Monday, July 13, 2020
The weekend was marked by packing and cleaning around our house. It was like a ritual sacrifice to the gods of consumerism. De-cluttering the house surfaced all sorts of questions - why do I own a Yonana (a frozen banana yogurt maker)? How many unopened packages of writeable CD-ROMs does a nephrologist need in 2020? Will I ever again read the 2001 Handbook on Urgent and Ambulatory Medical Procedures? And, at what point is something vintage-cool rather than just outdated? The sunk-cost fallacy can be a deep mental pit from which to climb. The irony, of course, is we are contemplating a house with a bit more space for our now smaller amount of stuff. As painful as it is to clean and pack, it was a comforting respite from the news.
---Latest Data---
Nothing uplifting in this section today.
https://ourworldindata.org/coronavirus-data-explorer?yScale=log&zoomToSelection=true&time=2020-04-16..&country=USA~GBR~CAN~BRA~AUS~IND~DEU~FRA~ITA~SWE&deathsMetric=true&dailyFreq=true&aligned=true&perCapita=true&smoothing=7
FT data - the second graph down now has state-level data - I suggest setting it to cases, per million, linear, and add your state to the highlighted list.
https://ig.ft.com/coronavirus-chart/?areas=usa&areas=gbr&cumulative=0&logScale=1&perMillion=0&values=deaths
The NY Times has hotspot map is an excellent quick glace of rolling 2-week case change: https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html
State Details:
https://public.tableau.com/views/Coronavirus-ChangeovertimeintheUSA/2_Corona?:display_count=y&:origin=viz_share_link
Rt data: https://rt.live/
COVID risk by US county: https://globalepidemics.org/key-metrics-for-covid-suppression/
Each of the above sites reports its source data. Please review sources like https://covidtracking.com/ to understand the quality of that data.
------------
Canberra, Australia, has been using wastewater monitoring to estimate coronavirus in the community. It is a great example of how to use this technique to monitor when your infection rate is very low.
https://www.abc.net.au/news/2020-07-03/canberra-free-from-known-coronavirus-cases-sewage-confirms/12418272
Pooled human plasma for critically ill COVID patients has not been highly successful in previous articles. Here is information on using a small dose of plasma in healthy individuals. Unfortunately, it appears this has some controversy or politics behind it. Indeed, finding a more scientific-oriented reporting outlet (rather than Yahoo news) would also be helpful.
https://news.yahoo.com/plasma-shot-could-prevent-coronavirus-130023057.html
I have not encountered patients in my office who "refuse" to wear a mask. However, there are now discussions about the implications of merely having such patients in the office waiting room. A physician cannot abandon (in the legal sense) a patient, but also must protect other patients and staff. Here is an enlightening discussion on the topic:
https://www.mdedge.com/infectiousdisease/article/225259/coronavirus-updates/patients-who-refuse-wear-masks-responses-wont
Dr. Fauci will be hosting a virtual Q&A later today (10:30 AM PST /1:30 PM EST) with the Dean of Stanford's School of Medicine.
https://www.newsweek.com/dr-anthony-fauci-watch-livestream-stanford-university-school-medicine-interview-covid-19-1517280
There are now some sporadic anecdotal US case reports of second infections or re-infections. PLEASE bear in mind that confirming these case reports needs to be done very rigorously. I am not certain about the patient, the symptoms, or the types of testing used except it was PCR swabs. I am certain the physician author (and the physicians on the linked podcast) are giving the data they have, but if re-infection is possible, it is very concerning. There are many unknows: patients with prolonged symptoms; reservoirs of virus or viral particles that could demonstrate intermittent PCR-positivity; and variation in the long-term immune response.
https://www.vox.com/2020/7/12/21321653/getting-covid-19-twice-reinfection-antibody-herd-immunity
and
https://dailyvoice.com/new-jersey/monmouth/news/central-jersey-doctor-reports-patients-reinfected-with-coronavirus/790555/
and
https://www.microbe.tv/twiv/
And, Florian Krammer has some thoughts on this too:
https://twitter.com/florian_krammer/status/1282462250343829506
On our team Q&A call last week, the notion that a 1% mortality was small came up. Take a look at this data.
https://www.quora.com/How-can-a-disease-with-1-mortality-shut-down-the-United-States/answer/Franklin-Veaux
Read the comments - the author cites sources and his assumptions. While the exact numbers may be imprecise, the notion that there is a huge potential for morbidity and mortality should not be lost.
How rumors get started is now of greater interest to me than ever. Here is some news and then follow up corrections on "new unknown pneumonia" from Kazakhstan. It is probably not new or unknown. Read the thread.
https://twitter.com/florian_krammer/status/1281612543765684225
I heard this piece on NPR on Friday - someone broke down the COVID-19 conspiracy theory and was able to see, like a virus, how 5G, Bill Gates, implantable chips, and all the disparate elements formed into the intellectual casserole of bad ideas we now have.
https://www.npr.org/2020/07/10/889037310/anatomy-of-a-covid-19-conspiracy-theory
Infographic of the day #1 - Let there be light!
One of my favorite ramifications of the Amazon economy (numerous, highly-specific choices in a single product category that are differentiated on small technical details) is the education you must have to understand what you are buying. Have you tried to purchase a small LED flashlight recently? Learn about lumens, lux, and candela (which all sound like a big-haired 80's metal band - here's to you Great White Lion Snake!).
https://i.redd.it/8itmyq6l3fa51.jpg
Infographic of the day #2 Metadata
Take a look at this: https://www.truepeoplesearch.com/insights/image?alttext=What%20info%20tech%20companies%20collect%20from%20you&filename=info-giant-tech-companies-collect-5_compressed.png
from https://www.truepeoplesearch.com/insights/info-tech-companies-collecting-from-you
----- Bonus Round - Conspiracies and Truth
It appears the history of science is a road filled with intellectual potholes, some of which are mine and some of which will never be filled in (see item #3).
Early germ theory had many opponents, one of whom was Hippolyte Rossignol. Rossignol was a French veterinarian who has gone down in history as the man who challenged Louis Pasteur to "prove" his theory of live attenuated vaccinations through a public case/control study of an Anthrax vaccine, in 1882. Pasteur's vaccine worked well, and the first public anti-vaxxer challenge made Pasteur that much more famous. BUT - if you dig into the story more, you will find that Pasteur made all sorts of logical leaps (like all diseases could be cured through vaccines) and may have taken credit for some techniques for viral attenuation that were not his discoveries. Either way, the "germ theory deniers" have ended up on the wrong side of history.
Pasteur background: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1087873/
More succinct reading: See page 81-82
https://books.google.com/books?id=hdRWAAAAQBAJ&lpg=PA82&ots=x88f68EJGT&dq=Hippolyte%20Rossignol%20vaccine&pg=PA81#v=onepage&q=Hippolyte%20Rossignol%20vaccine&f=false
Germ theory denialism: https://en.wikipedia.org/wiki/Germ_theory_denialism
On our call the other day, a question arose about whether "increased hygiene in the early 20th century resulted in more polio cases in the 1950s." It turns out that there is much more to this story. Polio has been around for centuries, transmitted from human to human (fecal-oral contamination), and has a wide range of clinical impacts. Interestingly, the younger you are when you get it, the less likely you are to get the paralytic symptoms. SO, as the late 1800s saw the development of organized municipal water systems, the age cohorts of those impacted by polio dramatically shifted from the pre-1900s most common of < 2-year-olds to 10-30-year-olds. Kids were just more clean—young kids in particular. So, in the early 1900s, polio was suddenly a devastating disease of paralysis. Hence the March of Dimes, the public attention, and ultimately the Salk and Sabine vaccines. Thank you, Nick Fallon, for educating me! Here is the .pdf: https://web.archive.org/web/20081207154734/http:/www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mmed.section.2862
Here is one last crucial conspiracy to explore. I don't know that we will ever know the truth on this one (and I cannot think of a good test to explore the hypothesis). However, I am grateful to the loyal reader who brought this to my attention. Enjoy.
https://www.upworthy.com/theory-of-the-golden-girls-being-an-organized-criminals
Clean hands and sharp minds, team
-Adam
The weekend was marked by packing and cleaning around our house. It was like a ritual sacrifice to the gods of consumerism. De-cluttering the house surfaced all sorts of questions - why do I own a Yonana (a frozen banana yogurt maker)? How many unopened packages of writeable CD-ROMs does a nephrologist need in 2020? Will I ever again read the 2001 Handbook on Urgent and Ambulatory Medical Procedures? And, at what point is something vintage-cool rather than just outdated? The sunk-cost fallacy can be a deep mental pit from which to climb. The irony, of course, is we are contemplating a house with a bit more space for our now smaller amount of stuff. As painful as it is to clean and pack, it was a comforting respite from the news.
---Latest Data---
Nothing uplifting in this section today.
https://ourworldindata.org/coronavirus-data-explorer?yScale=log&zoomToSelection=true&time=2020-04-16..&country=USA~GBR~CAN~BRA~AUS~IND~DEU~FRA~ITA~SWE&deathsMetric=true&dailyFreq=true&aligned=true&perCapita=true&smoothing=7
FT data - the second graph down now has state-level data - I suggest setting it to cases, per million, linear, and add your state to the highlighted list.
https://ig.ft.com/coronavirus-chart/?areas=usa&areas=gbr&cumulative=0&logScale=1&perMillion=0&values=deaths
The NY Times has hotspot map is an excellent quick glace of rolling 2-week case change: https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html
State Details:
https://public.tableau.com/views/Coronavirus-ChangeovertimeintheUSA/2_Corona?:display_count=y&:origin=viz_share_link
Rt data: https://rt.live/
COVID risk by US county: https://globalepidemics.org/key-metrics-for-covid-suppression/
Each of the above sites reports its source data. Please review sources like https://covidtracking.com/ to understand the quality of that data.
------------
Canberra, Australia, has been using wastewater monitoring to estimate coronavirus in the community. It is a great example of how to use this technique to monitor when your infection rate is very low.
https://www.abc.net.au/news/2020-07-03/canberra-free-from-known-coronavirus-cases-sewage-confirms/12418272
Pooled human plasma for critically ill COVID patients has not been highly successful in previous articles. Here is information on using a small dose of plasma in healthy individuals. Unfortunately, it appears this has some controversy or politics behind it. Indeed, finding a more scientific-oriented reporting outlet (rather than Yahoo news) would also be helpful.
https://news.yahoo.com/plasma-shot-could-prevent-coronavirus-130023057.html
I have not encountered patients in my office who "refuse" to wear a mask. However, there are now discussions about the implications of merely having such patients in the office waiting room. A physician cannot abandon (in the legal sense) a patient, but also must protect other patients and staff. Here is an enlightening discussion on the topic:
https://www.mdedge.com/infectiousdisease/article/225259/coronavirus-updates/patients-who-refuse-wear-masks-responses-wont
Dr. Fauci will be hosting a virtual Q&A later today (10:30 AM PST /1:30 PM EST) with the Dean of Stanford's School of Medicine.
https://www.newsweek.com/dr-anthony-fauci-watch-livestream-stanford-university-school-medicine-interview-covid-19-1517280
There are now some sporadic anecdotal US case reports of second infections or re-infections. PLEASE bear in mind that confirming these case reports needs to be done very rigorously. I am not certain about the patient, the symptoms, or the types of testing used except it was PCR swabs. I am certain the physician author (and the physicians on the linked podcast) are giving the data they have, but if re-infection is possible, it is very concerning. There are many unknows: patients with prolonged symptoms; reservoirs of virus or viral particles that could demonstrate intermittent PCR-positivity; and variation in the long-term immune response.
https://www.vox.com/2020/7/12/21321653/getting-covid-19-twice-reinfection-antibody-herd-immunity
and
https://dailyvoice.com/new-jersey/monmouth/news/central-jersey-doctor-reports-patients-reinfected-with-coronavirus/790555/
and
https://www.microbe.tv/twiv/
And, Florian Krammer has some thoughts on this too:
https://twitter.com/florian_krammer/status/1282462250343829506
On our team Q&A call last week, the notion that a 1% mortality was small came up. Take a look at this data.
https://www.quora.com/How-can-a-disease-with-1-mortality-shut-down-the-United-States/answer/Franklin-Veaux
Read the comments - the author cites sources and his assumptions. While the exact numbers may be imprecise, the notion that there is a huge potential for morbidity and mortality should not be lost.
How rumors get started is now of greater interest to me than ever. Here is some news and then follow up corrections on "new unknown pneumonia" from Kazakhstan. It is probably not new or unknown. Read the thread.
https://twitter.com/florian_krammer/status/1281612543765684225
I heard this piece on NPR on Friday - someone broke down the COVID-19 conspiracy theory and was able to see, like a virus, how 5G, Bill Gates, implantable chips, and all the disparate elements formed into the intellectual casserole of bad ideas we now have.
https://www.npr.org/2020/07/10/889037310/anatomy-of-a-covid-19-conspiracy-theory
Infographic of the day #1 - Let there be light!
One of my favorite ramifications of the Amazon economy (numerous, highly-specific choices in a single product category that are differentiated on small technical details) is the education you must have to understand what you are buying. Have you tried to purchase a small LED flashlight recently? Learn about lumens, lux, and candela (which all sound like a big-haired 80's metal band - here's to you Great White Lion Snake!).
https://i.redd.it/8itmyq6l3fa51.jpg
Infographic of the day #2 Metadata
Take a look at this: https://www.truepeoplesearch.com/insights/image?alttext=What%20info%20tech%20companies%20collect%20from%20you&filename=info-giant-tech-companies-collect-5_compressed.png
from https://www.truepeoplesearch.com/insights/info-tech-companies-collecting-from-you
----- Bonus Round - Conspiracies and Truth
It appears the history of science is a road filled with intellectual potholes, some of which are mine and some of which will never be filled in (see item #3).
Early germ theory had many opponents, one of whom was Hippolyte Rossignol. Rossignol was a French veterinarian who has gone down in history as the man who challenged Louis Pasteur to "prove" his theory of live attenuated vaccinations through a public case/control study of an Anthrax vaccine, in 1882. Pasteur's vaccine worked well, and the first public anti-vaxxer challenge made Pasteur that much more famous. BUT - if you dig into the story more, you will find that Pasteur made all sorts of logical leaps (like all diseases could be cured through vaccines) and may have taken credit for some techniques for viral attenuation that were not his discoveries. Either way, the "germ theory deniers" have ended up on the wrong side of history.
Pasteur background: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1087873/
More succinct reading: See page 81-82
https://books.google.com/books?id=hdRWAAAAQBAJ&lpg=PA82&ots=x88f68EJGT&dq=Hippolyte%20Rossignol%20vaccine&pg=PA81#v=onepage&q=Hippolyte%20Rossignol%20vaccine&f=false
Germ theory denialism: https://en.wikipedia.org/wiki/Germ_theory_denialism
On our call the other day, a question arose about whether "increased hygiene in the early 20th century resulted in more polio cases in the 1950s." It turns out that there is much more to this story. Polio has been around for centuries, transmitted from human to human (fecal-oral contamination), and has a wide range of clinical impacts. Interestingly, the younger you are when you get it, the less likely you are to get the paralytic symptoms. SO, as the late 1800s saw the development of organized municipal water systems, the age cohorts of those impacted by polio dramatically shifted from the pre-1900s most common of < 2-year-olds to 10-30-year-olds. Kids were just more clean—young kids in particular. So, in the early 1900s, polio was suddenly a devastating disease of paralysis. Hence the March of Dimes, the public attention, and ultimately the Salk and Sabine vaccines. Thank you, Nick Fallon, for educating me! Here is the .pdf: https://web.archive.org/web/20081207154734/http:/www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mmed.section.2862
Here is one last crucial conspiracy to explore. I don't know that we will ever know the truth on this one (and I cannot think of a good test to explore the hypothesis). However, I am grateful to the loyal reader who brought this to my attention. Enjoy.
https://www.upworthy.com/theory-of-the-golden-girls-being-an-organized-criminals
Clean hands and sharp minds, team
-Adam
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