Two quick updates about the CDC’s surveillance efforts for COVID-19 and other diseases:
The CDC has provided a short-term wastewater surveillance contract to Verily, the biotech company that’s affiliated with Google, so that data collection can continue at about 400 sewage testing sites while a longer-term contract is in dispute. This temporary measure will help keep up surveillance during the winter respiratory virus season, though Verily still has a lot of logistical work ahead to actually start testing at sites where another company, Biobot Analytics, was previously in charge. (Verily will need to contact the sites, send them equipment, set up sample collection procedures, etc.) The CDC’s National Wastewater Surveillance System is also working on an updated COVID-19 dashboard, according to POLITICO’s story about the short-term contract. For more context, see my coverage of the contract switch and POLITICO’s previous reporting.
The CDC is expanding its testing program for international travelers arriving at U.S. airports, in a three-month pilot program for the winter virus season. This program, called the Traveler-Based Genomic Surveillance program, has screened travelers for coronavirus variants over the last two years, primarily using PCR tests among travelers who volunteer for a nasal swab. This winter’s pilot program expands surveillance in two ways: adding about 30 testing targets (including flu, RSV, other common diseases, and markers of antimicrobial resistance), and adding wastewater testing at three airports. One airport, San Francisco’s international airport, was already providing samples from plane sewage. See my article in Science News for more details.
Deaths in U.S. prisons: Throughout the pandemic, the UCLA COVID Behind Bars Data Project has been a leading source for data on COVID-19 cases and deaths in carceral settings. As COVID-specific data on prisons and jails have become more sporadic, the project recently turned its attention to overall mortality data in these settings. Last week, the UCLA team released a new dataset sharing all-cause deaths in prisons through 2020, which combines data from public reports and records requests. The full dataset is available on GitHub, and a summary of this project’s findings on all-cause mortality was published in the New York Times last weekend.
BIOFIRE syndromic trends data: BIOFIRE Diagnostics is a biotech company focused on diagnostic testing, offering tests for a variety of viruses, bacteria, and other pathogens. The company publishes anonymized test results from its labs on its Syndromic Trends dashboard; this dashboard is a helpful way to get an overview of test positivity for COVID-19 compared to other common diseases. (H/t Force of Infection.)
R&D roadmap for COVID-19 vaccines: The University of Minnesota’s Center for Infectious Disease Research and Policy has published a new report outlining the research and development steps needed for the world to produce coronavirus vaccines that are “broadly protective,” not tied to a specific variant. It includes recommendations for research on virology, immunology, and vaccine technologies, along with information on using animal models and guidance on vaccine policy. Related: the CDC’s Advisory Community on Immunization Practices met this week to discuss COVID-19 and other vaccines.
CDC reports on travel surveillance: Two new studies about COVID-19 among international travelers to the U.S. were published in this week’s CDC Morbidity and Mortality Weekly Report. Both studies describe results from the agency’s Travel Surveillance program, which is a collaboration with biotech company Ginkgo Bioworks and testing company XpresCheck. One report compares traveler test results from before and after the U.S. ended its pre-departure testing requirement for international flights, finding that travelers were much more likely to have COVID-19 after the requirement was lifted. The second report provides results from a pilot program testing airplane wastewater at JFK Airport; this report found that the vast majority of plane samples tested were positive for SARS-CoV-2, and researchers identified a variety of Omicron variants. More work is needed to really get airplane wastewater testing going in the U.S., but it’s good to see early results showing this program’s feasibility.
Early data from XBB.1.5 in NYC: Another notable study in CDC MMWR this week provided analysis from New York City’s health department on Omicron XBB.1.5. The subvariant was first identified in the city in October 2022 (though it may have evolved somewhere else), and quickly spread through the region; it accounted for 81% of sequenced COVID-19 test samples by early January. The NYC health department linked sequencing data with patient outcomes data, finding that people infected with XBB.1.5 were not significantly more likely to be hospitalized or to die from COVID-19 compared to those infected with other variants. In other words, XBB.1.5 appears to not cause more severe disease, based on this report.
Predicting COVID-19 cases based on wastewater results: One more newsworthy study to share this week: researchers at Hokkaido University developed a mathematical model to predict COVID-19 cases based on coronavirus concentration levels in Sapporo, Japan. I’m always on the lookout for studies like this, as wastewater data become increasingly important to track true infection numbers. (Here’s a prior example, from the University of Florida.) Of course, it’s worth noting that the Hokkaido researchers had consistent wastewater and case data from spring 2020 through 2022 to use for their model; for wastewater researchers working in the U.S. now, that consistency is often harder to achieve.
This week, I had a new article published in The Atlantic about how COVID-19 wastewater surveillance can be useful beyond entire sewersheds, the setting where this testing usually takes place. Sewershed testing is great for broad trends about large populations (like, an entire city or county), the story explains. But if you’re a public health official seeking truly actionable data to inform policies, it’s helpful to get more specific.
My story focuses on one wastewater testing setting that’s been in the news a lot lately: airplane bathrooms, from which researchers can identify new variants arriving with international travelers. But airplanes are far from the only place where specific wastewater surveillance can be valuable. Here are some of those other places, highlighting some information that I learned in reporting this story (but couldn’t fit in the final article).
K-12 schools
Early in the pandemic, colleges and universities became a hub for wastewater surveillance innovation. At campuses like Columbia University in NYC, researchers tested the sewage at individual dorms in order to determine exactly which students were getting sick—and take quick action, usually by requiring students at the infected dorm to get PCR-tested and quarantining the people who tested positive.
But the same technique can apply to schools with younger students. In late 2020, the University of California San Diego expanded its testing program to elementary schools, in an initiative called the Safer at School Early Alert System. The program started with 10 schools in the 2020-21 school year, then expanded to 26 in the 2021-22 year. Wastewater testing at specific sewershed points next to the schools led researchers to identify asymptomatic COVID-19 cases with high accuracy, program leader Rebecca Fielding-Miller told me.
The San Diego program isn’t alone: other public school systems have tried out building-level wastewater testing, usually in collaboration with nearby research groups. While the research projects tend to successfully show that wastewater surveillance can pick up infections, it’s challenging for school systems to get the funding to do these programs long-term. (Unlike universities, which are in total control of their funding, public schools need to rely on local governments).
As a consequence of these funding challenges, the San Diego program wasn’t renewed for the 2022-23 school year. “We really would have wanted to keep doing it, but funding ran out,” Fielding-Miller said.
Hospitals, other healthcare facilities
Much of the U.S.’s health strategy throughout the pandemic has focused on keeping hospitals from becoming overwhelmed—or at least helping hospitals weather COVID-19 surges. Wastewater surveillance can help accomplish this, by giving hospital administrators warnings about potential increased transmission; wastewater trends usually predict hospitalization trends by a week or more. And when wastewater surveillance is happening at hospitals themselves, these warnings can be really specific.
At NYC Health + Hospitals, the city’s public hospital system, administrators can get these warnings from wastewater testing at the system’s eleven hospitals. The surveillance program includes weekly tests for COVID-19, flu, and mpox (formerly called monkeypox), in collaboration with local researchers. The resulting data “gives us better situational awareness,” said Leopolda Silvera, a global health administrator at Health + Hospitals. If the health system notices a coming surge at one hospital, they can adjust resources accordingly—such as sending more staff to the emergency department.
The Health + Hospitals wastewater program has been running for about a year, Silvera said. At this point, it’s the only program she knows of that does building-level surveillance at hospitals. In the future, the hospital system might start testing for other pathogens and health threats like antimicrobial resistance.
Congregate facilities
Congregate facilities like nursing homes and senior living facilities can include a lot of vulnerable people who are at higher risk for severe COVID-19, all living in close quarters. As a result, this is another category of settings where it could be helpful to have building-level wastewater surveillance: facility administrators could learn quickly about upcoming surges and respond, by doing widespread PCR testing or instituting a temporary mask mandate.
The state of Maryland used to have a program doing exactly this, with a focus on correctional facilities throughout the state—particularly facilities housing the most vulnerable residents. The wastewater surveillance program ran through May 2022, at which point it “quietly ended,” according to local outlet the Maryland Daily Record. An initial $1 million in funding for wastewater testing in Maryland ran out; while the CDC National Wastewater Surveillance System picked up testing at wastewater treatment plants, no new entity was able to continue testing at the congregate living facilities.
According to the Daily Record, the building-level wastewater testing was incredibly helpful for informing COVID-19 measures at correctional facilities and helped keep cases down. I hope the Maryland program isn’t the last example we see of this testing in the U.S.
Large, communal workplaces
Early in the pandemic, some of the U.S.’s worst COVID-19 outbreaks happened at factories, particularly large food processing plants. People in these settings are often working in close quarters, easily able to infect each other—and when an outbreak happens, there are ramifications for both individual employees and the company’s business.
These large facilities could be another target for wastewater surveillance: if company administrators see a warning about rising COVID-19 from their buildings’ sewage, they could institute basic public health measures to curb the spread. Such is the strategy for some mine companies in rural Canada, which work with biotech company LuminUltra to test their wastewater. People often live and work at these sites, making them relatively closed settings for transmission.
At these locations, COVID-19 was previously “kind-of out of control, clinical testing was very reactive,” said Jordan Schmidt, director of product applications at LuminUltra. With wastewater testing, the mining companies can keep outbreaks “to a handful of people.” Fewer people get sick and there’s less interruption to business, he said.
Neighborhood-level testing
As public health agencies face lower budgets and overall lower awareness about COVID-19, some officials want to maximize their limited resources. If you only have the funding and staff for two mobile PCR testing sites this week, you’d want to make sure they go to a neighborhood where the testing would be most helpful, right?
The Boston Public Health Commission had this goal in mind when they launched a new neighborhood-level wastewater testing program, in collaboration with Biobot Analytics. The program includes testing twice a week at 11 sites across Boston, selected to provide good coverage of the city and also enable testing without too much disruption to traffic. While testing just started in January, the program is already helpful for identifying specific COVID-19 patterns, said Kathryn Hall, deputy commissioner for the health agency.
Boston’s program is focused on COVID-19 right now, but could expand to other diseases as needed, Hall said: “Now that we have the infrastructure in place, it allows us to be really be prepared and also to ask novel and interesting questions.”
Airplanes
Airplane surveillance fits into a slightly different category than the other settings I described here. When researchers test airplane wastewater, they aren’t seeking to get advanced warnings of new surges or inform public health policies. Instead, the goal is to track variants—with a focus on any new coronavirus mutations that might come into the U.S. from abroad. (Read the Atlantic story for more details on how this works!)
Other transportation hubs could be useful for tracking variants too, experts told me. This could mean large train stations, bus stations, shipping ports—any location that involves a lot of people moving from one place to another. After all, variants can evolve in the U.S. as easily as they can in other parts of the world.
Overall, the specific wastewater testing settings described here could be valuable pieces of expanding the U.S.’s overall surveillance network, along with the more-traditional sewershed testing. But all these testing sites need sustained funding to actually provide valuable data in the long run, something that could be in jeopardy as the federal public health emergency ends.
NIH launches at-home testing telehealth program: This week, the National Institutes of Health announced the first location for “Home Test to Treat,” a new program that will make it easier for people in vulnerable communities to receive Paxlovid after testing positive on at-home, rapid tests. The Biden administration first announced this program in September, but it’s formally launching now with Berks County, Pennsylvania as the first participating community. As Paxlovid shifts to a drug that must be privately purchased instead of provided for free by the federal government, more programs like this one will be needed to fill access gaps.
Study estimates global Long COVID prevalence: A large team of researchers, led by population health scientists at the University of Washington, conducted an extensive review of Long COVID symptoms. The analysis used 54 prior studies and two medical record databases, incorporating data from 1.2 million people in total. Overall, about 6% of patients reported at least one class of Long COVID symptoms three months after their initial infections, with the vast majority of cases occurring in people who had mild acute cases. The study was published in JAMA in October, but gained attention this week thanks to an article that its leading authors wrote in The Conversation.
China’s COVID-19 data are unreliable: It’s been about a month since China loosened its COVID-19 protocols in the wake of protests and contagious Omicron subvariants, and the country is now facing a massive surge—with as many as one million new cases a day according to some modeling estimates. Yet COVID-19 deaths reported in the country have been very low, fewer than five a day. This discrepancy suggests that China’s authorities are not correctly counting their COVID-19 deaths, while the country’s dismantled testing infrastructure has also led to less reliable case numbers. Officials from the World Health Organization have formally called on the country to “be more forthcoming with information” about its COVID-19 surge, reports Helen Branswell at STAT News.
CDC testing airplane wastewater on flights from China: In response to surveillance concerns, the CDC is working to test wastewater on flights arriving from China in select U.S. airports. This method is, of course, more efficient than testing every single traveler from the country in the interest of identifying any new variants that might arise. (Though it’s worth noting that some experts are skeptical about the potential of new variants arising in China.) Scientists from Concentric, a company that works with the CDC on traveler surveillance, previously talked about plane wastewater testing during our interview in November.
Race/ethnicity differences among child vaccination rates: Finally, a notable study in this week’s CDC Morbidity and Mortality Weekly Report: researchers at the CDC and collaborators examined vaccination rates among children ages five to 17 using data from the National Immunization Survey. They found vaccination coverage (with at least one dose) was highest among Asian children (at about 75%), followed by Hispanic or Latino children (49%), white children (45%), and Black children (43%). The researchers also noted differences among vaccination rates by other socioeconomic factors, and by parents’ mask-wearing habits.
In the program—which is a collaboration between the agency’s Travelers Health Branch, biotech company Ginkgo Bioworks, and airport wellness company XpresSpa Group—travelers at four major airports can volunteer to be swabbed right after they get off the plane. The travelers’ test results are pooled by country of origin, meaning that analysts at Ginkgo combine their samples and PCR-test them together.
In addition to test positivity, Ginkgo also sequences the samples to identify variants spreading around the world. The program has included about 60,000 people between November 2021 and September 2022, according to the CDC. It’s now expanding to add more airports, with the CDC and Ginkgo working together to select international flights that should be targeted for testing.
Earlier this week, I talked to bioinformatics experts Andy Rothstein and Casandra Philipson, who work on the CDC travel surveillance program at Concentric (Ginkgo’s COVID-19 testing initiative), to learn more about how the program works. Swati Sureka from Ginkgo’s communications team also took part in the interview.
Here are a few key insights I learned from the conversation:
Travelers who volunteer to be tested don’t actually receive individual results back from Ginkgo, due to the company’s pool testing method. But they receive free at-home tests that can provide individual results.
Despite a relatively small sample size, the surveillance program tends to match global coronavirus variant trends from GISAID (a global repository of variant sequences).
The CDC uses data from this program as a complementary surveillance system, in coordination with the agency’s domestic variant surveillance, wastewater testing, and other systems.
Along with expansions to more airports, the Concentric scientists are working on testing wastewater from airplanes as another way to pull COVID-19 data from international travelers.
The experts named BQ.1 and BQ.1.1 as the most concerning variants they’re following right now, though the program has also picked up XBB.
This interview has been lightly edited and condensed for clarity.
Betsy Ladyzhets: I wanted to start by asking about the backstory behind the traveler-based genomic surveillance program. I’ve read a bit about it, but I’m curious to hear from you guys about how it got started and choices that have been made as you’ve expanded the program.
Andy Rothstein: Gingko has long recognized that biosecurity is an integral component to the growing bio-economy, even before COVID. But when spring 2020 came around, Ginko as an organization rapidly responded with a large commitment to the sequencing effort across the country… That really showed that there was an opportunity to grow a biosecurity business unit within Gingko, which became Concentric.
We built a K through 12 testing program, where we implemented this novel approach of pooled testing. We could have kindergarteners basically swabbing their noses in the classroom, everyone could put it one tube, it simplified the process, and we were able to get those results out quickly. But we really recognized that this is just one interface that can be a part of the biosecurity infrastructure.
We saw that travelers were this really important sentinel for bringing in new things like variants or tracking lineages. And we could combine the pooled testing approach with our sequencing capability at Ginkgo. Then, we got in contact with XpresSpa [now XpresCheck], which was pivoting their business model as well, because no one was going in the airports for manicures and massages. We approached them, as well as the CDC branch that deals with travel histories, quarantining, and things like that. We came to them to launch a pilot program in September 2021 as a proof of concept to say like, “Is this an interface that could provide valuable insights for public health and the CDC?”
We didn’t really know whether or not the pilot would work out. But we were one of the first to detect Omicron coming into the country in November [2021]. The program has now expanded, as of August 2022, into a two year program. And we’ve consistently been able to show that there’s real value in early warning, early detection through this novel interface.
Casandra Philipson: Gingko is an organism engineering company, we know that we’re going to be living with engineered organisms in the future. I think, because of that our founders have always had this prerogative to be able to have an early warning system or anomaly detection system for threats, whether or not they’re natural or manmade. And we have a lot of really smart people who had previous experience, in, like, Department of Defense surveillance exercises in the past. So I think there was an interest in early warning signals.
It’s also hard to be able to do surveillance in other countries, at least at that early, pandemic phase. And so this was a really easy way to have access to things that were coming in from other countries, that we otherwise wouldn’t have had access to.
BL: Yeah, that makes a lot of sense. I’m curious, building off of that, how is the CDC using the data that comes out of this program? Is it mostly about new variants? Or are there other things they’re kind of doing with it?
AR: CDC has a lot of complimentary surveillance systems ongoing, especially for SARS-CoV-2, that they’ve built up, whether it be clinical or whether it be wastewater. This is a novel interface for them to be detecting new things coming into the country. And so we really help source and, I guess, consolidate what is coming into the country and whether or not it’s a bad thing, or part of the existing evolution of SARS-CoV-2.
We work in tandem with them weekly, to not only optimize this program, but also give insights into the data that’s coming out. The [travel surveillance page of the] COVID Data Tracker has been a good culmination of all of this work that we’ve been doing. We can broadcast that publicly and show, almost side-by-side, here’s what’s happening in United States; here’s what’s happening, potentially coming into the United States.
BL: I did want to ask more about that new page on the COVID tracker, because I’m curious what you would want the average viewer to take from those charts. What should folks be getting out of both the test positivity rate and the variants?
AR: The first part is this test positivity rate. What we’ve seen is that, as testing declines in countries around the world, whether that’d be the appetite for testing or the funding for testing, we have a new sentinel to see what, potentially, the positivity looks like around the world. There’s been a number of times that we, in our program, have matched positivity rates in a country of origin [for a group of travelers]. Then as testing stopped [in that country], we still are picking up a positivity rate. For the public that is looking at this chart, it’s an opportunity to see into the window: What’s the global picture of what’s coming into this country?
Positivity is the first lens of data. The next is that we actually sequence, and we are understanding what is the breakdown or the frequencies of different variants coming into the country. You can see how what’s happening on [the CDC’s U.S. variant surveillance page] is lining up with the frequencies in our program. And because we’re finding new things, we end up sort-of being ahead of the curve in terms of what those frequencies might end up being in the United States.
BL: So you’re talking about comparing the CDC’s variant proportions estimates versus the travel estimates.
AR: Yeah, exactly. And the wastewater estimates… Not everybody is necessarily going and seeking testing when they’re sick with COVID, they might be doing an at-home test. So we’re using all of those [data systems] in a complementary sense to find, like, what’s a holistic picture of the SARS-CoV-2 coming in and outside of the United States?
BL: I also wanted to ask about, so like, if I’m a traveler coming into the U.S. at one of these airports where you have this program, how is it advertised? And what do people learn about it when they decide to volunteer to get tested?
AR: We have these pop-up testing booths, in collaboration with XpresCheck. They’re our on-the-ground infrastructure to basically be recruiting folks coming off of international flights. All the international flights go into one bottleneck where you’re going to leave the terminal, and you have an opportunity to see this booth that has some information about like, testing for public health, with the CDC logo—basically recruiting folks to come in. Folks that volunteer, they swab their noses and then we are pooling [tests] by those countries. We also have been giving them free, individual tests to take home.
We’re not collecting or giving back individual testing data to [the volunteers]. But we are showing that this is a part of the public health program. What we’ve found, through survey results, is that participation has really been increased by the fact that people feel like they’re being a part of this public health program and they want to help. We have great recruiters on the ground.
BL: So people don’t get their individual results, but you said they get an at-home test that they can use?
AR: Yeah. And then they can get their individual results [from that test]… They don’t get the pooled result.
BL: Are the data that you’re getting from this program linked to any other data? Because I know one big concern with variants is like, is a new variant going to be more severe? Is it going to be more likely for people to be hospitalized? So is there any capacity to link the tests that you’re doing with, say, hospitalization records?
AR: I think it’s a great idea, a great direction. Right now, we haven’t been linking those clinical data… We can try to look at the data within our program, and then contextualize it [using other sources] on what might be happening, in the United States or in origin countries.
But we’ve also been really excited about expanding our passive detection through wastewater. We’ve done an R&D project where we were looking at wastewater testing off of aircraft. So, that’s another complimentary data set off of the aircraft itself to help get a more holistic picture—not everyone is going to be using the bathroom [on the plane], but not everyone is going to be volunteering in this program.
BL: Testing the wastewater off the airplane seems like a great idea, I would not have thought of that.
AR: Yeah, we’re really excited about the opportunity to do something along those lines, since folks aren’t always going to volunteer to swab their nose.
We’re pooled testing by country, so we know that folks are coming from specific places. We can also—they can volunteer to give us any past travel history, so that we can try to link those data on our own. But there’s no systematic way to link [our results] to clinical data.
CP: Our sweet spot is microbes and viruses. So we actually don’t collect individual data that would allow us to associate an individual with their health record at all. I just wanted to emphasize that.
BL: That makes sense. I know that [linking datasets] is something that is very challenging to do, even with established health systems. I was just curious.
Swati Sureka: I can add one thing, just in terms of the knock-on benefits of the program. Say we do get early warning of an emerging variant that could potentially be of concern, that we don’t know on the global stage yet. We work directly with the CDC on getting them access to those [test] samples so that they can do direct viral characterization. Because, with emerging variants, it’s hard to get your hands on samples of it to be able to conduct research on how the virus behaves. I think that’s one of the side benefits, being able to actually pull those samples and share them directly with the CDC.
BL: Are there any variants that you’re all particularly watching right now? Like, I know, there’s been a lot of news about XBB, that’s spreading in East Asia. From your perspective, what are you seeing as concerning hotspots at the moment?
AR: Yeah. This is a big part of what our team does: as this data comes in, understanding what might be the trends happening globally. We have repeatedly shown that we can do early warning, [our data are] some of the first to identify a variant of concern. We can look and say, like, there’s certain mutations that we know, either from past variants or in predictive space, that [indicate this new variant is] going to be a problem for immune escape.
Variants that I think we’ve been really keeping an eye on and telling our CDC partners about are BQ.1 and BQ.1.1, which have been split out by CDC in the last couple of weeks. Our program was one of the first to identify and actually designate this BQ.1 variant. So we saw, early on, that it had characteristics because of its mutational profile [allowing it to] take hold. We continue to watch that.
The United States has been, pretty much, a few weeks to a month behind trends that we see in Western Europe. So I think it’s been pretty clear that BQ.1 is going to be something to watch for, as it sort of expands in its frequency… We also see XBB in our program, we’ve seen it as well. I think it’s going to be an interesting new chapter of SARS-CoV-2 evolution where we have potentially co-circulating variants of concern that have different dynamics in different parts of the world.
BL: Yeah, it’s very interesting… One other thing I wanted to ask you about is sample size. It seems like, from the data on the CDC dashboard, that you’re working with a small number of airports and a limited sample, compared to the number of international travelers coming into the U.S. So how do you think about analyzing that, and potentially expanding the sample?
AR: Definitely part of our plan is to ramp up the number of samples that we can get, as well as the number of airports that we might be operating out of.
But I think it’s just remarkable to talk about this program, when you see such a small sample size, and we’re still able to find new things and match GISAID, or global variant frequencies. It highlights, even with a small sample size, that the way that we’ve designed the program and the way our CDC counterparts think about where we’re going to be, what flights are we going to be choosing—that has been really, really successful so far. You always want more samples in science, but I think we’re working with what we have, and we’re excited to be expanding.
BL: That makes sense. So you’re able to say, “We want to send people to these flights, because this country has concerting variants right now,” that kind of thing?
AR: Yeah. Our CDC counterparts are tapped into both the CDC-wide conversations about variants and the global, WHO conversations about variants. So they’ll give us indications when there might be something to think about. And, again, this program is super nimble in its ability to pivot. When we think we want to focus on certain regions of the world, [we can recruit from specific flights].
It’s nice to be working in airports that have these direct flights and these long-haul flights. But thinking about how we prioritize is definitely—the CDC folks are thinking about this, and we sort-of help support them.
BL: The last main thing I wanted to ask about is, obviously in the U.S. and globally, we’re seeing so much less PCR testing now than we had at earlier points in the pandemic. How are you and—to any extent that you can talk about it—how are partners at the CDC thinking about making sure that we’re collecting a lot of samples from diverse settings, and looking in different places, looking at wastewater, and just continuing to keep track of what variants are circulating?
AR: I think back to, finding novel places to sample things. Like, the fact that we’ve invested and tried to build capability to do aircraft wastewater testing is just adding a complementary [data layer]. We’re going to have this layered interface or layered system where we might have some PCR tests, we might have wastewater, we might have sequencing, we might not have sequencing.
We’re figuring out, how do we just keep adding and keep building on this biosecurity infrastructure. I mean, the worst thing that could happen from this is we build all this and then no one uses it again, until something pops up. We’re really invested in finding new and novel ways to sample and to detect, and eventually sequence if we can get more robust data, like on variants.
BL: That makes sense. I wonder to what extent it can one day be useful for other viruses, too. I know we’re in a bad flu moment right now, or at least the beginnings of maybe a more intense flu season this year. And I know experts always talk about, like, “Can we read the tea leaves from the Southern hemisphere?” So that makes me think, “Okay, could we actually sample people who are coming in? And see if they have the flu, and not just COVID?” Or other things of that nature?
CP: This is something that keeps me up at night. Without being too forward-looking, absolutely, I would say, there are some commercial products out there right now—like from Illumina, which is a massive sequencing behemoth, they’ve just released some new sequencers on their end. They have this panel of, like, 66 viruses that you can detect in one panel. I think we’re gonna see more of that from many different types of partners who are looking at surveillance.
Moving beyond SARS-CoV-2, could samples be used for that? We’ve seen lots of publications that definitely prove that’s true. I think it’s right on cue, hopefully, with where we’re all headed.
BL: Yeah, I hope so. Well, those were all my main questions. Is there anything else you all think would be important for me to know about the program?
Swati Sureka: Stepping back, seeing how this [program] has played out over the past year, I’ve just been floored by, like, tens of thousands of people who have mobilized and participated and given samples in service of public health. For me, as a person who works in the communications space, I think we often hear a lot of these narratives of like, “People aren’t gonna do anything” or take any measures that they’re not forced to do.
People are inherently self-interested in all of these narratives that we hear. And it’s been really impressive to watch the participation that we’ve seen from travelers who want to help public health and want to help stop the spread, want to help pick up new variants. I don’t want to lose that thread of things.
BL: Totally. I can just envision, if you’re coming off a long flight, you just want to get through customs and get home. Taking a few extra minutes to get swabbed is not nothing.
AR: Yeah. And you could be doing that and say, “Oh, it doesn’t matter.” But we’re consistently seeing how helpful this data is, to inform all these complementary systems for building a biosecurity infrastructure. It’s really important data as we move forward.
BL: Yeah. When folks sign up, do you give them a link to the dashboard?
AR: Now we do. Now we can, right, it’s now live. It’s been really nice to have that public-facing thing, so that folks know where their efforts are going towards.
The CDC is no longer publishing data about COVID-19 outbreaks on cruise ships.
Last week, 93 out of 94 cruise ships reporting COVID-19 data to the CDC had active outbreaks, meeting the agency’s threshold of cases in at least 0.3% of passengers and crew.
As of July 18, 2022, CDC’s COVID-19 Program for Cruise Ships is no longer in effect. CDC will continue to publish guidance to help cruise ships continue to provide a safer and healthier environment for passengers, crew and communities going forward.
This seems a bit suspicious, considering that the U.S. (including cruise ships) is in the middle of a COVID-19 surge driven by the highly transmissible Omicron BA.5 variant. In a statement to the Washington Post, CDC spokesperson Kristen Nordlund said: “CDC has determined that the cruise industry has access to the necessary tools… to prevent and mitigate COVID-19 on board.”
But there have been no substantial changes to COVID-19 safety measures on cruise ships that might merit this change, according to the Post; in fact, cruises have only become more lenient since the beginning of 2022. Some cruise lines have stopped requiring tests before passengers board a ship.
Cruise lines will continue to report COVID-19 data to the CDC, but the process is voluntary. And without public data from cruise ships, passengers trying to decide whether they should proceed with a trip will need to call a cruise line directly to ask about potential outbreaks.
I’ve heard some commentators say that the end of the mask mandate on airplanes in April was a turning point in U.S. attitudes towards the pandemic. The end of cruise ship data feels like another potential turning point, demonstrating how the CDC is slowly pulling resources out of its COVID-19 response—even as the country faces a dangerous surge.
National report from the White House Coronavirus Task Force: The Center for Public Integrity, a nonprofit newsroom focused on investigations of democracy, has been periodically releasing reports of COVID-19 statistics intended for internal use by the White House Coronavirus Task Force and state governors. Reporters at the Center are often only able to obtain state-level reports, but last week, they released a national report including summary data and recommendations for all 50 states. The report is dated November 29.
Searchable database of PPP loans: On December 1, the Small Business Administration released extensive data on loans issued through the Paycheck Protection Program (PPP), including specific loan amounts and company names. Accountable.US, a nonpartisan watchdog group, has made this information available in an easy-to-navigate database. You can search for a specific business or filter by different geographic regions and industries.
Searchable database of federal COVID-19 purchases: Since March, ProPublica has tracked where federal government spending on the pandemic is going. The database represents $28 billion, 14,209 government contracts, and 6,832 individual vendors. Data can be sorted by spending categories, vendor types, and contract sizes.
COVID-19 Global Travel Restrictions and Airline Information: The Humanitarian Data Exchange is an international repository run by the United Nations Office for the Coordination of Humanitarian Affairs. One of the repository’s COVID-19 datasets displays travel restrictions and airline restrictions for nearly 300 jurisdictions, updated every day.
COVID-19 Data Dispatch 