It’s clear that BA.2 is finishing what BA.1 started. Because of this, the shape of the overall Omicron wave (which includes all the sublineages— BA.1, BA.1.1, BA.2, BA.3) is varying across the globe. We saw a similar phenomenon last spring with Alpha. In general, there are four Omicron wave shapes:
This is far and away the best summary of current status I have read anywhere. Nuanced and clearly communicated as always, avoiding the fear mongering in many recent articles in national press while clearly describing the range of pathways. And thank you thank you for highlighting base effects for these enormous percentage changes! Best COVID-19 newsletter out there.
"avoiding the fear mongering. . . while clearly describing the range of pathways" is why I recommend this site as the main place to get COVID info! Excellent work.
As always, thank you for the excellent update. Is there a link to access the old and new CDC transmission maps that Dr. Salemi found that are interactive with click-through county specific transmission rates? Thanks.
Clearly, your reporting underscores the tragedy that last week, congress scrubbed the Covid-19 preparedness funding from the $1.5 trillion spending bill. Haven't we learned? What were they thinking?
I can't seem to paste in the link, but the old transmission map is still on the CDC Covid Data Tracker. I had it bookmarked but got there again from the main Data Tracker page by selecting "Cases, Deaths, & Testing" and then "County Data & Trends." So it seems like it's still in the same place, the only change is that Data Type is now defaulting to Cases instead of Community Transmission. At first it didn't look like CT was an option for Data Type but it's just above Cases in the drop-down menu.
Dr. Hart - thanks. This is very useful. But was also seeking a simple color-coded click and view graphic (as per Dr. Salemi's community transmission maps in today's YLE update) for informing pubic and policy-makers displaying new CDC and old CDC guidance when comparison can be useful as we learn more over time. Thanks again.
I deleted the post and posted a new reply with a link that will take one to the Community Transmission data.
As for the old and new CDC maps, I don't know how Dr. Salemi constructed those. If you follow the link in Dr. Jetelina's article to his Twitter feed, you will see the 2 maps she used in this article today, along with quite a bit of additional analysis. To see the maps side-by-side on an ongoing basis would be a welcome feature, but I have no idea how that would be done..
I wish we could come up with a kind of "self funding" model for managing pandemic risk, paid for with instruments like:
1. A modest tax on insurance companies, paid into a reinsurance pool
2. A nominal fee for testing. It could be used to help guarantee treatment and paid time off from work in the event that you test positive.
3. A modest tax penalty for not getting vaccinated...against everything recommended by ACIP. Doesn't have to be at the federal level.
4. A lending program where instead of the feds giving money to the states for their pandemic response, they loan money to the states (and the states would have to pay back the loans with interest)
5. Fines for non-compliance with local mask mandates, collected at point of sale ("What's this line on my receipt? Oh, that's the penalty for not wearing a mask")
I like #1 as having some possibilities. I fear that the other options could backfire. This is a "public" health and, in my opinion, requires "public" funding support thus underscoring the community responsibility for tackling pandemic/endemic. I also believe that funding mostly at federal level is important as viruses do cross state lines:-). The federal portion needs to be an incentive to encourage states to participate. Just a few thoughts but do appreciate creative thinking as this problem ain't going away!
Right, but since this appears to have gotten hopelessly politicized, I kind of think an apolitical funding mechanism similar to reinsurance might be our only option, especially with money getting diverted to....other things right now.
An extremely informative post. Thank you for pointing out that, *"According to the new CDC guidelines, you can take off your mask in these areas because hospitals won’t reach capacity any time soon". This is very different from taking off masks for your own protection against infection, which is an important distinction I fear is lost among the public*. I can almost guarantee you that this crucial distinction seems totally LOST on many folks up here along the Minnesota/Wisconsin border, where mask-wearing indoors (e.g. grocery stores) has zipped down to essentially zero, like a rabbit disappearing in some kind of stage-magic trick. As well, on the technically speaking side, the Boston sewerage data plot that you reviewed is a Semi-Log plot -- its time axis is linear, not logarithmic. Only the vertical axis is logarithmic.
Excellent summary. And very timely! I'm the only Virologist most of my friends know, so people have been asking me "how do you think BA.2 will go in the US?"
Your excellent post saved me the time of writing a reply to my friends.
I'm stocked up on masks and I don't "spend" them during troughs, three reasons.
1. The testing, hospital, and antiviral capacity are adequate if I contract Covid during a relative lull.
2. During a peak, when there's a higher risk, I'll probably want to change masks frequently (30 hours per mask)
3. Solid waste from disposable masks is a real problem. So I can balance my conflicting values by using no mask or cloth masks (for source control) when cases are low.
As usual, very helpful discussion on current situation. In an upcoming letter, please discuss the recent applications for a fourth shot (second booster) submitted by Moderna and Pfizer. Are there public guidelines on when or if one should get the additional booster.
I am vaxed and boosted; haven't had Covid yet. The CDC's new "it's okay to take off your mask indoors" guidance makes me feel like there's an unspoken policy at work: the CDC wants as many of us to get Covid as quickly as possible (as long as we don't run out of hospital beds). As long as you survive Covid, there's the benefit of natural immunity, which is a way of "vaxing" the un-vaxed, and bestowing super-immunity on the vaxed/boosted. It's almost as if "masks off" is an admonition by the CDC that our vaccines no longer work against omicron and future variants. It's the CDC's way of sticking to their "vaccines are the only way out of the pandemic" without admitting "vaccines are not enough to end the pandemic."
I heard recently that the J&J vaccine is holding it's own against Pfizer and Moderna. Really? Isn't J&J the least effective of the 3 vaccines? If J&J is now "holding its own," that means Pfizer and Moderna are no longer very effective.
The article that I read is that the J&J data is still very inconclusive, but it MAY be that J&J immunity holds strong or even gets stronger over time and that it MAY be more effective vs newer variants than mRNA. It did say that it is way too early to write J&J off, that it might be the perfect thing for places where vaccines have to travel a lot before being given, but, unfortunately, so many people around the world got the message that it is "bad," that many will only hold out for mRNA when it may turn out that J&J is just as good in the long run.
There are two important ways that the vaccines still work against Omicron and probably most variants that we might see:
1. They dramatically reduce severity.
2. They reduce transmission, when you zoom out to the population level. A 50% reduction in getting infected doesn't seem that great at the individual level, but it also implies a 50% reduction in the transmission rate. That's a big deal.
A question: It seems one could conjecture that reported cases are diminishing in part because home test results may not be reported to local health authorities. Can we measure how the mass distribution of home testing kits has impacted state and local case reporting?
I hear this quite a bit, and I'm really quite skeptical of this theory. Here's why. It's one thing to say that people who do home tests might be less likely to get PCR tests. It's quite another to speculate about what those people *would* do if they didn't have access to home tests. Would they be running out and getting PCR tests? I kind of doubt it. In other words, in the alternate universe where people don't have home tests, they just...don't get tested. So the impact on case counts is minimal. Sure, there's undercounting, but that same amount of undercounting exists with or without rapid tests.
I follow my local county data pretty closely. It was easy to see the uptick when Delta first made a small inroad. It was actually harder with Omicron because it hit so fast and labs fell behind so quickly (the "reported date" data in GA is pretty noisy as therecare bumps when data comes in late. The "onset date" - which I assume is sample collection date - is incomplete, but more reliable for seeing trends. Not every record has this field completed, I guess)
Right now, I can't tell what's happening. Reported cases are ticking up, but onset date data shows nothing. TPR has stopped dropping. Nearby wastewater data is really noisy. I backed into a relative count from using the CDC reported 15 day change. It was up two weeks ago for while, then way back down, now up bit.
So, I conclude: who knows? I think things will be much clearer in a couple weeks. ...hoping for the best.
...and no new out-of-the-blue variants. We're closing in on six months since Omicron popped up.
Appreciate all the detailed info. Question about the new variants-i am seeing a lot of patients (in the Northeast) with what would appear to be Covid symptoms-sudden onset of muscle aches, nasal congestion, +/- cough, sore throat. Home tests are all negative. Any info about current home test reliability with BA strains? Any info would be greatly appreciated! Thank you!
Thank you, excellent summary. The challenge is anticipating change in patterns, especially impact on the local environment - positive cases that reduce folks available to work from amazon to nursing homes to hospitals, workload on ER, workload on hospital admits. A four fold increase when the starting numbers are low, has hardly any impact. The second task are mitigation efforts that have an actual impact. For example, if a firm is a programming shop and the firm has folks returning to office. Which is better masking or going back to remote work for 3 weeks.
More of a question than a comment. As a pediatrician, people ask me all the time when we should mask or not mask in my community (Omaha,NE). I used to use less than 20 cases for 100,000 prevalence and 10% or less test positivity rates. These numbers don’t seem quite as accurate as they used to be. What would you use to decide masking in our community? Thank you so much!
This is off-topic but of interest to me. Apologies.
About the three types of deer so similar to humans for ACE2, one of which is Père David's Deer:
Père David’s Deer were originally Chinese but were hunted almost to extinction there. All the surviving deer in the PRC are highly inbred deer from one captive population.
In China there is a health myth associated with eating its venison that it would provide good fortune and a long life.
Is it possible that this may be a possible food route for the initial infections at the food market?
Where I encountered the reference to that work (a recent piece on White Tailed Deer infections from deer to deer):
Comparison of the human ACE2 protein demonstrated a high degree of homology between the human ACE2 protein and its orthologues in multiple animal species [9]. Among the species that the ACE2 protein shares a high degree of homology with human ACE2, are three species of deer, including Père David’s deer (Elaphurus davidianus), reindeer (Rangifer tarandus), and white-tailed deer—WTD (Odocoileus virginianus), suggesting potential susceptibility of these species to the ancestral SARS-CoV-2 virus [9]
END QUOTE
From their bibliography:
9. Damas J, Hughes GM, Keough KC, Painter CA, Persky NS, Corbo M, et al. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. Proc Natl Acad Sci U S A. 2020;117: 22311–22322. pmid:32826334
Personally, I would also like to know much more about the three (four?) sister viruses found in Laos and possibly in Cambodia (a mention in just one past ref I encountered).
University of Washington's Health Metrics Institute is forecasting that the US will not go through another surge. Would love to hear your take on this in comments on in your next update.
It certainly doesn't contradict our heroine's prediction that it's going to be different in different parts of the country. Cases can go down overall, while surging in certain areas.
This is far and away the best summary of current status I have read anywhere. Nuanced and clearly communicated as always, avoiding the fear mongering in many recent articles in national press while clearly describing the range of pathways. And thank you thank you for highlighting base effects for these enormous percentage changes! Best COVID-19 newsletter out there.
"avoiding the fear mongering. . . while clearly describing the range of pathways" is why I recommend this site as the main place to get COVID info! Excellent work.
I have alerted everyone I know to the excellence of the information and expertise here!
As always, thank you for the excellent update. Is there a link to access the old and new CDC transmission maps that Dr. Salemi found that are interactive with click-through county specific transmission rates? Thanks.
Clearly, your reporting underscores the tragedy that last week, congress scrubbed the Covid-19 preparedness funding from the $1.5 trillion spending bill. Haven't we learned? What were they thinking?
I can't seem to paste in the link, but the old transmission map is still on the CDC Covid Data Tracker. I had it bookmarked but got there again from the main Data Tracker page by selecting "Cases, Deaths, & Testing" and then "County Data & Trends." So it seems like it's still in the same place, the only change is that Data Type is now defaulting to Cases instead of Community Transmission. At first it didn't look like CT was an option for Data Type but it's just above Cases in the drop-down menu.
Based on a link in a Twitter thread in Dr. Salemi's post, the link below will take you directly to the Community Transmission.
https://covid.cdc.gov/covid-data-tracker/#county-view?list_select_state=all_states&list_select_county=all_counties&data-type=Risk&null=Risk
That's the one, thank you!
Thank you Lara - very helpful
Dr. Hart - thanks. This is very useful. But was also seeking a simple color-coded click and view graphic (as per Dr. Salemi's community transmission maps in today's YLE update) for informing pubic and policy-makers displaying new CDC and old CDC guidance when comparison can be useful as we learn more over time. Thanks again.
You're welcome, sir.
I deleted the post and posted a new reply with a link that will take one to the Community Transmission data.
As for the old and new CDC maps, I don't know how Dr. Salemi constructed those. If you follow the link in Dr. Jetelina's article to his Twitter feed, you will see the 2 maps she used in this article today, along with quite a bit of additional analysis. To see the maps side-by-side on an ongoing basis would be a welcome feature, but I have no idea how that would be done..
Again appreciated.
I wish we could come up with a kind of "self funding" model for managing pandemic risk, paid for with instruments like:
1. A modest tax on insurance companies, paid into a reinsurance pool
2. A nominal fee for testing. It could be used to help guarantee treatment and paid time off from work in the event that you test positive.
3. A modest tax penalty for not getting vaccinated...against everything recommended by ACIP. Doesn't have to be at the federal level.
4. A lending program where instead of the feds giving money to the states for their pandemic response, they loan money to the states (and the states would have to pay back the loans with interest)
5. Fines for non-compliance with local mask mandates, collected at point of sale ("What's this line on my receipt? Oh, that's the penalty for not wearing a mask")
6. Congestion taxes for large indoor events
I like #1 as having some possibilities. I fear that the other options could backfire. This is a "public" health and, in my opinion, requires "public" funding support thus underscoring the community responsibility for tackling pandemic/endemic. I also believe that funding mostly at federal level is important as viruses do cross state lines:-). The federal portion needs to be an incentive to encourage states to participate. Just a few thoughts but do appreciate creative thinking as this problem ain't going away!
Right, but since this appears to have gotten hopelessly politicized, I kind of think an apolitical funding mechanism similar to reinsurance might be our only option, especially with money getting diverted to....other things right now.
An extremely informative post. Thank you for pointing out that, *"According to the new CDC guidelines, you can take off your mask in these areas because hospitals won’t reach capacity any time soon". This is very different from taking off masks for your own protection against infection, which is an important distinction I fear is lost among the public*. I can almost guarantee you that this crucial distinction seems totally LOST on many folks up here along the Minnesota/Wisconsin border, where mask-wearing indoors (e.g. grocery stores) has zipped down to essentially zero, like a rabbit disappearing in some kind of stage-magic trick. As well, on the technically speaking side, the Boston sewerage data plot that you reviewed is a Semi-Log plot -- its time axis is linear, not logarithmic. Only the vertical axis is logarithmic.
Excellent summary. And very timely! I'm the only Virologist most of my friends know, so people have been asking me "how do you think BA.2 will go in the US?"
Your excellent post saved me the time of writing a reply to my friends.
And restock on masks. They are cheap and plentiful for the time being.
I'm stocked up on masks and I don't "spend" them during troughs, three reasons.
1. The testing, hospital, and antiviral capacity are adequate if I contract Covid during a relative lull.
2. During a peak, when there's a higher risk, I'll probably want to change masks frequently (30 hours per mask)
3. Solid waste from disposable masks is a real problem. So I can balance my conflicting values by using no mask or cloth masks (for source control) when cases are low.
As usual, very helpful discussion on current situation. In an upcoming letter, please discuss the recent applications for a fourth shot (second booster) submitted by Moderna and Pfizer. Are there public guidelines on when or if one should get the additional booster.
As usual, excellent timely updates. We are so blessed to have you do these updates! Thank you!
I am vaxed and boosted; haven't had Covid yet. The CDC's new "it's okay to take off your mask indoors" guidance makes me feel like there's an unspoken policy at work: the CDC wants as many of us to get Covid as quickly as possible (as long as we don't run out of hospital beds). As long as you survive Covid, there's the benefit of natural immunity, which is a way of "vaxing" the un-vaxed, and bestowing super-immunity on the vaxed/boosted. It's almost as if "masks off" is an admonition by the CDC that our vaccines no longer work against omicron and future variants. It's the CDC's way of sticking to their "vaccines are the only way out of the pandemic" without admitting "vaccines are not enough to end the pandemic."
I heard recently that the J&J vaccine is holding it's own against Pfizer and Moderna. Really? Isn't J&J the least effective of the 3 vaccines? If J&J is now "holding its own," that means Pfizer and Moderna are no longer very effective.
The article that I read is that the J&J data is still very inconclusive, but it MAY be that J&J immunity holds strong or even gets stronger over time and that it MAY be more effective vs newer variants than mRNA. It did say that it is way too early to write J&J off, that it might be the perfect thing for places where vaccines have to travel a lot before being given, but, unfortunately, so many people around the world got the message that it is "bad," that many will only hold out for mRNA when it may turn out that J&J is just as good in the long run.
There are two important ways that the vaccines still work against Omicron and probably most variants that we might see:
1. They dramatically reduce severity.
2. They reduce transmission, when you zoom out to the population level. A 50% reduction in getting infected doesn't seem that great at the individual level, but it also implies a 50% reduction in the transmission rate. That's a big deal.
Thank you for your work, it is so valuable.
A question: It seems one could conjecture that reported cases are diminishing in part because home test results may not be reported to local health authorities. Can we measure how the mass distribution of home testing kits has impacted state and local case reporting?
I hear this quite a bit, and I'm really quite skeptical of this theory. Here's why. It's one thing to say that people who do home tests might be less likely to get PCR tests. It's quite another to speculate about what those people *would* do if they didn't have access to home tests. Would they be running out and getting PCR tests? I kind of doubt it. In other words, in the alternate universe where people don't have home tests, they just...don't get tested. So the impact on case counts is minimal. Sure, there's undercounting, but that same amount of undercounting exists with or without rapid tests.
I follow my local county data pretty closely. It was easy to see the uptick when Delta first made a small inroad. It was actually harder with Omicron because it hit so fast and labs fell behind so quickly (the "reported date" data in GA is pretty noisy as therecare bumps when data comes in late. The "onset date" - which I assume is sample collection date - is incomplete, but more reliable for seeing trends. Not every record has this field completed, I guess)
Right now, I can't tell what's happening. Reported cases are ticking up, but onset date data shows nothing. TPR has stopped dropping. Nearby wastewater data is really noisy. I backed into a relative count from using the CDC reported 15 day change. It was up two weeks ago for while, then way back down, now up bit.
So, I conclude: who knows? I think things will be much clearer in a couple weeks. ...hoping for the best.
...and no new out-of-the-blue variants. We're closing in on six months since Omicron popped up.
FWIW, I've got my masks and tests stockpiled....
Interesting that India and Bangladesh have had minimal cases. Do you think there is any relationship to the fact that they have been using Corbevax?
Appreciate all the detailed info. Question about the new variants-i am seeing a lot of patients (in the Northeast) with what would appear to be Covid symptoms-sudden onset of muscle aches, nasal congestion, +/- cough, sore throat. Home tests are all negative. Any info about current home test reliability with BA strains? Any info would be greatly appreciated! Thank you!
Thank you, excellent summary. The challenge is anticipating change in patterns, especially impact on the local environment - positive cases that reduce folks available to work from amazon to nursing homes to hospitals, workload on ER, workload on hospital admits. A four fold increase when the starting numbers are low, has hardly any impact. The second task are mitigation efforts that have an actual impact. For example, if a firm is a programming shop and the firm has folks returning to office. Which is better masking or going back to remote work for 3 weeks.
More of a question than a comment. As a pediatrician, people ask me all the time when we should mask or not mask in my community (Omaha,NE). I used to use less than 20 cases for 100,000 prevalence and 10% or less test positivity rates. These numbers don’t seem quite as accurate as they used to be. What would you use to decide masking in our community? Thank you so much!
This is off-topic but of interest to me. Apologies.
About the three types of deer so similar to humans for ACE2, one of which is Père David's Deer:
Père David’s Deer were originally Chinese but were hunted almost to extinction there. All the surviving deer in the PRC are highly inbred deer from one captive population.
In China there is a health myth associated with eating its venison that it would provide good fortune and a long life.
Is it possible that this may be a possible food route for the initial infections at the food market?
Where I encountered the reference to that work (a recent piece on White Tailed Deer infections from deer to deer):
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010197
QUOTE from Introduction:
Comparison of the human ACE2 protein demonstrated a high degree of homology between the human ACE2 protein and its orthologues in multiple animal species [9]. Among the species that the ACE2 protein shares a high degree of homology with human ACE2, are three species of deer, including Père David’s deer (Elaphurus davidianus), reindeer (Rangifer tarandus), and white-tailed deer—WTD (Odocoileus virginianus), suggesting potential susceptibility of these species to the ancestral SARS-CoV-2 virus [9]
END QUOTE
From their bibliography:
9. Damas J, Hughes GM, Keough KC, Painter CA, Persky NS, Corbo M, et al. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. Proc Natl Acad Sci U S A. 2020;117: 22311–22322. pmid:32826334
Personally, I would also like to know much more about the three (four?) sister viruses found in Laos and possibly in Cambodia (a mention in just one past ref I encountered).
Whoah!!!! Thanks!
University of Washington's Health Metrics Institute is forecasting that the US will not go through another surge. Would love to hear your take on this in comments on in your next update.
https://twitter.com/AliHMokdad/status/1506291082451107855
It certainly doesn't contradict our heroine's prediction that it's going to be different in different parts of the country. Cases can go down overall, while surging in certain areas.