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Weekly coronavirus-related chat, questions, and minor updates - week of December 28
This thread is posted weekly, and is intended as a place for more-casual discussion of the coronavirus and questions/updates that may not warrant their own dedicated topics. Tell us about what the situation is like where you live!
I've been watching US data for any signs of a post-Thanksgiving surge and ... I'm not really seeing it.
What there is are both:
This doesn't absolutely mean that there was no "Thanksgiving bump", and it's possible that there was a slight increase which will show up down the road. As it is though, daily new cases peaked on December 18 at 662/1million, and are now trending downwards. Canada follows a nearly identical trend, whilst the UK are moving sharply upward (still just below the US in incidence/million).
Otherwise ... the thing about pandemics is that they're difficult to predict, behaviour is exceedingly dependent on human response, though viral behaviour (notably mutations, of which much recent discussion) and environment (seasonal changes, other variables) can also have effects. The North American Holiday Bump so far has, thankfully, been a bust.
Yes, it’s hard to see much of a Thanksgiving bump in the data. It’s too soon to say for Christmas.
The holidays result in delays in most government reporting, and now there is another holiday period. I’ve read that during holiday periods, only hospital data should be trusted. This graph looks very bad. One reason you can’t see a Thanksgiving bump in particular is that it keeps going up.
Also it seems that a big increase in California is matched by a decline in the Midwest, so nationwide averages can be misleading.
Massachusetts had a noticeable bump in positive test rates shortly after Thanksgiving that's been more or less sustained since then.
Latest daily /r/boston post
Direct stats link page 1
Direct stats link page 2
I'm not excited to see what these charts look like in a week or two when we start to see the results of all the Christmas/New Year gatherings.
If you look at the Massachusets new daily case values from ~ Nov 20 to Dec 10, what you see is a continuation of existing trend, with the reporting sigmoid I mentioned: falling Thanksgiving week, rising the following week, but not persisting. Since the 10th, new reported cases fall, but that gets into any current data lags and possibly underreported cases. An actual increase in new cases tends to persist, as active cases are the source of new cases, possibly mitigated by harsher shutdowns. Shutdowns themselves take about two weeks to appear in data. Data artefacts --- delays in testing and reporting --- more typically describe what is being seen here. Holiday periods stand out very sharply in healthcare data generally as people tend to to, or not to be able to, seek out care, and that which is administered is not promptly reported. Unfortunately this makes holiday-induced infectious disease influences harder and slower to tease out of data.
The real kicker is the Rt trend, which shows Massachusetts transmission decreasing through the Thanksgiving weekend, though it has potentially risen very slightly (1.05 to 1.08) in December. As those values are . 1.0, total new cases are still increasing, though fairly slowly.
Contrast California and Vermont. Both have seen Rt . 1, in California begining 23 September and rising to 1.18 on November 16, and falling since, to just aabout spot on 1.0 now. California's tremendous run-up in cases resulted from that slight but prolonged trend which has been reversing through the holiday period. Having started with an already considerable active cases rate, the effects were huge. Vermont's Rt has been >1 since 16 August, rising as high as 1.33 (through 16 October), and falling since though still about 1.10. Vermonts daily cases have exploded ... but from a far lower level: 3 implied infections on 16 August, 14 on 16 October, and rising despite the falling Rt to 109 currently. (Absolute numbers, not thousands). That's a 33x increase. California's implied infections on 23 September were 3,530, today 17,354, much larger in absolute terms but less than a 6x increase. Vermont's trend if continued is the more troubling.
With infectious disease, it is spread rate * time that is most critical, and is why higher doubling rates, even from a far lower initial infected population, are so concerning. The same applies to any exponential growth dynamic.
It won't be until the 3rd or 4th week of January before the Christmas/New Years effects are evident.
Another week, another reason to be pissed off at Belgium's increasingly incompetent handling of the pandemic.
Coronavirus: Vaccinations set to begin in nursing homes, health workers in March
MARCH.
HEALTH WORKERS IN MARCH.
NINE MONTHS TO PREPARE.
Seriously, nine months to prepare, and they're acting like Edward Jenner just showed up two weeks ago.
If you dig into why those numbers look bleak, you'll quickly understand that the problem is two-fold:
Back to Belgium. First, some population statistics:
So, 1.5 million high priority vaccine targets, and another 8.5 million lower priority. We most likely want a penetration of ~80% in the high priority group (1.2m), and ~70% overall (7m, target source), which gives us 1.2 million high priority seniors to vaccinate (with some margin for health care personnel), and 7 million lower priority targets.
Now, the Pfizer vaccine has special storage requirements, but that doesn't prevent it from being made available to pharmacies the day of (as it has to thaw anyway). But if we are just counting hospitals able to store it, there are 19 centres in Wallonia, 6 in brussels, and another 20 in flanders.
Let's make some reasonable assumptions (or at least, reasonable expectations). A shot takes ~12 minutes to process end to end, including paperwork. So 5 patients per pipeline per hour. A single hospital, depending on its size, can handle a concurrent 5-10 patients for the shot, so let's be liberal and say 10. So we're able to vaccinate … 50 patients per hour per hospital, or 18000 per day in Belgium over an 8 hour day.
That is… drumroll… 540k per month, or roughly the correct calculations the government has made to say "we're going to vaccinate health workers in March".
I think it's reasonable to be pissed off at how unprepared the country is. These numbers suck ass. There are ~5k pharmacies in Belgium. If one tenth of those were able to distribute the vaccine, we would be done by March.
Would it require money? Yes. Money we're losing as long as the lockdown continues.
Would it require training? Yes. We had time to train.
Would it require special logistical handling to distribute the Pfizer version? Yeah, THIS IS NOT NEW.
Fucking doy.
America's vaccine rollout is already a disaster
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While disappointing, it seems like this could change rapidly? Bob Wachter tweeted that “@UCSF
we started w/ ~600 people/day & will hit ~3x that next wk”.
It would be good to know the overall rate of growth in vaccinations. This seems better than assuming a constant rate?
One also
prays to literally every diety ever concocted by mankindhopes that the incoming administration has a more thought out distribution plan than the current approach of “let the states undergoing various levels of budget crisis plan and fund the vaccination roll out “. Jan. 20th can’t come soon enough if for no other reason than the change in pandemic management, although obviously the change will not be instantaneous (and may have been further delayed by the current administration’s intransigence...)But words can’t describe how depressing it will be if/when some non-trivial percentage of this initial wave of vaccines expires unused.
Rant
It’s so stereotypically American to partake in the largest worldwide scientific outpouring of all time to create a miracle vaccine, only to fail because we can’t figure out how to efficiently distribute it over our fractured health systems (not to mention the last decade of underfunded rural hospital closures). I can’t wait for members of Congress to start calling for elimination of public health funding for the pandemic because “the vaccine is available.” (satire, I fucking pray).I'm reading stories about why there are delays and not really getting it. It seems like at a hospital or nursing home level, they should already have the management and staff to give a shot. Why shouldn't a decentralized approach work?
Probably logistics. Storage, transportation, etc. is inconvenient. This vaccine doesn't come in single-dose vials that you chuck in a fridge, they come in vials that contain many doses that need to be stored at -70°C for long-term storage and needs to be at fridge-temp for administration. But it can't be refrozen, so you have to administer the entire vial of 100 doses in a day.* Particularly for smaller hospitals in lower-density areas, this is hard to do if you also have conditions like wanting to vaccinate the risk groups first.
*Details here might vary, these are just some of the concerns I've heard.
Each vial contains 5 doses, however they are deliberately overfilled to compensate for normal waste, and it's sometimes possible to get 6 or 7.
I'm arguably an "essential worker" and so should be able to get my vaccine relatively early, but with the way it's been going I am honestly thinking it's more likely that I'll be able to import the UK vaccine before that happens.
Last week, I posted about the TSA saying that on December 23 they screened the highest number of airline passengers since March.
This page on the TSA's site shows their daily numbers, and they set another record on December 27. Other than December 24th and 25th they've been in the area of 1 million - 1.2 million every day since a week before Christmas. That's still only about half of what their volume was at this time last year, but that's still a lot of people flying. The volume has been closer to 25% for most of the year.
Incoming US House representative Luke Letlow (Louisiana, Republican) died at 41 from COVID-19 complications. He was supposed to be sworn in this Sunday, as the youngest rep in the state. A doctor from the hospital was very specific that his death was caused by COVID, and that it's absolutely not a situation like, "oh, he died from something else entirely, but because he tested positive they blame it on COVID":
I received the first shot of the Moderna vaccine on the 31st. As a 911 dispatcher, I qualified as a first responder(Texas being one of the few states that recognize dispatchers as first responders).
The overall process was extremely smooth.
Three lines of vehicles lined up outside of the building where the shot was being given. As people got the shot and moved on, people left their vehicles where they were, ran inside, got the shot, and then went back to their vehicles where they relocated to another part of the parking lot to wait 15 minutes for reactions. An ambulance with two paramedics was waiting close by. If anyone had a reaction, all they had to do was honk their car horn and the medics would come check them out.
I was in and out in less than 30 mins, including the 15 mins waiting time
So far, I can't say I've had any real negative side effects. A slightly sore arm is about the extent of it. Although I have been told that it's after the second shot that any side effects are likely to kick in.
Congratulations, and thank you for the work that you do.
Why getting COVID-19 vaccines to rural Americans is harder than it looks, and how to lift the barriers
And a similar story in the Washington Post:
Why a Michigan doctor is driving coronavirus vaccines from hospital to hospital in his Honda pickup truck
I still don’t understand why it’s hard. It seems like it should be possible to reach community health centers with iceboxes, dry ice, and and a lot of driving? It shouldn’t be hard to hire people or even recruit volunteer drivers to help with an important cause like this. Businesses that do a lot of shipping might help too.
I think there's a couple factors behind it.
One is that the response at the federal level in the US continues to be a fucking joke. So each state is probably being left to figure it out on their own.
In a sane world, we'd have a team of smart people in the federal government, working solely on the problem of rural vaccine delivery, and coordinating with rural health centers in all 50 states about best practices and resources etc. I seriously doubt the Trump administration has a team like that as part of their Covid task force.
Another factor is that no one is willing to gamble with wasting doses due to logistics fuckups. The Pfizer vaccine, for example, is shipped in units of 975 doses. If there's a snowstorm, or a truck broken down in the middle of nowhere, or a dry ice shipment never arrives, or whatever, you risk losing that entire batch.
Or, if you hold a mass-vaccination drive at some rural health center, you might have less than 1000 people show up due to vaccine misinformation, and end up wasting part of the batch.
And the whole thing needs to be done all over again 4ish weeks later, including making sure all the people who got the first dose show up for the second one.
Again, imagining a fantasy world with a well-functioning US federal government, the thing you'd want to do is do trial runs in maybe 4-6 rural counties around the US, have actual experts in public health and logistics weighing in and observing, and then distill what they learned into a guide they could send to every county in the US. And again...I sorta doubt that's happening right now, or will happen before February.
Some kind of appointment system, along with a few extra people on standby from slightly further down the priority list, should be enough to make sure someone gets vaccinated.
I don't know why we worry about people getting the second dose. I don't expect to get a chance to get the vaccine for quite a while, but when I do get a chance, I am going to cancel the second appointment, because I think it's unethical to get a second dose when other people didn't even get their first dose.
Like, if you had a chance to get vaccinated, and you could give one dose to your spouse, wouldn't you do it?
I would guess they are too rule-bound to do anything other than follow the official schedule, but shouldn't be so rule-bound that they're not willing to "look the other way" or cut corners when people decide to do the right thing.
My understanding is that you need both injections to be properly vaccinated. Is that not the case?
Yes, that is officially how they are doing it, because it's the same way the trials were run and we don't know for sure whether immunity from just one dose would wear off.
However, there is a big debate going on. It sure looks like people get immunity within 14 days of the first dose. Here are two commonly reshared graphs from the trials. Here is Zeynep Tufekci making a respectable argument for this.
Unfortunately, it looks unlikely that anyone is going to do a scientific study to prove whether one dose is enough.
So it's an educated guess. Our risk is low anyway because we are early-retired and don't go out much, so I'm comfortable with that risk for myself.
It really sucks that nobody is going to find out for sure whether our limited supply of vaccines can be stretched to twice as many people. But hey, at this point, what's another 100,000 deaths?
There's early evidence that just one dose is effective, but somewhat less effective than two doses:
I think it's entirely possible that by the time I get vaccinated (I'm in 0 high-risk groups, so my current estimate is a 50/50 chance I can get vaccinated in the first half of 2021) we'll have more data and based on that the medical guidance might be reduced to only a single dose. But I'm also hoping by that time, vaccine logistics are fairly well sorted out, and by getting a second dose I won't be taking one away from someone else in a zero-sum way.
It's also possible, AFAIK, that we could end up with some sort of "2 doses for healthcare workers and high-risk groups, 1 dose for general herd immunity" tiered system. Right now everyone who's getting vaccinated is in the high-priority groups, so getting the second dose for full ~95% immunity makes sense (especially with the more infectious strain spreading like wildfire right now). That might change as it rolls out to more people.
Personally, I'm going to follow the advice of the doctor or pharmacist giving it to me. If they say 1 dose, I'll be fine with that. If they say come back in a month, I'll be fine with that too.
Tweet thread from Trevor Bedford, professor at UW and Fred Hutch here in Seattle and one of the experts I've been following since the very beginning of the pandemic:
Colorado announced yesterday that they had found a case with that variant. I think that's the first known case of it in the US.
California as well
B117 variant is very serious. It's considerably more transmissible. https://twitter.com/dgurdasani1/status/1344774555718590464
L.A. County hospitals turn away ambulances, put patients in gift shop: ‘I’ve never seen anything like this’
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South Africa hits 1 million coronavirus cases as new variant spreads rapidly
South Africa imposes strict new rules as it surpasses 1 million covid-19 cases
[Reposted in the right place.]
Israel zooms past 1 million vaccinations in sprint to vanquish pandemic
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43 San Jose Kaiser Staff Members Test Positive in COVID Outbreak
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Are you eligible for a COVID-19 vaccine? Washington state to launch tool, rely on honor system
I'm a Washington state resident and I think this is fucking fantastic.
For an example of the opposite strategy: $1 million fines, licenses in peril for COVID-19 vaccine fraud in NY
Pharmacists and doctors have enough to worry about right now without having to exhaustively check the documentation of everyone they vaccinate, and worrying about huge fines or losing their license if they get duped.
People will inevitably cheat and skip the line. Oh well. They're still getting vaccinated. Out of all the undesirable outcomes, I'd prefer 100 people getting vaccinated who don't "deserve" it over 1 single dose of wasted vaccine, as we've seen in many other states.
You summed up my thoughts on the matter perfectly. I'm also a Washington state resident and in general have been proud of our states response to the pandemic.
Heartbreaking first-hand account from a nurse in the southeast US
Some healthcare workers refuse to take COVID-19 vaccine, even with priority access
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I think these quotes are equally important, as I was trying to figure out why this would be the case:
Seems like a combination of lack of trust in the government and the vaccine seems to be the case largely along with fear of uncertainty of what the long-term effects (if any) may be.
It is also weird to see "...; or they believed the dangers of COVID-19 had been exaggerated." come from healthcare workers at this stage of the pandemic.
Zeynep Tufekci: The Mutated Virus Is a Ticking Time Bomb
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Covid variant found in Florida; more cases identified in California
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I don't think people fully appreciate how serious B117 variant is. It doesn't appear to be more lethal, but it is considerably more infectious. https://twitter.com/dgurdasani1/status/1344774555718590464
Dozens of residents die at Belgian care home after Santa visit
L.A. homeless sites ‘overwhelmed’ by COVID-19: ‘These are the toughest times’
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U.K. Delays Second Covid-19 Vaccine Dose as Europe Ponders How to Speed Up Immunization
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Here is the official justification for why the UK is doing this:
Optimising the COVID-19 vaccination programme for maximum short-term impact
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Also, a Twitter thread by a virologist supporting the decision.
Doctors criticize UK health officials for changing Pfizer Covid vaccine plan
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A Continent Where the Dead Are Not Counted
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The Worst Of COVID-19 Should Be Over For Manaus, Brazil. But It's Not
Here is a graph on Twitter.