Omicron BA.4 and BA.5 (shown here in teal) have been spreading rapidly in the U.S. in the last month. CDC data are as of June 4.
In the past week (June 4 through June 10), the U.S. reported about 760,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 110,000 new cases each day
233 total new cases for every 100,000 Americans
8% more new cases than last week (May 28-June 3)
In the past week, the U.S. also reported about 29,000 new COVID-19 patients admitted to hospitals. This amounts to:
An average of 4,100 new admissions each day
8.8 total admissions for every 100,000 Americans
8% more new admissions than last week
Additionally, the U.S. reported:
2,100 new COVID-19 deaths (0.7 for every 100,000 people)
62% of new cases are Omicron BA.2.12.1-caused; 13% BA.4/BA.5-caused (as of June 4)
An average of 90,000 vaccinations per day (per Bloomberg)
As I predicted last week, the brief dip in reported COVID-19 cases was a result of the Memorial Day holiday, not an actual signal of the BA.2/BA.2.12.1 wave reaching its peak. National case counts are up again this week, with the country still reporting over 100,000 new cases a day. And remember, the true infection rate could be five or more times higher, thanks to under-testing.
Hospital admissions, a more reliable metric (less impacted by holiday interruptions) also went up this week. The number of Americans admitted to the hospital with COVID-19 has risen steadily each week since early April.
Even as millions of people are protected from severe symptoms by vaccination or prior infection, many are still susceptible—whether they’re too young to be vaccinated or have not yet received booster shots for which they are eligible. Plus, the U.S. continues to have next to zero data on Long COVID cases, a debilitating, long-term condition that can impact even people who are fully vaccinated and boosted.
Highly contagious Omicron subvariants continue to drive this surge. BA.2.12.1, the subvariant first identified in New York, is now causing almost two-thirds of cases nationwide, according to the CDC’s latest estimates. Meanwhile, the agency is finally listing separate estimates for BA.4 and BA.5, subvariants with greater capacity to reinfect people (even those who already had other versions of Omicron.)
BA.4 and BA.5 caused about 13% of cases combined in the week ending June 4, and are spreading fast. These two subvariants are currently more prevalent in parts of the Midwest and South, while BA.2.12.1 is more dominant in the Northeast. This pattern might partially explain why the Northeast is seeing virus transmission decrease or plateau, while other regions report increases.
Wastewater data from Biobot show a similar picture: a downward trend in the Northeast, offset by upward trends in the other regions. Cities like Boston and New York City are showing somewhat confusing signals right now, as Memorial Day travel and gatherings may have interrupted the decline.
We’ve received several questions about the recent divergence between the @MWRA_update North & South Systems—our Epidemiology team found that this is not an abnormal divergence. 1/3 pic.twitter.com/0hihJHJazn
According to the CDC’s old community transmission levels (which are based on cases, not hospitalizations), about 96% of U.S. counties are currently reporting high transmission—and should recommend masking in public. But new mask requirements or other safety measures have been few and far between as this surge remains largely invisible.
While the CDC is not yet reporting BA.4 and BA.5 separately, the subvariants are included in B.1.1.529; this grouping is driving increased transmission in some Midwestern and Southern states. Chart via the CDC variant dashboard.
America’s current COVID-19 surge is being driven by BA.2 and its sublineage BA.2.12.1. But there are other versions of Omicron out there to which we need to pay attention—namely, BA.4 and BA.5. Here’s a brief FAQ on these two subvariants, including why scientists are concerned about them and where they’re spreading in the U.S.
What are BA.4 and BA.5?
Remember how, when South African scientists first sounded the alarm about Omicron in November, they identified three subvariants—BA.1, BA.2, and BA.3? BA.1 first spread rapidly around the world, followed by BA.2.
Then, in the winter, South African scientists again identified new Omicron subvariants, called BA.4 and BA.5. These two variations split from the original Omicron lineage, and tend to be discussed together because they have similar mutations. (Specifically, they have identical spike protein mutations; this article discusses the mutations in more detail).
It’s important to note that, while South African scientists characterized these subvariants, they likely didn’t originate in the country. South Africa has a better variant surveillance system than many other countries, particularly compared to its neighbors, allowing the country’s scientists to quickly identify variants of concern. BA.4 and BA.5 also caused a new surge in South Africa, allowing for study of the subvariants’ performance.
Why are scientists concerned about these subvariants?
Early studies of BA.4 and BA.5 indicate that not only are these subvariants more transmissible than other forms of Omicron, they’re also more capable of bypassing immunity from prior infection or vaccination.
While the differences between BA.4/BA.5 and BA.1/BA.2 are less dramatic than the differences between the Omicron family and Delta, scientists hypothesize that there is still enough distinction between these two Omicron sub-groups that people who already had Omicron BA.1 or BA.2/BA.2.12.1 could potentially get reinfected by BA.4 or BA.5.
My guess based on this: BA.4/BA.5 escape, while not as dramatic as Omicron escape from vaccine or Delta immunity, is enough to cause trouble and lead to an infection wave. But not likely to cause much more severe disease than the previous wave, especially in vaccinated.
What are BA.4 and BA.5 doing in South Africa and other countries?
BA.4 and BA.5 have been detected in over 30 countries, according to CNN. But scientists have again focused on South Africa, as this country has better surveillance than many others—particularly as PCR testing declines around the world.
In South Africa, the BA.4/BA.5 wave that started in April has peaked and is now on the decline. Hospital admissions and deaths were lower in this recent wave than in the Omicron BA.1 wave in November and Decenter, largely thanks to high levels of immunity in the country. Still, the continued Omicron infections suggest that reinfection is a real concern for these subvariants.
Brief trip back into Covid data today:
Promising news from South Africa, where the BA.4 / BA.5 variant wave has passed quietly, with high levels of immunity meaning this wave has had little impact on rates of severe illness or death pic.twitter.com/C5W6iZzDLK
South Africa never really had a BA.2 wave, so BA.4 and BA.5 mostly competed with other Omicron lineages in that country. But in the U.K., which did face BA.2, recent data suggest that BA.4 and BA.5 have a growth advantage over even BA.2.12.1. In other words, BA.4 and BA.5 could potentially outcompete BA.2.12.1 to become the most transmissible Omicron subvariants yet.
What are BA.4 and BA.5 doing in the U.S.?
The subvariants are definitely here and spreading, but we have limited visibility into where and how much thanks to declined testing and surveillance. The CDC has yet to separate out BA.4 and BA.5 on its variant dashboard; according to White House COVID-19 Data Director Cyrus Shahpar, this is because the CDC has yet to identify these subvariants as causing 1% or more of new national cases in a given week.
Updated variant proportions just posted. BA.2.12.1 now estimated to be ~59% of specimens sequenced last week. BA.4 and BA.5 not yet meeting the 1%+ threshold to be listed separately https://t.co/YIeQkH8YmEpic.twitter.com/SsSyoVO5Gh
— Dr. Cyrus Shahpar Archived (@cyrusshahpar46) May 31, 2022
But the CDC does include BA.4 and BA.5 in its Omicron B.1.1.529 category, which has grown from causing 1% of new cases in the first week of May to causing 6% of new cases in the last week of the month. The number of cases sequenced in a week has dropped this spring compared to the first Omicron surge, leading me to wonder: are BA.4/BA.5 really causing fewer than 1% of new cases each, or do we just not have the data to detect them yet?
CDC data do show that the B.1.1.529 group (which includes BA.4/BA.5) is causing over 10% of new cases in the Plain States, Gulf Coast, and Mountain West—compared to under 5% in the Northeast, where BA.2.12.1 is more dominant. This data aligns with local reports of BA.4 and BA.5 spreading in wastewater in some Midwestern states that track variants in their sewage. For example, scientists at the Metropolitan Council in the Twin Cities recently said they expect BA.4 and BA.5 to “replace BA.2.12.1 as the dominant variants” in the next few weeks.
What could BA.4 and BA.5 mean for future COVID-19 trends in the U.S.?
As I noted above, data from the U.K. suggest that BA.4 and BA.5 could outcompete BA.2—and even BA.2.12.1—to become the dominant Omicron subvariants in the U.S. Early data from U.S. Omicron sequences are showing a similar pattern, reported variant expert Trevor Bedford in a recent Twitter thread.
“Focusing on the US, we see that BA.2.12.1 currently has a logistic growth rate of 0.05 per day, while BA.4 and BA.5 have logistic growth rates of 0.09 and 0.14 per day,” Bedford wrote. The country’s rising case counts can be mostly attributed to BA.2.12.1, he said, but BA.4 and BA.5 are clearly gaining ground. And, he noted, these two subvariants may be able to reinfect many people who already had BA.1 or BA.2.
Thus, we expect at least some portion of the BA.4 / BA.5 epidemics to be driven by increased vaccine breakthrough and increased reinfection relative to current BA.2 circulation. 12/12
In short: even more Omicron breakthrough infections and reinfections could be coming our way. Even if BA.2.12.1 transmission dips (as it seems to be doing in the Northeast), we could quickly see new outbreaks driven by BA.4 and BA.5—leading overall case numbers to plateau or rise again.
“For the summer, going into the winter, I expect these viruses to be out there at relatively high levels,” Dr. Alex Greninger from the University of Washington’s clinical virology lab told CNN. “Just the number of cases, the sheer disruptions of the workforce — It’s just a very high, high burden of disease.”
In the past week (May 28 through June 3), the U.S. reported about 700,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 100,000 new cases each day
215 total new cases for every 100,000 Americans
9% fewer new cases than last week (May 21-27)
In the past week, the U.S. also reported about 27,000 new COVID-19 patients admitted to hospitals. This amounts to:
An average of 3,800 new admissions each day
8.1 total admissions for every 100,000 Americans
5% more new admissions than last week
Additionally, the U.S. reported:
1,700 new COVID-19 deaths (0.5 for every 100,000 people)
94% of new cases are Omicron BA.2-caused; 59% BA.2.12.1-caused (as of May 28)
An average of 70,000 vaccinations per day (per Bloomberg)
The BA.2/BA.2.12.1 surge continues. According to the CDC, the number of new cases reported nationwide dropped last week, compared to the prior week; but this drop is more likely a result of the Memorial Day holiday than of an actual slowdown in transmission. (As I frequently note in these updates, holidays always result in case reporting dips as public health workers take time off.)
Despite the holiday, the country reported over 100,000 new cases a day last week. And, of course, this is a massive undercount. A new preprint from researchers at the City University of New York suggests that actual coronavirus infections during the BA.2/BA.2.12.1 surge may be 30 times as high as reported case counts—and that’s in New York City, which has better PCR infrastructure than most. (More on this study later in the issue.)
Unlike official case counts, the number of COVID-19 patients newly admitted to hospitals across the country rose last week: an average of 3,800 patients were admitted each day, a 5% increase from the prior week. Hospital admissions are more reliable than case counts, especially after a holiday, suggesting that we are indeed still on the upswing of this surge.
Similarly, coronavirus levels in the country’s wastewater keep rising. Biobot’s dashboard shows a continued national increase, as well as increases in the Midwest, West, and South regions. In the Northeast, virus levels dipped last week and now appear to be at a plateau.
Has the Northeast peaked? Optimistically, I would like to say yes, but a combination of spotty data and the Memorial Day holiday makes it tough to say for sure. In New York City, case rates dropped last week—but so did testing. In Boston, coronavirus concentrations in wastewater seem to be on a downturn—but the data are noisy.
And even if the Northeast is coming out of its BA.2/BA.2.12.1 surge, the rest of the country is on the opposite side of the wave. Reported case numbers in Southern and Midwest states like Missouri, Wyoming, Alabama, Utah, Mississippi, and Texas shot up by over 20% last week, while Hawaii and Florida now have the highest reported case rates, according to the June 2 Community Profile Report.
Even the CDC’s highly lenient Community Levels are beginning to light up yellow and orange, suggesting that counties from Florida to central California should reinstate indoor mask requirements. But are any leaders actually putting these measures in place? It seems unlikely, leaving the increasingly-smaller COVID-concerned minority to fend for ourselves.
New Surgeon General advisory on health worker burnout: This week, U.S. Surgeon General Dr. Vivek Murthy released a new advisory on COVID-19 burnout among health workers, summarizing research on the issue and highlighting it as a public health priority. The advisory discusses a variety of societal, cultural, structural, and organizational factors contributing to health worker burnout, while tying this burnout to growing shortages of doctors and other health professionals. From the one-page summary of the advisory: “If not addressed, the health worker burnout crisis will make it harder for patients to get care when they need it, cause health costs to rise, hinder our ability to prepare for the next public health emergency, and worsen health disparities.”
CDC may change COVID-19 reporting for hospitals: The CDC is planning a few changes to its reporting requirements for hospitals in order to simplify the reporting process and cut down on redundant information, according to a draft plan shared with Bloomberg. Among the changes: hospitals may no longer be required to report suspected COVID-19 cases (i.e. those cases not yet confirmed with a PCR test); with most hospitals testing all patients when they’re admitted, suspected cases are less common and the data are less useful than they had been at earlier points in the pandemic. The CDC may also stop requiring COVID-19 reporting from some types of facilities, such as mental health centers, and may change the frequency of required reporting.
New preprint about Omicron BA.4 and BA.5: While the U.S. mostly worries about BA.2.12.1, additional Omicron subvariants BA.4 and BA.5 have been spreading in South Africa and other countries. A new study from a highly-regarded consortium of Japanese researchers suggests that BA.4 and BA.5 are about 20% more transmissible than BA.2 (similarly to BA.2.12.1). Also, even more concerning: the researchers found that BA.4 and BA.5 are more capable of resisting protection from a prior Omicron infection than BA.1. While the study has not yet been peer-reviewed, it garnered a lot of attention on Twitter this week from scientists warning that we need to watch out for these subvariants.
U.S. gets closer to a vaccine for kids under five: The FDA has set new dates for its vaccine advisory committee to review data on COVID-19 vaccines for children under age five: the committee will discuss both Moderna’s and Pfizer’s under-five vaccines on June 15, after discussing Moderna’s vaccine for children ages six to 17 on June 14. This announcement came after Pfizer and BioNTech released new data on their under-five vaccine, saying that a series of three doses provided strong protection against severe disease. There are some caveats for the data (which were shared via press release), but this is great news for children under age five and their families.
NIH sharing some COVID-19 technology (but not patents): I missed this news from earlier in May: the National Institutes of Health has made a deal with the World Health Organization’s COVID-19 Technology Access Pool and the Medicines Patent Pool to lisense 11 technologies used in COVID-19 vaccines and therapeutics. This lisense will allow pharmaceutical manufacturers around the world to make the coronavirus spike protein, RNA virus tests, and other COVID-19 components, increasing access to these technologies in low- and middle-income countries. Of course, it would be better for these countries if the NIH had shared full vaccine patents, but apparently that’s asking too much.
It’s not all mild cases: new COVID-19 hospital admissions have been rising at a similar rate to cases in the last couple of weeks. Chart via the CDC.
In the past week (May 21 through 27), the U.S. reported about 770,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 110,000 new cases each day
234 total new cases for every 100,000 Americans
8% more new cases than last week (May 14-20)
In the past week, the U.S. also reported about 25,000 new COVID-19 patients admitted to hospitals. This amounts to:
An average of 3,600 new admissions each day
7.7 total admissions for every 100,000 Americans
8% more new admissions than last week
Additionally, the U.S. reported:
2,200 new COVID-19 deaths (0.7 for every 100,000 people)
97% of new cases are Omicron BA.2-caused; 58% BA.2.12.1-caused (as of May 21)
An average of 70,000 vaccinations per day (per Bloomberg)
America’s largely-ignored BA.2 surge continues: the U.S. reported over 100,000 new cases a day last week, while an average of 3,600 new COVID-19 patients were admitted to hospitals each day. Both of these metrics rose about 8% from the week prior.
Of course, as I am frequently reminding everyone these days, current case numbers are a drastic undercount of actual infections, thanks to at-home testing and increasingly-fractured PCR access. Our current surge might actually be the country’s “second-largest wave of COVID-19 infections since the pandemic began,” Wall Street Journal reporter Josh Zumbrun wrote last week.
The culprits for this wave of infections are BA.2 and its sublineage BA.2.12.1; the latter is now causing more than half of new cases in the U.S., according to CDC estimates. Northeast states, which have been BA.2.12.1 hotspots for a few weeks now, continue to report the highest case rates: these include Rhode Island, Delaware, New Jersey, Massachusetts, D.C., and New York.
There are some promising signs that the BA.2 wave in these Northeast states may soon be on a downturn, if it isn’t already. Data from Biobot show that coronavirus levels in wastewater are dropping in this region, with reports from Bostonand from Maine contributing to this pattern. New York City, where I live, has reported a case plateau for the last week or so, but I’m hopeful that it could turn into a downturn soon.
what's up with COVID-19 in NYC right now? official case numbers have plateaued, and I think we could see a downturn soon. a cautiously optimistic thread: (1/9) pic.twitter.com/3T96FagCts
— betsy ladyzhets 📊 (@betsyladyzhets) May 26, 2022
But will this encouraging pattern in the Northeast withstand the holiday weekend of largely-unmasked travel and gatherings? It may be a couple of weeks before we know for sure, because the holiday will interrupt data reporting (as holidays always do). The CDC itself is taking a long weekend off, with no Weekly Review this past Friday and no data updates at all Saturday, Sunday, and Monday.
Meanwhile, COVID-19 deaths—the most lagging pandemic metric—are going up once again. More than 300 Americans died of the disease each day last week, in a 13% increase from the week prior. These are the consequences of our country’s continued failure to protect the vulnerable.
After appearing to peak in mid-April, COVID-19 case rates in New York City began going up again as BA.2.12.1 took over. Chart from NYC Health.
In the past week (May 14 through 20), the U.S. reported about 710,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 101,000 new cases each day
216 total new cases for every 100,000 Americans
19% more new cases than last week (May 7-13)
In the past week, the U.S. also reported about 23,000 new COVID-19 patients admitted to hospitals. This amounts to:
An average of 3,300 new admissions each day
6.9 total admissions for every 100,000 Americans
24% more new admissions than last week
Additionally, the U.S. reported:
2,000 new COVID-19 deaths (0.6 for every 100,000 people)
98% of new cases are Omicron BA.2-caused; 48% BA.2.12.1-caused (as of May 14)
An average of 140,000 vaccinations per day (per Bloomberg)
The Omicron BA.2 surge continues in the U.S., with a 19% increase in officially-reported COVID-19 cases in the past week to over 100,000 new cases a day. Of course, the official case numbers severely underestimate true infections, as PCR testing sites close and more people use rapid tests; actual case counts may be five or more times higher.
New hospital admissions are also increasing: about 23,000 COVID-19 patients were admitted for care nationwide last week, up from 11,000 one month ago. While millions of Americans have some protection against severe disease from vaccination and/or prior Omicron infections, many are still susceptible. Hospitals are beginning to fill up again in almost every state, and as Ed Yong points out, the numbers don’t capture continued burnout among healthcare workers.
🚨I wrote about how the health-care system is faring. In many places, things are better than the winter's surge. But that's scant comfort. The system is now locked in a chronic, cumulative crisis that exerts a toll regardless of what COVID is doing. 1/ https://t.co/zZItleYRg5
BA.2.12.1, the most transmissible version of Omicron BA.2 now spreading in the U.S., accounted for almost half of new cases in the week ending May 14, according to CDC estimates. Northeast states remain hotspots: BA.2.12.1 caused about three in four new cases in New York and New Jersey last week.
One thing I’ve been wondering, in recent weeks, is when we might see cases peak in the Northeast. In New York City, where I live, case trends seemed to turn downward in mid-April; but then after about a week, the numbers went up again — perhaps a consequence of BA.2.12.1 taking over from BA.2.
COVID-19 trends from wastewater surveillance for the Northeast look similar to the case trends in NYC: a slow increase through March and April, followed by a potential plateau or further increases in May.
And other regions are catching up, according to Biobot’s tracker: states in the Midwest and South continue to see their coronavirus levels increase as the Northeast stagnates. Official case data from the latest Community Profile Report suggest that states such as Nebraska, Montana, Missouri, Kansas, and Kentucky reported the sharpest increases over the last week.
One piece of good news: new COVID-19 vaccinations rose slightly over the last week, going above 100,000 new shots administered daily for the first time in several months. Second booster shots in older adults and those with severe medical conditions are likely driving this increase, though, rather than shots for the previously unvaccinated.
As local leaders like NYC mayor Eric Adams refuse to institute new mask mandates and the country overall seems apathetic to this COVID-19 surge, it’s unclear how long we’ll be dealing with these Omciron subvariants — or how much we’ll invite the virus to keep mutating.
The US’s second Omicron surge is fully here.
At the end of Jan / beginning of Feb, my hypothesis was that if there wasnt a clear national surge by the end of March we would be basically surge-free until the fall.
Omicron BA.2.12.1 (shown here in red) is taking over from BA.2 (pink) in much of the country, with the Northeast in the lead. Chart via the CDC, data as of May 7.
In the past week (May 7 through 13), the U.S. reported about 590,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 85,000 new cases each day
181 total new cases for every 100,000 Americans
31% more new cases than last week (April 30-May 6)
In the past week, the U.S. also reported about 18,000 new COVID-19 patients admitted to hospitals. This amounts to:
An average of 2,600 new admissions each day
5.6 total admissions for every 100,000 Americans
18% more new admissions than last week
Additionally, the U.S. reported:
1,900 new COVID-19 deaths (0.6 for every 100,000 people)
99% of new cases are Omicron BA.2-caused; 43% BA.2.12.1-caused (as of May 7)
An average of 80,000 vaccinations per day (per Bloomberg)
New COVID-19 cases continue to rise in the U.S., with an average of 85,000 cases reported nationally each day last week—double the daily average from three weeks ago. This is a significant undercount, of course, as the majority of COVID-19 tests conducted these days are done at home.
The country is also reporting more COVID-19 patients admitted to hospitals: about 18,400 people were admitted last week, an 18% increase from the prior week. While this is far lower than the numbers reported during the peak of the Omicron wave (and includes some incidental hospitalizations), it’s still a concerning signal: even as immunity from prior vaccinations and infections protects many Americans from severe disease, plenty of people remain vulnerable.
This current increase is largely driven by the Omicron subvariant BA.2 and its offshoot BA.2.12.1, which is the most transmissible version of this lineage yet. BA.2.12.1 caused about 43% of new cases nationwide in the week ending May 7, according to CDC estimates; in parts of the Northeast, Midwest, and South, that ratio is over 50%.
The Northeast, which has the most BA.2.12.1, also continues to report the highest coronavirus levels in wastewater regionally, according to Biobot. After a potential plateau in recent weeks, the Northeast is now continuing to show a clear uptick; wastewater data from other parts of the country also indicate a slow increase in coronavirus transmission.
The CDC’s wastewater data somewhat reaffirm these trends, but are currently difficult to interpret as a number of sites have gone offline recently. (More on that later in the issue.)
States with the highest COVID-19 case rates continue to include Northeast states: Rhode Island, Massachusetts, New York, Maine, Vermont, New Jersey, and Washington, D.C. But some Midwest states (Illinois, Michigan, Wisconsin) as well as Hawaii are also reporting over 250 new cases per 100,000 people in the last week, showing how this BA.2 surge is spreading to other regions.
If you look at the CDC’s Community Level guidance, you may think that, even if you live in one of these surging Northeast states, you can go out in public without a mask. But other metrics, such as the agency’s old Community Transmission levels (which are based more on cases than hospitalizations), suggest otherwise.
1. Based on this week's @CDCgov transmission levels, 89% of the US population lives in a county classified as "substantial" or "high".
— Jason L. Salemi, PhD, FACE (@JasonSalemi) May 13, 2022
In short: if you want to protect yourself and others in your community, especially if you live in the Northeast, now is a good time to mask up, test often, and avoid large indoor gatherings.
As cases rise in the U.S. and other parts of the world, Omicron subvariants are a continued culprit. Experts are watching closely to see if further mutations of the virus may become even more contagious, or may gain the ability to evade immunity from prior infections and vaccinations.
BA.4 and BA.5 in South Africa
When South African scientists sounded the alarm about Omicron in November, they identified three versions of the variant, called BA.1, BA.2, and BA.3. BA.1 first spread rapidly through South Africa and the rest of the world in December and January; BA.2 then outcompeted BA.1 to become the dominant strain globally.
Now, South African scientists are sounding the alarm again: this time about new Omicron lineages, dubbed BA.4 and BA.5. These two lineages have driven another new surge in the country, with both cases and hospital admissions rising sharply in recent weeks. The surge might be starting to slow, as of late this week, but it’s unclear if this trend will continue.
Sigal and his collaborators tested neutralizing antibodies—a commonly-studied aspect of immune system protection—from BA.1 against BA.4 and BA.5. They found that a BA.1 infection offered relatively limited protection against BA.4 and BA.5, especially if the person who had BA.1 was unvaccinated. “BA.4 and BA.5 have potential to result in a new infection wave,” the authors wrote.
This study is a preprint, not yet peer-reviewed. But it’s still a major warning sign for the U.S. and other countries: watch out for BA.4 and BA.5.
In New York and New Jersey, BA.2.12.1 is causing over 60% of new cases; it’s no coincidence that these states are also reporting some of the highest case and hospitalization rates in the country right now. New England, mid-Atlantic, South, and Midwest states are also seeing high proportions of BA.2.12.1.
The CDC’s variant proportions estimates don’t yet include BA.4 and BA.5, but other reports suggest that these subvariants are already in the U.S. and starting to compete with our homegrown BA.2 lineages. Marc Johnson, a leading wastewater expert in Missouri, posted on Twitter yesterday that he’s seeing “a circus of Omicron sublineages” in his state, including BA.4 and BA.5.
So here is the latest Missouri sewershed data. It's a circus of Omicron sub-lineages. There are literally 5 strains competing against each other that each have a different residue at position 452. pic.twitter.com/T1CObdJdeD
Also worth noting: a new U.S. study (shared as a preprint last week) found that, actually, Omicron is not inherently less severe than other variants. In comparing hospitalization and mortality risks after accounting for vaccination and medical risk factors, the researchers behind this study found little difference between the Omicron wave and prior periods. While this study also has yet to be peer-reviewed, it doesn’t bode well for future Omicron-driven surges.
These maps from the May 5 Community Profile Report look pretty different from the CDC’s all-green “Community Levels” map, huh?
In the past week (April 30 through May 6), the U.S. reported about 450,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 65,000 new cases each day
138 total new cases for every 100,000 Americans
21% more new cases than last week (April 23-29)
In the past week, the U.S. also reported about 16,000 new COVID-19 patients admitted to hospitals. This amounts to:
An average of 2,200 new admissions each day
4.7 total admissions for every 100,000 Americans
17% more new admissions than last week
Additionally, the U.S. reported:
2,300 new COVID-19 deaths (0.7 for every 100,000 people)
98% of new cases are Omicron BA.2-caused; 37% BA.2.12.1-caused (as of April 30)
An average of 70,000 vaccinations per day (per Bloomberg)
New COVID-19 cases are still rising in the U.S., as the country continues to face the Omicron subvariant BA.2 and its offshoots. While at levels much lower than what we saw in December and January, daily new cases have more than doubled in the last month.
And, as I frequently note these days, case numbers are capturing a small fraction of actual COVID-19 infections, as PCR testing becomes less available and at-home rapid tests become more popular. Hospital admissions, a more reliable metric, have also shot up in recent weeks, with about 50% more COVID-19 patients admitted to U.S. hospitals last week than in the first week of April.
Wastewater data suggest that COVID-19 transmission nationwide may be increasing slightly or in a plateau, far from the kind of exponential increase we saw during the first Omicron surge. Biobot’s dashboard shows that coronavirus levels in wastewater in the Northeast, South, and Midwest continue to increase slightly, while in the West, virus levels have shifted back down in the most recent week of data.
The CDC’s wastewater dashboard similarly suggests that fewer parts of the country are seeing major coronavirus upticks than the national system reported a couple of weeks ago. But this dashboard is a bit incomplete at the moment, with hundreds of sites reporting no recent data, so I take that finding with a grain of salt.
Northeast states continue to report the highest case rates, according to the May 5 Community Profile Report. Maine, Rhode Island, Vermont, Massachusetts, Hawaii, New York, New Jersey, Illinois, New Hampshire, and Connecticut all reported more than 200 new cases for every 100,000 residents in the last week, passing the CDC threshold for a medium “Community Level” (or, under the agency’s old guidance, more than double the threshold for high transmission).
The map on the L is what CDC wants you to see. The map on the R is what you need to see. The map on the L says all but 13% of US is low risk. The map on the R says only 13% is low risk. Hosps have increased 20% over the last 2 weeks. Get boosted & wear a mask in crowded spaces. pic.twitter.com/cUDn8WMink
The BA.2 subvariant is now causing almost 100% of new COVID-19 cases in the country, according to CDC estimates, with the even-more-contagious BA.2.12.1 sub-subvariant causing about one in three of those cases. In the coming weeks, we’ll see how well protection from vaccines and recent Omicron BA.1 infections holds up against these more-transmissible versions of the virus.
On the left, the CDC’s current Community Levels indicate that 90% of the U.S. is in a “low risk” region. On the right, the CDC’s old Transmission Levels indicate that only 15% of the country is in a “low risk” region.
In the past week (April 23 through 29), the U.S. reported about 370,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 53,000 new cases each day
113 total new cases for every 100,000 Americans
25% more new cases than last week (April 16-22)
In the past week, the U.S. also reported about 13,000 new COVID-19 patients admitted to hospitals. This amounts to:
An average of 1,900 new admissions each day
4.0 total admissions for every 100,000 Americans
19% more new admissions than last week
Additionally, the U.S. reported:
2,300 new COVID-19 deaths (0.7 for every 100,000 people)
97% of new cases are Omicron BA.2-caused; 29% BA.2.12.1-caused (as of April 23)
An average of 80,000 vaccinations per day (per Bloomberg)
Nationwide, new COVID-19 cases have increased in the U.S. for the fourth week in a row. The daily case average has doubled since early April, and that’s just the cases that we’re reporting; with less PCR testing availability and more people using at-home tests, we have very limited visibility into this current uptick.
New hospital admissions, a more reliable metric than cases, have also continued to rise this week. U.S. hospitals reported about 13,200 COVID-19 patients admitted this week, up from under 10,000 in the first week of April.
Wastewater data similarly continue to indicate increased coronavirus spread. The Northeast is still in a high plateau, according to Biobot’s dashboard, while other parts of the country are reporting upticks.
This mirrors the reported case data: Northeast states Vermont, Rhode Island, New York, and Massachusetts reported the highest case rates in the week ending April 27, according to the latest Community Profile Report. But states in the South and West, such as North Carolina and Nebraska, reported the sharpest increases.
Almost one-third of new cases were caused by the BA.2.12.1 subvariant in the week ending April 23, according to the CDC’s latest estimates. This version of Omicron, first identified by the New York state health department, is even more transmissible than BA.2. It’s causing more than half of cases in the New York and New Jersey region, the CDC estimates.
Despite all of these concerning signals, the vast majority of the country seems unaware that we are in a new COVID-19 spike. Indeed, I’m writing this from the plane back to New York City, on which I’m one of few mask-wearers.
And I can’t really blame my fellow travelers for their lack of awareness: if you just look at the CDC’s Community Level map—as the agency recommends people do—you’d think that the whole country is in a green, low-risk zone. The agency’s old guidance, with more stringent, case-based thresholds, paints a very different picture.
Here are the 2 CDC COVID maps. The one on the left is the community level map which suggests 90% of the US has low risk. The map on the right of actual virus transmission levels shows a different story where only 15% of the country is low risk. pic.twitter.com/gf2NyF9OKf
The U.S. has “reached the choose-your-own-adventure stage of the pandemic,” as Maryn McKenna put it in a recent WIRED article. We’re taking “individual responsibility” to a whole new level.
COVID-19 Data Dispatch 