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.
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?
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.
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.
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 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.
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):
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 . 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 
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.