BA.2.75, a newer subvariant that evolved from BA.2, has been driving increased coronavirus transmission in some other countries recently. You might also see it referred to as “Centaurus” on social media. This lineage has yet to be identified in large numbers in the U.S., but I was inspired by a recent reader question to share what we’ve learned about it since my previous post in July.
Scientists are concerned about BA.2.75 because it has several new mutations that are distinct from BA.2, most of those in the spike protein (where the virus binds to human cells). And some preliminary research, including recent studies in the Lancet Infectious Diseases and in the New England Journal of Medicine, have found that BA.2.75 is less susceptible to neutralizing antibodies from prior infections or treatments than past variants.
This could mean people who previously caught BA.2 or other versions of Omicron could be susceptible to BA.2.75, reports Hannah Flynn in Medical News Today. Of course, more research and data are needed on the new variant. But BA.2.75 has been driving new surges in India, Nepal, and other countries—another signal that it’s worth watching.
As I noted in today’s National Numbers post, the CDC is not yet reporting BA.2.75 prevalence estimates separately from other versions of BA.2. But it has reported an increase in BA.2 overall in recent weeks, from 0.6% of new cases in the week ending August 27 to 1% in the week ending September 10. This is probably BA.2.75, given that older versions of BA.2 haven’t been competitive in the U.S. for a few months.
Helix, a COVID-19 testing company that works with the CDC and other agencies on variant surveillance, is tracking BA.2.75 separately from BA.2 on its dashboard. According to Helix’s data, original BA.2 has stayed at very low prevalence in recent weeks while BA.2.75 has risen to 1% of cases sequenced.
It’s currently unclear—as it was in July—to what extent BA.2.75 might be able to compete with BA.5 or BA.4.6, which are the main subvariants of concern spreading across the U.S. right now. But if BA.2.75 does become dominant, it will be helpful that the newly-authorized booster shots include genetic material from the original, Wuhan variant, not just BA.4 and BA.5.
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.
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.
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.
Coronavirus levels in wastewater may be plateauing in the Northeast, while the remaining regions of the country catch up. Chart via Biobot, retrieved on April 24.
In the past week (April 16 through 22), the U.S. reported about 300,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 43,000 new cases each day
91 total new cases for every 100,000 Americans
35% more new cases than last week (April 9-15)
In the past week, the U.S. also reported about 11,000 new COVID-19 patients admitted to hospitals. This amounts to:
An average of 1,600 new admissions each day
3.4 total admissions for every 100,000 Americans
8% more new admissions than last week
Additionally, the U.S. reported:
2,600 new COVID-19 deaths (0.8 for every 100,000 people)
93% of new cases are Omicron BA.2-caused; 19% BA.2.12.1-caused (as of April 16)
An average of 100,000 vaccinations per day (per Bloomberg)
After weeks of me warning about it, a BA.2 surge is upon us. Nationwide, new COVID-19 cases have gone up for the third week in a row; we’ve seen a 68% increase since the last week of March.
And that’s just the reported cases: Americans may be doing about four times more at-home tests than they’re doing lab-based PCR tests, according to Mara Aspinall, a COVID-19 testing expert (who cowrites a testing-focused newsletter). The vast majority of these at-home tests are never reported to public health officials and don’t make it into our trends analysis.
But there are other metrics that similarly indicate a national rise in coronavirus transmission. Viral levels in wastewater are going up, according to both Biobot’s tracker and the CDC’s national monitoring system; the CDC’s COVID-19 data team noted in this Friday’s Weekly Review that “more than half of all sites reporting wastewater data are experiencing a modest increase in SARS-CoV-2 levels.” Some of these increases are going from very low to still low, but they’re still worth watching.
The U.S. is also reporting an increase in new COVID-19 patients admitted to hospitals: about 11,000 people this week, up from 10,000 last week. New hospitalizations lag behind cases slightly, but they are a more reliable metric, as anyone with symptoms severe enough to require hospitalization generally will seek care (so, underreporting is less of a concern.)
At the regional level, the Northeast is still seeing the highest case rates: leading jurisdictions include Vermont, Washington D.C., New York, Rhode Island, and Massachusetts, according to the April 21 Community Profile Report. The Northeast—particularly New York and New Jersey—is also a hotspot for the Omicron sub-subvariant, BA.2.12.1.
To borrow an analogy from my sister (an engineering student): the emergence of these new Omicron sublineages feels like when you’re trying to do a problem set that claims to have five problems, but then each problem has several sub-problems, and those sub-problems themselves have more sub-problems. In the coming weeks, we’ll see just how much more transmissible Omicron can get.
There’s some good news, though: cases in some parts of the Northeast might be plateauing. It’s hard to tell for sure because of the aforementioned unreliable data, but wastewater data for the region (as well as for individual cities like Boston) seem to be leveling off; we’ll see next week if this trend continues.
BA.2 levels are particularly high (93% prevalence) in the New York/New Jersey region, and new sublineages have recently been identified in New York. Chart via the CDC.
As though it’s not already confusing enough to distinguish between Omicron BA.1 and BA.2, more sublineages have popped up in recent weeks as Omicron continues to spread and mutate. Here are two that I’m watching, though they don’t seem to be major causes for concern at this time.
BA.2 sublineages in New York
Last week, the New York State Department of Health announced that it has identified new sub-variants of BA.2, called BA.2.12 and BA.2.12.1, through testing and sequencing. The BA.2 lineage overall accounts for the vast majority of cases in New York, and these two new strains are causing over 90% of new cases in the central part of the state.
These two sublineages seem to be spreading even faster than original BA.2 in New York, with a growth advantage of about 25%—perhaps explaining in part why the state is once again seeing higher case rates than other parts of the country. It’s unclear so far whether these BA.2 offshoots will have any impact on severity or vaccine effectiveness; the health department is looking into this.
Also worth noting: New York has a more robust variant surveillance system than a lot of other states. It’s very possible that Omicron is mutating elsewhere in the country, too; but those potential sublineages haven’t been identified yet.
The number of cases so far may seem to be insignificant compared with the steep Omicron peak of the winter, but “we’re essentially back at levels of case rates back to the Delta wave,” said Eli Rosenberg, deputy director for science at the New York State Department of Health. “This would have been a very significant wave already by last year’s standards.”
XE recombinant in the U.K. and other countries
This new offshoot hasn’t been identified in the U.S. yet, but it deserves some attention. Essentially, BA.1 and BA.2 have combined—likely in regions or even in individual people that are experiencing simultaneous infections of both strains—and formed what scientists call a “recombinant” variant, with some genetic material from both. The BA.1/BA.2 conglomerate has been labeled XE.
According to research so far, XE may have a slight growth advantage over BA.2. The World Health Organization (WHO) estimated that XE is about 10% more transmissible than BA.2, but further study is needed to confirm this number. Over 600 XE cases have been identified in the U.K., according to TIME, along with smaller numbers in India, Thailand, and other countries.
Scientists aren’t particularly concerned about XE at this point because it hasn’t been spreading rapidly and outcompeting other variants, like the original Omicron did in the winter. But agencies like the U.K.’s Health Security Agency and the WHO are monitoring for any worrying signals.
In the past week (April 9 through 15), the U.S. reported about 220,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 31,000 new cases each day
67 total new cases for every 100,000 Americans
19% more new cases than last week (April 2-8)
In the past week, the U.S. also reported about 10,000 new COVID-19 patients admitted to hospitals. This amounts to:
An average of 1,400 new admissions each day
3.1 total admissions for every 100,000 Americans
1% more new admissions than last week
Additionally, the U.S. reported:
2,900 new COVID-19 deaths (0.9 for every 100,000 people)
100% of new cases are Omicron-caused; 86% BA.2-caused (as of April 9)
An average of 100,000 vaccinations per day (per Bloomberg)
New COVID-19 cases in the U.S. have gone up for the second week in a row, and the increase was sharper this week. While the daily average of new cases (about 31,000) remains low compared to the Omicron surge, this trend is still concerning—especially when factoring in all the at-home rapid tests that are going unreported right now.
Wastewater trends suggest that cases will continue rising in the coming weeks. Biobot’s dashboard suggests a national increase (most pronounced in the Northeast region), while about 60% of sites in the CDC’s network have reported increasing coronavirus levels in the last two weeks.
Newly hospitalized COVID-19 patients, an indicator that’s typically behind cases but more reliable, is also showing a small increase as of this week. This will be an important metric to watch in the next few weeks: will BA.2 strain hospitals the same way that Omicron BA.1 did in December and January?
BA.2, it’s important to note, is now causing the vast majority of new COVID-19 cases in the U.S. The CDC’s latest estimates suggested that this sublineage made up 86% of cases in the week ending April 9. And some parts of the country may be seeing further mutation of BA.2—more on that later in the issue.
The Northeast continues to be a leader in this surge, as shown by both the wastewater trends and case data. According to the April 14 Community Profile Report, states with the highest case rates in the last week include: Vermont, Washington D.C., Rhode Island, New York, Massachusetts, Alaska, New Jersey, Maine, Connecticut, and New Hampshire.
All of these states are seeing high transmission, according to the CDC’s old guidance. But the new guidance places most counties in these states in low or medium “community levels;” largely because hospitalizations—which, again, are a lagging indicator—haven’t started rising yet.
This week, Philadelphia became the first major U.S. city to once again require masks in public indoor spaces, in response to rising cases and hospitalizations. I hope to see other cities and localities follow Philadelphia’s lead, but I know current attitudes make this unlikely.
COVID-19 Data Dispatch 