COVID-19 Megathread 6: Return of the Omicron

[Tintrlvr]

I generally don’t support muting people, but Bandit is really challenging that. He has been shown the facts/reasoning many times and yet refuses to ever stray from his #populist “Fauci bad” stupidity. It seems like either deliberate trolling, or serious cognitive issues at this point.

Did you not realize this about Bandit independent of coronavirus? He's not to be engaged with seriously on any topic.

[Tintrlvr]

Why are people who get Covid in CT or RI TEN! times more likely to die than someone who gets Covid in ID or NE.  That's weird right?  It seems to really hit the north east the hardest (just like gingivitis!), is it because they got hit earlier and we didn't know as much about  keeping people alive?  Where their hospitals overrun?  Or just worse?  It's not black people driving the numbers, are people in Hartford just that much fatter than Boise?  Population density?


Ten times more is a LOT, there has to be a reason for the difference.

Testing levels were well under a tenth of what they are now back then, so only a tiny fraction of cases, mostly only the most severe, were reported during that initial outbreak. In actuality, there were still more cases in New York in March-April than there have been in any other state, by far. It’s as simple as that. I don’t think you’re a fool, and this should be obvious to anyone paying attention.

Death rates from new cases in the region now from the virus are no different than anywhere else.

[Tintrlvr]

Why are people who get Covid in CT or RI TEN! times more likely to die than someone who gets Covid in ID or NE.  That's weird right?  It seems to really hit the north east the hardest (just like gingivitis!), is it because they got hit earlier and we didn't know as much about  keeping people alive?  Where their hospitals overrun?  Or just worse?  It's not black people driving the numbers, are people in Hartford just that much fatter than Boise?  Population density?


Ten times more is a LOT, there has to be a reason for the difference.

Testing levels were well under a tenth of what they are now back then, so only a tiny fraction of cases, mostly only the most severe, were reported during that initial outbreak. In actuality, there were still more cases in New York in March-April than there have been in any other state, by far. It’s as simple as that. I don’t think you’re a fool, and this should be obvious to anyone paying attention.

Death rates from new cases in the region now from the virus are no different than anywhere else.

but NY doesn't have the same levels that the rest of New England does



why is NY 1/5 of what CT is?

I assume this is just something wonky with how they are generating their “estimates”. For example, they may be assuming that positivity rates are the right thing to consider when trying to determine the “real” number of cases in March-April, which could result in an undercount of cases in places that were testing a lot, like RI. But that method carries with it a prior assumption that death rates *were* different in different places. Instead, I assert that death rates themselves are the best indicator of how many cases there were in March-April, i.e., death rates should have been roughly the same elsewhere.

I do agree death rates were lower after June or so, as ventilators were used less, infections caught earlier, and dexamethasone and other steroids used to prevent cytokine storms.

[Tintrlvr]

We're going to be over 100,000 cases a day on Friday (if not earlier), aren't we?

[Tintrlvr]

I'm sure we've been well over 100,000 months ago. We don't know it, because the testing capacity was much less back then.

Yes, and it would be great if things were just like they were in late March again, wouldn't it? I lived through that here in NYC; you can shut your mouth on this.

[Tintrlvr]

What is the source for the claim that testing has decreased?  

It is true that positivity rate has increased.  But according the Covid Tracking Project and the Johns Hopkins tracker, testing is also still increasing this week as it has been for the last 6-8 weeks.



https://coronavirus.jhu.edu/testing/individual-states

It's possible he is looking state-by-state. For example, while New York has massively increased testing in the past month, it is not the location of a major outbreak at the moment. And Rhode Island just this week passed the threshold of being the first state to have (over the course of the pandemic) undertaken more coronavirus tests than there are residents in the state. But many of the states with the highest new case rates have much, much lower testing rates than the top-tier testing states.

[Tintrlvr]

We're going to be over 100,000 cases a day on Friday (if not earlier), aren't we?

Well, I hoped I wasn't going to be right.

[Tintrlvr]

Biden won't become President until 20 January.

At which point we could be at much higher daily figures, unfortunately.

[Tintrlvr]

According to my mother (she does pulmonary research) a few of the extracted RNA sequences that a research group got from post-Covid patients (severe illness) look a lot like those of IPF.

I’m not saying it is the exact same, but that alone should be concerning. The life expectancy of those with IPF is three years upon diagnosis. So...yeah Del Taco you ed up.

What is IPF?

According to Google, "Idiopathic Pulmonary Fibrosis", which seems to be a generic term for scarring of the lungs for unknown reasons. It seems like it would be hard to generalize about outcomes for a medical term that is specifically for an illness with an unknown cause.

[Tintrlvr]

Deadliest day since the start of the pandemic?

Thursday last week had 9 more deaths than yesterday, but I am sure today will be a new record based on trajectory and day-of-the-week effects.

[Tintrlvr]

You can't have a stay at home order for just the old and sick because it violates the Equal Protection clause of the 14th Amendment. At most you could strongly encourage them to stay home.

No it doesn't. Since the distinctions are not being made on the basis of a "suspect classification" (race, gender, religion, etc. — you could maybe argue age here, but certainly not "sickness"), the plaintiffs would have to demonstrate that there was no rational basis for the difference in treatment. The rational basis clearly exists for sick people!

Age is also not a Constitutionally protected class; that's well-trodden ground.

[Tintrlvr]

In the meantime... today was the first day with more than 300k new cases in the United States. Just like the recent 4k daily deaths milestone, it's going largely unreported (NYT did talk briefly about the 4k deaths; we'll see if they comment on 300k cases).

[Tintrlvr]

On Jan 11, the 7-day average for new cases was 255k. One month later, there's a real chance of it being below 100k. That's crazy.

Well, actually it's science.

True. The way things were looking though, I didn't think it would decrease that fast.

I do wonder if vaccines are having a bigger effect than initially expected. Perhaps more spread than we actually realized was happening through healthcare workers getting exposed at work and then spreading the virus in their daily lives outside of work, so vaccinating them (really the only group that has achieved "herd immunity" levels of vaccination already) has had a more disproportionate effect than we expected.

[Tintrlvr]

I know this guy is a moron but has he never been to another country? At least most tropical countries make you show a vaccination card to get in. There’s no difference between Honduras making me show a yellow fever vaccine than there is Greece and a COVID vaccine.

The US itself also requires you to get a vaccine in order to arrive/return from a lot of countries, even if you are a US citizen.

[Tintrlvr]

Pfizer CEO believes third dose will likely be needed.

https://www.cnbc.com/2021/04/15/pfizer-ceo-says-third-covid-vaccine-dose-likely-needed-within-12-months.html

Which is not what the article says, or what the CEO said. CNBC and the rest of the media are just fishing for clicks here.

The quote: "So I think for planning purposes, planning purposes only, I think we should expect that we may have to boost."

He's just hedging that they don't know how long the vaccine will be effective for without a booster. He didn't say "likely" anywhere, just that there was a chance it would be needed, which is fair because we don't have definitive data on the length of effectiveness (though the evidence seems to suggest that it will probably be effective for a long time and not require a booster this year, at least, given that there's been no observed decline in effectiveness over six months in the trial volunteers).

[Tintrlvr]

New Hampshire becomes the first U.S. state to report more than 50% of its population being fully vaccinated! (I guess some data backlog just got cleared)

Washington state surpasses the milestone of having 40% of its population fully vaccinated

New Hampshire is now reporting 85% of its population (not adult population, population) having received at least one dose, which seems obviously wrong as this would mean 95+% vaccine uptake among New Hampshire adults. Their data has seemed off for a while, ever since they "corrected" their percentage vaccinated down a couple of weeks ago. Someone is either incompetently running the reporting or just plain old cooking the books in New Hampshire.

On a positive note, the 7-day average of cases nationwide is now lower than reported at any time since late June 2020, having fallen below the late September 2020 low in the past two days. Also, since testing was still quite scarce across much of the country in June 2020 compared to now, this is almost certainly the time with the lowest rate of actual new cases in the country since the early days of the initial outbreak (maybe early March 2020, before any major lockdowns came into effect).

[Tintrlvr]

Damn. Is that the lowest number of new cases and deaths yet?

Ever since I started recording case numbers on 3/26/2020, yes.

What were they on March 14, the day I was sent home from work never to return?

According to Wikipedia, which is one of the only sources I can find that has data by day going back that far, there were 662 cases and 7 deaths officially recorded in the US on 3/14/2020. (Of course, in reality there were probably tens of thousands, maybe even hundreds of thousands, of new infections that day, particularly in and around NYC.)

[Tintrlvr]

There's a large segment of the population in this country that remains unvaccinated, not to mention those that are under 12 and cannot get the vaccine. This is only allowing for new mutations and variants to develop as the virus gets an exponential chance to keep replicating. It's apparently not common sense that stopping transmission stops replication. Every day and every chance this virus gets to mutate is one that could render our vaccines useless or even just far less effective.

Why don't you have this concern for the flu? Every person it infects is a chance for it to mutate into something deadlier that evades all our vaccines. Right?

I have some understanding of virology. Coronaviruses and influenza viruses are very different. These vaccines we currently have are the first vaccines to ever be used against a human coronavirus. We should all be lucky they are as effective as they currently are. Influenza vaccines are generally made in advance of the upcoming season and often have a fairly low efficacy rate. (So far, we're lucky that the highly lethal avian strains haven't passed from human to human. They appear to be harder to vaccinate against. From what I recall, something in either human respiratory physiology or the shape of the virus makes it currently virtually impossible to pass from person-to-person. That prospect does scare me.) In recent years, influenza vaccine efficacy rates have varied from 10-60%. However, the flu is of highest concern among the elderly, the very young, and the immunocompromised. Vaccines in general may either be problematic or not even work for those that are immunocompromised. As for coronaviruses in general, this virus (SARS-CoV-2) is the third known fatal coronavirus in humans. Its predecessors were SARS (SARS-CoV-1) with a fatality rate of about 10% and MERS (MERS-CoV) with a fatality rate of about 35%. Generally, viruses trade off virulence for transmissibility. However, that are many instances of viruses becoming more virulent with time (examples include Ebola, West Nile, and the Spanish flu).

Right now, we have a virus running rampant across the world and replicating exponentially in every new host. So far, the vaccines are holding up, although not as much as when they were first released to the general public. But we're always one mutation away from something that will render our vaccines either useless or far less effective. I believe in erring on the side of caution. Wear masks in most indoor places when you're with strangers and maintain a certain distance from those you don't know. In restaurants, go ahead and eat normally if you're vaccinated. I plan on going to the movies soon and I'm not going to wear a mask watching the movie (but I'll still wear it other indoor public places). I want businesses to be open, but considerations need to be made, particularly in restaurants (such as reduced capacity or working to space people apart more effectively or asking for vaccine status). I think this is all a matter of risk mitigation and balancing.

Since you seem more knowledgeable than others on the issue, I have to actually ask a question. Given the extremely high risk of a mutation rendering the vaccines useless, I've long asked myself the question of: Would humanity actually be better off if a vaccine had not been developed?

My reasoning here is quite similar as to why the excessive use of anti-biotics is allowing the creation of anti-biotic resistent bacteria. People taking needless antibiotics means the bacteria can somehow "learn" how to defeat the antibiotics and create a mutation that makes it anti-biotic resistance.

So similarly, is the fact that covid is spreading to vaccinated people, and in some cases being able to infect them and what not creating a vaccine-resistant strain of covid?

Meanwhile with no vaccine, humanity would be worse off in the short term, but covid would be unable to "learn" how to become vaccine resistant (since there would be no vaccine) and eventually it would be gone in 3 years or so (much like every other epidemic in human history).

Basically my fear is that partial vaccination might somehow drag on the pandemic (meaning instead of lasting for 3-4 years it lasts a whole decade) as well as giving the virus more chances to mutate and create a worse version of itself.

Note I am borderline biology-illiterate given I dropped that class in year 7 or so so perhaps I am just saying stupid things.

This makes zero sense. The no-vaccine scenario and the incomplete-vaccination scenario have the same ultimate result - eventually COVID burns itself out through infecting a large portion of the population. In the latter scenario, though, a significant number of vaccinated people are never infected and survive where in the no-vaccine scenario they would have died or had a serious illness with long-term effects and significant societal costs.

The concern re: bacteria and antibiotics is because we, humans, don't really develop much resistance to bacterial infections, and there are no vaccines for most common and dangerous bacterial infections. If you get exposed to strep again after a strep infection is cleared with antibiotics, you'll just get the same strep infection again. So the concern is that the next infection will become harder to treat if the second strep infection is antibiotic resistant. That's irrelevant for vaccines, though, since a vaccine isn't a treatment; it's prevention. And a virus (or bacteria, for that matter) that evades a vaccine isn't "stronger" than a virus that doesn't, it's just better attuned specifically to evading that particular vaccine (same is true for antibiotic-resistant bacteria, of course - the infection itself isn't worse, but it's harder to treat because the antibiotics don't work).

[Tintrlvr]

I simply said that children getting infected and spreading the virus will result in a lot more deaths and long COVID etc.

False.

It is difficult to pinpoint exactly how much spread occurred on campuses. But throughout the pandemic, government studies showed that infection rates in schools did not exceed those in the community at large, Dr. Ladhani said. In schools that experienced multiple virus cases, he added, there were often “multiple introductions” — meaning that infections were likely acquired outside the building

+

if parents are vaccinated, covid is as dangerous as regular flue, if not — they likely get it anyway (yeah, Delta is that transmittable, herd immunity (vaccines or "natural) should be probably around ~90% to totally stop it).

It may be true that transmission rates in schools were no different from the general population before vaccines were available. But that datapoint is completely meaningless now, when schools are by far the likeliest gathering place for large numbers of entirely unvaccinated people (children). Clearly schools are a major transmission risk currently. The solution isn't to keep schools closed - it's to hurry up and approve and mandate vaccines for all school-aged children.

[Tintrlvr]

https://twitter.com/sirimahanthesh/status/1446162069250789384

Is it still the case that the Covid death rate is higher for men than women? If so, what might be causing it-are there any factors that happen to be correlated with being a man that would increase the risk?

Men generally have weaker immune systems than women. By contrast, women have much higher rates of auto-immune disease than men. Vaccines shouldn't change that calculus. Men are also likelier to die from the flu and many other contagious diseases than women.

[Tintrlvr]

Wow, and anti-virals have been really disappointing compared to their perceived potential generally, so a very effective anti-viral is really a huge surprise (much more so than a successful vaccine).

[Tintrlvr]

Remember that still means a small percentage of vaccinated end up in the ICU. Because not many end up in the ICU, vaccinated or not.

Some small number of people go to the ICU for the flu, too, or for any number of other contagious diseases.

[Tintrlvr]

Quite a bit of medical jargon that I'm too lazy to repeat here, but it all boiled down to "this is a serious matter, but there's a fine line between justifiable concern and sensational panic."

I have a friend of mine fighting off a breakthrough case right now.  She went to a party where she was exposed to a girl who (a) was experiencing symptoms and (b) knew that she could potentially be positive, but this girl attended the party anyway because she was "tired of talking about COVID".  

Now most folks aren't this brazen or inconsiderate, but just be smart and be responsible -- vaccinated or not.

I've been reading a lot of conflicting reports. Some are saying that South Africa is faring better than expected. However, others studies are saying there's no evidence Omicron is any less severe than previous variants. I think what we do know for sure is that Omicron is far more infectious than previous variants. It seems to me that even if we're fortunate in having a less virulent variant (which  is too early to say one way or the other), the biggest problems are the substantial increase in infectiousness and serious decrease in effectiveness of the vaccine prior to being boosted. For example, if the new variant were somehow 25% less severe than the previous, it wouldn't do us much good if the new variant was even just twice as infectious. Those are random numbers, but the fact we know is that infectiousness is significantly higher. I'd say the primary worry, apart from everything else we've been worrying about, is that the hospitals will be completely overrun. That's been the scariest thing in my view since the start of the pandemic. Early on, the thought of not nearly enough ventilators left me with dread. A completely overrun healthcare system affects everyone.

I got my booster just before Thanksgiving, almost seven months after my second dose (I've stuck with Pfizer all the way). What I've been reading is that, for those of us with the mRNA vaccines, effectiveness of the vaccine after the second dose goes down rapidly. It seems to me like the CDC is either behind or inept. If the second dose loses most of its effectiveness after 4-5 months, we're in big trouble if the waiting period is 6 months for boosting after the second dose. On the other hand, boosters haven't been available for that long overall. We have no idea how long boosted immunity lasts against Omicron. So far, they're holding up well and that is very good news, but we don't know what it looks like six months from now.

"No evidence" is mostly bad-at-communicating-scientist-speak for "No one has published a peer-reviewed study in a well regarded journal yet," which should be obvious because it's only been a month since the variant was identified but is also a totally meaningless statement. Unfortunately, occasionally they will use this way of speaking in an opposite way to describe things where there is actually affirmatively strong evidence against the statement being asserted (such as "no evidence that vaccines cause fertility problems," which really means "strong evidence exists that vaccines do not cause fertility problems"), and this creates confusion, but unless there is contrary evidence being cited (there isn't any evidence being cited that says omicron is as severe as delta, or as the original COVID), you can safely ignore "no evidence" statements.

[Tintrlvr]

Pretty stunning numbers in NYC. The hospitalization rate for vaccinateds actually decreased last week, despite the huge overall surge.
https://twitter.com/cooperlund/status/1476612381153411077?s=21

A big part of that is the replacement of Delta with Omicron. Three or four weeks ago, most new cases in NYC were still Delta, which was much more likely to cause hospitalization generally. NYC isn't of course Upper New England or the rural Midwest, where cases are still falling because the Delta wave is fading while Omicron hasn't quite hit with full force yet. But it looks that way from the hospitalization statistics because Omicron is so much less severe.

As an aside, there's a very obvious pattern right now of surges in areas that are more interconnected, both within the country and internationally - most striking not in the cities, which are perhaps more obvious but could be attributed to density, but in the ski counties, which are behaving more like the big cities and less like surrounding rural areas. Omicron will eventually get widespread everywhere, of course, but some rural, very disconnected parts of the country might not see too many cases until late in January.

[Tintrlvr]

Since December 20th, when Omicron really began to take off in the US, about 2.28% of the US population has tested positive for COVID. The idea that Omicron will just work its way through the entire population, and we'll reach some level of herd immunity probably has some truth to it (assuming no new variants in the near future), but it still has a long way to go, if that's the plan.

Most tests are at home nowadays, and I suspect most positive home test results are not getting reported to the govt. I've read that some counties, notably Fairfax VA, are not even accepting submission of home test results.

There is also tons of asymptomatic omicron that is presumably not being tested for.

Right - accounting for the relatively low rate of test reporting (probably most reported tests are through institutions - hospitals, school, and other entities that require all employers/entrants to be regularly tested), almost certainly at least 10%, and possibly as high as 20% of the United States has already had omicron, with the percentages much higher in areas where Omicron arrived earlier (maybe as high as 70-80% in NYC, e.g.) and more like 2-3% only in places where Omicron didn't show a presence until the New Year, like much of the rural Mountain West.