Corona Virus: It's a Marathon, Not a Sprint

[Alefroth]

There's always excess deaths. I think the question you should be asking is "When will excess deaths go back to historical (i.e. pre 2020) levels?"

I don't think that what he's asking. When will they not be considered excess, but rather just regular modern let er rip deaths?

Yep. Excess deaths implies some kind of baseline. Do Covid deaths ever become part of the baseline?

[Smoove_B]

Yep. Excess deaths implies some kind of baseline. Do Covid deaths ever become part of the baseline?

Well...yes? We keep a list of the top causes of death and not surprising covid is on that list (the exact spot changes based on age or other demographic features). How that baseline moves over the next decade is anyone's guess, but if the people reporting are correct, America will continue to decline (in terms of looking at our overall health outcomes / death rates / life span with respect to comparable countries).

The fact that we're collectively willing to just accept all this new level of death and chronic illness does not bode well at all.

[Kraken]

High levels of immunity have helped avoid "excess mortality" in Mass.

The COVID-19 vaccines have helped Massachusetts avoid “excess mortality,” or deaths exceeding the expected number at any given time of year, during two surges in the pandemic, according to a study published Monday by researchers at Brigham and Women’s Hospital, and Harvard and Yale universities.

“This is good news, and it suggests that, in our highly vaccinated state, we are benefitting from a high level of immunity, which likely helped to protect individuals at highest risk,” Dr. Jeremy Faust, a Brigham and Women’s emergency medicine physician and an author of the study, said in a statement.
...
During the pandemic, Massachusetts has seen “periods without excess mortality, corresponding to times of low prevalence” of the virus, the study found. But there also were two periods when researchers observed no excess mortality despite “substantial outbreaks” of COVID-19. One such period came between late February 2021 and June 2021, while the second occurred between late February 2022 and June 2022.

“The uncoupling of excess mortality and new COVID-19 cases, in the absence of decreases in the mean age of infected individuals ... suggests that in our highly vaccinated state, current levels of immunity are considerable, leaving many, if not most, individuals at high risk with substantial protection against the most severe outcomes of SARS-CoV-2 infection,” the study said.

Seventy-seven percent of Massachusetts residents are considered fully vaccinated against COVID-19, according to a weekly state report updated Aug. 17.

[gbasden]

Yep. Excess deaths implies some kind of baseline. Do Covid deaths ever become part of the baseline?

Well...yes? We keep a list of the top causes of death and not surprising covid is on that list (the exact spot changes based on age or other demographic features). How that baseline moves over the next decade is anyone's guess, but if the people reporting are correct, America will continue to decline (in terms of looking at our overall health outcomes / death rates / life span with respect to comparable countries).

The fact that we're collectively willing to just accept all this new level of death and chronic illness does not bode well at all.

How do they figure out what that baseline is? How do we separate "normal" deaths from excess?

[Max Peck]

Excess mortality - statistics

In this article, excess mortality refers to the number of deaths from all causes measured during a crisis, above what could be observed under ‘normal’ conditions. The excess mortality indicator simply takes the number of people who died from any cause, in a given period, and compares it with a historical baseline from previous years in a period which was not affected by the pandemic. In this case, the baseline consists of the average number of deaths that occurred in each month during the period 2016-2019. The higher the value, the higher the amount of additional deaths compared to the baseline. In the case of a negative indicator, this means that fewer deaths occurred in a particular month compared with the baseline period.

[gbasden]

Excess mortality - statistics

In this article, excess mortality refers to the number of deaths from all causes measured during a crisis, above what could be observed under ‘normal’ conditions. The excess mortality indicator simply takes the number of people who died from any cause, in a given period, and compares it with a historical baseline from previous years in a period which was not affected by the pandemic. In this case, the baseline consists of the average number of deaths that occurred in each month during the period 2016-2019. The higher the value, the higher the amount of additional deaths compared to the baseline. In the case of a negative indicator, this means that fewer deaths occurred in a particular month compared with the baseline period.

Thanks! I guess I'm just fascinated by the concept of how you make such a baseline. If we have COVID going on and want to know how many excess deaths occurred, does it matter what year we pick? Do natural disasters, too much bacon eating, obesity and whatnot in the background become part of that baseline, or are those filtered out somehow? Sorry, I don't mean to go down a pedantic wormhole, I just got struck with the difficulty of figuring out what the correct number of deaths should be per year.

[Smoove_B]

Thanks! I guess I'm just fascinated by the concept of how you make such a baseline. If we have COVID going on and want to know how many excess deaths occurred, does it matter what year we pick? Do natural disasters, too much bacon eating, obesity and whatnot in the background become part of that baseline, or are those filtered out somehow? Sorry, I don't mean to go down a pedantic wormhole, I just got struck with the difficulty of figuring out what the correct number of deaths should be per year.

It's all done on a population level, so the numbers are gigantic. If something like a large-scale emergency event were to occur (let's say a hurricane related flood) during a year we're using for comparison, there would be a "blip" in the data for that ~30 days (probably closer to week) and then it would go back to that background level.

I think it helps if you think of it outside of the context of the pandemic. Namely, we do our best to categorize each and every death (starting at a local level, but then aggregated up to state, then reported to feds) so that we can get a handle on what it is that's killing people - noting the trends and changes over time by looking at death certificates. But for various reasons not everything is categorized and not everyone agrees with how to categorize or represent things ("Was this a death directly related to cancer or did they just happen to die of pneumonia?" "Was obesity the cause of the heart attack that killed them or was it just contributing?") so the "excess death" label gives us a broad, general handle on how to think about things in the bigger picture.

With the pandemic we're still interested in all that, but our systems are all overwhelmed (still), so this "excess death" measurement is a way for us to quantify (indirectly) the level of death that's happening that is above and beyond what we would typically expect to see in any given time frame (monthly, annually, etc...) looking at historical data. Here we're using it as a way to infer a potential connection to the pandemic, though again, people argue.

Either way, it's telling us people are dying at a level higher than we'd been seeing and there seems to be an association with the waves of the pandemic - suggesting a connection.

That's a bit of a ramble (sorry, I'm chugging coffee trying to get going today), but hopefully helpful.

[gbasden]

That's a bit of a ramble (sorry, I'm chugging coffee trying to get going today), but hopefully helpful.

Thanks! It's absolutely helpful. It's just really interesting statistical analysis that I hadn't ever considered before.

[Smoove_B]

Thanks! It's absolutely helpful. It's just really interesting statistical analysis that I hadn't ever considered before.

It's all stuff way above my pay grade for reference - part of the research and epi level wing of the field. But it's a cornerstone element of trying to figure out what might be happening across populations of people and something we're ultimately tasked with performing (population health monitoring). But to give a non-COVID related example, it's been something that's helped us figure out syndemics (a term that thankfully the media hasn't ruined yet). Basically the idea is that you have some type of known disease condition (let's use HIV/AIDS) that is having a previously unknown synergistic interrelationship with some environmental/social factor that hasn't been established yet.

As you dig into the excess death data and start to look for patterns, you notice (over time) HIV infections are up in a specific region and that a certain community is seeing increased levels of excess deaths (above what you'd expect for a similar population). As you dig more, you realize that there's a connection between HIV and hunger that puts people with an HIV infection at increased risk for hospitalization and death if they are food insecure. And that is the syndemic - when you have two (or more) epidemics (HIV; food insecurity) interacting with each other and creating a previously unrecognized negative outcome that is the product of both.

Personally I love reading about this stuff and seeing how they connect the dots, but the math and mathematical analysis involved is waaay above me. However, going back to comments that I'd made at some point here about the Affordable Care Act and the information sharing that was legislatively encouraged between hospitals/clinics and the public sector after it was passed, this is an example (discovering syndemics) of something that can emerge - and we all potentially benefit (which I guess makes some people unhappy).

And that's my random tangent for a Friday morning.

[Smoove_B]

Since I know there are a few of y'all in the Chicago area, I'm sure you already know how things are going:

Week one is over for thousands of Chicago Public Schools students as they head home for the weekend, but a few students and staff never made to their buildings this week.

CPS data shows 311 adults and 296 students self-reported positive COVID cases.

The number is much higher compared to last year's first week of school, which had 65 adult and 139 student cases.

"I don't think it's surprising we have higher numbers of COVID compared to last year," said Dr. Tina Tan of Lurie Children's Hospital. "Of the current variant or Omicron BA 5 is actually the most transmissible."

I know I'm ramming my head into the wall on this, but it's *so goddamn frustrating* that we completely understand how to lower risk and yet refuse to do so. Refuse.

[Isgrimnur]

I say this with no sarcasm or humor.

I am so sorry that the general public is not only unworthy of your efforts but also actively rejecting the help that your work and that of others attempt to provide.

[malchior]

Today was the 8th time this year that my every other week recycling pick up was delayed 'between 1-2 days' because of 'staff shortages'. I looked it up when I said to my wife that it felt like half the pick ups had been delayed. I was close to right. I'm sure it's nothing.

[malchior]

USA! USA! USA! #1...in lifespan decrease in the advanced world

The average life expectancy of Americans fell precipitously in 2020 and 2021, the sharpest two-year decline in nearly 100 years and a stark reminder of the toll exacted on the nation by the continuing coronavirus pandemic.

In 2021, the average American could expect to live until the age of 76, federal health researchers reported on Wednesday. The figure represents a loss of almost three years since 2019, when Americans could expect to live, on average, nearly 79 years.

The reduction has been particularly steep among Native Americans and Alaska Natives, the National Center for Health Statistics reported. Average life expectancy in those groups was shortened by four years in 2020 alone.

...

“This signals a huge impact on the population in terms of increased mortality,” he added.

Dr. Steven Woolf, director emeritus of the Center on Society and Health at Virginia Commonwealth University, characterized the diminution of life expectancy in the United States as “historic.”

While other high-income countries were also hard hit in 2020, the first year of the pandemic, most had begun to recover by last year, he said.

“None of them experienced a continuing fall in life expectancy like the U.S. did, and a good number of them saw life expectancy start inching back to normal,” Dr. Woolf said.

Those countries had more successful vaccination campaigns and populations that were more willing to take behavioral measures to prevent infections, such as wearing masks, he said, adding: “The U.S. is clearly an outlier.”

[Isgrimnur]

Well, this should lighten the burden on the Social Security pyramid scheme.

[Smoove_B]

Yeah, I was looking at something yesterday (Monday? Time is meaningless) that had NJ/NY losing 3 years but I think Texas was like 2.1 years. We were on a slight decline before COVID-19; this just made it much, much worse.

[LawBeefaroni]

Yeah, I was looking at something yesterday (Monday? Time is meaningless) that had NJ/NY losing 3 years but I think Texas was like 2.1 years. We were on a slight decline before COVID-19; this just made it much, much worse.

Driving out marginalized populations that you don't take care of is a great way to improve average life span.

[Smoove_B]

Driving out marginalized populations that you don't take care of is a great way to improve average life span.

Indeed. And once the data started coming out last year confirming what we already suspected (how the pandemic was disproportionately riskier for people of color), is it any wonder large swaths of white America declared it over and refused to do anything to stop it from getting worse?

Shithole country. That's what we are now.

[Smoove_B]

I know everyone is over it, but the third Covid autumn is upon us:

The toll will depend on whether new variants emerge and how humans behave. Will many Americans, for example, decide to get the new, Omicron-tailored booster that could be available as soon as this weekend? Will we continue to see a shapeshifting of the Omicron variant, or will something entirely different appear that’s not as good a target for the vaccines?

...

But with Covid, a reprieve is a relative state: Even as hospitalizations and deaths fall, more than 400 people are still dying a day. It’s also expected to be temporary: Most experts envision cases to start increasing again as the factors that encourage spread — from more people going back to work and school to people spending more time indoors — mount. The country as a whole is no longer taking the steps to reduce spread that it once was. Federal health officials have in effect blessed that by rolling back their guidelines, signaling that such measures are too costly societally and economically to continue with at this point, given that nearly everyone has some protection against Covid-19.

That last point is crucial. Despite how many deaths may occur this winter, by no means is the United States in a situation like earlier in the pandemic. Even though several hundred people are dying a day — and not to minimize the tragedy of that — overall, the number of deaths are near all-time lows even as transmission has been skyrocketing. That shows both how death rates have dropped as population immunity has grown, and simultaneously how even with lower death rates, the country can still lose thousands of people each week when millions of infections are occurring.

I personally think the disparity issue is going to be even larger for Fall/Winter 2023 based not only on the population demographics, but where you live in the United States - even down to a zip code level. In just looking around my own area vaccination rates are embarrassingly low. But as you drive east, they increase significantly across all population groups.

I think the biggest X factor is for kids right now. They're largely unvaccinated and getting ready to get back to school. Are they going to be drivers in the next wave? Are the higher rates of hospitalizations and deaths (still far lower than other cohorts) going to persist?

We're going to find out.

None of this addresses Long Covid either, as more and more studies are coming out showing how potentially problematic and concerning it should be.

[LawBeefaroni]

If you would just stop with the doom and gloom, perception could become reality. Haven't you read The Secret?





Our kids have been back to school since August 22. Already one confirmed case in a classroom. Mitigation? Everyone has to wear a mask. COVID positive child comes back after 5 day quarantine. Things are fine.

Also, everyone is coughing/sneezing now. Just a cold? Wear a mask, I can do without a cold.

[LordMortis]

I think the biggest X factor is for kids right now. They're largely unvaccinated and getting ready to get back to school. Are they going to be drivers in the next wave? Are the higher rates of hospitalizations and deaths (still far lower than other cohorts) going to persist?

We're going to find out.

None of this addresses Long Covid either, as more and more studies are coming out showing how potentially problematic and concerning it should be.

This has long been my belief so it must be true. Since well before COVID, parents of young children were always the vector to being sick in to work. This went to 11 when work became "open office".

I don't know if it will drive higher hospitalizations and deaths and long COVID anymore, as my area has long since been in FAFO phase one and deaths are high enough and hospitalizations are already up. Long COVID is the elephant no one talks about. FAFO phase two starts on Tuesday. I plan to hole up until I get the revised vaccine, short of shopping. I do have grand opening shop with a big coupon scheduled for the 9th. It's in a big warehouse, but will still be the single largest exposure for me in 2.5 years, not a week after school starts. I'll likely go N95 instead of cloth mask that day.

[Isgrimnur]

[Isgrimnur]

The Atlantic

Earlier this year, a team of British researchers rendered the invisible nature of brain fog in the stark black-and-white imagery of MRI scans. Gwenaëlle Douaud at the University of Oxford and her colleagues analyzed data from the UK Biobank study, which had regularly scanned the brains of hundreds of volunteers for years prior to the pandemic. When some of those volunteers caught COVID, the team could compare their after scans to the before ones. They found that even mild infections can slightly shrink the brain and reduce the thickness of its neuron-rich gray matter. At their worst, these changes were comparable to a decade of aging. They were especially pronounced in areas such as the parahippocampal gyrus, which is important for encoding and retrieving memories, and the orbitofrontal cortex, which is important for executive function. They were still apparent in people who hadn’t been hospitalized. And they were accompanied by cognitive problems.

[malchior]

Huh. It's almost like let 'er rip without knowing the risks was a bad idea.

[Isgrimnur]

[LawBeefaroni]

There's your zombie apocalypse.

[Smoove_B]

In case you're wondering what's on tap (as we finish the current BA.5 wave)

BA.2.75.2 exhibits more extreme antibody escape than any variant we've seen so far.

...

In 18 random blood donor samples in Stockholm, sampled just a couple of weeks ago, BA.2.75.2 was neutralised, on average, five-fold less potently than BA.5. These are recent samples in a city that has good vaccine coverage and likely relatively high prior infection rates.

[Smoove_B]

Not interesting enough? Ok, how about this new milestone moment:

And according to the latest briefing document by @IHME_UW: Total deaths due to COVID-19 in the last week increased to 590 per day on average compared to 570 the week before (Figure 3.1). This makes COVID-19 the number two cause of death in the US this week (9/9/22).

[Grifman]

Just reinforcing what Smoove posted:

[Smoove_B]

Some more (informed) fortune telling:

What should we expect from #SARSCoV2 this autumn?

I think it would be smart to prepare for both an increase in #COVID19 due to seasonal (behavioural) change & a new variant.
As so many others have elegantly illustrated, new lineages of SC2 are sparking interest.

...

We've learned in the past that predicting impact from a list of mutations alone isn't completely straightforward. However, the mutations we see in BQ.1.1 & BA.2.75.2 (& others, as noted above) are in locations that could impact immune evasion & receptor binding. Currently, we expect that selection pressure on the virus is largely to get around immunity, with so much of the world having a level of protection due to vaccination, infection, or both. This is a long-term game for many endemic viruses. So it's not surprising, but...

...

So, question 3 - What should we do?

Given the time of year and what we are seeing in mutations & growth, I think we may well face a double-impact of autumn & a new variant in the next couple of months. We should prepare for this, & hope we don't need those preparations. We don't know & can't currently predict 'how bad' such a wave might be. But, even if it's fairly 'not bad', we saw a notable impact of BA.5 (which was 'not bad') this summer due to absences , particularly in hospitals & airlines . While hospitalizations & deaths are obviously the most critical of outcomes, we do seem to be stuck in a bit of a black-&-white that if these are low, everything else is fine

I think we need to change that. Huge workplace absences can really impact our society

So, WHAT should we do?
- Start & encourage booster roll-out
- Decide our 'thresholds of action'
- Make a plan for how to react
- Publicise so people are prepared

No govt is keen to encourage masks or homeoffice again, I know!
But in my opinion, it's better to have these on the table to prevent disruptions to schools, transport, infrastructure & deliveries, if cases & absences start to threaten those this autumn/winter.

In a personal way, you can help too:
When cases rise and/or you're in a crowded, ill-ventilated place, wear a mask!
If you're sick (with anything at all!) stay home if at all possible. Even if not COVID, nobody wants your cold! (And those cause absences too!)

We've got a lot of experience (& immunity!) under our belt now - we'll never be back to those first pandemic times. But at the same time, it's smart to stay alert & prepared. This winter will be tough in many ways - let's do what we can to stop #COVID making it tougher!

[Zaxxon]

Smoove, if there is one positive that could come out of this godawful pandemic, I hope it's tweet 16 from that thread:



It has boggled my mind since decades prior to COVID why so many people insist on cavalierly spreading disease to others (note that this is distinct from and significantly worse than so many who insist on cavalierly failing to take precautions while feeling entirely healthy).

If you're actually sick, stay the fuck at home!

[Isgrimnur]

[Smoove_B]

If you're actually sick, stay the fuck at home!

It would be nice yes. But then we're spiraling out into a situation where workers aren't directly or indirectly punished by their employers for using sick time or taking unpaid time off work to recover. Remember, all workers are constantly trying to steal from you so they must be present and visibly working in order to pay them. The idea that a place like Chipotle - which people love despite repeated food safety violations and outbreaks - just had to pay NYC over failure to allow workers to use sick time (among other things) is still where we're at.

[Zaxxon]

If you're actually sick, stay the fuck at home!

It would be nice yes. But then we're spiraling out into a situation where workers aren't directly or indirectly punished by their employers for using sick time or taking unpaid time off work to recover. Remember, all workers are constantly trying to steal from you so they must be present and visibly working in order to pay them. The idea that a place like Chipotle - which people love despite repeated food safety violations and outbreaks - just had to pay NYC over failure to allow workers to use sick time (among other things) is still where we're at.

I knew you'd come back on that tangent--I should have amended my statement to If you're actually sick and can very easily stay the fuck at home, stay the fuck at home!

Which is what I really meant, and which describes the folks that boil my blood. Clearly a large number of people can't simply stay at home whenever they should. Millions upon millions could but do not, including many doctors in my orbit prior to the pandemic.

[LawBeefaroni]

Ha! Now when people show up to work sick, they just say, "I tested negative for COVID" and it's all good.

And I don't mean the jobs that have a WFH option. They stay home for a stubbed toe.

I mean former "front line" retail and service workers.

Worker A: *cough cough*

Worker B: *Side eye*

Worker A: "It's OK, tested negative."

Worker B:*Nods*

[Smoove_B]

Which is what I really meant, and which describes the folks that boil my blood. Clearly a large number of people can't simply stay at home whenever they should. Millions upon millions could but do not, including many doctors in my orbit prior to the pandemic.

There's a (former) friend of family that would send their kid to school no matter what because this child wanted the perfect attendance certificate. Fever? Dripping mucous and or hacking up a lung? Medicate to mask symptoms to get credit for going because nothing is more important than getting that certificate.

New study published today in Nature. Lots of tables to read through covering the types of things people are experiencing one year after a Covid-19 infection. Not surprisingly they're all over the place, but if you just look at the raw data there's an incidence of reporting some type of mental/physical/muscular/neurological effect at a rate of 71/1000 people. When you scale that out to population levels, that is significant. What's also interesting are the two final caveats:

The risks and burdens were elevated even in people who did not require hospitalization during acute COVID-19. Limitations include a cohort comprising mostly White males. Taken together, our results provide evidence of increased risk of long-term neurologic disorders in people who had COVID-19

So even "mild" causes causing chronic problems and the populations being examined were largely white males.

[Smoove_B]

More studies yesterday - two independent studies (one from Norway; one from United States) suggesting a connection between Covid-19 and the development of diabetes in children.

Norway:

After adjusting for age, sex, country of origin, geographical area and socio-economic factors, the analyses found that young people who contracted COVID-19 were around 60% more likely to develop type 1 diabetes 30 days or more after infection compared to those without a registered infection or who tested negative for the virus (see figure in full abstract).

“The exact reason for the increased risk of type 1 diabetes in young people after COVID-19 is not yet fully understood and requires longer-term follow-up and further research into whether the risk could be different in children who are infected with different variants”, says Gulseth.

United States:

In this study, new T1D diagnoses were more likely to occur among pediatric patients with prior COVID-19 than among those with other respiratory infections (or with other encounters with health systems). Respiratory infections have previously been associated with onset of T1D,6 but this risk was even higher among those with COVID-19 in our study, raising concern for long-term, post–COVID-19 autoimmune complications among youths.

[Smoove_B]

Hello darkness my old friend

[Zaxxon]

I was told this is behind us.

[Isgrimnur]

Time is a flat circle. And full of selfish assholes.

[Smoove_B]

I was told this is behind us.

That's to keep you from looking at what's ahead:

The Institute for Health Metrics and Evaluation at the University of Washington and other experts, including Dr. Anthony Fauci, the nation’s top infectious disease expert, foresee a wave beginning to swell in late October, and peaking in late December or January.

It could kill another 20,500 Americans, according to the IHME.

...

The wave may be carried by one variant, Dr. Raj Rajnarayanan, assistant dean of research and associate professor at the New York Institute of Technology campus in Jonesboro, Ark., told Fortune this week.

“But if you look closer, they may all have the same set of mutations.”

And they may all end up with the same disastrous effect: rendering current COVID countermeasures like drugs and vaccines powerless.