Last week, several variant experts that I follow on Twitter (which I refuse to call by its new name, thanks) started posting about a new SARS-CoV-2 variant, first detected in Israel. They initially called it Omicron BA.X while waiting for more details to emerge about the sequence; it’s now been named BA.2.86.
Scientists and health officials are concerned about BA.2.86 because it has many mutations on its spike protein, showing significant deviation from other versions of Omicron. This variant evolved from an earlier Omicron strain (BA.2) rather than XBB, which is the primary lineage spreading across the world right now—and is the primary focus of booster development for this fall.
Here are two relevant threads with more info (the first for a more general audience, the second going into more details about mutations):
Quick summary of the "BA.X" variant that trackers are watching closely. Bear in mind, there are only a few sequences of it so far and it may not be able to compete with currently dominant variants and may not take off. But it's interesting and *potentially* concerning.
Virologists hypothesize that BA.2.86 may have evolved in someone with a chronic infection—essentially gaining more and more mutations as the same person stayed sick for many months. Similar hypotheses apply to Delta and Omicron, though it’s hard to get definitive answers without actually finding those patients.
Another reason for concern: as of today, BA.2.86 has been detected on three different continents. In addition to Israel, scientists have found it in Denmark and the U.S. Since most countries are not doing rigorous genomic surveillance these days, the cases found so far suggest that this variant is actually far more widespread; it just went undetected until now.
I’m keeping today’s post about BA.2.86 short due to the limited information we have so far. But I’d like to dive into it more next week. So, send me your questions about this variant or about genomic surveillance more broadly, and I will answer them in next Sunday’s newsletter.
In the past week (March 2 through 8), the U.S. officially reported about 170,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 24,000 new cases each day
52 total new cases for every 100,000 Americans
25% fewer new cases than last week (February 23-March 1)
In the past week, the U.S. also reported about 20,000 new COVID-19 patients admitted to hospitals. This amounts to:
An average of 2,800 new admissions each day
6.1 total admissions for every 100,000 Americans
13% fewer new admissions than last week
Additionally, the U.S. reported:
1,900 new COVID-19 deaths (270 per day)
90% of new cases are caused by Omicron XBB.1.5; 2% by XBB.1.5.1; 1% by CH.1.1 (as of March 11)
An average of 50,000 vaccinations per day
Following the same pattern we’ve seen for the last few weeks, COVID-19 spread is still on the decline nationally. Official case counts, hospital admissions, and wastewater surveillance data all continue to point in this direction.
This week, the decline in CDC-reported cases was sharper than it’s been in a couple of months (with 25% fewer cases reported than the prior week). But this may be due to reporting issues, rather than an actual change in transmission patterns: the CDC’s case trends page explains that Florida, Washington State, and Utah all did not report cases in the week ending March 8.
Still, I’m heartened by the fact that hospital admissions—which are reported more reliably—dropped by 13% this week, compared to smaller week-over-week changes over the last month. Wastewater surveillance data from Biobot also continue to show steady declines, though we’re still not close to the national lows observed during this time in 2021 and 2022.
Biobot’s data suggest declining surveillance in all four major regions of the country, with coronavirus levels in the Northeast now dropping below the Midwest, South, and West coast. Some individual counties in the Midwest are still reporting increased viral concentrations in their wastewater; I specifically noted Sheridan County and Teton County, Wyoming in Biobot’s data.
Omicron XBB.1.5 has been the dominant variant in the U.S. since mid-January, and we have yet to see a new subvariant rise to meaningfully compete with it. CH.1.1, which has driven increased transmission in other parts of the world, has remained under 2% of new cases nationally, per the CDC’s estimates.
The CDC’s latest variant update also breaks out XBB.1.5.1, an offshoot of XBB.1.5, at about 2% of new cases nationally. I have yet to see much discussion of this offshoot or how it differs from XBB.1.5; I’ll cover it more in future issues as we learn more. In addition, variant experts are keeping an eye on XBB.1.9, XBB.1.16, and other subvariants that have further mutated from the XBB lineage.
In his latest Substack newsletter, long-time COVID-19 commentator Eric Topol suggests that the U.S. might be in a welcome “break from COVID-19 waves.” He points to XBB.1.5’s dominance and the fact that its rise “was not associated with a surge of COVID-19 hospitalizations or deaths in the United States or elsewhere in the world” despite the subvariant’s increased capacity to spread.
At the same time, Topol explains the problem with our current “high baseline” of continued COVID-19 spread, which leads to continued severe cases among vulnerable people and the ongoing risk of Long COVID. He also explores the potential for another Omicron-like event, which would potentially cause another major surge. His article is helpful for understanding our current COVID-19 moment.
In NYC, where I live, COVID-19 case rates and test positivity are lower than they’ve been since early 2022—while still much higher than we saw last spring post-Omicron BA.1, or in spring 2021 as vaccines were widely rolled out. And the numbers are likely going to get more unreliable soon, as the city begins to wind down public testing sites.
As if BA.4 and BA.5 aren’t already enough to worry about: some COVID-19 experts are sounding the alarm about BA.2.75, a new version of Omicron that evolved out of BA.2.
This subvariant was first identified in India in late May, and has now been reported in the U.K., Germany, and several other countries, according to the World Health Organization. Scientists are concerned because it has new spike protein mutations that could heighten its ability to bypass immunity from past infections or vaccinations—including, potentially, from BA.4 or BA.5.
— World Health Organization (WHO) (@WHO) July 5, 2022
At least three BA.2.75 cases have been reported in the U.S. so far, according to a Friday press release from the surveillance company Helix. Two of these cases were on the West Coast, in Washington and California. These cases are currently lumped in with other versions of BA.2 on the CDC dashboard.
The information on BA.2.75 is fairly preliminary at this point; the WHO is monitoring it as an additional lineage of Omicron, not a separate variant of concern, and watching for new data. It’s unclear how competitive it might be with BA.5, now dominant in the U.S., but is worth keeping an eye on. As Dr. Katelyn Jetelina points out in a recent issue of Your Local Epidemiologist, the spread of BA.2.75 could further complicate fall booster shot plans.Â
BA.4 and BA.5 caused more than 20% of new COVID-19 cases nationwide in the week ending June 11, according to CDC estimates.
This week, I had a new story published at TIME’s online news site, explaining what Omicron BA.4 and BA.5 could mean for COVID-19 trends in the U.S.
The story makes similar points to my FAQ post on these subvariants from earlier in June: basically, BA.4 and BA.5 have evolved to get around antibodies from a prior coronavirus infection or vaccination, and the U.S. is likely to see a lot of reinfections from these subvariants—even among people who already had BA.1 or BA.2 earlier this year. BA.2.12.1 has mutated in a similar way, leading experts to suspect that one of these subvariants (or all three) will dominate the next phase of the pandemic.
When I talked to variant experts for my TIME story, I asked them for their thoughts on surveillance. “Is it getting harder to identify and track new linages like BA.4 and BA.5 as fewer people use PCR tests and more use at-home tests?” I asked. “What improvements or shifts would you like to see in surveillance?”
All three experts I spoke to had different perspectives, which I found interesting—and worth sharing in the COVID-19 Data Dispatch, since I wasn’t able to include this (somewhat wonkier) information in my TIME story.
Here’s what they said:
Marc Johnson, a microbiology and immunology professor at the University of Missouri who leads the state’s wastewater surveillance program, thinks that expanding wastewater monitoring is the way to go (though he admitted his bias, as someone who works in this area). “Sewershed monitoring is a really good way to track variants going forward,” he said. “It gives you a comprehensive view without costing you hundreds of thousands of dollars… or without having to sequence a thousand people.”
Shishi Luo, associate director of bioinformatics and infectious diseases at Helix (a genomics and viral surveillance company), is thinking about how to ensure her company consistently receives enough PCR test samples to get useful data from sequencing. At the moment, pharmacies and community testing sites are still providing enough samples that Helix has sufficient information to track variants, she said. But, anticipating that those numbers may dwindle, Helix is connecting with urgent care clinics and hospitals that do diagnostic testing. “I think those places will continue to collect samples and perform qPCR tests,” she said.
Paul Bieniasz, a professor at Rockefeller University who studies viral evolution, thinks that the current levels of surveillance are sufficient—at least, when it comes to policymaking and updating vaccines. “I would like to keep surveillance at a level such that such that we can have a pretty accurate picture about what’s going on,” he said. But he wants to prioritize “the really important things”: namely, understanding changes to vaccine effectiveness, which treatments to use, and identifying a new “major antigenic shift” like the one that produced Omicron as soon as it occurs.
“But it can always be better,” he said. “The more intense the surveillance, the more sensitive it is, and the earlier you detect things that might be of concern in the future.”
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.”
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.
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.
A moderate size BA.4/5 wave starting to slow in South Africa 🇿🇦 https://t.co/klBaulq3xL
— Meaghan Kall has moved to Bluesky (@kallmemeg) May 4, 2022
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.
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.
COVID-19 Data Dispatch 