Thursday Throughput: BA5 Edition
COVID-19 Memorial Field of White Flags 14 – RFK Stadium September, 2021. Photo by Amaury Laporte via Flickr
[ThTh1] It seems like everyone and their dog has come down with a case of COVID case in the last few weeks. While the official number show only a minor increase, the massive increase in in-home testing means that most cases are going unreported. The CDC now estimates that, for every reported case, we have seven unreported cases. For comparison, during the height of the pandemic, we were only detecting one in three. Hospitalizations have become to tick up, hitting levels we haven’t seen in six months. Deaths are, so far, mercifully flat although still at a rate that will take 100,000 lives over the course of the year.
So what’s going on?
The culprit is the BA5 variant. This new variant now comprises the majority of new cases. It has three mutations to the spike protein, which not only makes it far more infectious — it is approaching measles levels of infectiousness — but able to avoid antibodies, whether obtained from vaccination or “naturally”. We don’t know yet if it’s more severe because very few people have not been exposed to COVID, either through vaccination or infection. And an increasing number of people have had COVID multiple times. But even if it doesn’t kill, the variant can still cause significant illness and long COVID. But the massive infectiousness is the bigger concern. Not only does it mean this variant is spreading like wildfire and may evade many of the methods — masking, outdoor activities, etc. — that have worked to slow down previous variants.
Basically, we seem to be in a cycle where COVID is throwing new things at us every six months or so as it continues to circulate through populations. What we are doing is blunting its edge. But short of shutting down the entire planet, we seem to be stuck with the scenario we feared 2.5 years ago — a new endemic virus that emerges every six months to a year to extract a new toll in sickness and death.
The good news? Vaccines still work in preventing severe disease and death. If it has been six months since your last vaccination or infection, it is probably a good idea to seek one out if you are eligible. Very few people are, unfortunately. Masking indoors is still a good idea. If you are sick, stay home as much as possible. We are currently testing bivalent vaccines that show promise not only in defending against BA5 but against future variants. Paxlovid still shows great effectiveness against the new variant and new treatments are in the pipeline. And, ultimately there is a hope of a universal coronavirus vaccine.
In short, the war has not ended or even gone into a stalemate. We missed our chance to defeat this, assuming we even had one. But our weapons continue to work and our geniuses continue to refine and improve them. The worst-case scenario would be a much more deadly variant. But the most likely scenario seems to be a new immune-evading variant every six months to a year until we develop universal vaccines.
[ThTh2] Speaking of COVID-19 vaccines, you may have heard of a new study claiming the vaccines do more harm than good. This study is garbage. In fact, vaccines may have saved 31 million lives making them one of the most effective public health efforts in history.
[ThTh3] The rocket stage that recently impacted the moon is not a huge mystery. It’s from China.
[ThTh4] CERN has fired up their collider again. It hasn’t destroyed the Earth yet, but it has found some new and crazy particles.
[ThTh5] Why do we send space probes out to asteroids? Because sometimes they are very different than what we expected. See the video of what happened when we landed on Bennu.
[ThTh6] Math is crazy sometimes:
[ThTh7] We may have identified the cause of Long COVID. This may have implications for the long-term health of COVID victims.
[ThTh8] Vortices!
Watch a vortex reach up from the sea and climb the side of a 470m cliff pic.twitter.com/zC0tg4jz93
— Science girl (@gunsnrosesgirl3) June 30, 2022
[ThTh9] Unravelling the mystery of Angel’s Glow.
[ThTh10] Using black holes to do particle physics? Just might work.
We might be the one household that has somehow seemingly avoided any Covid infections.Report
I think that switching from Greek letters to “BA” variants is bad.
I understand that the optics and I guess I see why the bees that power went with the new convention, but I still think that it’s bad.Report
yeah, it almost makes them feel ….less concerning? than the Greek lettered variants. Then again, they may be afraid of running out of alphabet.
I am at home today, recuperating from booster #2 (uptick in cases in my area, I”m over 50 and have asthma and interact with some folks on long term chemo). Kind of like booster #1: muscle aches, chills, mild fever. At least today I can set my AC at 82 to save energy (and money!) and not suffer….Report
At some point COVId is it will be endemic, like Flu. Every year the fly variants get names and every year (or every 6 months) Covid variants will have to get names. You have to make a ch age at some pointReport
I would have liked to have hit Omega before we made that concession.Report
As long as Charlton Heston isn’t involved!Report
ThTh7, the article is paywalled. Any chance there’s a link to another article? Or, at least, an elevator pitch summary from our gracious host?Report
I had my COVID infection in May which was probably not BA.5 and as I understand it, my prior infection means bubkus to BA.5. One of the interesting things though is that now everyone thinks any signs of upper-respiratory infection are COVID. This is true even if they test negative again and again. No one believes in the common cold anymore.Report
There’s also a similar RSA virus running rampant …Report
We all got covid a little over 2 weeks ago (just in time to mess up our vacation). It was surprisingly unpleasant. The acute period only had me down for a day (my wife and son a bit longer, they got fevers, I didn’t) but the lingering effects have been different than anything I can remember. I had muscle aches, brain fog, stomach issues coming and going, and a bunch of other junk. I was finally able to return to exercising yesterday can tell I’m still not 100%.Report
I continue to mask in crowded indoor conditions, but I really, really wish that I could read a reputable and robust study proving exactly how much of a difference masking makes (or doesn’t). Two years in and I still can’t find a reputable source that tells me how much of a difference masking makes for me and my immunocompromised wife.Report
Not sure what you mean by reputable, but there have been a number of studies published in reputable medical journals that n-95 respirators are highly effective, KN-95s slightly less effective, medical procedure masks moderately effective and double layer cotton cloth masks slightly less effective then medical
procedure masks. The cotton ones can be made better apparently either a medical procedure mask behind them.Report
Yeah if you need to see the source documents (the full papers) I have access to some.Report
Sorry I forgot this thread. My apologies.
I am not trying to be in any way argumentative. But using your examples, are you suggesting that there is a consensus that wearing an N95 reduces getting Covid by X %? That similarly it reduces transmitting it to others by Y%? I am aware of some studies that show that they theoretically may help, but am unaware of actual well controlled replicated human trials that reveal the answers to my questions (which I have a very open mind toward).
This is something which science can empirically answer. It is something which after two years we deserve an empirical answer to. But is it something we actually DO have?Report
It’s my understanding that doing a controlled study would violate medical ethics.Report
“you could read–”
“no I mean a REPUTABLE study”
“…what do you mean by ‘reputable’?”
“it agrees with what I already think.”Report
No, I have an open mind on the issue. I use them in crowded conditions, but would like more empirical data. If studies reveal no benefit, I will stop using them. If they show small benefit I will probably use them more.Report
I would like to know REALLY how much it benefits me if I am the only person in a space masking.
because very often I am. If it’s doing absolutely nothing for me, I might as well give it up. The weird looks I get from my fellow citizens are transporting me back to junior high, when I *always* wore the wrong thing and was the target of scorn.
OTOH: if it’s even 5% less likely I get covid/a bad case of it, then it’s worth it
One of the things that frustrates me at this stage in the pandemic is how all of us – nearly all of us laypeople – are expected to make decisions based on partial and sometimes-contradictory information. It really does feel like we’re all in this alone, something I’ve felt much of this pandemic. Most recently it was “do I get the second booster? Do I get it now or wait until a couple weeks before classes start? DO I wait until the omicron one comes out?”Report
Yes, exactly. We need more empirical answers on a lot of questions.Report
ThTh1 – I’m not denying anything, I’m not, but isn’t this the “usual” season for a covid increase? Has anyone checked the regional distribution, or is the data too sparse?Report
Hard to measure right now because the case testing is so disjoined from actual cases. Wastewater testing is much better but it’s not universally deployed.Report
ThTh6: Graph theory is not crazy. It’s a very useful field of study for discovering “hidden” structure within discrete data. Ask me about the Christmas gift I made for my mother based on the game “Instant Insanity” and graph theory.Report
ThTh8: This makes my inner fluid dynamics geek happy.Report
“Basically, we seem to be in a cycle where COVID is throwing new things at us every six months or so as it continues to circulate through populations.”
We desperately needed to avoid this, and we didn’t. And we will pay for it.Report
What realistically could have been done to stop this? For the sake of argument, assume that you have the power to crush your political enemies like ants.Report
Also… control other countries.
How many variants emerged in other countries? How do we prevent that? And/or their impact here?
There undoubtedly missteps along the way but the idea there were some major inflection points where we could have made the outcomes dramatically different seems farfetched. Unless we went the totalitarian route which is not without major costs of its own.Report
And in the long run, even the totalitarian approach didn’t work, as seen in China.
The genie was out of the bottle before we even knew it existed.Report
Isolation worked well against original COVID (though expecting the majority of people to not act like insane idiots is apparently too much to ask), and our original vaccine seemed to be sufficient for Delta (New Zealand was on the brink of conquering it, even with minimal restrictions at the start of the year). But Omicron is a different beast. We need better vaccines, both more up to date and able to handle greater diversity of variants so we can actually get ahead of the mutations, that means we need our regulatory agencies to work faster to approve vaccines and make sure the research efforts are well-funded.Report
Isolation wasn’t an option for pretty much any non-island nation.
Also, how do vaccines get developed with a strict universal isolation approach? How do people get food?
Whether as an individual or a nation, isolation only works if either A) you can be totally self-sufficient or B) you rely on outsiders not isolating to provide for you.Report
With the original strain, some combination of isolation (for those who could), masking, and elimination of recreational indoor gatherings might have been sufficient to contain it, but good luck getting the whole world to coordinate. Without total eradication, you’re just kicking the can down the road.Report
Isolation for individuals, yes.
Isolation for nations much less so.
But I think folks underestimate how many can truly isolate without making massive societal changes.
How many people does it take to run a grocery store? More than anyone realizes. It’s not just clerks and shelf stockers. Who makes sure the refrigeration is working properly? Who cleans up the store? Who coordinates deliveries?
Then circle out from there… where’s the electricity come from? Who drives the trucks? Services them? Who runs the gas station? Who delivers the gas? Where’s the gas come from? Where’s the food come from? Etc etc etc.
Yes, lots of us could have isolated — and sadly many gave up on doing so far too early. But far more people than most realize couldn’t isolate.
“Just isolate” isn’t a plan.Report
Right, that’s why I said a combination of isolation for those who can and masking for those who can’t. The goal is not to totally stop transmission, but to get the effective reproduction rate below 1 and keep it there long enough to eradicate the virus.
I think that with the original strain, and maybe even delta, this was feasible in wealthy countries if everyone cooperated. I don’t know how feasible it would have been in developing countries, which is why I expressed skepticism in the comment that started this chain. Probably we would have ended up getting omicron anyway, sooner or later.Report
I see Omicron as a poor man’s vaccine that South Africa gave to the world. It’s free and even anti-vaxers get it whether they want it or not.
It doesn’t do an excellent job in that you still get sick and you are still infectious, but at least it’s much less deadly than any of its predecessors and seems to have stopped them and their nasty ways.Report
@kazzy
I’m pretty certain I do understand what a country-wide isolation strategy looks like, since I lived through one. It’s true that not everyone can stay home, the plan was that of a large enough fraction do stay home (expect for essential activity like buying food or medicine) the chains of transmission can be cut back enough that the disease can’t propagate. To be clear, this doesn’t work with Omicron (it didn’t work terribly well with Delta without vaccines), but original COVID could be eliminated using this approach.
If more than a handful of countries has taken this approach in the first place, we could have prevented COVID from mutating too far by denying it opportunities to spread, but apparently expecting
basic responsibility from most the rest of the world is too much to ask.Report
James,
I don’t know all the ins and outs of New Zealand. Or, really, any ins and outs. So, please pardon my ignorance.
How much of NZ’s food is produced domestically versus how much comes from overseas? Did this change at all during the pandemic?
What about other goods?
Did NZ develop its own vaccine? Or did it use a vaccine developed elsewhere?
I don’t ask these to be snarky in any way… to me they go a long way towards evaluating how scalable any particular Covid response was.Report
Our food is a mix of domestic and foreign, but note that we never stopped freight coming in (or moving around the country), it got to a point where special freight-only flights were being sent here because there weren’t enough passengers for the amount of air freight we needed.
We didn’t develop our own vaccine, we went with Pfizer, though vaccine development would have been considered and essential activity so even under Alert Level 4 it would have continued if we were doing any.
This is why it took seven weeks to suppress COVID to the point where a full lockdown wasn’t needed – people were still leaving their homes, so transmission continued, just at a much lower rate (the R value got as low as 0.5 during Alert Level 4, meaning cases would halve every 2 weeks or so).Report
Thanks, James.
That gets at my point… it’s easier to impose a lockdown when you rely on other nations to provide food and vaccines.
How many more people would have needed out of lockdown to support a fully independent vaccine R&D program? Then manufacturing and delivery?
It’s not just scientists… it’s everyone from the bottom up… janitors, bus drivers, etc etc etc.Report
Honestly, probably not many. Drug development isn’t a labour-intensive process. Equally, New Zealand’s food mills were still running during Level 4. Everyone staying home isn’t necessary, you just have to reduce movement enough that the virus can’t spread quickly enough.Report
It’s hard to measure all that. At the start of the pandemic… when New Jersey was among the Metro NY epicenter, we were more or less locked down and still saw exponential spread.
I guess it could have been worse… hard to know alternate timelines.Report
Here’s a map to get you started:
http://lotrproject.com/map/#zoom=2&lat=-1692.5&lon=1500&layers=BTTTTTTTT
Mordor is to the southeast, while the Shire is up to the left.Report
Kicking the can down the road is a good plan! I mean, if you’re hoping to make it, oh, a year so you can get some vaccines out the door.
I will say that the promise of the vaccines in 2021 was awesome. Get vaccinated and you won’t have to mask anymore! Get vaccinated and you won’t get the covid! Get vaccinated and, okay, maybe you’ll get the covid but it won’t be bad enough for you to be hospitalized! Okay, maybe it’ll be that bad but get vaccinated and you won’t *DIE*.
You just have to kick the can long enough to get to that point.
I will say that the whole “elected leaders not following their own freaking mandates” was exceptionally frustrating and I could not comprehend people defending politicians for not following their own mandates.
I mean, it made the mandates look like they weren’t *REALLY* mandates.Report
Yeah I will never again accept “Hey do this thing and everything will be peachy!” because here four vaccines in I’m still masking and still being careful for the sake of a friend on long-term chemo, and I don’t know when I’ll go to a movie in a theater again.
Not that it’s really anyone’s FAULT but they WAY oversold the “get vaccinated and it’s OVER!” part of it. I’m still wrestling with the idea that the however-many-more years of life I have left are going to be radically different from the first fifty, and I can’t quite make it to the point of acceptance on that.Report
The difficulty is, it’s hard to know how much of that was intentional deception and how much was just not knowing how it’d go.
Fauci’s… um… prediction about herd immunity didn’t help.Report
I have often said that no matter what your theory about COVID is, it’s possible to find data that supports it.
I guess the only change is to say that if your theory was “it’ll go away within 18 months”, well, not so much.Report
I’m surprised by the confusion with the math problem. The idea of the loops guaranteeing the initial number in it makes sense. The more advanced math I couldn’t have solved myself but seems pretty straightforward. Were people overthinking it?Report
I suspect the big hurdle is the idea that you can put the slips under the boxes entirely at random and always get loops, with every box in exactly one loop. Not because that’s particularly hard to show, but because most people don’t think about a function that maps a finite set onto itself in terms of what that function might represent and what properties it might have (eg, the loops and that the loop that includes the box labeled “1” must include the slip labeled “1”).
Walking through why the probability of a loop of length 100 is 1/100 and then waving his arms (“it’s a general rule”) is sort of cheating. The case for a loop of length greater than 50 and less than 100 is somewhat more complicated.Report