Today we got our first Omicron lab data! A week and half since Omicron broke the news. Just beautiful. As the scientist of the study said, “If I don’t die from the virus, I’ll die of exhaustion”. We’re getting more and more epidemiological data, too. Together they give us a dense, but clear(er) picture of Omicron.
Thanks—every single post,thanks! If you have a moment, I was confused by this statement: “We can have a virus that leads to mild cases, but isn’t less severe.” Does that means mild cases on an individual level (generalized, of course), but potentially still severe impacts at a broader scale (hospitals filling up and having to ration care, etc.)? Or am I missing the point? Thanks!
Thanks for a great summary, and for acknowledging Long Covid. I always see Long covid as an afterthought in many articles(at best). It would be great if you can share how the scientific community is doing on understanding the causation of Long Covid. We have a bias in the medical establishment that puts more resources towards heart attack and sudden illness rather than chronic illness. I have had a long covid since mid-2020 and it is indeed something that you want to avoid. Not saying morbidity should be treated on par with mortality but it needs a separate lens altogether
These are excellent newsletters, thanks for doing them. I recently "joined" your audience and I paid my dues, and now I'm wondering about something: Would you provide a carefully constructed explanation of the Test Positivity Rate (Positive RT-PCR Tests/All RT-PCR Tests Performed/24 hrs)? This particular "daily index" (usually its seven-day rolling average is reported and plotted religiously) is ballyhooed here in Minnesota (and I presume elsewhere in the USA) by public health functionairies, yet no credible authority has ever provided an honest, plain English explanation of how exactly TPR is reliably supposed to be useful in decision-making regarding any element of pandemic response. The veribage we hear locally is the following boilerplate: "TPR tells us if we are testing enough patients". HUH ?? Incredibly, top leadership figures at the Minnesota Department of Health were heard on a local TV interview last summer encouraging citizens to *Please come in and just get tested so that we can Wash Out all of these positive PCR test values*. . . . . I'm not exaggerating here. Those were the actual words.
Obviously, a problem with TPR is that it's a synthetic variable, a weird kind of compromise made under "battlefield conditions". TPR does not necessarily (and actually CANNOT) measure accurately the actual variance over time in "new case prevalence" -- this inconvenient reality is something that most lay folks are not equipped to understand. Background gumming-up of remarks to the public also is assured due to conflation of, or confusion about, the meanings of terms like "case" and "infected" and "sick", etc.
RT-PCR testing in my state (and presumably all others) is done not only for symptomatic people who may or may not be suffering from COVID, but also for an interesting menagerie of other folks too. Plenty of people get tested here (often ~ 25-40,000 tests per day) and not because they all feel sick or look sick to some ER doctor or clinic nurse, but because some are about to undergo an elective operation or because they are getting ready to travel overseas, or because they think that they may have been exposed, or perhaps because they are just earnest members of the "worried well club", etc. This blending of "healthcare customers" gives rise to a conceivably pesky issue: the effects that a concealed MIXED denominator might have when we attempt to sense the meanng of changes in TPR over time. At issue: a denominator whose actual composition may change every day, and in various ways, and that can affect computed TPR values in distorted ways -- e.g. if TPR "goes down" over two time periods in some state who can be certain about the extent to which a contributory cause in the observed "good" fluctuation was a significant shift in denominator composition per se? I would guess that one of several elephants in the public health living room could be that government luminaries have not taken the time to simply put themselves in the shoes of a layman and then intentionally and carefully "come clean" to clear the air by explaining that (1) TPR is not based on daily, random, statistical sampling of any segment of our population and (2) TPR is the result of making a strikingly crude compromise. Sadly, my state is in the middle of a scary "Delta outbreak" and high-level state health figures here are these days being quoted by local media when making official statements about either "our concerning data" or " the improving picture" whenever 7-day averaged TPR values have changed from (for example, the actual numbers here) 11.0 to 10.4 per cent or vice-versa, respectively, over some two-week period.
In sum, the "TPR Meaning Issue" has been a constant hornets' nest, and for about 18 months in my opinion. Ancillary communication issues inevitably have arisen, they are not being admitted or addressed responsibly by epidemiologists in any state to my knowledge, and we have a situation of "misleading messaging". Thanks very much. -- James T. Lee, MD PhD FACS FIDSA FSHEA.
Seems like 16-17 year olds will be (maybe) eligible for boosters soon, but not 12-15 year olds. Understanding younger patients usually, but don't always, have milder cases, should we still be concerned once our younger adolescents start hitting the 8-10 month post-vaccination timeframe? Seems like that could be when Omicron really hits the U.S. hard. There is also the concern of long-COVID in this population as well.
Also, what is the concern for elderly patients who received boosters ASAP? I have an elderly family member whose antibodies (Roche semi-quantitative) dropped from over 2,500 to just over 100 in just 5 months. I know antibodies don't tell the whole story, but many of my family/friends had antibodies tested, and most were still in the 400-700 range well more than 8 months post 2nd dose. I'm afraid this relative, who was boosted in mid-September, will again experience a huge drop in antibodies just as Omicron slams the U.S.
Thank you again for another incredibly helpful update. Are you hearing of any studies of correlation between antibody levels and infection incidence? it seems intuitive, but a few months ago, there was skepticism that the relationship had been proved out.
@Katelyn, Great summary. And since I'm officially on vacation, I'm not doing additional research myself! Random thought I've been entertaining: An anonymized registry of Ag-test results keyed to zipcodes. It would be a crowd-sourced testing pool. Thought?
I have concerns about irregularities in covid-19 testing. I perform nasal swab testing at a hospital and my technique follows all the CDC and WHO guidelines. Lately many patients report having recently been tested elsewhere and state “they didn’t go that far”. Over the past year I too have had to be tested and only 1 in 5 went to the air pocket past the nasal bone (space just near the sinus labyrinth). The spores are back there, not in the nasal drip where we would swab for MRSA. Can you, in your limited spare time, address this issue.
How long after the inoculations and inoculations/infection was the test performed? Pfizer report used 21 days for the double injections and one month for three dose data - it looks a LOT different.
These posts have been so incredibly helpful. Thank you!
I’m struggling a little to understand the time series analysis w/r/t severity. It seems to me that comparing ICU occupancy or hospital admissions at day 10 of two waves doesn’t tell us that much unless the number of infections are comparable because hospital admissions are dependent on infections not time. It follows that if there are more infections in less time we’d see a higher rate of usage of healthcare resources in that time as well. Wouldn’t it make more sense to compare those against the number of confirmed infections for example?
I recognize that this would also be imperfect given the high and rising test positivity rate, but given that SA saw similar test positivity rates in previous waves it seems not unreasonable.
I’m excited to learn why I’m thinking about this in the wrong way!
Thank you for this post and for all you do! I was hoping you could clarify one sentence (I tried to look at the original article to clarify for myself but wasn’t able to do so). It says that 9 people have covid pneumonia, and 8 of them are unvaccinated and one is a child. Is the child one of the 8 unvaccinated, meaning that there is one vaccinated adult with covid pneumonia? Or are they referring to the child - who I presume is unvaccinated given that their other charts have “n/a” for vaccine status for the peds floor?
(On another note dear lord can the FDA please say something about last week’s EUA request for boosting 16-17yos?!)
You showed that 2 shots plus prior infection creates real protection. But if that prior infection was from the Delta variant, and our vaccines / boosters are still targeted against the original virus, then this may not indicate any benefit from the booster, but rather from Delta exposure.
Is Omicron a derivative of Delta? Does it share most/all of Delta's mutations?
Thanks—every single post,thanks! If you have a moment, I was confused by this statement: “We can have a virus that leads to mild cases, but isn’t less severe.” Does that means mild cases on an individual level (generalized, of course), but potentially still severe impacts at a broader scale (hospitals filling up and having to ration care, etc.)? Or am I missing the point? Thanks!
Thanks for a great summary, and for acknowledging Long Covid. I always see Long covid as an afterthought in many articles(at best). It would be great if you can share how the scientific community is doing on understanding the causation of Long Covid. We have a bias in the medical establishment that puts more resources towards heart attack and sudden illness rather than chronic illness. I have had a long covid since mid-2020 and it is indeed something that you want to avoid. Not saying morbidity should be treated on par with mortality but it needs a separate lens altogether
These are excellent newsletters, thanks for doing them. I recently "joined" your audience and I paid my dues, and now I'm wondering about something: Would you provide a carefully constructed explanation of the Test Positivity Rate (Positive RT-PCR Tests/All RT-PCR Tests Performed/24 hrs)? This particular "daily index" (usually its seven-day rolling average is reported and plotted religiously) is ballyhooed here in Minnesota (and I presume elsewhere in the USA) by public health functionairies, yet no credible authority has ever provided an honest, plain English explanation of how exactly TPR is reliably supposed to be useful in decision-making regarding any element of pandemic response. The veribage we hear locally is the following boilerplate: "TPR tells us if we are testing enough patients". HUH ?? Incredibly, top leadership figures at the Minnesota Department of Health were heard on a local TV interview last summer encouraging citizens to *Please come in and just get tested so that we can Wash Out all of these positive PCR test values*. . . . . I'm not exaggerating here. Those were the actual words.
Obviously, a problem with TPR is that it's a synthetic variable, a weird kind of compromise made under "battlefield conditions". TPR does not necessarily (and actually CANNOT) measure accurately the actual variance over time in "new case prevalence" -- this inconvenient reality is something that most lay folks are not equipped to understand. Background gumming-up of remarks to the public also is assured due to conflation of, or confusion about, the meanings of terms like "case" and "infected" and "sick", etc.
RT-PCR testing in my state (and presumably all others) is done not only for symptomatic people who may or may not be suffering from COVID, but also for an interesting menagerie of other folks too. Plenty of people get tested here (often ~ 25-40,000 tests per day) and not because they all feel sick or look sick to some ER doctor or clinic nurse, but because some are about to undergo an elective operation or because they are getting ready to travel overseas, or because they think that they may have been exposed, or perhaps because they are just earnest members of the "worried well club", etc. This blending of "healthcare customers" gives rise to a conceivably pesky issue: the effects that a concealed MIXED denominator might have when we attempt to sense the meanng of changes in TPR over time. At issue: a denominator whose actual composition may change every day, and in various ways, and that can affect computed TPR values in distorted ways -- e.g. if TPR "goes down" over two time periods in some state who can be certain about the extent to which a contributory cause in the observed "good" fluctuation was a significant shift in denominator composition per se? I would guess that one of several elephants in the public health living room could be that government luminaries have not taken the time to simply put themselves in the shoes of a layman and then intentionally and carefully "come clean" to clear the air by explaining that (1) TPR is not based on daily, random, statistical sampling of any segment of our population and (2) TPR is the result of making a strikingly crude compromise. Sadly, my state is in the middle of a scary "Delta outbreak" and high-level state health figures here are these days being quoted by local media when making official statements about either "our concerning data" or " the improving picture" whenever 7-day averaged TPR values have changed from (for example, the actual numbers here) 11.0 to 10.4 per cent or vice-versa, respectively, over some two-week period.
In sum, the "TPR Meaning Issue" has been a constant hornets' nest, and for about 18 months in my opinion. Ancillary communication issues inevitably have arisen, they are not being admitted or addressed responsibly by epidemiologists in any state to my knowledge, and we have a situation of "misleading messaging". Thanks very much. -- James T. Lee, MD PhD FACS FIDSA FSHEA.
Thanks for all you do. I know it can’t be easy with a family.
Seems like 16-17 year olds will be (maybe) eligible for boosters soon, but not 12-15 year olds. Understanding younger patients usually, but don't always, have milder cases, should we still be concerned once our younger adolescents start hitting the 8-10 month post-vaccination timeframe? Seems like that could be when Omicron really hits the U.S. hard. There is also the concern of long-COVID in this population as well.
Also, what is the concern for elderly patients who received boosters ASAP? I have an elderly family member whose antibodies (Roche semi-quantitative) dropped from over 2,500 to just over 100 in just 5 months. I know antibodies don't tell the whole story, but many of my family/friends had antibodies tested, and most were still in the 400-700 range well more than 8 months post 2nd dose. I'm afraid this relative, who was boosted in mid-September, will again experience a huge drop in antibodies just as Omicron slams the U.S.
Thank you again for another incredibly helpful update. Are you hearing of any studies of correlation between antibody levels and infection incidence? it seems intuitive, but a few months ago, there was skepticism that the relationship had been proved out.
@Katelyn, Great summary. And since I'm officially on vacation, I'm not doing additional research myself! Random thought I've been entertaining: An anonymized registry of Ag-test results keyed to zipcodes. It would be a crowd-sourced testing pool. Thought?
Thank you for all this info. You’re such a wealth of information and it’s understandable.
I have concerns about irregularities in covid-19 testing. I perform nasal swab testing at a hospital and my technique follows all the CDC and WHO guidelines. Lately many patients report having recently been tested elsewhere and state “they didn’t go that far”. Over the past year I too have had to be tested and only 1 in 5 went to the air pocket past the nasal bone (space just near the sinus labyrinth). The spores are back there, not in the nasal drip where we would swab for MRSA. Can you, in your limited spare time, address this issue.
How long after the inoculations and inoculations/infection was the test performed? Pfizer report used 21 days for the double injections and one month for three dose data - it looks a LOT different.
These posts have been so incredibly helpful. Thank you!
I’m struggling a little to understand the time series analysis w/r/t severity. It seems to me that comparing ICU occupancy or hospital admissions at day 10 of two waves doesn’t tell us that much unless the number of infections are comparable because hospital admissions are dependent on infections not time. It follows that if there are more infections in less time we’d see a higher rate of usage of healthcare resources in that time as well. Wouldn’t it make more sense to compare those against the number of confirmed infections for example?
I recognize that this would also be imperfect given the high and rising test positivity rate, but given that SA saw similar test positivity rates in previous waves it seems not unreasonable.
I’m excited to learn why I’m thinking about this in the wrong way!
Thank you for this post and for all you do! I was hoping you could clarify one sentence (I tried to look at the original article to clarify for myself but wasn’t able to do so). It says that 9 people have covid pneumonia, and 8 of them are unvaccinated and one is a child. Is the child one of the 8 unvaccinated, meaning that there is one vaccinated adult with covid pneumonia? Or are they referring to the child - who I presume is unvaccinated given that their other charts have “n/a” for vaccine status for the peds floor?
(On another note dear lord can the FDA please say something about last week’s EUA request for boosting 16-17yos?!)
Thanks!!
Thanks for the great summary! Would you help us make sense of this when you’re able to ?
https://twitter.com/cieseksandra/status/1468465347519041539?s=21
You showed that 2 shots plus prior infection creates real protection. But if that prior infection was from the Delta variant, and our vaccines / boosters are still targeted against the original virus, then this may not indicate any benefit from the booster, but rather from Delta exposure.
Is Omicron a derivative of Delta? Does it share most/all of Delta's mutations?
Maybe this is the time to mix in that Moderna booster if you got a Pfizer initial course.