16 Comments

I applaud your time consuming efforts to keep us informed. I'd still appreciate better info on what data and the source of that data is used in your graphs- especially for deaths. If the latter is from the CDC website I'd appreciate it if you could help navigate their site to what stats you are relying on. The fact that the CDC stopped reporting deaths after the Emergency was declared over calls into question the quality of their reporting. They also changed the way expected deaths were forecast to include pandemic related deaths, which of course reduced "excess death" reports. The rationale for this obfuscation is poorly described by the CDC. Most people I know would say that I am not a stupid person but I find it incredibly hard to find what I'm looking for on the CDC website and to fully understand it when (I think) I have located it. And their search function is almost useless. Help please.

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DM, I agree the CDC website data is hard to interpret. It's why I follow wastewater surveillance like Biobot instead. I would like to see CDC go back to tracking levels of Covid community transmission, too. Loss of information definitely makes it harder to understand what's going on with this virus. Something to consider with respect to death numbers: deaths are a lagging indicator as to how fast the virus is spreading within communities. And death isn't the only harm Covid causes - long term morbidity is equally important, millions of people have disabling Long Covid, and many will eventually die from the long term ill health effects of developing Long Covid. People vaccinated and boosted still get breakthrough cases leading to both death and Long Covid. Until the CDC starts to focus on how to slow the spread of transmission of an aerosol virus, Covid will continue will continue to find hosts and mutate, and it's only a matter of time until current vaccines and treatments offer us less protection. Meanwhile, get vaccinated or boosted, be careful and find some good quality N95 masks like 3M Aura or V-flex to wear indoors in high-risk settings.

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Thanks, Pamela.

I agree that it would be good to have statistics on community transmission, but I must say that I long ago gave up on those numbers as I feel they are almost worthless due to poor reporting and home testing. Better wastewater tracking would be good, but is too spotty now and comparisons with the past are not terribly useful since the past wastewater surveillance was very poor. I know deaths are a lagging indicator, but I consider them much more reliable than other measures because they are widely and generally completely reported - i.e. they are the best we have now to see how the overall pandemic is afflicting the country as compared to past reports. I don't know exactly how the CDC was compiling weekly data before the Emergency was announced "over" but I believe it was much closer to "real time" than what we have now. I believe it was reports that were mandated during the emergency to be reported in more timely fashion and that that mandate is gone. The CDC announced that it would no longer be reporting deaths and directed those interested to go to an alternative source which, as you note, very much lags real time, given the sources and delays in reporting its data. I still believe that it is the best we have right now and - with a lag - would at least all us to see changes by looking at very complete past data to see trends. Those trends would only lag current time by six or seven weeks I think despite being less than fully reported even then. That would help to dispel (or corroborate) claims about the "current levels" of COVID deaths. I agree that "long COVID" is a major concern that is being inadequately measured and addressed. But, for now, at least I prefer to look at the most reliable, if very much less than perfect measure, which is deaths.

You clearly understand the problems with current data and I much appreciate the inputs, especially your suggested source on waste water data. Thanks for taking the time to respond to my concerns.

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DM, all excellent points. Thank you for replying and further sharing your perspective. I'll be watching both trends to the extent I can.

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Not sure which files Benjay and Jeremy are pulling from on CDC - in a previous comment he mentioned he added the linked sources, but I don't see, will wait for him to reply.

In the meantime, yes, I agree, the CDC website can be overwhelming, not particularly well organized, and you can get drowned in hundreds of reports which seem to show the same thing, but don't really match up precisely. That said, here are some suggested places to look for data that I have found helpful:

1) The Wonder Database - This is the pinnacle of CDC data, the central hub which allows you pull data in millions of ways as you see fit. If you are familiar with pivot tables, database theory, this is the place to do. You can choose your own variables, groupings, date ranges

This "Quick Start Guide" is a great place to start, maybe check out YouTube tutorials too. Again, no familiar with your level of data analysis, but even if a novice, this is worth learning as the fundamentals are applicable beyond mortality

https://wonder.cdc.gov/wonder/help/QuickStart.html

2) My personal favorite way to gather mortality data from the CDC is from the "Weekly deaths by state" report which is published every Wednesday afternoon.

https://data.cdc.gov/NCHS/Weekly-Provisional-Counts-of-Deaths-by-State-and-S/muzy-jte6

It's a simple CSV file with death totals reported in a variety of categories (but not nearly all).

It is important to realize this is an evolving spreadsheet, where each week the previous weeks get updated. The most recent week reported 38K deaths, but that will grow eventually to ~55K once enough time has passed (generally by 6 weeks you have 95% of total deaths, last 5% might take months). If you happen to use this feel free to message with any questions on it's use and shortcomings.

3) Excess death forecasts of course are not an exact science, it involves a lot of nested hypotheses, assumptions, modeling caveats. There are competing arguments on whether we should include pandemic related deaths into baseline. And at a country level look, each country is different. The US declined in 2022 closer back to baseline (3.2 million deaths against predicted 3 million if no pandemic existed), but you could argue since so many elderly died in 2020-2021, by 2022 we should have potentially been below 3 million forecast. Or, since Covid is here to stay and will be part of life, we have to accept that instead of .88% of the population dying each year, it will be .97% of the population dying, and that is the new baseline?

It seems tough call, and testing various hypotheses on different countries provides different results. Some countries suddenly had massive death spike in 2022 (Korea, Australia). Some hit an elevated high in 2020 and have maintained that level since (Portugal, Israel, Germany). Some returned back to pre-pandemic baselines (Sweden).

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I just was looking around the CDC website again. I found again its announcement that after the Emergency ended that they wouldn't be reporting deaths but sending those interested to the NVSS site. Just saw a notice on its website that they aren't publishing them any longer either. The CDC will only let us see "trends" from week to week - not absolute numbers ANYWHERE. They just don't want anyone to know and perhaps point out how bad the actual raw numbers are - still not enormously improved from prior periods. And to make it impossible to compare to historical disease tolls especially compared to historical rates of death from flu. This is gross bureaucratic and political concealment of information to encourage/sustain a false narrative. I haven't tried to use the state by state data, because I didn't want to add the info up to compare the whole country's deaths to the past national reports. And to have to do it every week. And I'm not even sure I could do it now, if so inclined, since it may have been suppressed like the national data on deaths has been.

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CDC is still updating this file (for now):

https://data.cdc.gov/NCHS/Weekly-Provisional-Counts-of-Deaths-by-State-and-S/muzy-jte6

As noted above it provides all cause mortality by state, by week, with a few select causes of deaths broken out. If you want to know Covid deaths, you can dump this into a pivot table and filter to any state (or the US), and choose "Covid-19 (U071, Multiple Cause of Death) to see recorded Covid deaths which largely match what they will eventually add to wonder. You can also get "accidental deaths" by subtracting "Natural Cause" from "All Cause".

Note the the data lags, if you are interested in using this table and have questions feel free to message me, I have taken a snapshot of it every week for the last 3 years and understand its strengths and weaknesses quite well.

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As always, appreciate your time spent in data, analysis, and communication! I still worry about accuracy of data (not you) as fewer people test now in terms of cases, and hospitals can and do put down cause of death or even hospitalization as the comorbidity which patient may have been managing fine until they got COVID. There doesn't seem to be a correlation between states that have highest amount of cases and states with highest amount of hospitalizations. And it's pretty clear that COVID caused much $$ loss for hospitals and the managing industry as they lost patient visits, tests, elective and non-elective surgeries due to fear of COVID. Seeing really bad related outcome of poorly administered medical services in Western MA due to reduced staffing, reduced patient time, poor communication, and reduced access to long time docs. Never mind that we are in an election year and with patients, general population, and medical folks suffering from pandemic fatigue, no candidate or party wants to touch the subject. I also feel as a severely immune-compromised person with loved ones also immune-compromised that we can't live in that bubble that says COVID is "gone" as a serious issue until we see a lack of a fall/winter COVID surge...which hasn't happened yet. Thanks for your vigilance.

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"And it's pretty clear that COVID caused much $$ loss for hospitals and the managing industry as they lost patient visits, tests, elective and non-elective surgeries due to fear of COVID. "

Yes and No. Large wealthy hospital systems thrived and had record breaking profits, smaller and rural hospitals took a beating.

https://www.washingtonpost.com/us-policy/2021/04/01/hospital-systems-cares-act-bailout/

(bypasses paywall) https://archive.li/HhF2S

https://publichealth.jhu.edu/2022/federal-subsidies-kept-covid-strapped-hospitals-financially-stable-in-2020-first-year-of-pandemic

https://www.npr.org/2021/05/18/996207511/hospitals-serving-the-poor-struggled-during-covid-wealthy-hospitals-made-million

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Absolutely, in the end the "industry" did financially better after their initial fear and hit, due to gov subsidies, and certainly CEO's continued to make out like bandits. Take a look at this more recent article in my area and CEO's doubled salaries . And sadly, that hasn't filtered down to the docs, nurses, and staff. So quality of care of patients has gone down in larger and smaller hospitals distinctly, more stress for staff, less access and follow-through for patients, but those at the top seem to still find a way to protect themselves and the private equity firms. https://www.bostonglobe.com/2023/08/17/metro/hospital-ceo-pay-millions-2021/?p1=Article_Recirc_Most_Popular&fbclid=IwAR2Eh0fNYZrD78l433IPFsS582OOk047xBXeOiWxGPxrJNwMPJONyMgR768

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"remember, we knocked flu and RSV out for two winters, thanks to Covid mitigation"

I repeatedly see this claim, but there are a number of arguments which appear to falsify this hypothesis, while a much simpler explanation remains - viral interference:

1) Flu and RSV were also knocked out in countries which didn't participate in Covid mitigation at the level of the rest of the world - specifically the Nordic countries all returned children to school spring 2020, had very brief lockdowns, the lowest mask usage in the world - yet flu and RSV disappeared there as well. Flu in Australia (typically April - Oct) also disappeared, but mask wearing didn't take off in Australia until September 2020.

2) Additionally, you have pockets of the US that also sent kids back to school, brief lockdowns, and weren't masking nearly as much as the rest of the world (South Dakota, Florida, Texas, rural Georgia, all private schools in the US outside of possibly NY and CA) - no flu or RSV, correct?

3) Countries that did mask prior to 2020 still had flu, Japan for example had a bad flu year in 2019 [1] - granted this is short of school closures and business closures, but still shows example of 1 piece of the Swiss Cheese model being penetrated by flu.

4) South Korea, which has one of the highest high quality masking rates in the entire world, recently had their worse flu season since 2000 [2] - despite having similar behavior 2020-2023 and continued wearing of high quality masks.

5) When flu disappeared, almost everyone was only wearing cloth masks, which are now regarded as ineffective (at worst) or the bare minimum (at best) - how could it be that the weakest masks made Flu disappear?

6) Finally, why did our mitigation strategies only work for Flu and RSV but not Covid? How could Covid continue to explode while two other virus families of similar size, transmission method, and life cycle were temporarily wiped? The explanation that "Covid is so transmissible, so contagious, that it would have been even more widespread without these mitigation methods" ignores that Nordic countries had the best Covid outcome, that the US states not participating in Covid mitigation had similar outcomes as their more diligent neighbors, and, to me the bigger falsification - Covid didn't roar out of control once we stopped masking despite predictions it would be like "throwing gas on fire".

I feel these 6 points offer compelling refutation of the "It was the mitigations" hypothesis for why Flu and RSV left.

Meanwhile, the theory of Viral Interference bypasses each of those 6 points without needing to construct an elaborate number of conditions to maintain the Mitigation hypothesis.

We have even seen this happen before, for example in 2009 the annual RSV summer peak didn't happen when H1N1 was surging [3], and from what I understand - this is the explanation of why certain strains of circulate while others lay dormant. Experiments in animal populations have been able to reproduce results as well [4].

What are your thoughts?

______________

[1] https://www.upi.com/Top_News/World-News/2019/02/01/Millions-in-Japan-affected-as-flu-outbreak-grips-country/9191549043797/

[2] https://www.koreaherald.com/view.php?ud=20230522000636

[3] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5657134/

[4] https://academic.oup.com/jid/article/212/11/1690/2911897

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Just went to the address you provided the link for and saw this statement: "Effective September 27, 2023, this dataset will no longer be updated. Similar data are accessible from wonder.cdc.gov." I believe this was what I saw prior to writing my first email. I don't know how they will "add it to Wonder"- eventually or otherwise - if it isn't updated and available. And "similar data" -what does "similar" mean?This is what I meant by suppressing data. Can you tell me what your review of the data says the national death toll in the US has been in the first 6 months of 2023. That should be enough of a lag to provide a reasonable, at least ballpark, figure. Anyway, I think you can feel my frustration.

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Thanks, Michael. I will be back to you to go over the steps when I have a chance to experiment first. I know it lags if the source is the NVSS numbers from death certificates that they no longer show us. They certainly aren't trying to make the data very simple to find are they. The NVSS page was at least easy to pull the data out of, even if it lagged. Thanks again. This info will probably disappear soon too, I imagine. BTW, I looked at Wonder and it appeared that there was nothing there either - except maybe very old data?

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Jeremy and Benji grateful for the dashboard. Could you give a tutorial on the county graphs? Just want to make sure I understand how to read the lines😂, English Major over here and just don’t know if I am understanding. Where we are compared to hospital capacity? How many beds. Sorry as it is total user error on my part!

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Dr. Faust and Benjy, any chance of doing a "deep dive" update on the development of universal, variant-proof and/or pancoronavirus vaccines and the clinical trials that are underway? I've only been able to find limited data about: UB-612 from Vaccinity, Mosaic-8b from Caltech, RBD-scNP from Duke University, SpFN 1B-06-PL and RFN from Walter Reed Army Institute of Research and Yale's intranasal booster? Thanks.

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Now that school is back in session, in Southern California we are seeing a huge surge of covid-19 cases. All due to school districts not being preventive againt covid-19, like they were when covid-19 first hit. No one is wearing a mask. Sure we have a few students and staff that still mask up but a great majority don’t. School nurses are pretty much the only ones wearing their N95 mask 24/7. Some districts are even going back to their masks mandates due to excessive absenteeism. California districts also used to provide covid-19 testing, rapid and PCR. That’s not happening anymore. But they still provide us with rapid tests. When any given student or staff comes to the health office with symptoms of covid-19, we send them home with a rapid test. If a parent asks for a rapid test, we will also provide them. Several districts also updated their ventilation systems during the first initial lockdown. I read an article recently that spoke of some districts back east who had to shut down and go back to virtual learning because they had numerous cases of covid-19. All school nurses nationwide continue to be on those frontlines of covid-19 within the school setting.

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