All of my final exams came due last night at midnight — they were all fortuitously scheduled for the last day of finals week — so I got to open my mailbox this morning to find an expected mountain of papers to grade. Oh joy. There goes my weekend. Also, my flies arrived late yesterday, so I’ve got to go in to the lab today and get the stocks set up for my spring genetics course. That course, by the way, is going to be taught entirely in person, because my university has been applying some gentle pressure on the faculty to pretend the pandemic is completely over and we can all go back to normal. To be fair, I really want to get back to normal, too, but I’m also realistic enough to know that what I desire isn’t necessarily what I’ll get. The university is not adjusting any of its policies to deal with the threat of the new Omicron variant, and is in fact loosening them. As usual, we’ll wait until a crisis is upon us and only then start changing things, too little and too late, to try and catch up to a disease that’s running ahead of us right now. And my university is relatively progressive compared to the western Minnesota community, and the Minnesota governor!
My next few days are going to be bogged down in work, and then my so-called Christmas “break” I’m going to be tied up in that magic word, preparation, for the next semester, which I’m required to take seriously, unlike the administration. Wouldn’t it be nice if I could submit my grades next week and then take a nap or play with spiders or you know, just relax, until 18 January, when classes resume? Nope, isn’t going to happen. Especially since I have a looming dread that this is going to be an abortion of a semester, that we’ll go in assuming an air of nonchalant normalcy, and at some point we’re going to get screaming panicky emails from the administration telling us the quarantine spaces are all full, the local hospital is full, the pandemic is spiking, change your class management and go into lockdown. I figure I’ve got to prepare for two classes, not just one, an in-person version and a remote version. Thanks, procrastinators on high!
And then Ed Yong has to come along and splash stinky reality all over me.
OK, I can’t blame him. I know this stuff, but hey, I’ve been trying to close my eyes and pretend it isn’t as bad as it probably will be. Omicron should open everyone’s eyes to the new normal, that because we refuse to do what needs to be done, we’re going to get new variants every year, and we’re going to have to learn to live with new levels of unpredictability.
America was not prepared for COVID-19 when it arrived. It was not prepared for last winter’s surge. It was not prepared for Delta’s arrival in the summer or its current winter assault. More than 1,000 Americans are still dying of COVID every day, and more have died this year than last. Hospitalizations are rising in 42 states. The University of Nebraska Medical Center in Omaha, which entered the pandemic as arguably the best-prepared hospital in the country, recently went from 70 COVID patients to 110 in four days, leaving its staff “grasping for resolve,” the virologist John Lowe told me. And now comes Omicron.
Will the new and rapidly spreading variant overwhelm the U.S. health-care system? The question is moot because the system is already overwhelmed, in a way that is affecting all patients, COVID or otherwise. “The level of care that we’ve come to expect in our hospitals no longer exists,” Lowe said.
Because we don’t know what is going to happen, we need more discipline, more cohesive action, more cooperative behavior in our communities. That’s not the American way!
The real unknown is what an Omicron cross will do when it follows a Delta hook. Given what scientists have learned in the three weeks since Omicron’s discovery, “some of the absolute worst-case scenarios that were possible when we saw its genome are off the table, but so are some of the most hopeful scenarios,” Dylan Morris, an evolutionary biologist at UCLA, told me. In any case, America is not prepared for Omicron. The variant’s threat is far greater at the societal level than at the personal one, and policy makers have already cut themselves off from the tools needed to protect the populations they serve. Like the variants that preceded it, Omicron requires individuals to think and act for the collective good—which is to say, it poses a heightened version of the same challenge that the U.S. has failed for two straight years, in bipartisan fashion.
We’re not ready for omicron. How about pi, and rho, and sigma, and phi, and…we’re going to run out of Greek letters long before this is over. Oh, wait, “over”? It may not ever be over, at least, not until the recalcitrant and deluded are all dead. I was letting my guard down after I got my third booster, but I’m going to have to look forward to my fourth, and fifth, whatever it takes (at least we run no risk of running out of numbers), and I’m going to have to be less cocky. He says, while preparing to abandon isolation and spend 16 weeks in a classroom.
First, the bad news: In terms of catching the virus, everyone should assume that they are less protected than they were two months ago. As a crude shorthand, assume that Omicron negates one previous immunizing event—either an infection or a vaccine dose. Someone who considered themselves fully vaccinated in September would be just partially vaccinated now (and the official definition may change imminently). But someone who’s been boosted has the same ballpark level of protection against Omicron infection as a vaccinated-but-unboosted person did against Delta. The extra dose not only raises a recipient’s level of antibodies but also broadens their range, giving them better odds of recognizing the shape of even Omicron’s altered spike. In a small British study, a booster effectively doubled the level of protection that two Pfizer doses provided against Omicron infection.
Second, some worse news: Boosting isn’t a foolproof shield against Omicron. In South Africa, the variant managed to infect a cluster of seven people who were all boosted. And according to a CDC report, boosted Americans made up a third of the first known Omicron cases in the U.S. “People who thought that they wouldn’t have to worry about infection this winter if they had their booster do still have to worry about infection with Omicron,” Trevor Bedford, a virologist at Fred Hutchinson Cancer Research Center, told me. “I’ve been going to restaurants and movies, and now with Omicron, that will change.”
I guess I’ll be self-isolating at home from now on, except every day when I go in to work.
Omicron might not actually be intrinsically milder. In South Africa and the United Kingdom, it has mostly infected younger people, whose bouts of COVID-19 tend to be less severe. And in places with lots of prior immunity, it might have caused few hospitalizations or deaths simply because it has mostly infected hosts with some protection, as Natalie Dean, a biostatistician at Emory University, explained in a Twitter thread. That pattern could change once it reaches more vulnerable communities. (The widespread notion that viruses naturally evolve to become less virulent is mistaken, as the virologist Andrew Pekosz of Johns Hopkins University clarified in The New York Times.) Also, deaths and hospitalizations are not the only fates that matter. Supposedly “mild” bouts of COVID-19 have led to cases of long COVID, in which people struggle with debilitating symptoms for months (or even years), while struggling to get care or disability benefits.
And even if Omicron is milder, greater transmissibility will likely trump that reduced virulence. Omicron is spreading so quickly that a small proportion of severe cases could still flood hospitals. To avert that scenario, the variant would need to be substantially milder than Delta—especially because hospitals are already at a breaking point. Two years of trauma have pushed droves of health-care workers, including many of the most experienced and committed, to quit their job. The remaining staff is ever more exhausted and demoralized, and “exceptionally high numbers” can’t work because they got breakthrough Delta infections and had to be separated from vulnerable patients, John Lowe told me. This pattern will only worsen as Omicron spreads, if the large clusters among South African health-care workers are any indication. “In the West, we’ve painted ourselves into a corner because most countries have huge Delta waves and most of them are stretched to the limit of their health-care systems,” Emma Hodcroft, an epidemiologist at the University of Bern, in Switzerland, told me. “What happens if those waves get even bigger with Omicron?”
Ha ha, I know! Nothing! Nothing will change! The people in charge will keep pushing everyone to go back to work, the media will amusingly report without condemnation on all those assholes protesting against basic hygiene, and Republicans will be passing laws against accurate information and public health measures.
And then I die because I can’t get healthcare from a system clogged with people on ventilators who refused to get vaccinated. I’m calling it now.
Omicron appears to be incredibly transmissible. The UK has been averaging around 30-50K daily infections during the delta wave. Now in the last 3 days its been 59K, 79K, 88K.
What’s getting more irritating every day is that the assholes who are complaining the loudest about the restrictions in place because of covid are the leading cause of the restrictions in place because of covid. I do my part to stem the spread and these fucknuts make it worse every day. (I live in small city midwest, so I’m just generally fucked anyway with regards to me views and values)
I’d move, but I have a good job and I actually like it here. It’s the people I can do without
Ah yes, the Enlightenment-era conceit that human beings are rational, are intrinsically “good,” and will act out of “enlightened self-interest” reaches it ultimate conclusion: A plague-ridden nation populated by superstitious, racist, greedy clods whose government is teetering on the edge of fascism because our outdated Constitution/Bill of Rights prevents anything to stop it.
All because a bunch of 18th century, slave-owning, rich, white, bastards convinced a bunch of illiterate, uncultured, colonial peasants that they could “govern themselves.” History keeps repeating itself. it seems.
The UK doubling rate is now 1.7 days, with delta it was more like 11 days. Omicron is very very much more contagious than any of the stains we have yet seen.
Yeah, this.
Right now in parts of the USA, the hospitals are already overwhelmed and have gone to emergency triage.
The level of care has gone down for everyone, both Covid-19 and non-Covid-19 care such as heart attacks, cancer, emergency, etc..
And with the 6th Omicron wave just starting it will get worse.
A lot of people will get a Covid-19 virus infection for Xmas and some will die and some of the survivors will be long haulers.
This is going to be another winter of sickness and death.
This NYT Morning Newsletter arrived in my email inbox this morning: Omicron Threatens Red America. There’s a chart about midway down the article that shows just how much worse Omicron will be for the unvaccinated, and Trump America is very much in that category.
@3
It’s not just the USA or North America.
Europe — East and West — is showing massive resistance to any measures to slow down the epidemic.
I get the impression (from the rather unreliable US press, supplemented by Rhiannon’s reports) that East Asia is doing better in this way, but they also have their share of “COVIDiots.”
And I gather Africa is also doing a lot better than expected, though no one seems to know why.
At the very least, it seems to be a particular problem with the European imperialist culture, which BTW North America, Australia, and New Zealand share. The solution to all problems (and non-problems) is to steal more and kill more. He (gender intentional) who has the most gold on top of the highest pile of corpses wins.
It’s kind of like a Ponzi scheme, actually.
I don’t know much about science ,so forgive me if I ask ,why is covid 19 mutating so fast ?
All the other variants over the last few years didn’t seem to spread so fast.
Another thing I have noticed, the religious nutjobs haven’t leaped on covid 19 as a sign
that the big sky daddy is pissed at us again .
Seems like they shot themselves in the foot by declaring it a govt hoax .
SARS-CoV-2 isn’t the only spreading virus now. H3N2 is spreading, too.
https://healthweather.us/analysis/the-problem-child-of-flu-strains-is-gaining-ground
Add obsessive handwashing and alcohol wipes back to your daily routine.
I’m going to ditch my cloth mask and find some KN95 masks.
robro @ 6 Good. Maybe I can look forward to having a significant chunk of the population of Wyoming wiped out. no, I’m not feeling grumpy at all today, why do you ask?
drksky @ 2 Same. And the fewer people there are, the fewer 4x4s I have to look out for while I’m out riding.
@8- davidc1
I don’t think anyone really knows. This major variant (shifted strain?) could have been mutating under the radar as testing for COVID is not the same as doing sequencing of the virus detected. But the apparently sudden changes could have been going on in immune comprised people. Or another idea making its rounds is that Omicron could be the result of infected mammals spilling the variant back to humans. As with how this variant will play out in populations around the world per fatality rate it seems too early to tell. It appears that immune escape in those previously infected or vaccinated will be an issue. Hybrid immunity (previously infected plus vaccinated) might be a boon or hopefully boosters will be sufficient for most of us. The higher transmissibility of this one now seems almost a given. The window for the unvaxxed is quickly slamming shut. Hopefully for them this thing is less lethal. It could be months before more is known and there will still be plenty of uncertainty. I went from enjoying not wearing a mask for almost a month back to begrudgingly wearing it again. Thanks Omicron!
I’m borrowing a bit from the prognostication of Med-tuber John Campbell, but given the spread of this thing, herd immunity may not be an issue after its done with us. His early notion that we will all be exposed at some point is hard for me to digest and seems too alarmist. If true I don’t know how Omicron immunity plays out for future strains or if SARS-CoV-2 becomes a common cold in the future. Your vaccination and infection history with this coronavirus could have positive or negative consequences with future exposures to variants.
At this point I wonder what coinfection with Delta and Omicron looks like. Plus flu. Bites nails. At least I’m COVID vaccine boosted and vaccinated against flu. Ugggh!
Agree with drksky @2. The authorities seem to have been doing a fairly good job of promoting masks, distancing, and vaccination. It is the inherent irrationality of humans (Akira @3) that is letting the virus get out of hand.
I think that there will be a collapse of services, especially medical, but also other public services as the workers get sick, especially in red states. Not much that any government can do anything about. And yes, now is not the time to get sick from other causes, or to need other public services.
What we need is for Omicron to actually turn out to not cause as serious illness, or at least in the vaxxed and boosted. And for it to be maximally transmissable to all those who aren’t. To close down the big pool of easy targets, which rationally should have been closed by masking and vaccination. And then, a quick mRNA vaccine tailored for Omicron. If I was Pfizer and Moderna, I’d bet that that’s where the big money for me is going to be.
I know this may seem cold-blooded but there is a solution for acceptable levels of medical care now: triaging medical resources and set a hard % limit for all medical resources (bed, ICU, staffing, whatnot) for COVID patients who can get vaccinated but haven’t, and reserve the rest for others, including breakthrough cases.
Also, given that many COVIDiots are actively attacking medical staff, some exceptions should be made to the law where the hospital is required to accept ER patients and get them stable before discharge.
Scary stuff PZ. In Australia governments, even some of the Labor ones, are dismantling every protection on the grounds that there has been a good vaccination rate. Even very minor protections like masks indoors, or check-ins for restaurants have been discarded because of a few morons demonstrating about “freedom”. The result already is a skyrocketing third wave in the face of inadequate stocks of booster injections for people like me (old and with health problems). Be afraid, be very afraid. Take care everyone.
@12- garnetstar
Strain specific boosters sound good and I’m for it, but the logistics are a downer. It takes months for development and approval and when done part of the race against the clock is lost. How many will be already exposed to Omicron when it hits the market? Will the effort be putting all eggs in one basket for a variant that may become irrelevant not long down the road? Will future variants be similar to Omicron? Did Omicron stem from Delta or an earlier less prevalent strain? So would a future variant escape Omicron immunity rendering a variant (strain?) specific vaccine less effective? Was Omicron an antigenic drift or shift due to recombination of coinfection with variants of SARS-CoV-2 or another human coronavirus? Would coinfection recombinant be common or rare flukes?
Cutting to the point are variant specific vaccines better than trying to develop a more universal coronavirus vaccine that takes all comers?
OTOH would a vaccine tailored to Omicron broaden our immune response in a manner similar to having a universal vaccine? Having some B- and T-cell immunity toward the ancestral spike would Omicron immunity select for mutant B immunocytes away from that or would ancestral spike and Omicron immunity coexist? I hate to call it original sin, especially as the concept is flu-specific, but I wonder what antigenic imprinting could mean in the long-term for populations or people as new variants crop up.
Also after reading Offit’s book Vaccinated where he introduces Hilleman’s notion of long term HA specific flu strain cycling, I wonder a century down the road what will coronavirus immunity look like.
After herd immunity becomes established what would something like original 2003 SARS or MERS do in exposed people with immunity to 2019 SARS virus?
Davidc1
Viruses mutate, it’s what they do.
Mutations may or may not affect transmission rate, you can’t conflate the two.
By the way it’s word, comma, space.
Only trying to be helpful.
@16 Yes I know they mutate ,it seems that this bastard is doing it faster this time round .
Also , the dimwits refusing to be vaccinated ,how much have they hindered the fight against covid 19 ?
Yeah ,the word ,comma space bollox again .
Still don’t know what you mean by it ,if you could write a sentence the way I do ,and a proper sentence like what the rest of the world does ,that might help .
AstrySol @13, I believe that a version of that kind of triage was what they did during the previous Delta surge, in hospitals that were overwhelmed. If you’re unvaxxed with COVID, you’re in the category of more-likely-to-die-even-if-you-do-get-care, and that’s the lowest priority.
But, hospitals have to get to the point where they cannot provide care to everyone: they don’t go to triage without that. I think, like you, that they shouldn’t have to wait for that.
davidc1 @17
should be
You should never put a space before punctuation.
Oh the joys of good timing. I’m heading to the UK to help care for my 90 year old mom on Monday, and I have to travel through London to get there. I’m boosted, stocked up on KF94 and KN95 masks, etc. so there’s nothing much more I can do except hope not to be exposed. Not worried about me, but very concerned about passing it on to her. Will have to be very careful for the first few days.
Been reading reports from people in London who went to office parties recently, or were simply in the office with a bunch of other people, and having six, seven, eight or more people they know all coming down with Covid as a result. Omicron really is a game changer in terms of infectiousness, and I’m not looking forward to seeing the full havoc it’s going to be causing here in the US before long.
They believe Omicron comes from a pre-Alpha strain of Covid and evolved alongside Alpha and Delta into its current form.
Vaccines can only attack the targets the virus presents to them, so it all depends on whether you can find a target that (a) can used used to effectively neutralize the virus and (b) doesn’t mutate out of reach of the vaccine.
Developing an effective vaccine against Omicron is clearly the highest priority because we already have an effective vaccine against all the other known variants of concern. I’m guessing but it seems logical that an effective Omicron vaccine has a better chance of knocking down any future variants of concern that arise from Omicron than the original vaccine.
I don’t doubt they’re looking for commonalities between the variants the can exploit with a single vaccine, but given the pace of mutation, it could be a never-ending struggle to keep up with the virus.
@17
Yes vaccine refuseniks not helping.
@19 is being very patient and helpful re punctuation.
I’m sorry but if you can’t get that, unless you are being particularly obtuse, you never will.
Virus’s mutate rapidly because RNA is much less stable than DNA and the copying process has a lot of errors. The rate of new mutations is product of the error rate and the rate that new copies are being made. Since so many people are unvaccinated Covid petri dishes there are a lot of new copies being made. If a variant is faster and more infectious it ends up having the most copies. Interestingly, omicron is not related to any of the other major variants. ( https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant )
However, if you think Covid19 is bad, look at HIV – the mutation rate is so high that within a month of infection a person is populated with a vast swarm of variants different from the initial infecting population. This is partly because HIV has a lot more stuff in it and thus more things that can change. The mutation rate is one reason there still is no HIV vaccine after forty years.
Its upsetting that in Australia we had this licked. Then the murdoch mouthpieces, economy above all else and anti vax bastards tore down the wall.
Re: marner @ #19…
Much as I agree with that rule about punctuation (and include parentheses), there is some posting software that will turn some constructs into emoticons, especially when ending a parenthetical remark. In those cases, I insert a space ahead of the closing parenthesis to avoid the conversion.
California has reverted “masks indoor everywhere”. This will mostly affect the “red” counties (Central Valley and the areas east of San Diego known as the Inland Empire). Where I live (SF Bay Area), we never dropped indoor masking in the first place.
As for higher educational institutions… Stanford University (known to those from UC Berkeley as Leland Stanford Junior-University) is going to start their Winter Quarter in January with at least two weeks of remote classes.
@19 Ah,I see said the blind man.But when I do it yourself way,the red squiggle pops up .
Thank you for taking the trouble,I only had a secondary education,but I have tried to educate
myself by reading books on subjects that interest me,such as history.
Also what used to be known as Natural History,also the history of science.But actual hard
science like what the Doc deals in is way about my head.
Plus I know I use far too many commas,and I don’t know when I should use ; instead.
Over here in GB,there is The Open University .I did start on a Humanities course,A101.
I passed that,but personal things came up so I had to stop it.
But a university isn’t everything,most of the bastards in the tory cabinet went to uni,and they are thick as shit.
@22 HAHA,I just did.
I’m confused. I thought we all agreed that space commas were a kind of tardigrade.
I saw a news story within the last couple of days reporting that people who’ve had the vaccine, but no booster, still have pretty high levels of antibodies to delta, but not omicron. However, those who’ve had the booster had high levels of antibodies to both. I sure hope that’s true.
And are there investigations into why Africa seems to be having a relatively milder time with COVID than, say, the US or the UK? I don’t mean they’re getting off scot-free, but it does seem to be less severe there, and I don’t think anyone knows why. (Maybe it’s not real — maybe it’s just poorer reporting or something. But Nigeria reports fewer cases than Australia, despite having over 8x as many people.)
@29 wot
davidc1, you’re close but not quite there yet. You’ve just got to put a space after the comma now.
@32 I fought I did do done doed that, like that, you mean?
Good question. Not that I know of but there should be.
.1. Part of it is just poor reporting.
To take one example, India is reporting 477,000 deaths.
The actual number is probably more like 4 million deaths.
Worldwide reported is 5 million dead, the actual number is probably more like 20 million dead.
In a lot of third world countries, they don’t have the systems in place to even collect this kind of data.
In a lot of countries, they don’t even bother collecting such statistics. It makes the governments look bad when huge numbers of people are dying from a pandemic virus.
This is also happening here in the USA. AFAICT, Florida’s Covid-19 numbers are just fantasy right now.
Out of sight, out of mind.
.2. Part of it is different age structures in the population. The West and parts of Asia have an average older population. Africa has a young average population. Younger people are more resistant to the effects of the virus than older people. Same goes with obesity, which is a major risk factor for Covid-19 virus disease outcomes.
It is hard to figure out what is actually going on in Florida with their questionable reporting systems.
Most public health experts consider Florida to be deliberately undercounting Covid-19 deaths as much as possible. This is common in some parts of the USA.
In a lot of Red, rural areas in the South and Midwest, there is a lot of pressure to leave Covid-19 virus off of death certificates. I guess this is because it is embarrassing to die of a preventable disease that doesn’t even exist.
Good job Nebraska.
If you don’t report Covid-19 virus deaths, then they never happened.
The difference between Nebraska and a third world country isn’t much.
Remember: that which does not kill us mutates and comes back to try again.