Coronavirus levels in wastewater are now rising in all regions of the country, according to Biobot. Screenshot taken on April 9.
In the past week (April 2 through 8), the U.S. reported about 190,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 27,000 new cases each day
57 total new cases for every 100,000 Americans
5% more new cases than last week (March 26-April 1)
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
3.0 total admissions for every 100,000 Americans
10% fewer new admissions than last week
Additionally, the U.S. reported:
3,500 new COVID-19 deaths (1.1 for every 100,000 people)
100% of new cases are Omicron-caused; 72% BA.2-caused (as of April 2)
An average of 100,000 vaccinations per day (per Bloomberg)
After several weeks in a plateau, new COVID-19 cases in the U.S. are once again going up at the national level. The CDC reported an average of 27,000 new cases a day last week—less than one-tenth of what we saw during the Omicron surge, but still a notable uptick from the week prior.
National numbers of newly hospitalized patients and COVID-19 deaths are both still trending down; this is unsurprising, as trends in hospitalizations and deaths typically follow cases by several weeks.
That wastewater signal likely means that cases will keep going up in the next couple of weeks. BA.2 is a clear culprit for this: the more-contagious Omicron sublineage is now causing about three in four new COVID-19 cases in the U.S., according to the CDC’s latest estimates. BA.2’s dominance led the FDA to pull its emergency use authorization for Sotrovimab, a monoclonal antibody drug that works against Omicron BA.1—but not against BA.2,
As we’ve seen for the last couple of weeks, the Northeast continues to be a leader in case increases. Jurisdictions with the highest cases per capita in the week ending April 6 are Alaska, Vermont, Rhode Island, Washington, D.C., New York, Massachusetts, New Jersey, and Maine. All reported more than 100 new cases for every 100,000 residents, per the latest Community Profile report.
Under the CDC’s old community level guidance, all of these Northeast states (and Alaska) would be classified as seeing high transmission. But under the new, more lenient guidance, 99% of the country—including most counties in these states—are classified as “low” or “medium” community levels.
These lenient levels don’t account for warnings in our wastewater, not to mention under-testing as PCR sites close and at-home tests go unreported. As Katherine Wu wrote in The Atlantic this week, the U.S. may be facing a new surge, but it’s harder to accurately track COVID-19 now than it has been since spring 2020. Don’t let the low numbers fool you into thinking all is well.
BA.2 caused more than two-thirds of new COVID-19 cases in the Northeast in the week ending March 26, according to CDC estimates. It’s no coincidence that this region is also seeing cases start to tick up.
In the past week (March 26 through April 1), the U.S. reported about 180,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 26,000 new cases each day
55 total new cases for every 100,000 Americans
3% fewer new cases than last week (March 19-25)
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
3.3 total admissions for every 100,000 Americans
16% fewer new admissions than last week
Additionally, the U.S. reported:
4,400 new COVID-19 deaths (1.3 for every 100,000 people)
100% of new cases are Omicron-caused; 55% BA.2-caused (as of March 26)
An average of 90,000 vaccinations per day (per Bloomberg)
Nationwide, COVID-19 cases in the U.S. have reached a plateau. New cases decreased only 3% from the previous week to this week, following an 8% decrease the week before that. New hospitalizations and deaths are also declining slightly, approaching the same plateau pattern.
Wastewater is showing a similar pattern, too. The overall, national trend of coronavirus levels in wastewater has been in a plateau for a couple of weeks now, according to the Biobot dashboard. Regionally, the Northeast saw a slight uptick followed by an even slighter downturn, and the South may be seeing a slight uptick now.
BA.2, the Omicron sublineage that is more transmissible than the version of this variant that first reached us in the U.S., is now causing over half of new COVID-19 cases nationwide, according to CDC estimates. Two weeks ago, I wrote that 50% prevalence was a threshold for cases starting to increase in Europe; if the U.S. follows Europe (as we usually do), that means we’ll start seeing case increases here in the next week.
According to the CDC’s estimates, BA.2 is already causing almost 75% of new cases in the New England and New York/New Jersey regions. It’s unsurprising, then, that several Northeast states have reported case increases in the last week. According to the latest Community Profile Report, states that reported increases above 25% week-over-week include: Arizona, Alabama, Ohio, Delaware, North Carolina, Hawaii, Massachusetts, and New York.
New York City—an early hotspot for BA.2, as it was for the original Omicron strain in December—reported more than 100 cases for every 100,000 residents last week, according to both city data and the CDC’s figures.
Under the old CDC thresholds, this would have put the city in a “high transmission” zone, indicating that all residents should mask up in public, indoor spaces. However, the new CDC guidance places New York City in a “low” level, meaning masks are not recommended—a clear example of the lenience in this new guidance.
It’s good news that we’re not seeing a sharp BA.2-driven increase here in the U.S. yet, either within coronavirus levels in wastewater or within the case data. A BA.2 surge here may likely be a small bump rather than a huge wave. Still, the new lenience in safety measures—combined with federal funding running out for free testing, vaccinations, and other COVID-related coverage—is making me pretty nervous.
This week, I had a big retrospective story published at FiveThirtyEight: I looked back at the major metrics that the U.S. has used to track COVID-19 over the past two years—and how our country’s fractured public health system hindered our use of each one.
very excited to share this one: for @FiveThirtyEight, I looked back at the metrics that the U.S. has used to track COVID-19 over the last two years — and how our fractured public health system doomed each one. (1/5) https://t.co/wgzTYL8Dh9pic.twitter.com/sqxwIrufQT
The story is split into seven sections, which I will briefly summarize here:
Case counts, January to March 2020: Early on in the pandemic, the U.S. had a very limited picture of COVID-19 cases due to our very limited testing: after rejecting a test made by the WHO, the CDC made its own test—which turned out to have contamination issues, further slowing down U.S. testing. In early March 2020, for example, the majority of cases in NYC were identified in hospitals, suggesting that official counts greatly underestimated the actual numbers of people infected.
Tests administered, March to September 2020: Test availability improved after the first wave of cases, with organizations like the COVID Tracking Project keeping a close eye on the numbers. But there were a lot of challenges with the testing data (like different units across different states) and access issues for Americans with lower socioeconomic status.
Hospitalizations, October to December 2020: By late 2020, many researchers and journalists were considering hospitalizations to be a more reliable COVID-19 metric than cases. But it took a long time for hospitalization data to become reliable on a national scale, as the HHS launched a new tracking system in the summer and then took months to work out kinks in this system.
Vaccinations, January to June 2021: When the vaccination campaign started in late 2020, it was “tempting to forget about all other COVID-19 metrics,” I wrote in the story. But the U.S.’s fractured system for tracking vaccinations made it difficult to analyze how close different parts of the country were to prospective “herd immunity,” and distracted from other public health interventions that we still needed even as people got vaccinated.
Breakthrough cases, July to November 2021: The Delta surge caused widespread infections in people who had been vaccinated, but the CDC—along with many state public health agencies—was not properly equipped to track these breakthrough cases. This challenge contributed to a lack of good U.S. data on vaccine effectiveness, which in turn contributed to confusion around the need for booster shots.
Hospitalizations (again), December to January 2022: The Omicron surge introduced a need for more nuance in hospitalization data, as many experts asked whether COVID-19 patients admitted with Omicron were actually hospitalized for their COVID-19 symptoms or for other reasons. Nuanced data can be useful in analyzing a variant’s severity; but all COVID-related hospitalizations cause strain on the healthcare system regardless of their cause.
New kinds of data going forward: In our post-Omicron world, a lot of public health agencies are shifting their data strategies to treat COVID-19 more like the flu: less tracking of individual cases, and more reliance on hospitalization data, along with newer sources like wastewater. At this point in the pandemic, we should be fortifying data systems “for future preparedness,” I wrote, rather than letting the systems we built up during the pandemic fall to the wayside.
I did a lot of reporting for this piece, including interviews with some of the U.S.’s foremost COVID-19 data experts and communicators. As long as the piece is, there were a lot of metrics (and issues with these metrics) that came up in these interviews that I wasn’t able to include in the final story—so I wanted to share some bonus material from my reporting here.
Long COVID:
As I’ve discussed in previous issues, the U.S. has done a terrible job of collecting data on Long COVID. The NIH estimates that this condition follows a significant share of coronavirus infections (between 10% and 30%), but we have limited information on its true prevalence, risk factors, and strategies for recovery.
Here’s Dr. Eric Topol, the prolific COVID-19 commentator and director of the Scripps Research Translational Institute, discussing this data problem:
[Long COVID has] been given very low priority, very little awareness and recognition. And we have very little data to show for it, because it hasn’t been taken seriously. But it’s a very serious matter.
We should have, early on, gotten at least a registry of people —a large sample, hundreds of thousands of people prospectively assessed, like is being done elsewhere [in the U.K. and other countries]. So that we could learn from them: how long the symptoms lasted, what are the symptoms, what are the triggers, what can be done to avoid it, the role of vaccines, the role of boosters, all this stuff. But we have nothing like that.
The NIH’s RECOVER initiative may answer some of these questions, but it will take months—if not years—for the U.S. to actually collect the comprehensive data on Long COVID that we should have started gathering when the condition first began gaining attention in 2020.
Demographic data:
In the testing section of the story, I mention that the U.S. doesn’t provide much demographic data describing who’s getting tested for COVID-19. There is actually a little-known provision in the CARES Act that requires COVID-19 testing providers to collect certain demographic data from all people who seek tests. But the provision is not enforced, and any data that are collected on this subject aren’t making it to most state COVID-19 dashboards, much less to the CDC’s public data dashboard.
Here’s Dr. Ellie Murray, an epidemiologist at the Boston University School of Public Health, discussing why this is an issue:
We don’t collect reason for seeking a test. We don’t collect age, race, ethnicity, occupation of people who seek a test. Those kinds of things could provide us with some really valuable information about who is getting tested, when, and why—that could help us figure out, what are the essential occupations where people are having a lot of exposures and therefore needing to get a lot of tests? Or are there occupations where we’re seeing a lot of people end up in hospital, who have those occupations, but they’re not getting tests, because actually, the test sites are nowhere near where they need to work, or they don’t have the time to get there before they close.
And so we don’t really know who is getting tested, and that, I think, is a bigger problem, than whether the numbers that are being tested tell us anything about the trajectory of COVID. Because we have case data, and hospitalization data, and death data to tell us about the trajectory. And the testing could really tell us more about exposure, and concern, and access—if we collected some more of this data around who is getting tested and why.
Test positivity:
Speaking of testing: another metric that I didn’t get into much in the story was test positivity. Test positivity—or, the share of COVID-19 tests that return a positive result—has been used from the CDC to local school districts as a key metric to determine safety levels. (For more on this metric, check out my FAQ post from this past January.)
But even when it’s calculated correctly, test positivity faces the same challenges as case data: namely, bias in who’s getting tested. Here’s Lauren Ancel Meyers, director of the University of Texas at Austin’s COVID-19 Modeling Consortium, explaining this:
Test positivity is just as fraught [as cases]. It’s just as difficult, because you need to know the numerator and the denominator—what’s influencing the numerator and the denominator? Who is going to get tested, who has access to tests? … It used to be, at the very beginning [of the pandemic], nobody could get a test who wanted a test. And now, today, everybody has a test in their medicine cabinet, and they don’t get reported when they test. It’s different issues that have ebbed and flowed throughout this period.
Often, if you’re a good data analyst or a modeler, and you have all the information, you can handle those kinds of biases. But the problem is, we don’t know the biases from day to day. And so even though there are statistical tools to deal with incomplete bias, without knowing what those biases are, it’s very hard to do reliable inference, and really hard to understand what’s actually going on.
Genetic surveillance:
Also related to testing: genetic surveillance for coronavirus variants of concern. Genetic surveillance is important because it can help identify new variants that may be more transmissible or more likely to evade protection from vaccines. It can additionally help track the qualities of concerning variants once they are identified (if variant data is linked to hospitalization data, vaccination data, and other metrics—which is not really happening in the U.S. right now.)
Our current genetic surveillance systems have a lot of gaps. Here’s Leo Wolansky, from the Rockefeller Foundation’s Pandemic Prevention Institute (PPI), discussing how his organization seeks to address these challenges:
[We’re trying to understand] where our blind spots are, and the bias that we might experience with a lot of health system reporting. One of the things that PPI has been doing is identifying centers of excellence in different parts of the world that can improve the sequencing of new cases in underrepresented countries. And so for example, we’ve provided quite a bit of support to the folks in South Africa that ultimately rang the alarm on Omicron.
We’re also doing this by actually trying to systematically assess countries’ capacity for this type of genomic surveillance. So thinking about, how many tests have been recorded? What’s that test positivity rate? Do we have confidence in the basic surveillance system of the country? And then, do we also see enough sequences, as well as sequencing facility data, to demonstrate that this country can sequence and just isn’t doing enough—or cannot sequence because it needs foundational investment in things like laboratories and devices. We’ve been mapping this capacity just to make sure that we understand where we should be investing as a global community.
The Pandemic Prevention Institute is taking a global perspective in thinking about data gaps. But these gaps also exist within the U.S., as is clear when one looks at the differences in published coronavirus sequences from state to state. Some states, like Wyoming, Vermont, and Colorado, have sequenced more than 10% of their cumulative cases, according to the CDC. Others, like Oklahoma, Iowa, and South Dakota, have sequenced fewer than 3%. These states need additional investment in order to thoroughly monitor coronavirus transmission among their residents.
Cohort studies:
In a cohort study, researchers follow a group of patients over time in order to collect long-term data on specific health conditions and/or the outside factors that influence them. The U.S. has set up a few cohort studies for COVID-19, but they haven’t been designed or utilized in a way that has actually provided much useful data—unlike cohort studies in some other countries. (The U.K., for example, has several ongoing cohort studies collecting information on COVID-19 symptoms, infections in schools, seroprevalence, and more.)
Here’s Dr. Ellie Murray explaining the lost potential of these studies in the U.S.:
There are a number of existing cohort studies that have been asked or who asked to pivot to collecting COVID information and therefore collecting long-term COVID information on their cohorts. But there doesn’t seem to be any kind of system to [determine], what are the questions we need answered about COVID from these kinds of studies? And how do we link up people who can answer those questions with the data that we’re collecting here, and making sure we’re collecting the right data? And if this study is going to answer these questions, and this one is going to answer those questions—or, here’s how we standardize those two cohorts so that we can pull them together into one big COVID cohort.
And so, we end up in this situation where, we don’t know what percent of people get Long COVID, even though we’ve been doing this for over two years. We don’t even really know, what are all the different symptoms that you can get from COVID? … There are all these questions that we could be sort-of systematically working our way through, getting answers and using them to inform our planning and our response. [In addition to having] standardized questions, you also need a centralized question, instead of just whatever question occurs to someone who happens to have the funding to do it.
Excess deaths:
Excess deaths measure the deaths that occur in a certain region, over a certain period of time, above the number of deaths that researchers expect to see in that region and time period based on modeling from past years’ data. Excess deaths are the COVID-19 metric with the longest lag time: it takes weeks from initial infection for someone to die of the disease, and can take weeks further for a death certificate to be incorporated into the public health system.
Once that death information is available, however, it can be used to show the true toll of the pandemic—analyzing not just direct COVID-19 deaths, but also those related to isolation, financial burden, and other indirect issues—as well as who has been hit the hardest.
Here’s Cecile Viboud, a staff scientist at the NIH who studies infectious disease mortality, discussing this metric:
We’ve been using the excess death approach for a long time. It comes from flu research, basically starting in 1875 in the U.K. And it was used quite a lot during the 1918 pandemic. It can be especially good in examining historical records where you don’t have lab confirmation—there was no testing ability back in those days…
So, I think it’s kind of natural to use it for a pandemic like COVID-19. Very early on, you could see how useful this method was, because there was so little testing done. In March and April 2020, you see substantial excess, even when you don’t see lab-confirmed deaths. There’s a disconnect there between the official stats, and then the excess mortality… [We can also study] the direct effect of COVID-19 versus the indirect effect of the pandemic, like how much interventions affected suicide, opioids, death, accidents, etc. The excess approach is also a good method to look at that.
Viboud also noted that excess deaths can be useful to compare different parts of the U.S. based on their COVID-19 safety measures. For example, one can analyze excess deaths in counties with low vaccination rates compared to those with high vaccination rates. This approach can identify the pandemic’s impact even when official death counts are low—an issue that the Documenting COVID-19 project has covered in-depth.
The Northeast has seen a small uptick in coronavirus levels in its wastewater in recent weeks, followed by a plateau. Chart via Biobot Analytics.
In the past week (March 19 through 25), the U.S. reported about 190,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 27,000 new cases each day
58 total new cases for every 100,000 Americans
5% fewer new cases than last week (March 12-18)
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 1,800 new admissions each day
3.9 total admissions for every 100,000 Americans
21% fewer new admissions than last week
Additionally, the U.S. reported:
5,200 new COVID-19 deaths (1.6 for every 100,000 people)
100% of new cases are Omicron-caused; 35% BA.2-caused (as of March 19)
An average of 100,000 vaccinations per day (per Bloomberg)
New COVID-19 case numbers for the U.S. overall are still decreasing, according to the CDC’s data. But the drop from the previous week’s cases to this week’s cases (about 5%) is lower than any week-over-week change since Omicron peaked in January, suggesting that we’re heading for a plateau—if not a new increase.
Last week, I discussed a potential new surge in the U.S. driven by the Omicron sublineage BA.2, which is more transmissible than the version of Omicron we faced a couple of months ago. BA.2 caused about 35% of new COVID-19 cases nationwide in the week ending March 19, according to CDC estimates, up from 22% in the prior week.
As BA.2 slowly outcompetes the other Omicron sublineages in the U.S., we also continue to see case upticks in some parts of the country. States that reported case increases in the last week include Arkansas, Kentucky, Maine, New York, Colorado, Massachusetts, and Vermont, according to the March 24 Community Profile Report. (Arkansas and Kentucky reported week-over-week increases above 25%, while the other states here reported increases above 10%.)
Wastewater data align somewhat with these case increases. Biobot’s tracker shows a slight uptick (followed by a plateau) in coronavirus levels in the Northeast’s wastewater, at a regional level, along with plateaus in other parts of the country. And about 40% of sites in the CDC’s national wastewater network have reported increases over the last two weeks—though the CDC’s data are difficult to interpret, as this tracker doesn’t provide context on actual wastewater levels at each site.
To be clear, it’s good news that we aren’t seeing major case increases yet, just some small upticks. At the same time, numbers of newly hospitalized COVID-19 patients and deaths are dropping to levels not seen since last summer; this week, about 750 people died of the disease each day, according to the CDC—the first time this number has been under 1,000 in several months.
The 7-day avg for new hospital admissions in the U.S. (confirmed + suspected COVID) is now also at an all-time low pic.twitter.com/99LPzBCYKw
In a recent TIME article, several experts suggested that vaccines plus lingering immunity from the Omicron wave in December and January may protect the U.S. from a major surge with BA.2. Still, with safety measures dropping across the country, in the event that we do see a major new surge (from BA.2 or otherwise), we won’t be prepared to curb virus transmission in a meaningful way.
BA.2 caused about one in four U.S. COVID-19 cases in the week ending March 12, according to CDC estimates.
Two years into the pandemic, we now know some basic truisms about the coronavirus. For example: outdoor events are always safer than indoor events; older age is the most significant risk factor for severe symptoms; hospitalization trends typically follow case trends by a couple of weeks; and whenever Europe has a new surge, the U.S. is likely to also see a surge in the next month or so.
That last truism is particularly relevant right now, because Europe is experiencing a new surge. Cases are increasing in the U.K., Germany, the Netherlands, and many other countries. The new surge is likely due to European leaders’ decisions to end all COVID-19 safety measures in their countries, combined with the rise of Omicron sublineage BA.2.
As BA.2 prevalence increases here in the U.S.—and our leaders also end safety measures—we seem poised to follow in Europe’s footsteps once again. But a BA.2 surge is likely to look different from the intense Omicron surge that we experienced in December and January, in part because of leftover immunity from that Omicron surge.
Let’s go over what we know about BA.2, and what might happen in the next few weeks.
What is BA.2?
It’s important to note that this isn’t a new variant, at least not compared to the original Omicron strain. As I noted in a FAQ post about this strain back in January, South African scientists who originally characterized Omicron in November 2021 identified three sub-lineages: BA.1, BA.2, and BA.3.
BA.1 spread rapidly through the world, driving the surge that we experienced here in the U.S. in December through February. But BA.2, it turns out, is actually more transmissible than BA.1—allowing it to now outcompete that strain and contribute to case increases in countries that already faced major BA.1 surges.
How does BA.2 differ from BA.1, or original Omicron?
The main difference between these two strains is that BA.2 is more contagious: scientists estimate that BA.2 is about 30% more transmissible than other Omicron strains, if not more. (Note that this is a smaller difference than Omicron’s advantage over Delta and other earlier variants.)
In a recent report, the U.K. Health Security Agency estimated that someone infected with BA.2 would infect about 13.6% of their households and 5.3% of contacts outside of their households, compared to 10.7% of households and 4.2% outside contacts for other Omicron strains. The modest difference between these rates demonstrates why BA.2 is not outcompeting other Omicron strains as quickly as Omicron outcompeted Delta a couple of months ago.
Another notable feature of BA.2 is that, unlike BA.1, it can’t be identified with a PCR test. BA.1 has a mutation called S drop-out, which causes a special signal in PCR test results, allowing the variant to be flagged without sequencing; BA.2 doesn’t have this mutation. To be clear, a PCR test will still return a positive result for someone who is infected with BA.2—it’ll just take an additional sequencing step to identify that they have this particular strain.
Finally, one major challenge during the Omicron BA.1 surge has been that two of the three monoclonal antibody treatments used in the U.S. did not work well for people infected with Omicron. BA.2 may exacerbate this challenge, as some studies have suggested that the third treatment—called sotrovimab—continued working against BA.1, but may not hold up against BA.2. Luckily though, Eli Lilly (which developed one of the treatments that failed for BA.1) has produced an updated monoclonal antibody cocktail that does work for both Omicron strains.
How is BA.2 similar to BA.1, or original Omicron?
Two major pieces of good news here: 1) our existing COVID-19 vaccines work similarly well against BA.2 as they do against BA.1, and 2) prior infection with BA.1 seems to be protective against infection with BA.2.
Essentially, studies are showing that the two strains are close enough in their genetic profiles that antibodies from a BA.1 infection will provide some immunity against a BA.2 infection. And the same thing goes for vaccination, at least when it comes to protection against severe disease. A recent CDC study showed that, even during the Omicron surge, COVID-19 patients who had received three vaccine doses were far less likely to require mechanical ventilation or die from the disease than those who weren’t vaccinated.
There’s a flip side to this, though: for both BA.1 and BA.2, prior infection with a previous variant is not very protective against an Omicron infection. CDC seroprevalence data suggest that between 40% and 45% of Americans got infected with BA.1 during the winter surge; this means the remaining 55% to 60% of the population is susceptible to BA.2. Vaccines protect against severe disease and death from BA.2, but they don’t protect against BA.2 infection to the degree that they did against past variants.
This means that in terms of protection against infection, populations with high rates of vaccination or prior infection remain essentially naive to it. Though vaccines and prior infections still protect from severe disease and death (thanks to T-cell protection). 3/ pic.twitter.com/gmwlk2l7ZV
— Prof Francois Balloux (@BallouxFrancois) March 19, 2022
BA.2 and BA.1 are also similar in their severity. Both strains are less likely to cause severe disease than Delta; BA.1 had a 59% lower risk of hospital admission and 69% lower risk of death than Delta in the U.K., according to a new paper published this week in the Lancet.
It’s important to remember, however, that Delta was actually more severe than other variants that preceded it. As a result, “Omicron is about as mild/severe as early 2020 SARSCoV2,” wrote computational biologist Francois Balloux in his Twitter thread (referring to both BA.1 and BA.2).
What are the warning signs for a BA.2 surge in the U.S.?
First of all, many U.S. experts consider case increases in Europe to be an early indicator of increases in the U.S. As I said at the top of the post, Europe is seeing a surge right now, and many of the countries reporting case increases have estimated over 50% of their cases are caused by BA.2.
In the U.S., our BA.2 levels are lower: the CDC’s most recent estimates suggested that BA.2 was causing about 23% of new cases nationwide as of March 12. If BA.2 continues growing at the same rate we’ve seen in recent weeks, we have one or two more weeks before this variant hits 50% prevalence in the U.S.
“The tipping point seems to be right around 50%,” Keri Althoff, an epidemiologist at Johns Hopkins Bloomberg School of Public Health, told CNN. “That’s when we really start to see that variant flex its power in the population” as far as showing its severity.
At the same time, several Asian countries are also seeing major BA.2 surges at the moment. For example, Hong Kong was able to deal with early Omicron cases earlier in the winter, former COVID Tracking Project lead Erin Kissane pointed out in her Calm Covid newsletter; but now, the territory is facing a terrible BA.2 wave, driving what is now the world’s highest case fatality rate.
NEW: I’m not sure people appreciate quite how bad the Covid situation is in Hong Kong, nor what might be around the corner.
First, an astonishing chart.
After keeping Covid at bay for two years, Omicron has hit HK and New Zealand, but the outcomes could not be more different. pic.twitter.com/1Ol4HHs9kT
Here in the U.S., we’re also seeing warning signals in the form of rising coronavirus levels in wastewater. (Wastewater is considered an early indicator for surges, because coronavirus material often shows up in sewer systems before people begin to experience symptoms or get tested.) About one-third of sewershed collection sites in the CDC’s wastewater monitoring network are reporting increased virus prevalence in the two-week period ending March 15.
The CDC wastewater data must be interpreted cautiously, however, as this surveillance network is biased towards states like Missouri and Ohio, which have over 50 collection sites included in the national network. 12 states still do not have any collection sites in the network at all, while 23 states have fewer than 10. This recent Bloomberg article includes more context on interpreting wastewater data.
New York City is one place that’s reporting increased viral levels in wastewater, at the same time as the city health department reports that case numbers have plateaued—or may even be ticking up. An excellent time to loosen all mask and vaccination requirements, am I right?
What might a BA.2 surge in the U.S. look like?
Between the warning signals from Europe and the newly-lax safety measures throughout the U.S., it seems very likely that we will see a BA.2 surge in the coming weeks. The bigger question, though, is this surge’s severity: to what extent will it cause severe disease and death?
As I mentioned above, estimates suggest that about 40% to 45% of Americans have some Omicron antibodies from an infection earlier in the winter. At the same time, about 65% of the population is fully vaccinated and 45% of those fully vaccinated have received a booster shot, according to the CDC.
That’s a lot of people who are protected against severe COVID-19 symptoms, if they get infected with BA.2. But the U.S. has lower vaccination coverage than other countries, particularly when it comes to boosters. For example, in the U.K., 86% of eligible people are fully vaccinated and 67% are boosted, according to CNN. These lower vaccination rates contributed to the U.S.’s high mortality rate during the Omicron surge compared to other wealthy countries.
While the vaccines offer great protection, the U.S. appears to have given up on many other COVID-19 safety measures, like masks, social distancing, and limits on in-person gatherings. Without reinstating some of these measures, we would essentially be left without any tools to slow down the spread of BA.2; and even if some states and cities put safety measures in place, they’ll likely face more pushback now than they did in earlier surges.
To quote from Kissane’s newsletter:
In practical terms, with work and school happening in-person and without high-filtration (or any) masks or serious ventilation requirements in the US and most of Europe, governments in North America and Europe have made increased covid exposure essentially mandatory for most citizens.
I want to emphasize that for most vaccinated people, this increased risk probably won’t be a huge deal even if BA.2 causes a new case surge—they’ve either already racked up enough immunity to fight off BA.2 or they’ll be sick for a week.
One big caveat to this, though: we don’t have great data yet on how Omicron (or BA.2 specifically) might contribute to Long COVID rates; collecting data on this condition is very challenging and takes a lot of time. Studies suggest that vaccination reduces an individual’s risk of long-term symptoms if they get infected, but it does not eliminate this risk.
What can you do to prepare for this potential surge?
Here are a few things that I’m doing to prepare for a potential BA.2 surge in the coming weeks:
Promoting vaccination—particularly booster shots—to family members and friends.
Stocking up on good-quality masks (i.e. N95s and KN95s) and rapid tests. (Reminder, order a new round of free tests from covidtests.gov if you haven’t yet!)
Researching my options for COVID-19 treatments (antiviral pills and monoclonal antibodies) in the event that I get infected.
Getting tested frequently, particularly before attending indoor events (such as gathering with a few other friends, or going out to a movie theater.)
Watching wastewater and case trends in my area, and preparing to cut down on riskier behaviors if(/when) cases start rising.
I don’t know what BA.2 will mean for the US.
I do know this:
It hinges on vaccination/booster rates *now*.
So: 👆+
4th doses & Evusheld for immunocompromised ASAP, if not done.
Know where you’d get Paxlovid & Sotrovimab.
Order rapids now.
Get N95s or best possible now.
— Jeremy Faust MD MS (ER physician) (@jeremyfaust) March 16, 2022
As always, if you have any COVID-19 questions (about BA.2 or otherwise) that you’d like me to address, please reach out.
As COVID-19 safety measures are lifted and agencies move to an endemic view of the virus, I’m thinking about my shifting role as a COVID-19 reporter. To me, this beat is becoming less about reporting on specific hotspots or control measures and more about preparedness: what the U.S. learned from the last two years, and what lessons we can take forward—not just for the future COVID-19 surges that are almost certainly coming, but also for future infectious disease outbreaks.
To that end, I was glad to see the Biden administration release a new COVID-19 plan focused on exactly this topic: preparedness for new surges, new variants, and new infectious diseases beyond this current pandemic.
From the plan’s executive summary:
Make no mistake, President Biden will not accept just “living with COVID” any more than we accept “living with” cancer, Alzheimer’s, or AIDS. We will continue our work to stop the spread of the virus, blunt its impact on those who get infected, and deploy new treatments to dramatically reduce the occurrence of severe COVID-19 disease and deaths.
The Biden plan was released last week, in time with the president’s State of the Union address. I read through it this morning, looking for goals and actions connected to data collection and reporting.
Here are a few items that stuck out to me, either things that the Biden administration is already doing or should be doing:
Improving surveillance to identify new variants: The U.S. significantly improved its variant sequencing capacity in 2021, multiplying the number of cases sequenced by more than tenfold from the beginning to the end of the year. But the new Biden plan promises to take these improvements further, by adding more capacity for sequencing at state and local levels—and, crucially, “strengthening data infrastructure and interoperability so that more jurisdictions can link case surveillance and hospital data to vaccine data.” In plain language, that means: making it easier to track breakthrough cases (which I have argued is a key data problem in the U.S.).
Expanding wastewater surveillance:As I’ve written before, in the current national wastewater surveillance network, some states are very well-represented with over 50 collection sites; while other states are not included in the data at all. The Biden administration is committed to bring more local health agencies and research institutions into the surveillance network, thus expanding our national capacity to get early warnings about surges.
Standardizing state and local data systems: I’ve written numerous times that the U.S. suffers from a lack of standardization among its 50 different states and hundreds of local health agencies. According to the new plan, the Biden administration plans to facilitate data sharing, aggregating, and analyzing data across state and local agencies—including wastewater monitoring and other potential methods of surveillance that would provide early warnings of new surges. This would be huge if it actually happens.
Modernize the public health data infrastructure: One thing that could help health agencies better coordinate and share data: modernizing their data systems. That means phasing out fax machines and mail-in reports (which, yes, some health departments still use) and investing in new electronic health record technologies, while hiring public health workers who can manage such systems.
Use a new variant playbook to evaluate new virus strains: Also in the realm of variant preparedness, the Biden administration has developed a new “COVID-19 Variant Playbook” that may be used to quickly determine how a new variant impacts disease severity, transmissibility, vaccine effectiveness, and other factors. The new playbook may be used to quickly update vaccines, tests, and treatments if needed, by working in partnership with health systems and research institutions.
Collecting demographic data on vaccinations and treatments: The Biden plan boasts that, “Hispanic, Black, and Asian adults are now vaccinated at the same rates as White adults.” However, CDC data shows that this trend does not hold true for booster shots: eligible white Americans are more likely to be boosted than those in other racial and ethnic groups. The administration will need to continue collecting demographic data to identify and address gaps among vaccinations and treatments; indeed, the Biden plan discusses continued efforts to improve health equity data.
Tracking health outcomes for people in high-risk settings: Along with its health equity focus, the Biden plan discusses a need to better track and report on health outcomes in nursing homes, other long-term care facilities, and other congregate settings like correctional facilities and homeless shelters. Congregate facilities continue to be major COVID-19 hotspots whenever there’s a new outbreak, so improving health standards in these settings should be a major priority.
Studying and combatting vaccine misinformation, vaccine safety: The new plan acknowledges the impact of misinformation on vaccine uptake in the U.S., and commits the Biden administration to addressing this trend. This includes a Request for Information that will be issued by the Surgeon General’s office, asking researchers to share their work on misinformation. Meanwhile, the administration will also continue monitoring vaccine safety and reporting these data to the public.
Test to Treat: One widely publicized aspect of the Biden plan is an initiative called “Test to Treat,” which would allow people to get tested for COVID-19 at pharmacies, health clinics, long-term care facilities, and other locations—then, if they test positive, immediately receive treatment in the form of antiviral pills. If this initiative is widely funded and adopted, the Biden administration should require all participating health providers to share testing and treatment data. This would allow researchers to evaluate whether this testing and treatment rollout has been equitable across different parts of the country and minority groups.
Website for community risk levels and public health guidance: The Biden plan includes the launch of a government website “that allows Americans to easily find public health guidance based on the COVID-19 risk in their local area and access tools to protect themselves.” The CDC COVID-19 dashboard was recently redesigned to highlight the agency’s new Community Level guidance, which is likely connected to this goal. Still, the CDC dashboard leaves much to be desired when it comes to comprehensive information and accessibility, compared to other trackers.
A new logistics and operational hub at HHS: In the last two years, the Department of Health and Human Services (HHS) built up an office for coordinating the development, production, and delivery of COVID-19 vaccines and treatments. The new Biden plan announced that this office will become a permanent part of the agency, and may be used for future disease outbreaks. At the same time, the Biden administration has added at-home tests, antiviral pills, and masks to America’s national stockpile for future surges; and it is supporting investments in laboratory capacity for PCR testing.
Tracking Long COVID: Biden’s plan also highlights Long COVID, promoting the need for government efforts to “detect, prevent, and treat” this prolonged condition. The plan mentions NIH’s RECOVER initiative to study Long COVID, discusses funding new care centers for patients, and proposes a new National Research Action Plan on Long COVID that will bring together the HHS, VA, Department of Defense, and other agencies. Still, the plan doesn’t discuss actual, financial support for patients who have been out of work for up to two years.
Supporting health and well-being among healthcare workers: The new Biden plan acknowledges major burnout among healthcare workers, and proposes a new grant program to fund mental health resources, support groups, and other systems of combatting this issue. Surveying healthcare workers and developing systematic solutions to the challenges they face could be a major aspect of preparing for future disease outbreaks. The Biden plan also mentions investing in recruitment and pipeline programs to support diversity, equity, and inclusion among health workers.
More international collaboration: The new Biden plan also focuses on international aid—delivering vaccine donations to low-income nations—and collaboration—improving communication with the WHO and other global organizations that conduct disease surveillance. This improved communication may be especially key for identifying and studying new variants in a global pandemic surveillance system.
This week, a group of experts—including some who have advised the Biden administration— followed up on the Biden plan with their own plan, called “A Roadmap for Living with COVID.” The Roadmap plan also emphasizes data collection and reporting, with a whole section on health data infrastructure; here, the authors emphasize establishing centralized public health data platforms, linking disparate data types, designing data infrastructure with a focus on health equity, and improving public access to data.
Both the Biden administration’s plan and the Roadmap plan give me hope that U.S. experts and leaders are thinking seriously about preparedness. However, simply releasing a plan is only the first step to making meaningful changes in the U.S. healthcare system. Many aspects of the Biden plan involve funding from Congress… and Congress is pretty unwilling to invest in COVID-19 preparedness right now. Just this week, a $15 billion funding plan collapsed in the legislature after the Biden administration already made major concessions.
Readers, I recommend calling your Congressional representatives and urging them to support COVID-19 preparedness funding. You can also look into similar measures in your state, city, or other locality. We need to improve our data in order to be prepared for future disease outbreaks, COVID-19 and beyond.
In the past week (March 5 through 11), the U.S. reported about 260,000 new COVID-19 cases, according to the CDC. This amounts to:
An average of 37,000 new cases each day
79 total new cases for every 100,000 Americans
29% fewer new cases than last week (February 26-March 4)
In the past week, the U.S. also reported about 22,000 new COVID-19 patients admitted to hospitals. This amounts to:
An average of 3,100 new admissions each day
6.6 total admissions for every 100,000 Americans
28% fewer new admissions than last week
Additionally, the U.S. reported:
8,200 new COVID-19 deaths (2.5 for every 100,000 people)
100% of new cases are Omicron-caused; 12% BA.2-caused (as of March 5)
An average of 100,000 vaccinations per day (per Bloomberg)
Note: I’m shifting the format of these National Numbers posts to focus more on hospitalizations and wastewater, as case data become both less reliable and less available in many parts of the U.S.
Overall, new COVID-19 cases are continuing to fall across the U.S. The country reported about 37,000 new cases a day last week, according to the CDC, compared to ten times that number in early February.
Case numbers have become less reliable lately as testing sites close and people are redirected to use at-home rapid tests, which are generally not reported. Still, we’re seeing a similar trend in new COVID-19 patients admitted to hospitals: both new cases and new admissions dropped almost 30% last week from the week prior.
More than 98% of the U.S. population now lives in a location with a low or medium COVID-19 Community Level, according to the CDC. But a few places did see case increases last week: these include Nebraska, Kentucky, Alaska, and Delaware, according to the March 10 Community Profile Report.
BA.2, the Omicron sister variant that is even more transmissible than the original version of this strain, is slowly gaining ground in the U.S.: it’s gone from causing an estimated 1% of cases in the first week of February to 12% in the first week of March, according to the CDC’s modeling.
It hasn’t impacted case trends here yet, but deserves close attention in the coming weeks and months. Gothamist has a helpful article about BA.2’s potential impact in New York, where the variant’s prevalence in wastewater is doubling statewide every two weeks.
Meanwhile, several European countries—including the U.K., Germany, the Netherlands, and others—reported case increases this week. This is likely due to ending pandemic safety measures, Omicron gaining its second wind, or some combination of the two; regardless, it doesn’t bode well for the U.S., which is also ending pretty much all pandemic safety measures.
This week, the CDC added wastewater tracking to its COVID-19 data dashboard. Wastewater has been an important COVID-tracking tool throughout the pandemic, but it gained more public interest in recent months as Omicron’s rapid spread showed the utility of this early warning system. While the CDC’s new wastewater tracker offers a decent picture of national COVID-19 trends, it’s basically useless for local data in the majority of states.
Wastewater, as you might guess from the name, is water that returns to the public utility system after it’s been used for some everyday purpose: flushing a toilet, bathing, washing dishes, and so forth. In wastewater surveillance, scientists identify a collection point in the sewer system—either beneath a specific building or at a water treatment plant that handles sewage from a number of buildings. The scientists regularly collect wastewater samples from that designated point and test these samples for COVID-19 levels.
When someone is infected with the coronavirus, they are likely to shed its genetic material in their waste. This genetic signal shows up in wastewater regardless of people’s symptoms, so a wastewater sample may return a positive result for the coronavirus earlier than other screening tools like rapid antigen tests. And, because wastewater samples are typically collected from public sewer networks, this type of surveillance provides information for an entire community—there’s no bias based on who’s able to get a PCR or rapid test.
Scientists and organizations who utilize wastewater testing consider it an early warning system: trends in wastewater often precede trends in reported COVID-19 cases. For example, the coronavirus RNA levels identified in Boston’s wastewater shot up rapidly before Boston’s actual Omicron case numbers did, then also went down before case numbers did. Similarly, Missouri’s wastewater surveillance system—which includes genetic sequencing for variants—identified Delta cases last summer weeks before PCR testing did.
Wastewater surveillance is also a popular strategy for colleges and universities, which can set up collecting sites directly underneath student dormitories. Barnard College, where I went to undergrad, is one school that’s employed this strategy. At one point in the fall 2021 semester, the college instructed students living in the Plimpton residence hall (where I lived as a sophomore!) to get individual PCR COVID-19 tests because the wastewater surveillance program had found signals of the virus under their dorm.
The CDC has been coordinating wastewater surveillance efforts since September 2020, Dr. Amy Kirby, team lead for the National Wastewater Surveillance System, said during a CDC media briefing on Friday. “What started as a grassroots effort by academic researchers and wastewater utilities has quickly become a nationwide surveillance system with more than 34,000 samples collected representing approximately 53 million Americans,” Kirby said.
It’s a little unclear why it took the CDC so long to set up a dashboard with this wastewater data when surveillance efforts have been underway for a year and a half. Still, many researchers and reporters are glad to see the agency finally publishing this useful information. The dashboard represents wastewater collection sites as colored dots: blue dots indicate that coronavirus RNA levels have dropped at this site in the last two weeks; yellow, orange, and red dots indicate RNA levels have risen; and gray dots indicate no recent data. You can download data from a dropdown beneath the dashboard and on the CDC’s data portal site.
“More than 400 testing sites around the country have already begun their wastewater surveillance efforts,” Kirby said at the media briefing. But she failed to mention that, out of these sites—the actual total is 471, according to the CDC dashboard—more than 200 are located in just three states: Missouri, Ohio, and Wisconsin. Missouri, with 80 sites, has a long-established system to monitor wastewater, through a collaboration between state agencies and the University of Missouri. Ohio has 71 sites of its own, while Wisconsin has 61.
After these Midwest wastewater powerhouses, other states with a relatively high number of collection sites include North Carolina with 38, Texas with 35, New York with 32, Utah with 31, Virginia with 29, Colorado with 21, and California with 17. No other state has more than 10 wastewater collection sites, and 18 states do not have any wastewater collection sites at all.
So, the CDC dashboard is pretty useful if you live in one of these ten states with a high number of collection sites. Otherwise, you just have to… wait for more sites in your area to get added to the dashboard, I guess? (Kirby did say during the media briefing that several hundred more collection sites are in development.) Even within the states that are doing a lot of wastewater surveillance, though, reporting is uneven at more local levels; for instance, many New York sites are concentrated in New York City and surrounding suburbs.
In this way, biased wastewater surveillance coverage in the U.S. echoes biased genetic sequencing coverage, an issue I’ve written about many times before. (See the genetic surveillance section of this post, for example.) Some states, like California, New York, and others with high-tech laboratories set up for sequencing, have identified variants for a much higher share of their COVID-19 cases than states with fewer resources.
The CDC gives wastewater treatment plants, local health departments, and research laboratories the ability to join its national surveillance network. But again, this is much easier for institutions in some places than others. Consider the resources available for wastewater sampling in New York City compared to in rural parts of the Midwest and South.
In addition, for places that do have robust wastewater surveillance systems, there are some caveats to the data, the CDC expert told reporters. Data may be hard to interpret “in communities with minimal or no sewer infrastructure and in communities with transient populations, such as areas with high tourism,” she said. “Additionally, wastewater surveillance cannot be used to determine whether a community is free from infections.”
If you’re looking for more wastewater data beyond the CDC tracker, here are two sources to check out:
Biobot’s Nationwide Wastewater Monitoring Network,which I included in last week’s Featured Sources: This wastewater epidemiology company collects samples from water treatment facilities across the country; their dashboard includes both estimates of coronavirus levels in the U.S. overall and estimates for specific counties in which data are collected. Biobot’s data are available for download on Github. (Interestingly, it seems that some of the counties included in Biobot’s dashboard are not currently included in the CDC’s dashboard; I’ll be curious to see if that changes in the coming weeks.)
COVIDPoops19 dashboard: This dashboard, run by researchers at the University of California Merced, provides a global summary of wastewater surveillance efforts. It includes over 3,300 wastewater collection sites tied to universities, public health agencies, and other institutions; click on individual sites to see links to dashboards, align with related news articles and scientific papers.
KFF updates COVID-19 vaccine monitor: The Kaiser Family Foundation released a new report in its COVID-19 vaccine polling project this week, marking over a year since the U.S.’s vaccine rollout began. Notable updates from this report include: people are worried about Omicron’s impact on the economy and healthcare system, less worried about its impact on them personally; vaccine uptake “inched up in January” with more people getting their first doses; and gaps in booster shot uptake echo early gaps in vaccine uptake, with white Americans getting boosted at higher rates than Black and Hispanic Americans.
New version of the COVID-19 circuit breaker dashboard: A few weeks ago, I shared a dashboard from emergency physician Dr. Jeremy Faust and colleagues that estimates which U.S. states and counties are facing hospitals operating at unsustainable levels. The dashboard has now been updated, with help from Kristen Panthagani, Benjy Renton, Bill Hanage, and others; this new version includes hospital capacity and related metrics over time for states and counties, estimates of open beds, ICU-specific data, and more.
Biobot’s Nationwide Wastewater Monitoring Network: If you’re looking to monitor COVID-19 levels in U.S. wastewater, Biobot’s dashboard is a great source. The wastewater epidemiology company collects samples from water treatment facilities across the country; their dashboard includes both estimates of coronavirus levels in the U.S. overall and estimates for specific counties in which data are collected. The data are available for download on Github. (H/t Data Is Plural.)
Prisoners released in 2020, DOJ: A new report from the U.S. Department of Justice includes data on state and federal prisons during the COVID-19 pandemic. The number of inmates in these facilities declined about 15% from the end of 2019 to the end of 2020, according to this report. A large cause for this decline was overall disruption in the court system, not compassionate releases due to the pandemic: there was a 40% decrease in prison admissions from 2019 to 2020.
Companies requiring COVID-19 vaccinations: ChannelE2E, a news site covering the IT industry, has compiled this comprehensive list of major companies requiring their employees to get vaccinated. The list includes about 50 companies, and is regularly updated with links to news sources discussing policy changes. (H/t Al Tompkins’ COVID-19 newsletter.)
COVID-19 Data Dispatch 