It’s still wait-and-see time for many key characteristics of the Omicron variant. I think the fact that it’s going to cause more breakthroughs in vaccinated people, and re-infections in people with prior infections, is baked in. The rest will take some time.
Thank you so much, Zeynep, for continuing to write this posts. They are the best source of reliable data I've seen and I appreciate your efforts to continue this conversation.
While it may be too soon to know the course of Omicron, it is not too early to do the things that we should already have done: a) make rapid cheap screening tests for asymptomatic people massively available, get more people vaccinated with 1st 2nd or third shots c) update the vaccine recipe to optimize for Delta and Omicron d) improve indoor ventilation. e) cheer on firms and business venues that require at least two doses of vaccine for entry f) use those rapid cheap massively available tests to reduce the costs of certain social distancing measures such as quarantining all students when one student tests positive.
My personal take is that I'm planning two international flights between now and Dec 25. Oh yes, and getting more people vaccinated includes several billion who do not live in developed countries.
Particularly since we DO require use of masks. Why requires something relative ineffective and not something which is highly effective in preventing the infection of other passengers
First, some states make it difficult for people to prove their vaccination status, even banning businesses from checking vaccination status, and the federal government has been leery of creating direct conflicts there. (The airlines already need to violate these state rules if they're going to operate international flights from Texas or Florida, but the federal government seems to want to avoid testing the conflicts for domestic flights.)
Second, masks are visible to other passengers, and thus make a very visible signal that the air travel system is doing something. In this way, it's analogous to a lot of the post-9/11 security apparatus, which emphasizes visibility of restrictions over effectiveness of restrictions.
I'm not opposed to masking indoors, but airports are federal facilities and requiring vaccination to enter and to board would make sense as a low cost means of protecting other airport customers and passengers, just like smoking bans.
Always a relief to get a Zeynep update. I now filter out almost all other commentary on Covid. Sky News ran 2 stories a few days ago, within hours of each other, saying first that Omicron could overwhelm the UK health system and then that symptoms are 'mild'. The information landscape is ludicrous.
Agree. It just oscillates between the latest tiny piece of information rather than providing a proper framework that will let people understand what we know, why and how.
As an ICU nurse, could you help with some math? I'm in the middle of conservative Pennsylvania where the lines have been drawn and hardened in place re vaccinations. So we are swamped with unvaccinated vent patients now. We put them on the vent knowing full well that very, very, very few, will survive after weeks of mostly futile work. Is it possible to come up with a possible death toll considering how many live in my community with 500,000 people, a vaccination rate of 50 % maybe and what we know of the Delta transmissability? I used to live in Guadalajara Spain, population 250,000, vaccination rate of 80%, and 1 ICU patient as of last week! Thanks for your posts.
Sorry, man. I just stopped to think about what I just wrote, and what it would mean to your job/life, having to go through it first hand, face-to-face. I don't mean to come off as blithe. I don't know where we would be without people like you working in the trenches, and I can't thank you enough for all you do every day. Also, I'm sorry for how terrible the last 2 years have been. Everything we do as a society should be based on and measured by making things better for you guys in the hospitals, and keeping those ICu beds from filling up.
Thank you again, people care about you and appreciate you, keep up the good work!
Okay, here goes. Disclosure, i am not a scientist or an academic, just a person who has been carefully following the math on this. According to the cdc https://www.washingtonpost.com/context/cdc-breakthrough-infections/94390e3a-5e45-44a5-ac40-2744e4e25f2e/ check around slide 15, Fatality rate for SARS/Delta is between .1 and 1 percent. Or, between 1 in 1000 and 1 in 100. I have been using a range of 1 in 200, 1 in 250, but that is only true for an average 40yo. Gets worse when older, better when younger, blah blah blah...
You have 250,000 unvaccinated people in your community, but I'm betting most of the unvaccinated are young, and most of the old are vaccinated. Plus, you have to factor in the people who have gotten it already, so some immunity there.
So, if you are making a public appeal, 100,000 new cases very quickly could give you 400 dead neighbors in 6-8 weeks. That's a mid-case scenario.
Why we should vaccinate Africa, and what we can do to get Biden to move on this are two separate questions. Equity will work to some extent as an argument with him, but vaccinating Africa will then compete with a million other priorities, and the plan will be to take a look four years from now, and if there's still a problem then, to come up with a plan.
If he's scared, he'll think about the situation now. If Omicron is the "classic" version of the virus after a prolonged infection in an HIV+ person, we could get worse starting with Beta, Delta or Omicron. It looks like the lag before getting hit is something like six months to a year, so we're set to get hit again, and again while he's still serving his current term, and potentially with two or multiple new variants at the same time. This now becomes an urgent national security issue, and can be solved quite cheaply compared to buying a new aircraft carrier. This is separate from helping African countries produce locally, as that will be too slow. Long-term, local production is the answer though to make sure this mess doesn't happen again. India and Cuba, for example, can produce all the vaccine they need locally, and that is certainly feasible for Kenya, South Africa etc as well. Note that Cuba wasn't affected by the IP issues, as they developed and tested a vaccine from scratch, but that is trickier than producing something already known to work.
The IP issues are a red herring, difficulty of manufacture is the problem. Consider the difficulties of Novavax to ramp-up production (see NYT vax tracker) despite >$1B in funding. Also, the U.S. can be blamed for many things, but S. African vaccination is not one of them. They had all the doses their public wanted, and actually returned some excess doses. Their vax rate is at 25-35% because of refusal/hesitancy, not because of supply. I am, however, pretty sure this is NOT true for a lot of other countries.
There's a separate issue of whether pharma would lose motivation to produce vaccines if IP was stripped from them too aggressively. I'm staying out of that one since business and law aren't my things, but it seems that for the more capitalist-inclined, the US or EU getting sick of variants and simply paying them fair market price for one Africa's worth of vaccines would be an option. So I think there are options here at most points of the political scale.
The Novavax vaccine, the Medicago vaccine and the mRNA vaccines use methods that to my knowledge haven't been scaled up before. These might be very difficult to get to work in say Kenya without direct assistance from companies with experience in these. However, these are not the only ways of making vaccines. Recombinant protein vaccines would probably be the easiest to introduce and scale up. Some of these are in the pipeline for Sars-CoV-2, and if one works tweaking for Omicron or some other variant would be a two week or so job + whatever time it takes to inject people and measure antibodies. Killed virus vaccines (similar to the SinoVac one) should also be relatively easy, as this sort of vaccine has been manufactured for decades in many countries and the processes should be well understood. Killed virus vaccines might take a bit longer to upgrade if new variants come along, but this is done for flu.
Whether people will take the jabs is a different and important issue. However, both polio and smallpox were eliminated from Africa by vaccination, so there doesn't seem reason to despair here.
Thanks, and sorry for directing you to something you clearly know more about than me, as you work in that area. Phizer and Moderna, with their low-temp storage regimens, are clearly a no-go for Kenya et al. Disappointed that J&J has +side effects, -protection, that could have been really helpful.
As for the IP, the Warp Speed $ is a pretty good case for the USGOV remanding the patent protections, if it really became an issue. I have heard a lot of people fear it is an issue, but don't know of any instance where IP is holding anything up in the vax supply chain. Disclosure, in my job I do benefit from some protection via IP that I have access to, but it is plant material, so small stakes.
Not a problem. And I forgot to mention the adenovirus vaccines, which from a production viewpoint are probably not that difficult to make in say Kenya, and storage requirements are fairly relaxed. India is making AZ at a very large scale, and the process for J&J or Sputnik would be similar. J&J works better as a two dose series, and I think the side effects are less common than with AZ, so J&J could be considered if retargeted. The publicity with their Baltimore plant fiasco didn't help them though.
John, with the passage of time, to you have a better idea of the R0 of omicron? I'm thinking of that chart where its either hi R0 or hi immunity escape. I went back to that CDC slideshow from the end of July about the emergence of delta, and they were guessing an R0 range of 5-9, but now evidence points to 6? So be it, but it seems, intuitively, that omicron would HAVE to be a higher R0 (for ex, spreading in schools and hospitals, which are masked environments). I'd like your learned opinion.
Thank you for your update. I still miss you another topic: Longcovid. We all know that originally mild illness can turn into a severe illness like longcovid (wouldn't address it as mild given how much many longcovid haulers are suffering from it). So even if Omicron causes only mild symptoms in the majority of infections, we won't know about the risk of longcovid for another 2-3 months at least. And it raises another question: People with longcovid are also at risk of reinfection by omicron. How will their weakened immune system fight off omicron? They're supposed to have low antibody titers or a defect in T cells. So before I'm overly optimistic, I hope we get answers to this aspect, too.
I second this. I've done a fair amount of digging into this topic and still haven't founded particularly reliable numbers. The best episode for Delta is that breakthrough cases vs. unvaccinated are half as likely to get Long COVID, but my intuition tells me that the type of Long COVID should be different but AFAIK that's not tracked. Still having e.g. a cough or mild tiredness for a few weeks post infection is so different in nature from e.g. chronic fatigue symptom/brain fog for many months or longer. There really should be some form of severity & length bucketing to make this data make more sense. If a substantial % of breakthroughs lead to serious longterm consequences that would really change the equation IMO.
There's also a problem here that long Covid may be several different syndromes. Everything gets muddied by one study using a four week cutoff for persistence of symptoms, another study using an eight week, another six months etc. I'm sure this is driven partly by the fact that shorter timelines lead to faster publications, but leads to conflating slow recovery with long-term consequences. So I'm not sure if there are good apple-to-apple comparisons (there may be though), and honestly, what the studies need to concentrate on (till we have good definitions of specific long Covid syndromes) is long-term consequences.
There was a recent study which concluded that any of the several vaccines they tested could boost any of the others, which is great. The one exception is that the third dose of Astrazeneca doesn't boost people who received two doses of Astrazeneca previously. This is probably because an immune response is generated against the adenovirus vector used in the Astrazeneca vaccine, and will probably be a problem for J&J and Sputnik as well.
This is bad news for India since they're relying heavily on AZ and would have to scramble for dose 3, but might be good news for Africa because AZ (possibly already retargeted to Omicron) would be freed up for Covax. However, both regions have been hit hard with Delta, so there would be some hope that with most people it would be infection + vaccination providing protection, so boosting wouldn't be needed.
Seems like the early evidence is that "full vaccination" won't do much about spread (in the incident in a Hong Kong quarantine hotel where transmission went across the corridor both cases were fully vaccinated with mRNA vaccines). Boosters may be borderline. One of the cases in Israel had received an mRNA booster and infected one other person. However, he had also interacted with a huge number of possible contacts without precautions, and the ones other than the guy he shared a car with were negative. That is all very thin data, but it suggests that boosters for everyone + some moderate level of precautions (masking and reducing interactions) might do the trick. At least in places where people accept vaccines.
South Africa has been hit by three waves so far, six months apart, with the last wave about five months ago. All three waves were short and sharp. suggesting not a lot of migitation, and possibly a high infection rate each time. This suggests lots of pre-existing partial immunity in SA, which will almost certainly reduce the severity. I.e., we really won't know till we see how the people in the superspread event in Norway do. There's some reports from SA about children under 2 showing up in the hospital at a high rate with severe symptoms, but these are contradicted by other reports suggesting that's not true.
One thing to keep in mind is that antibody neutralization will take a big hit (we know that because the targets for some but not all of the monoclonals used for treatment have been altered). So, a lot less viruses will be taken out before they infect their first cell. There is an independent immune response involving killer T-cells and called cell-mediated immunity. This is completely independent of antibodies and targets infected cells for destruction. I don't want to go into this in detail, but cells send snippets of their own proteins to the cell surface. The T-cells have proteins on their surface with a structure similar to antibodies with which they monitor cells for known foreign proteins, and if something suspicious shows up they will destroy the cell. Vaccines induce the production both of antibody-producing B-cells and of killer T-cells that patrol for Spike, and in the case of infection or whole-virus vaccines other virus proteins as well. Omicron's mutations won't provide much defense here, but the T-cell patrols, like police, don't really clamp down till signs of trouble have already been started. There's lots of evidence that cell-mediated immunity reduces the severity of Covid infections, but it's not so good at preventing them.
How that plays out in actual practice is just a guessing game right now (we have every reason to hope that vaccinated individuals will still have important protection against severe disease, but we'll have to wait to be sure).
> Seems like the early evidence is that "full vaccination" won't do much about spread (in the incident in a Hong Kong quarantine hotel where transmission went across the corridor both cases were fully vaccinated with mRNA vaccines). Boosters may be borderline. One of the cases in Israel had received an mRNA booster and infected one other person.
This isn't actually evidence that vaccination or boosters "won't do much about spread". This is all evidence that there will be a lot of spread even with lots of vaccination and boosters. But it doesn't show us whether it would be *much* more spread without these things.
According to the CDC, no one except healthcare personnel should wear "good masks" (N95s), but cloth masks (which seem mostly ineffective) and surgical masks (which seem somewhat better than nothing) are a-okay! Updated Oct. 25, 2021.
If that's really the case, why doesn't the CDC mention that "standard" N95s can be used and instead heavily pushes relatively ineffective cloth and surgical masks? Also, the image that the CDC uses looks awfully like a standard N95. The "specially labeled 'surgical' N95 respirators" technicality looks like blatant ass-covering. It sure seems that the CDC wants people to "misunderstand" and not wear any kind N95.
An N95 respirator is a generic product and can be considered to be a mask or facemask, regardless of what an FAQ says. While in the technical literature they might usually be referred to as "respirators," that's not what we're talking about here. But if you want to split more hairs, maybe the CDC shouldn't have contradicted itself and placed a respirator in the "DO NOT choose masks that" category. Or are you going to suggest that facemasks aren't masks?
The CDC doesn't recommend the use of N95s by the general public for covid mitigation on that FAQ page or anywhere else, as far as I know. Show me where the CDC says otherwise. Obviously, the CDC recommends N95s for use in healthcare and industry where they've always been used, but that's not what we're talking about here.
In fact, Walensky claimed that wearing an N95 would eat your face off (I'm only slightly exaggerating).
We should defer to health departments then. LA Public health distributes cloth masks with your vaccine dose. Not surgical, certainly not N95. They are sending a strong message for cloth.
LA County Public Health and the State of California does recommend N95s. But they should definitely stop recommending the ineffective masks and start mentioning the way-better-than-N95s elastomeric respirators.
They may recommend N95 but they are literally handing out public-health branded masks at vaccination sites made of cloth. So either cloth masks are just as good as N95s since public health is literally handing them out even though N95s are easily available on Amazon, or local public health is sending mixed messages.
A couple neutralization assays are out done in different places using somewhat different methods (Zeynep retweets both if you want to check yourself). Both state about a 40x reduction in neutralizing ability from 2 doses Pfizer but with large person-to-person variation (but for one I see 7x reported in the tweet, but 40X in the abstract, and I don't have time to read through too carefully right now). There's an indication though that there is sufficient neutralization after infection + 2 Pfizer (and likely 2 Pfizer + booster). It's unlikely that when Pfizer releases its own results they'll be very different. Some things need to be kept in mind.
1) This is consistent with the thin data so far suggesting the double-dosed efficiently spread the virus.
2) According to an article in an Israeli newspaper, one person in Israel with a booster (he was interviewed for the article) didn't efficiently spread Omicron despite not taking precautions but did infect one other person he was in a car with for a prolonged length of time. This is consistent and promising as it suggests boosters might work at least long enough to bridge us to Omicron-specific vaccines. However, the usual caveats of doing statistics at N=1 apply. Doubtless, more data will show up with time.
3) Remember that cell-mediated immunity (killer T-cells) are unlikely to be much affected. The vaccines would likely significantly reduce illness (although not prevent infection) even with a worse variant where there was no antibody binding at all.
They claim a 25x loss of neutralization after two doses and that this is made up by a 25x increase in neutralization after boost with current vaccine.
Also, they claim that they will be ready in March with an anti-Omicron shot. But I imagine this would be the month they ship the first dose, not when most people can get it. So durability of the old booster will be an important question. Also, how closely spaced can mRNA shots be, given that myocarditis seemed to be an issue with dose 2 (after a three week interval) but much less with dose 3 (after a six month interval).
Thanks for this. Since the direction of Omicron is unknown, the question that seem most important to me is: What is strong and what is week about our response to Delta and other fairly well known variants. Strong: several vaccines that are effective at controlling Covid-19 in individuals that are free in the US and some other countries. Weak: 1) inadequate mfg capacity to produce enough jabs for most of world population; 2) 19th century level backwardness in IP law limiting an effort to produce adequate supplies and affordable jabs in many countries; 3) policies favoring medicine (drugs/vaccines) and undervaluing public health measures such as massive rapid testing, sequencing, contact tracing, improvement to ventilation, mask education and availability; and 4) failure to continually improve data collection methods and standards. The fourth in this list is probably first in importance. We are, in fact, still running blind as the gradual discovery of Omicron suggests. The rush of the CDC to drop masking as vaccines became available is characteristic of the impact of an unbalanced view of medicine vs public health. The delay in realizing the value of boosters is an example of not monitoring the evolution of the pandemic. The pressure to avoid boosters so that we can get more jabs world wide is an example of #1 above.
The timing of events in the past two weeks has made so clear the dysfunctional cadence of public health policy in the pandemic — obviously in the U.S. but also in the EU. Almost instantaneous clamping down on travel from SA (well, except for US citizens because apparently … well, no reason, really). When it became clear omicron is in many countries, and so many are pointing out the dangers of punishing transparent, fast alerts from SA? Silence. Nothing. Maybe a rollback in a week or two.
It’s like watching a chess player ignore Zugzwang. (Not sure that’s the right term but it’s the nearest ‘forced cadence’ term I know.)
Thanks so much. What's particularly hard at this point is the lack of guidance on the holidays from people that seem like they actually believe that "hunkering down" for the holidays is an extremely high cost. For example, the author's "it's time to hunker down" article from about a year ago. At this point the commentators that are covid-cautious are advising caution and the ones that are more open are advising wait-and-see. But with Xmas 3 weeks away and Xmas travel 2 weeks ago, "wait and see" is kind of not an option. To a significant extent, a lot of folks need to decide today (really, two weeks ago or more) whether to forgo the in-person indoor mixing of the holidays for a second year in the row. Wait and see to some extent means "go forward with the holidays more or less like normal," which may be fine, but Omicron has come at a very awkward time for planning purposes.
I think for people in wealth countries, get a booster now plus carry around rapid tests is a reasonable plan. If things look terrible, you can cancel at the last minute—not ideal, but justifiable. I would probably be more wary about elderly people or the immunocompromised, but we haven't yet heard of large number of vaccinated people get seriously sick, and someone with a booster now is likely even more protected. The one thing is, I think people should be prepared to have to stay somewhere longer than planned if they test positive—the hassle factor is real, even if the illness turns out to be really mild.
Thanks. If you had to guess, when will a positive test lose its "hassle factor?" In other words, in the Before Time, if you had the flu but were healthy enough to fly home, you would fly home rather than bear the (high) cost of airline change fees and more hotel rooms. When do you see it getting that way with COVID (if ever)?
Numbers seem to be suggestive that Omicron will be a small fraction of cases for the next couple weeks, but will become very significant in North America in January or February.
Indeed. Have tickets to fly to Paris just after Christmas. Or perhaps go visit friends in the US, but across the continent. Or stay home and hide. How long do we wait to decide now?
Getting a booster, packing some rapid tests and planning to go unless things go really south may be an option if you are comfortable with last minute changes to plans (potentially) and getting stuck somewhere—I think that may happen to people.
Is there an existing conversation about our approach to broader evolutionary dynamics? Ie fitness landscapes, uh, 'islands' and how public health policies play a role? Thinking about birds in Papau New Guinea. Relevant also for creative adaptation among scientists and civic spirit.
Thank you so much, Zeynep, for continuing to write this posts. They are the best source of reliable data I've seen and I appreciate your efforts to continue this conversation.
Thanks! Was waiting for your weekend read on this.
I appreciate this and all of your other posts Zeynep.
While it may be too soon to know the course of Omicron, it is not too early to do the things that we should already have done: a) make rapid cheap screening tests for asymptomatic people massively available, get more people vaccinated with 1st 2nd or third shots c) update the vaccine recipe to optimize for Delta and Omicron d) improve indoor ventilation. e) cheer on firms and business venues that require at least two doses of vaccine for entry f) use those rapid cheap massively available tests to reduce the costs of certain social distancing measures such as quarantining all students when one student tests positive.
A. A. A. - not to suggest your c., d., e. are not relevant and important, but AAAAAAAAAAAA
My personal take is that I'm planning two international flights between now and Dec 25. Oh yes, and getting more people vaccinated includes several billion who do not live in developed countries.
And, it is unbelievable that we have no requirements for vaccinations or preflight testing for domestic flights.
Particularly since we DO require use of masks. Why requires something relative ineffective and not something which is highly effective in preventing the infection of other passengers
First, some states make it difficult for people to prove their vaccination status, even banning businesses from checking vaccination status, and the federal government has been leery of creating direct conflicts there. (The airlines already need to violate these state rules if they're going to operate international flights from Texas or Florida, but the federal government seems to want to avoid testing the conflicts for domestic flights.)
Second, masks are visible to other passengers, and thus make a very visible signal that the air travel system is doing something. In this way, it's analogous to a lot of the post-9/11 security apparatus, which emphasizes visibility of restrictions over effectiveness of restrictions.
I'm not opposed to masking indoors, but airports are federal facilities and requiring vaccination to enter and to board would make sense as a low cost means of protecting other airport customers and passengers, just like smoking bans.
Always a relief to get a Zeynep update. I now filter out almost all other commentary on Covid. Sky News ran 2 stories a few days ago, within hours of each other, saying first that Omicron could overwhelm the UK health system and then that symptoms are 'mild'. The information landscape is ludicrous.
Agree. It just oscillates between the latest tiny piece of information rather than providing a proper framework that will let people understand what we know, why and how.
As an ICU nurse, could you help with some math? I'm in the middle of conservative Pennsylvania where the lines have been drawn and hardened in place re vaccinations. So we are swamped with unvaccinated vent patients now. We put them on the vent knowing full well that very, very, very few, will survive after weeks of mostly futile work. Is it possible to come up with a possible death toll considering how many live in my community with 500,000 people, a vaccination rate of 50 % maybe and what we know of the Delta transmissability? I used to live in Guadalajara Spain, population 250,000, vaccination rate of 80%, and 1 ICU patient as of last week! Thanks for your posts.
Sorry, man. I just stopped to think about what I just wrote, and what it would mean to your job/life, having to go through it first hand, face-to-face. I don't mean to come off as blithe. I don't know where we would be without people like you working in the trenches, and I can't thank you enough for all you do every day. Also, I'm sorry for how terrible the last 2 years have been. Everything we do as a society should be based on and measured by making things better for you guys in the hospitals, and keeping those ICu beds from filling up.
Thank you again, people care about you and appreciate you, keep up the good work!
Okay, here goes. Disclosure, i am not a scientist or an academic, just a person who has been carefully following the math on this. According to the cdc https://www.washingtonpost.com/context/cdc-breakthrough-infections/94390e3a-5e45-44a5-ac40-2744e4e25f2e/ check around slide 15, Fatality rate for SARS/Delta is between .1 and 1 percent. Or, between 1 in 1000 and 1 in 100. I have been using a range of 1 in 200, 1 in 250, but that is only true for an average 40yo. Gets worse when older, better when younger, blah blah blah...
You have 250,000 unvaccinated people in your community, but I'm betting most of the unvaccinated are young, and most of the old are vaccinated. Plus, you have to factor in the people who have gotten it already, so some immunity there.
So, if you are making a public appeal, 100,000 new cases very quickly could give you 400 dead neighbors in 6-8 weeks. That's a mid-case scenario.
Why we should vaccinate Africa, and what we can do to get Biden to move on this are two separate questions. Equity will work to some extent as an argument with him, but vaccinating Africa will then compete with a million other priorities, and the plan will be to take a look four years from now, and if there's still a problem then, to come up with a plan.
If he's scared, he'll think about the situation now. If Omicron is the "classic" version of the virus after a prolonged infection in an HIV+ person, we could get worse starting with Beta, Delta or Omicron. It looks like the lag before getting hit is something like six months to a year, so we're set to get hit again, and again while he's still serving his current term, and potentially with two or multiple new variants at the same time. This now becomes an urgent national security issue, and can be solved quite cheaply compared to buying a new aircraft carrier. This is separate from helping African countries produce locally, as that will be too slow. Long-term, local production is the answer though to make sure this mess doesn't happen again. India and Cuba, for example, can produce all the vaccine they need locally, and that is certainly feasible for Kenya, South Africa etc as well. Note that Cuba wasn't affected by the IP issues, as they developed and tested a vaccine from scratch, but that is trickier than producing something already known to work.
The IP issues are a red herring, difficulty of manufacture is the problem. Consider the difficulties of Novavax to ramp-up production (see NYT vax tracker) despite >$1B in funding. Also, the U.S. can be blamed for many things, but S. African vaccination is not one of them. They had all the doses their public wanted, and actually returned some excess doses. Their vax rate is at 25-35% because of refusal/hesitancy, not because of supply. I am, however, pretty sure this is NOT true for a lot of other countries.
There's a separate issue of whether pharma would lose motivation to produce vaccines if IP was stripped from them too aggressively. I'm staying out of that one since business and law aren't my things, but it seems that for the more capitalist-inclined, the US or EU getting sick of variants and simply paying them fair market price for one Africa's worth of vaccines would be an option. So I think there are options here at most points of the political scale.
The Novavax vaccine, the Medicago vaccine and the mRNA vaccines use methods that to my knowledge haven't been scaled up before. These might be very difficult to get to work in say Kenya without direct assistance from companies with experience in these. However, these are not the only ways of making vaccines. Recombinant protein vaccines would probably be the easiest to introduce and scale up. Some of these are in the pipeline for Sars-CoV-2, and if one works tweaking for Omicron or some other variant would be a two week or so job + whatever time it takes to inject people and measure antibodies. Killed virus vaccines (similar to the SinoVac one) should also be relatively easy, as this sort of vaccine has been manufactured for decades in many countries and the processes should be well understood. Killed virus vaccines might take a bit longer to upgrade if new variants come along, but this is done for flu.
Whether people will take the jabs is a different and important issue. However, both polio and smallpox were eliminated from Africa by vaccination, so there doesn't seem reason to despair here.
Thanks, and sorry for directing you to something you clearly know more about than me, as you work in that area. Phizer and Moderna, with their low-temp storage regimens, are clearly a no-go for Kenya et al. Disappointed that J&J has +side effects, -protection, that could have been really helpful.
As for the IP, the Warp Speed $ is a pretty good case for the USGOV remanding the patent protections, if it really became an issue. I have heard a lot of people fear it is an issue, but don't know of any instance where IP is holding anything up in the vax supply chain. Disclosure, in my job I do benefit from some protection via IP that I have access to, but it is plant material, so small stakes.
Not a problem. And I forgot to mention the adenovirus vaccines, which from a production viewpoint are probably not that difficult to make in say Kenya, and storage requirements are fairly relaxed. India is making AZ at a very large scale, and the process for J&J or Sputnik would be similar. J&J works better as a two dose series, and I think the side effects are less common than with AZ, so J&J could be considered if retargeted. The publicity with their Baltimore plant fiasco didn't help them though.
John, with the passage of time, to you have a better idea of the R0 of omicron? I'm thinking of that chart where its either hi R0 or hi immunity escape. I went back to that CDC slideshow from the end of July about the emergence of delta, and they were guessing an R0 range of 5-9, but now evidence points to 6? So be it, but it seems, intuitively, that omicron would HAVE to be a higher R0 (for ex, spreading in schools and hospitals, which are masked environments). I'd like your learned opinion.
Thank you for your update. I still miss you another topic: Longcovid. We all know that originally mild illness can turn into a severe illness like longcovid (wouldn't address it as mild given how much many longcovid haulers are suffering from it). So even if Omicron causes only mild symptoms in the majority of infections, we won't know about the risk of longcovid for another 2-3 months at least. And it raises another question: People with longcovid are also at risk of reinfection by omicron. How will their weakened immune system fight off omicron? They're supposed to have low antibody titers or a defect in T cells. So before I'm overly optimistic, I hope we get answers to this aspect, too.
I second this. I've done a fair amount of digging into this topic and still haven't founded particularly reliable numbers. The best episode for Delta is that breakthrough cases vs. unvaccinated are half as likely to get Long COVID, but my intuition tells me that the type of Long COVID should be different but AFAIK that's not tracked. Still having e.g. a cough or mild tiredness for a few weeks post infection is so different in nature from e.g. chronic fatigue symptom/brain fog for many months or longer. There really should be some form of severity & length bucketing to make this data make more sense. If a substantial % of breakthroughs lead to serious longterm consequences that would really change the equation IMO.
There's also a problem here that long Covid may be several different syndromes. Everything gets muddied by one study using a four week cutoff for persistence of symptoms, another study using an eight week, another six months etc. I'm sure this is driven partly by the fact that shorter timelines lead to faster publications, but leads to conflating slow recovery with long-term consequences. So I'm not sure if there are good apple-to-apple comparisons (there may be though), and honestly, what the studies need to concentrate on (till we have good definitions of specific long Covid syndromes) is long-term consequences.
There was a recent study which concluded that any of the several vaccines they tested could boost any of the others, which is great. The one exception is that the third dose of Astrazeneca doesn't boost people who received two doses of Astrazeneca previously. This is probably because an immune response is generated against the adenovirus vector used in the Astrazeneca vaccine, and will probably be a problem for J&J and Sputnik as well.
This is bad news for India since they're relying heavily on AZ and would have to scramble for dose 3, but might be good news for Africa because AZ (possibly already retargeted to Omicron) would be freed up for Covax. However, both regions have been hit hard with Delta, so there would be some hope that with most people it would be infection + vaccination providing protection, so boosting wouldn't be needed.
Seems like the early evidence is that "full vaccination" won't do much about spread (in the incident in a Hong Kong quarantine hotel where transmission went across the corridor both cases were fully vaccinated with mRNA vaccines). Boosters may be borderline. One of the cases in Israel had received an mRNA booster and infected one other person. However, he had also interacted with a huge number of possible contacts without precautions, and the ones other than the guy he shared a car with were negative. That is all very thin data, but it suggests that boosters for everyone + some moderate level of precautions (masking and reducing interactions) might do the trick. At least in places where people accept vaccines.
South Africa has been hit by three waves so far, six months apart, with the last wave about five months ago. All three waves were short and sharp. suggesting not a lot of migitation, and possibly a high infection rate each time. This suggests lots of pre-existing partial immunity in SA, which will almost certainly reduce the severity. I.e., we really won't know till we see how the people in the superspread event in Norway do. There's some reports from SA about children under 2 showing up in the hospital at a high rate with severe symptoms, but these are contradicted by other reports suggesting that's not true.
One thing to keep in mind is that antibody neutralization will take a big hit (we know that because the targets for some but not all of the monoclonals used for treatment have been altered). So, a lot less viruses will be taken out before they infect their first cell. There is an independent immune response involving killer T-cells and called cell-mediated immunity. This is completely independent of antibodies and targets infected cells for destruction. I don't want to go into this in detail, but cells send snippets of their own proteins to the cell surface. The T-cells have proteins on their surface with a structure similar to antibodies with which they monitor cells for known foreign proteins, and if something suspicious shows up they will destroy the cell. Vaccines induce the production both of antibody-producing B-cells and of killer T-cells that patrol for Spike, and in the case of infection or whole-virus vaccines other virus proteins as well. Omicron's mutations won't provide much defense here, but the T-cell patrols, like police, don't really clamp down till signs of trouble have already been started. There's lots of evidence that cell-mediated immunity reduces the severity of Covid infections, but it's not so good at preventing them.
How that plays out in actual practice is just a guessing game right now (we have every reason to hope that vaccinated individuals will still have important protection against severe disease, but we'll have to wait to be sure).
> Seems like the early evidence is that "full vaccination" won't do much about spread (in the incident in a Hong Kong quarantine hotel where transmission went across the corridor both cases were fully vaccinated with mRNA vaccines). Boosters may be borderline. One of the cases in Israel had received an mRNA booster and infected one other person.
This isn't actually evidence that vaccination or boosters "won't do much about spread". This is all evidence that there will be a lot of spread even with lots of vaccination and boosters. But it doesn't show us whether it would be *much* more spread without these things.
According to the CDC, no one except healthcare personnel should wear "good masks" (N95s), but cloth masks (which seem mostly ineffective) and surgical masks (which seem somewhat better than nothing) are a-okay! Updated Oct. 25, 2021.
Why haven't these people been fired yet?
https://www.cdc.gov/coronavirus/2019-ncov/prevent-getting-sick/about-face-coverings.html
https://www.science.org/doi/10.1126/science.abi9069
If that's really the case, why doesn't the CDC mention that "standard" N95s can be used and instead heavily pushes relatively ineffective cloth and surgical masks? Also, the image that the CDC uses looks awfully like a standard N95. The "specially labeled 'surgical' N95 respirators" technicality looks like blatant ass-covering. It sure seems that the CDC wants people to "misunderstand" and not wear any kind N95.
An N95 respirator is a generic product and can be considered to be a mask or facemask, regardless of what an FAQ says. While in the technical literature they might usually be referred to as "respirators," that's not what we're talking about here. But if you want to split more hairs, maybe the CDC shouldn't have contradicted itself and placed a respirator in the "DO NOT choose masks that" category. Or are you going to suggest that facemasks aren't masks?
The CDC doesn't recommend the use of N95s by the general public for covid mitigation on that FAQ page or anywhere else, as far as I know. Show me where the CDC says otherwise. Obviously, the CDC recommends N95s for use in healthcare and industry where they've always been used, but that's not what we're talking about here.
In fact, Walensky claimed that wearing an N95 would eat your face off (I'm only slightly exaggerating).
https://www.cnn.com/videos/health/2021/01/28/mask-guidance-n95-fauci-walensky-cnn-coronavirus-town-hall-sot-vpx.cnn
We should defer to health departments then. LA Public health distributes cloth masks with your vaccine dose. Not surgical, certainly not N95. They are sending a strong message for cloth.
LA County Public Health and the State of California does recommend N95s. But they should definitely stop recommending the ineffective masks and start mentioning the way-better-than-N95s elastomeric respirators.
http://publichealth.lacounty.gov/acd/ncorona2019/masks/
https://www.cdph.ca.gov/Programs/CID/DCDC/Pages/COVID-19/Get-the-Most-out-of-Masking.aspx
https://www.ncbi.nlm.nih.gov/books/NBK540078/#effi1
https://www.doi.org/10.1016/j.jamcollsurg.2020.05.022
https://www.doi.org/10.1001/jama.2008.894
They may recommend N95 but they are literally handing out public-health branded masks at vaccination sites made of cloth. So either cloth masks are just as good as N95s since public health is literally handing them out even though N95s are easily available on Amazon, or local public health is sending mixed messages.
A couple neutralization assays are out done in different places using somewhat different methods (Zeynep retweets both if you want to check yourself). Both state about a 40x reduction in neutralizing ability from 2 doses Pfizer but with large person-to-person variation (but for one I see 7x reported in the tweet, but 40X in the abstract, and I don't have time to read through too carefully right now). There's an indication though that there is sufficient neutralization after infection + 2 Pfizer (and likely 2 Pfizer + booster). It's unlikely that when Pfizer releases its own results they'll be very different. Some things need to be kept in mind.
1) This is consistent with the thin data so far suggesting the double-dosed efficiently spread the virus.
2) According to an article in an Israeli newspaper, one person in Israel with a booster (he was interviewed for the article) didn't efficiently spread Omicron despite not taking precautions but did infect one other person he was in a car with for a prolonged length of time. This is consistent and promising as it suggests boosters might work at least long enough to bridge us to Omicron-specific vaccines. However, the usual caveats of doing statistics at N=1 apply. Doubtless, more data will show up with time.
3) Remember that cell-mediated immunity (killer T-cells) are unlikely to be much affected. The vaccines would likely significantly reduce illness (although not prevent infection) even with a worse variant where there was no antibody binding at all.
Pfizer press release is here.
https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-biontech-provide-update-omicron-variant
They claim a 25x loss of neutralization after two doses and that this is made up by a 25x increase in neutralization after boost with current vaccine.
Also, they claim that they will be ready in March with an anti-Omicron shot. But I imagine this would be the month they ship the first dose, not when most people can get it. So durability of the old booster will be an important question. Also, how closely spaced can mRNA shots be, given that myocarditis seemed to be an issue with dose 2 (after a three week interval) but much less with dose 3 (after a six month interval).
Thanks for this. Since the direction of Omicron is unknown, the question that seem most important to me is: What is strong and what is week about our response to Delta and other fairly well known variants. Strong: several vaccines that are effective at controlling Covid-19 in individuals that are free in the US and some other countries. Weak: 1) inadequate mfg capacity to produce enough jabs for most of world population; 2) 19th century level backwardness in IP law limiting an effort to produce adequate supplies and affordable jabs in many countries; 3) policies favoring medicine (drugs/vaccines) and undervaluing public health measures such as massive rapid testing, sequencing, contact tracing, improvement to ventilation, mask education and availability; and 4) failure to continually improve data collection methods and standards. The fourth in this list is probably first in importance. We are, in fact, still running blind as the gradual discovery of Omicron suggests. The rush of the CDC to drop masking as vaccines became available is characteristic of the impact of an unbalanced view of medicine vs public health. The delay in realizing the value of boosters is an example of not monitoring the evolution of the pandemic. The pressure to avoid boosters so that we can get more jabs world wide is an example of #1 above.
The timing of events in the past two weeks has made so clear the dysfunctional cadence of public health policy in the pandemic — obviously in the U.S. but also in the EU. Almost instantaneous clamping down on travel from SA (well, except for US citizens because apparently … well, no reason, really). When it became clear omicron is in many countries, and so many are pointing out the dangers of punishing transparent, fast alerts from SA? Silence. Nothing. Maybe a rollback in a week or two.
It’s like watching a chess player ignore Zugzwang. (Not sure that’s the right term but it’s the nearest ‘forced cadence’ term I know.)
Also: love the cartoon.
Thanks so much. What's particularly hard at this point is the lack of guidance on the holidays from people that seem like they actually believe that "hunkering down" for the holidays is an extremely high cost. For example, the author's "it's time to hunker down" article from about a year ago. At this point the commentators that are covid-cautious are advising caution and the ones that are more open are advising wait-and-see. But with Xmas 3 weeks away and Xmas travel 2 weeks ago, "wait and see" is kind of not an option. To a significant extent, a lot of folks need to decide today (really, two weeks ago or more) whether to forgo the in-person indoor mixing of the holidays for a second year in the row. Wait and see to some extent means "go forward with the holidays more or less like normal," which may be fine, but Omicron has come at a very awkward time for planning purposes.
I think for people in wealth countries, get a booster now plus carry around rapid tests is a reasonable plan. If things look terrible, you can cancel at the last minute—not ideal, but justifiable. I would probably be more wary about elderly people or the immunocompromised, but we haven't yet heard of large number of vaccinated people get seriously sick, and someone with a booster now is likely even more protected. The one thing is, I think people should be prepared to have to stay somewhere longer than planned if they test positive—the hassle factor is real, even if the illness turns out to be really mild.
Thanks. If you had to guess, when will a positive test lose its "hassle factor?" In other words, in the Before Time, if you had the flu but were healthy enough to fly home, you would fly home rather than bear the (high) cost of airline change fees and more hotel rooms. When do you see it getting that way with COVID (if ever)?
Numbers seem to be suggestive that Omicron will be a small fraction of cases for the next couple weeks, but will become very significant in North America in January or February.
Indeed. Have tickets to fly to Paris just after Christmas. Or perhaps go visit friends in the US, but across the continent. Or stay home and hide. How long do we wait to decide now?
Getting a booster, packing some rapid tests and planning to go unless things go really south may be an option if you are comfortable with last minute changes to plans (potentially) and getting stuck somewhere—I think that may happen to people.
Being retired we have no problem with last-minute decisions, but getting stuck in Paris might be a mixed blessing... :-)
There you go.
At least if you fly to Paris, rather than domestically, you will be on a flight with people who are vaxed and/or tested. Domestically- no such rules.
Is there an existing conversation about our approach to broader evolutionary dynamics? Ie fitness landscapes, uh, 'islands' and how public health policies play a role? Thinking about birds in Papau New Guinea. Relevant also for creative adaptation among scientists and civic spirit.
See also: James Evans at University of Chicago
https://arxiv.org/abs/1910.09370
Letting so many people with HIV go untreated was both a moral stain and may well have turned into a variant generating force. This is very interesting: https://virological.org/t/selection-analysis-identifies-significant-mutational-changes-in-omicron-that-are-likely-to-influence-both-antibody-neutralization-and-spike-function-part-1-of-2/771