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Its been a week to decompress from the hyperbolic headlines of last week, but this is still not enough time to answer the important questions.
These are the only questions people should care about, and it seems like none of these questions have an answer yet.
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So I guess... lets wait another week and see if people have good answers to these questions. And if we don't have answers on Dec. 9th, then we will wait another week for Dec. 16th.
I'll venture some guesses here:
* How transmissible is Omicron?
Very. But how much? Based on current data, there's a sort of invariant involving a tradeoff between greater escape of post-infection/post-vaccination immunity and greater transmissibility where anything along that invariant line can explain it's aggressive rise. Either way, it doesn't really matter. If it continues to behave as it has, we'll see a lot more of omicron. ~60% confidence
* Are Omicron infections milder, or more severe?
That's the BIG question right now. I've seen one MD describe patients that they've seen with omicron as being mild. On the other hand, there's also been a significant rise in hospitalizations in affected areas, however, if there's simply more infected, that would be expected. I don't have a good guess here. We haven't had enough time to find out.
* Can Omicron become dominant in this Delta environment?
Given it's very rapid rise to dominance in the small subset of testing data I've seen, I'll put money on it out-competing delta. ~60% confidence
* How much can Omicron evade the vaccine-immunity and/or natural-immunity?
Another good question. Despite the fact it has a lot of spike-protein mutations, and many experts believe that immune escape is likely here: I'm not convinced that's the best metric, and I've only 20-30% confidence in my agreement with it. I'll revise this according to the following pieces of evidence I expect to see, in increasing order of how much confidence I'll gain in that assessment for each piece: I'll gain more after I hear a lot of anecdotes about vaccinated getting sick, more if I see lab results confirm lower antibody affinity, and more still after actual numbers to high statistical significance confirm that previously infected or people 2-6 months post-vaccination have a high rate of infection en par with the rest of the population.
I've got a simpler, though stupider, analysis.
The variants of concern (as defined by WHO) thus-far are Alpha, Beta, Gamma, Delta, and now Omicron. (The others were "variants of interest", but never graduated to a higher status than that).
So about 50% of the variants of concern (Alpha and Delta) became dominant in their time. The other 50% were concerning with their respective "superpowers", but were outcompeted by the others.
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So I give 50/50 odds that Omicron becomes dominant.
Maybe a bad analysis, but hey, everything is bad analysis right now until we get better data.
Note: there are many, many variants, including "Delta Plus" variants (offspring of Delta), Lambda, and other variants who grabbed the headlines. Gamma in particular took over South America (graduating into a Variant of Concern), but never managed to spread further than that.
Lambda also spread rapidly in South America, but also was vanquished by Delta.
So very high spread in a local area does not necessarily mean it will spread rapidly in other settings (especially since Delta seems so good at outcompeting all these variants).
> So very high spread in a local area does not necessarily mean it will spread rapidly in other settings (especially since Delta seems so good at outcompeting all these variants).
In South Africa omicron has replaced delta. Why should we expect delta to dominate omicron elsewhere?
Of course omicron may fail to be the dominant variant if there is a "better" one, but it seems more likely than not that delta will be replaced.
Some of these things are essentially unknowable without time. Yes, you can model them but stuff like sampling error and model error will bite you at this early stage.
I seem to recall one of the original arguments for the “artificial origin” hypothesis last year was that the virus was too different from other known viruses and therefore it was implausible that it had developed naturally.
But if we see here an apparently-sudden jump to a significantly different variant, does that make it less surprising that the original strain was novel?
I think there are few differences.
1) Covid-19 was more dissimilar from previous coronaviruses than Omicron is from current ones.
2) There is a lot more covid-19 in the world now so rare occurrences are more common.
3) There was other evidence for the lab leak hypothesis. A cover up from China, a viral research lab in the city with the outbreak, etc...
Just to be pedantic. Covid-19 is the disease, not the virus. SARS-COV-2 is the virus.
Not "too different". If it were too different it would be very unlikely to have been made by human hands. Different enough, in "suspicious places". For example, one of the major differences came from a spot on the spike protein. We now know that EHA had unsuccessfully applied for grants to study splicing in sequences from other coronaviruses into this spot of SARS (non-COV-2) at the WHI. It's not a stretch to think someone in an adjacent/partner lab was doing the same experiment on the actual COV-2 precursor.
But entire world has the virus now, every human is a potential "lab" for variants to come.
And I still don't think Omicron is as different from original Sars-Cov-2 as Sars-Cov-2 was to known predecessors.
What if that new variant is also engineered?
most "artificial origin" hypotheses centre around a lab-leak.
The number of scenarios where the new variant is engineered are vastly reduced, since it's less likely that this variant is a lab leak.
Other scenarios can still be within the realm of plausibility, but there are fewer of them.
What if new variants inevitably emerge given global mutations and lackluster vaccinations?
That is by far the best science article I have read on SARS-COV-2 yet. The summary is concise and relevent and the linked graphics are incredible and tell the story well:
https://covariants.org/variants/21K.Omicron
https://nextstrain.org/groups/neherlab/ncov/21K.Omicron
My naive understanding of why it's so difficult to stop coronaviruses in general from spreading is due to the virus moving between humans and animals. If that's true, and if that causes virus mutation, then is it possible to stop the mutations even with a theoretical 100% global vaccination?
It may have been possible to contain it early on. Way too late now. It's here to stay forever, with new strains constantly evolving.
I would say the goal of vaccinations is to minimize death and to prevent medical systems from being overwhelmed.
I don't think COVID-19 is a disease that can be eradicated.
The fewer hosts out there though, the fewer opportunities it has to mutate.
Since every household that has a pet has additional hosts, there is no way to meaningfully reduce the number of hosts.
I don't know much about virology. Is it possible for variants to 'blend'?
It sounds like Omicron has a number of variations vs Delta and other major variants.
Is it possible that someone who is simultaneously infected with both Delta and Omicron to generate virus particles that utilize proteins from both variants in the same viral particle?
If this can occur, would the genome of those viral particles get blended together, or would it just carry the genome of one or the other variants?
i.e. would co-infection of multiple variants simultaneously increase mutation rate, or could hybrid variants appear?
One thing I don't see being talked about is how virulent (rapid onset of severe illness) omicron is. The rate of spread isn't the only element. The viruses that are the common cold spread wildly but don't cause major issues for most people.
Why don't we talk about this more?
I see discussions of this all the time around Omicron, the problem is we have no idea how virulent Omicron is. The attributes we care about are immune evasion, transmissibility, severity. We know the most about immune evasion, we have a little data on transmissibility, but we know didly squat about severity.
People aren't talking about it much because we don't even have a bad guess about severity, much less a good guess.
It'll takes a while to figure out severity. Deaths happen 2-8 weeks after symptoms. Which means we're still probably several weeks before we have any good data on severity. And this data is still really hard to parse out especially with immune evasion which makes the average case more mild, even if the disease is more virulent.
Median time to death from onset of symptoms ~18.5 days:
https://www.drugs.com/medical-answers/covid-19-symptoms-prog...
Median time for first symptoms is ~4.5 days:
https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-guida...
Within a week, we should start to have a decent picture WRT severity. Obviously, as time goes by, that picture will only get clearer.
There are several other endemic human coronaviruses like HCoV-OC43 which cause common cold symptoms. Most of us catch them as youths and the resulting natural immunity protects us from severe symptoms during later reinfections. However they can still be deadly to frail and immunocompromised patients.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7252012/
Because the media/political narrative is to sustain continual panic. If you state that "the new strain is more contagious but the symptoms are basically the same as a common cold" then the panic will subside. Be we _immediately_ saw even greater panic and now even more "containment" actions that further disrupt society. Despite there being no evidence that it's more virulent. In fact, the evidence seems to be that it's much less virulent.
If this new strain is basically a common cold, then it's in our best interest for it to spread as quickly as possible. And that's normally what viruses do, they get less virulent. The vaccines have obviously failed at slowing the spread and have put evolutionary pressure on the virus to evade the very specific spike protein that the vaccines contain. If we all get broader protection, then this thing will be over without the need for liberty-crippling mandates.
Instead, it's almost impossible to get any sort of sober analysis of how this variant's symptoms differ from other variants.
I don't believe there's something along the lines of a conspiracy or anything nearly as dramatic as that, but it does surprise me how little the whole 'enragement is engagement' dynamic gets brought up in discussions around COVID coverage. Half the world being scared shitless of COVID and the other half being scared shitless of being plunged into yet another lockdown means lots of people doomscrolling news sites past ad after ad. There's no real incentive _not_ to sensationalise things, if later things turned out to be not so bad as the media outlet claimed they a) still get their ad revenue and b) nobody will care in a week's time when the next inevitable scandal happens and the news cycle moves on. If they choose to be cautious and not sensationalise things and it later turns out to be worse than reported then that's a lot of panicky, desperate scrolling not to get a slice of. I'm actually flirting with the belief that the post-War on Terror 24/7 news cycle combined with the above incentives is doing Western society a huge amount of avoidable harm.
I'm not sure how this issue can be solved to be honest, while my go-to answer is to have a strictly apolitical regulatory board which can demand retractions are published (after a transparent investigation) with the same headline prominence and ad spend as the initial article or video that was deemed to be alarmist or misleading but that has problems in itself; such a system introduces a "who is fit to determine objective truth?" debate where the regulatory board could determine 2 + 2 = 5 and there'd be very little that could be done to oppose this obvious falsehood.
While data is lacking, there is absolutely no reason to suppose that the symptoms are the same as the common cold for the unvaccinated. Vaccines have both reduced spread and more importantly yet reduced deaths. The strategy moving forward is to both continue to press the vaccination strategy as well as mass manufacture new antivirals so we can save as many of those too short sighted to vaccinate despite themselves. It's also liable that we will be stuck with another shot in 2022.
The strategy of just let it wash over us so we can get back to normal is not quite as horrifying as it was in 2020 when it meant hundreds of millions of damaged bodies and 3 million dead but it remains ridiculous. The unvaccinated who are liable to experience something no better than earlier strains aren't evenly distributed and areas where they are concentrated are especially vulnerable to their health care systems being overwhelmed but the truth is even in areas where ONLY 1 in 3 is unvaccinated we don't have the capacity for much of the population to linger in the hospital for weeks or months before deciding whether to die or not.
We don't have enough antivirals manufactured yet nor do we know the long term outlook of survivors even after we can manufacture more. We don't even know if they will be as effective with the new strain!
We don't have such a healthy economy that we can afford to go through another covid induced slump and believe me if deaths and illness start going up we will have another big ass slump whether an official lock down is declared or not.
For at least 2022 covid is going to be a substantial workplace hazard and it is absolutely reasonable that if someone gets sick at work and experiences substantial costs, disability, or death they treat it just like a workplace accident and if we do that then mandates become the only tenable option to reduce liability and OSHA will be only a convenient excuse for your employer is in fact doing to cover their own asses.
From the perspective of a worker why should I work at a place that wont even make you get a shot so you don't murder me. It seems to me a lot like letting you drive the forklift drunk an entirely unnecessary risk. It's a sellers market and I can sell my labor elsewhere.
Does anyone know if this blog still has an RSS feed? I think it has moved to a new domain.
Yes, but I can only find the link on the main page of the blog, not in individual posts. Here it is:
https://blogs.sciencemag.org/pipeline/feed
Refreshingly hype and agenda free reporting, as usual from Derek Lowe.
And still "[vaccination] is better than a naive immune system" with the conspicuous gap of where "already infected / recovered / might not have had symptoms even" might go.
"effective vaccines actually suppress variant formation" is going to get him yelled at for supporting antivaxer arguments, I bet.
you gotta explain to me how that's an antivaxer argument because suppressing variant formation is a good thing.
As he explains in the very next sentence strengthening the immune response lowers the risk of prolonged battles and chances for mutation which is what we want
Anti-antivaxer, i think.
I don't keep up with antivaxer arguments, and maybe I'm daft, but doesn't that mean if everybody were vaccinated then fewer variants would show up?
Yeah, I'm not sure how what the other commenter is saying follows from what Lowe wrote.
>"effective vaccines actually suppress variant formation" is going to get him yelled at for supporting antivaxer arguments, I bet.
Are you implying that since variants exist, then the vaccines aren't effective?
That's not what the data shows[1].
I'd point out that South Africa, where the Omicron variant was first characterized, vaccines have only ~30% penetration in the population[0], making it a good reservoir for mutated variants to spread.
[0]
https://ourworldindata.org/covid-vaccinations
[1]
https://www.news-medical.net/news/20211123/Systematic-review...
The current thinking is that new variants are most likely to evolve in immunocompromised patients who experience prolonged infections. While I encourage everyone eligible to get vaccinated, the vaccines aren't very effective in people with malfunctioning immune systems.
https://www.scientificamerican.com/article/covid-variants-ma...
>The current thinking is that new variants are most likely to evolve in immunocompromised patients who experience prolonged infections.
A very good point.
At the same time, in areas where vaccination rates are low, more folks are infected and a larger proportion of the immunocompromised (as well as the at-large) population will likely be infected.
Making places like South Africa, with less than 1/3 of the population vaccinated, more likely to be reservoirs for the virus, increasing the likelihood of both more variants _and_ an easier foothold for those variants to have their initial spread.
In the long run everyone including the immunocompromised population will likely be infected. I encourage everyone eligible to get vaccinated, however there will be no significant herd immunity effect to protect those who lack immunity. There may be some benefit to slowing this down however it can't be prevented.
https://www.businessinsider.com/delta-variant-made-herd-immu...
>In the long run everyone including the immunocompromised population will likely be infected.
That's as may be. But it's orthogonal to my point.
No, but increased vaccination rates and resultant lower case rates mean the conditions that are ideal for the formation of variants arise less often.
(Yes, I know the vaccine isn't completely sterilizing, but it still has significantly tamped down the degree of spread).
> While I encourage everyone eligible to get vaccinated, the vaccines aren't very effective in people with malfunctioning immune systems.
Isn't the fact that folks with malfunctioning immune systems are surviving rather than dying evidence that the vaccine is working? Granted, their survival has the side effect of a prolonged infection, but immunocompromised folks don't fare well against COVID.
> "effective vaccines actually suppress variant formation" is going to get him yelled at for supporting antivaxer arguments, I bet.
And yet you call this simple, scientific fact that wouldn't have been remotely controversial two years ago an "antivaxer argument"
I don't think it's an antivaxer argument but if you develop the reasoning it really becomes somewhat controversial.
The problem is that vaccines are not completely effective (efficacy goes down with time, is lower against new variants, there are breakthrough infections, etc.) so variant formation is not completely supressed.
Everything being equal (given one exposed or even one infected person) you may have less variant formation with vaccines. But when you have more infections you will end up having more variants.
That the number of infections would increase as people's behaviour adapted to the lower fatality rate was not unexpected: people take more risks because the prognosis of an infection is not so bad anyway, once infected they may have a mild, undiagnosed evolution and still contribution propagation...
And it's no longer an hypothetical scenario. In many European countries there are more infections now than ever before.
Why is that supposed to be an antivaxer argument? It doesn’t mean an effective vaccine eliminates variant formation.
I have no idea, I'm not the one who said it was. Even though the Covid vaccines don't prevent infection and transmission, by helping the body fight off the virus they absolutely do help prevent variant formation.
They also _do_ reduce infection and transmission, just not completely prevent it all the time.
They definitely do not reduce transmission, at least not with the currently circulating variants:
https://www.ucdavis.edu/health/covid-19/news/viral-loads-sim...
That doesn’t support your argument.
_Although vaccinated people with a breakthrough infection are much less likely to become severely ill than unvaccinated, the new study shows that they can be carrying similar amounts of virus and could potentially spread the virus to other people_
Could potentially spread is not the same as saying their equally likely to spread. Fewer infections and less severe cases both reduce transmission to the general population at least in the short term. Long term it may be that effectively everyone gets either COVID and or the vaccine.
When I say they don't reduce transmission, I mean (and the article backs up) that an infected vaccinated person transmits the virus just as much as an infected unvaccinated person. Probability of infection between the two groups is a different subject.
They specifically say: “Our study does not provide information on infectiousness.”
That said, if people are equally infections while sick, but their sick for a shorter period then their less likely to infect others.
Is he saying the current vaccines are not efficient?
I still don't get what makes covid different from the flu. Yes, covid is a little bit more deadly, but other than, why don't we just accept it as part of our lives like we did with the flu?
Currently in The Netherlands the hospitals are bracing for "code black" which means there are not enough beds and staff in the hospitals to treat everyone who needs it. Doctors will have to decide who gets treated and who doesn't - they will have to choose who lives and who dies.
What's more, regular care and non-urgent surgeries are put on hold, increasing the risk that patients experience more severe symptoms. Nurses and doctors are burned out and consider leaving their jobs.
That's why we can't "just accept it".
Over 700,000 (edit it’s now 800,000) dead Americans is about 20x as bad as the flu _even with all of these measures,_ that’s huge. But even that understates the difference when you measure years of life lost.
The flu typically kills the extreme elderly or people with extremely compromised immune systems. Aka they might die at 94 vs 95. COVID on the other kills people who are relatively much healthier, someone that dies at 75 vs 95 lost 20 years not 1.
This is also why people 70+ are almost fully vaccinated in the US. For that age range it’s an extremely serious disease with a high chance of killing them after infection.
COVID-19 is a serious public health problem but let's not exaggerate. In terms of years of life lost it's about 2-9x worse than the flu, not 20x.
https://www.nature.com/articles/s41598-021-83040-3
The average age of COVID-19 deaths in developed countries is about 80. Fortunately the vaccines and other treatments have greatly reduced the risk of death.
https://www.ons.gov.uk/aboutus/transparencyandgovernance/fre...
https://www.wsj.com/articles/the-covid-age-penalty-115920032...
From 2010-2020 the flu killed ~30,000 Americans per year.
https://www.cdc.gov/flu/about/burden/index.html
Edit COVID has actually killed 800,000 Americans.
20x of 30k < 800k. You can cut argue it should cover multiple years of flu, except the first US COVID case was less than 2 years ago and it really only got started in March 2020. Per month COVID has killed more people than the flu does per year on average and it’s not exactly stopping this winter.
Years lost are then on top of that deaths multiplier.
But in the long run Covid could actually kill less as younger people get it and grow old.
COVID is referring to a specific coronavirus, I hope it will go extinct relatively quickly.
That said coronavirus have long been one of the causes of the common cold and occasionally cause diseases of significant concern like SARS, COVID, etc. That’s likely around for the long haul unless some massive medical breakthroughs show up.
>This is also why people 70+ are almost fully vaccinated in the US. For that age range it’s an extremely serious disease with a high chance of killing them after infection.
Older people certainly dominate the vulnerable groups, but there are many other people living with various forms of immune system dysfunction. This is why the rest of us need to mask, vaccinate, and get boosters to minimize our chance of propagating the disease to the more vulnerable parts of our population. Not doing so is basically saying you don't care about other people.
Very honest and good faith question. Until when? What are the specific metrics for when we don't need masks or non-tweaked vaccines tailored to yearly variants like normal flu shots? At some point we need to say "if you are immunocompromised you need to take special precautions like you always did before covid". Just wondering out loud when that should be because for some of us it's sooner rather than later.
Where I live, precautions are specifically targeting hospital capacity. So I would expect that once hospitals are no longer under threat of being overwhelmed, requirements will be removed.
Reasonable question. I don't think we can answer that until most of the population has been vaccinated and we see how "quiet" the disease becomes. I think we are likely to be getting annual vaccinations for years to come. Don't forget that over 200,000 people in the US below age 70 have died. Most of those would not have been considered immunocompromised prior to COVID.
That's actually a good point because the "until most of the population has been vaccinated" is tricky. We don't really know how effective the vaccines are against new variants. Probably better than nothing I'd guess but it also doesn't completely stop transmission. An overly optimistic timeline is 100 days to get a tweaked vaccine for a new variant but we saw that's about how long it took for Delta to move completely through Florida. That plus the possibility of animal reservoirs and many high-compliance mask and lockdown areas getting large spikes anyway leaves me skeptical we can necessarily solve this through the public health policies that have been tried. I just want answers like everyone else and am trying to just learn to be healthy and live with this virus for the rest of my life. Happy to get an annual shot like the flu when/if this becomes endemic and seasonal.
And what is their BMI? The US was already dying.
Is your point that obese people deserve to die? It has been estimated that only 30% of COVID hospitalizations were related to obesity. Since 30% don't matter by your bookkeeping, do the other 70% count?
https://www.cdc.gov/obesity/data/obesity-and-covid-19.html
The number I've kept seeing is 78% of hospitalizations and death were obese.
https://www.cnbc.com/2021/03/08/covid-cdc-study-finds-roughl...
> why don't we just accept it as part of our lives like we did with the flu?
Because several areas are very near 100% hospital capacity with COVID patients still, and a COVID ICU visit is much more demanding from a timespan and resource perspective in terms of staff and equipment. We can't risk relaxing restrictions when hospitals are unable to bear an increase in patients.
From a cynical point of view, COVID policy is about protecting infrastructure - and only save lives as a side effect.
This is why many places had specific policy for essential services and essential workers, daycare and schooling, transportation, - as well as putting restrictions on private industry which in some countries has become significantly more centralized like meat processing.
> Yes, covid is a little bit more deadly, but other than, why don't we just accept it as part of our lives like we did with the flu?
Primarily because our health infrastructure has no capacity as is. Most places are really struggling, both with space and staff. Add to that the PTSD a lot of healthcare workers will be dealing with for decades to come.
And losing 1-3% of our total population isn't great.
But to your point: we will end up living with COVID as an endemic, so long as more people get vaccinated. We need to look at global vaccination rates beyond just local ones, too, as variants will continue to mutate throughout the world. With the vast, vast majority of folks winding up in the hospital being unvaccinated--taking up space, time and money--we're going to be struggling for a while.
And COVID patients are impacting the capacity for people to get routine check ups, and in some locations emergency work, done. It's bad for everyone. Until the numbers are low enough that our doctors and nurses aren't being pushed beyond their limit, we can't consider it sustainable.
COVID-19 is a serious public health problem but let's not exaggerate the risk. There was never any realistic chance of losing 3% of our population. The CDC estimated the fatality rate at 0.6% back when very few people were vaccinated. Now with widespread vaccination the fatality rate is much lower.
https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/burd...
Fair enough. I was using a range in order to address other countries as well.
Early on, before we had the vaccine and ways to help reduce mortality, the WHO said:
> Globally, about 3.4% of reported COVID-19 cases have died. By comparison, seasonal flu generally kills far fewer than 1% of those infected.
https://www.who.int/director-general/speeches/detail/who-dir...
We know this number was likely under-reporting the total cases, due to asymptomatic cases we didn't test for, but I think a range of 1-3% mortality for COVID, letting it go unchecked, is reasonable. This isn't even accounting for variants, as Delta evidenced.
Deaths will climb as our hospitals become encumbered, so we can't rely on the low-range estimates if fewer people are able to receive treatment. This is why we can't just accept COVID as something we live with and do nothing about quite yet.
It's very well possible if we let it rip the fatality rate could have been even lower. Isolate older population let everyone run about get it and we're done. Then let older/obese people back out after vaccinations.
> I still don't get what makes covid different from the flu. Yes, covid is a little bit more deadly, but other than, why don't we just accept it as part of our lives like we did with the flu?
The additional amount of hospitalizations from COVID19 is crushing our hospitals, even with some vaccine support. A number of states have run out of hospital beds in the August 2021 COVID19 Delta-variant surge.
Fortunately, we've got vaccines, monoclonal antibodies, and dexamethasone today compared to March 2020. With all of these new techniques, the death rate has dropped, and treatment of COVID19 has gotten easier.
Still, we're stressing our hospitals to severe limits in parts of the country. We'd ideally want more slack, so that our nurses / doctors can get a well deserved break from this pandemic.
Death rate dropped because everyone started listening to ventilation whistleblowers as well. If we listened to them earlier on we could have saved thousands of people in the US