change; we could determine what reasonabe/proactive/ protective steps could be done in our day to day lives.
Bottom line? Going forward I think we all, as residents on planet Earth, will truly need to reevaluate what we consider inconvenient and why.
I think Charity is right, especially for younger people. My college age son and friends can't yet be convinced that getting a booster is worth it. And I am much more cognizant of my schedule now and got my booster over the Thanksgiving holiday because I have Friday and Monday off. I really don't want to take any more time off for vaccine side effects, and I have a more flexible job than most.
Well, one meaning of the word "Nu" in Yiddish is "Well?" As in, "Well, what did you expect????"
Thank you for sharing such a thorough summary collated in a short period of time
Thank you so much for this rapid explanation of what's happening with this new variant. I also appreciated your discussion of travel bans, validating my impression of them as well.
travel bans are reactionary, meaning after the fact. By the time a government enacts a ban it is too late. The Nu variant was in the airplanes, airports, public transportation and hotel spread by the Hong Kong travelers.
The other thing that is dumb about them, at least in the US, is that so many people are excluded. Like the virus knows if you are a US citizen or not.
I know, right? It's almost certainly already in the US.
You mentioned PCR tests are able to detect the new variant. What about the antigen tests schools and families are using at home (eg. BinaxNOW)?
This is what I am wondering as well. Many healthcare facilities lean heavily on antigen tests. Thankfully it is pretty easy now to get results from a PCR in under 24-36 hours(at least at the time I am writing this comment). But I really want to know if the current batch of rapid tests would be able to detect Omicron as readily as they have with prior variants given the differences in how the antigen tests work vs PCRs.
"The BinaxNOW™ COVID-19 Antigen Self Test is a lateral flow immunoassay intended for the qualitative detection of nucleocapsid protein antigen from SARS-CoV-2."
BinaxNOW rapid antigen tests detect the N protein. Mutations in the Spike protein don't affect them, so they should work equally well for Omicron as for Delta (etc.)
On the other hand, they also can't distinguish Delta from Omicron.
Very helpful. Thx.
Thank you for the reliable information.
Hi Dr. Jetelina, if this variant has the ability to evade vaccines, therapies, and natural immunity as South African scientists suggest it may, could we not have both Delta and Omicron hitting us at the same time? Wouldn’t Delta not be able to stop Omicron because Omicron wouldn’t recognize Delta antibodies and be able to reinfect those people? Could people have both Delta and Omicron simultaneously?
Co-infection with 2 variants happens occasionally, usually in immunocompromised people.
Probably not, because antibodies are polyclonal and a constantly evolving population, even during a single infection. The antibodies you make on day 5 of an infection are better tuned to the virus than the antibodies you make on day 1. Also, there's more to the immune system than antibodies. T cells recognize a huge number of possible epitopes. What may happen is an increase in the number of breakthrough infections in vaccinated people, but most of them should still be protected from severe disease.
Reinfection of someone previously infected with Delta is a possibility. But the gold standard, hybrid immunity (previous infection/recovery followed by vaccination) seems to block a huge variety of variants. So get vaccinated, even if you were previously infected/recovered.
Thank you so much for your explanation! I’m vaxxed and boosted (Moderna) and wish more people would do the same.
Do we know how this is going to affect the vaccine trials for under 5s? If that vaccine is eventually approved but we're dealing with Omicron now, will our kids have to wait even longer for no real reason again?
One subject that may be of interest to your readers is the surveillance/sequencing effort. Questions like:
Is sequencing performed on all fully vaccinated breakthrough cases in the US?
Is sequencing performed on all partially vaccinated breakthrough cases in the US?
What is the rate of surveillance sequencing on vaccine naive cases the US?
What is the pipeline lag time from specimen collection to sequence availability in the US?
Are break-through specimens prioritized over non-breakthrough in the US?
How are these handled differently in other countries?
No, there's no systematic variant genotyping of breakthrough infections. A small percentage of positive PCR tests are sent for sequencing to track the emergence of new variants. One advantage for tracking Omicron is that it can be distinguished from Delta by PCR, because there's a deletion in the S gene that causes that channel to drop out on the qPCR. This potentially opens up the entire data set of PCR testing for variant tracking.
I would like to know if current B.1.1.529 positive cases appear to cause more severe disease?
I don't think that has been determined yet.
Too soon to tell
Is there any evidence to support you hypothesis that "So this likely means it mutated over time in one, likely immunocompromised, individual" What if we find that the mutations arose in a fully vaccinated individual? What if we find they occurred in an animal reservoir?
It's my understanding that most major variants appear to have emerged in this way - "supermutators" if you will
There are case studies tracking the diversity of variants in long-term infected, immunocompromised people, showing this kind of clonal evolution. In some cases it's happened over a period of months. In contrast, vaccinated people with breakthrough infections clear the virus *more* quickly than unvaccinated, so there's even less time for the virus to mutate and evolve in-host.
I find this concerning: "mRNA vaccines are really easy to alter. Once the minor change is made, only 2 dozen people need to enroll in a trial to make sure the updated vaccine works. Then it can be distributed to arms. Because the change is small, an updated vaccine doesn’t need Phase III trials and/or regularity approval. " Where is this codified? In what kind of "trial"? A challenge trial?
it would be a phase I trial. it would be like a flu vaccine every year. we don't have a new formula go through regulatory approval each year, that's because the formula is just changed a little for new variants.
@Katelyn, where are you getting your new variant info? I need an early source. Right now, for B.1.1.529, that was you. Thanks for the in-depth information. I'm now officially concerned.
honestly I just follow scientists (other epidemiologists and virologists) around the world on twitter. for example, Tom Peacock was the first to discover this variant and input it into GSAID
OK. I'll dust off the Twitter account. After all, that's where the first COVID reports surfaced. Thanks.
Not one to be a conspiracy theorist but: November 11, variant "Nu" detected. You know how those globalists love numerology...
Please don't.
https://www.coronaheadsup.com/
Looks like a collection of media sources. That's not the quality data I need. But thanks.
Any indication of if the existing lateral flow tests will still detect this variant?
"The BinaxNOW™ COVID-19 Antigen Self Test is a lateral flow immunoassay intended for the qualitative detection of nucleocapsid protein antigen from SARS-CoV-2."
BinaxNOW rapid antigen tests detect the N protein. Mutations in the Spike protein don't affect them, so they should work equally well for Omicron as for Delta (etc.)
Super helpful, thanks for all your hard work!
Read it'll be 100 days from now to shots in arm for reconfigured mRNA vaccine. Let's hope Omicron isn't much more transmissable than Delta so it'll take a long time to edge it out. Delta R0 is something like 6-7 - a beast of a respiratory virus. Hard to imagine something beating it by much...
I'm seeing it referred to as Omicron elsewhere, what gives?
yes this has now been named Omicron. This post came out before WHO announced
Damn! "Nu" would have been perfect. Catch up on sleep, if you can.
Do we know anything about the severity of symptoms in those in which B.1.1.529 has been detected? Hospitalizations? Deaths?
we don’t know yet. information we’re waiting on
That’s what I was coming to ask as well. My youngest gets her second dose of Pfizer tomorrow. I just want my life back. And convincing people to get another. Vaccine is going to be a nightmare.
I disagree -- speaking for my family (all vaccinated and boosted) we will roll up our sleeves for another vaccine, no problem. Those who've resisted thus far, will resist. I don't think anything has changed.
My husband has gotten all three willingly and will keep doing so because I can be a pain in the kiester but was wondering last week when we got our boosters at how many we are getting and how many times they will change their mind on what we need. He is pro-vaccine but people have their limits.
I hear you -- just saying that I (and I expect my family) would show up weekly, if that's what it took
Yes, but for many families, even getting the two shot sequence was difficult, even with our County Department of Health scheduling at home visits. People have caregiving duties or no transportation or no broadband access or no primary care physician or an unpredictable work schedule. I know in my county, they are still working to get hard to reach people to get the original vaccine - these are mostly in urban and rural areas, for more similar reasons than you might think.
I completely understand that there are people who may have limits. I don't agree that "they" keep changing their minds as to what we need. I believe we'd ultimately have to give credit to the virus for that.
The tolerance for, and acceptance of, the fact that there will inevitably be new/more/ worse mutations/ viruses which will then lead to development of updated vaccines/ boosters in general as time goes on, has to be done on an individual level. If we all accept what is known at the moment, while understanding it can- and likely will-change; we could determine what reasonabe/proactive/ protective steps could be done in our day to day lives.
Bottom line? Going forward I think we all, as residents on planet Earth, will truly need to reevaluate what we consider inconvenient and why.
Stay healthy, take care!
Agreed and well-said
I think Charity is right, especially for younger people. My college age son and friends can't yet be convinced that getting a booster is worth it. And I am much more cognizant of my schedule now and got my booster over the Thanksgiving holiday because I have Friday and Monday off. I really don't want to take any more time off for vaccine side effects, and I have a more flexible job than most.
If Omicron proves as scary as it first appears -- I think you'd change your mind. To be fair -- I've had zero vaccine side effects.
The hallmark of COVID-19 and SARS-CoV-2. A novel coronavirus (mis)behaving in ways we've not characterized before.