COVID-19 Data Dispatch

Category: Source spotlight

  • COVID source shout-out: Cryptic lineage investigation in Ohio

    Marc Johnson, a molecular virologist and wastewater surveillance expert at the University of Missouri, recently went viral on Twitter with a thread discussing his team’s investigation into a cryptic SARS-CoV-2 lineage in Ohio. I was glad to see the project get some attention, because I find Johnson’s research in this area fascinating and valuable for better understanding the links between coronavirus infection and chronic symptoms.

    A “cryptic lineage” is a technical term for, basically, a strange viral mutation that researchers have identified in a specific location. Unlike common variants that spread through the population (Delta, Omicron, BA.5, XBB, etc.), these lineages typically are contained in one place, or even in one person. They’re usually identified by wastewater surveillance, since that technique picks up more people’s infections than testing at doctors’ offices.

    Johnson has become a specialist in investigating these cryptic lineages over the last couple of years. His lab at the University of Missouri runs the state’s wastewater surveillance program, which includes genetic sequencing for sewage samples. And his team also collaborates on sequencing research for wastewater surveillance in other parts of the U.S. This Nature article from last year goes into more detail about how these investigations work.

    In the last few months, Johnson and his colleagues have been investigating one cryptic lineage in Ohio. The scientists have traced the lineage to Columbus and a town called Washington Court House; they believe it represents one sick person, who lives in Columbus and goes to Washington Court House for work. This individual is shedding a massive amount of coronavirus, orders of magnitude higher than the average COVID-positive person. See more details in this story by The Columbus Dispatch.

    Johnson and his colleagues would like to identify the person behind this lineage for two reasons. First, they can connect the person with doctors who can help treat their COVID-19 symptoms—it’s likely they’re having a pretty nasty gastrointestinal experience. Second, the scientists hope to better understand how viral particles that shed from a long-term infection might be related to chronic symptoms, as persistent virus in different organ systems is one of the leading hypotheses for why Long COVID occurs.

    I’ve interviewed Johnson before for stories about wastewater surveillance and I think he does fascinating work, so I was glad to see his Twitter thread get some attention. If you can help identify the Ohio resident with lots of coronavirus in their gut, get in touch with him!

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  • COVID source shout-out: Body Politic

    Body Politic, a health justice organization that has led Long COVID organizing over the last three years, shut down its Slack support group this week. The group has been a valuable place for long-haulers to connect and find resources; it’s also helped launch other important projects, such as the Patient-Led Research Collaborative and the Long COVID Survival Guide.

    The organization isn’t ending its support of long-haulers, though: it’s partnered with New Health, a mobile app developed to continue community Long COVID support. “New Health will be hiring Body Politic moderators and board members as their first paid staff, and members of our community are currently testing their app,” Body Politic leaders wrote in an April blog post describing the transition.

    I’ve written previously about Body Politic’s fundraising efforts as the group sought to transition form a grassroots, all-volunteer organization to a format that was more sustainable, and I’m glad to see that the group’s leaders have found this solution. But it’s a bit sad to see the original Slack group close—the end of an era.

    Thank you to all the volunteers who made the Body Politic group possible, from a journalist who has relied on many of its members and resources in my reporting on Long COVID!

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  • COVID source shout-out: Virginia’s new wastewater dashboard

    COVID source shout-out: Virginia’s new wastewater dashboard

    One of the visuals available on Virginia’s new wastewater dashboard.

    With the public health emergency ending, a lot of state and local health departments are sunsetting or paring down their COVID-19 dashboards. Wastewater surveillance data are an exception, though, with agencies continuing to test sewage (and share the results) as other forms of COVID-19 testing become less available.

    Virginia’s Department of Health is one notable example: this past week, the agency added a new wastewater surveillance section to its COVID-19 dashboard. The new section includes a map of testing sites, coronavirus trends by site, viral loads over time, and plenty of text explaining how to interpret the data.

    This dashboard will be a great resource for Virginia residents aiming to continue following COVID-19 spread in their communities. It’ll be updated weekly on Tuesdays, according to the department.

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  • COVID source shout-out: Wastewater testing at the San Francisco airport

    A few months ago, I wrote about how testing sewage from airplanes could be a valuable way to keep tabs on the coronavirus variants circulating around the world. International travel is the main way that new variants get from one country to another, so monitoring those travelers’ waste could help health officials quickly spot—and respond to—the virus’ continued mutations.

    This spring, San Francisco International Airport became the first in the U.S. to actually start doing this tracking; I covered their new initiative for Science News. The airport is working with the CDC and Concentric, a biosecurity and public health team at the biotech company Ginkgo Bioworks, which already collaborates with the agency on monitoring travelers through PCR tests.

    The San Francisco airport started collecting samples on April 20, and scientists at Concentric told me that they’re happy with how it’s going so far. Airport staff are collecting one sample each day, with each one representing a composite of many international flights. Parsing out the resulting data won’t be easy, but the scientists hope to learn lessons from this program that they can take to other surveillance projects.

    Both scientists at Concentric and outside experts are also excited about the potential to monitor other novel pathogens through airplane waste (though the San Francisco project is focused on coronavirus variants right now). Read my Science News story for more details!

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  • COVID source callout: Outbreak at a CDC conference

    Last week, we learned that a CDC conference—a gathering of experts in the agency’s epidemic intelligence service, no less—led to some COVID-19 cases, thanks to reporting by the Washington Post.

    Well, this past Tuesday, the Post published a follow-up story: more than 30 people got sick following the conference, and the CDC is working with the Georgia Department of Health to investigate. The case count was 35 as of Tuesday, and is surely higher now; about 2,000 people attended the conference.

    It’s now safe to say that this conference led to an outbreak. And that isn’t a surprising outcome, considering that it didn’t require masks or other COVID-19 safety measures. As I wrote last week, this outbreak basically signifies that the CDC considers ongoing COVID-19 spread at large events normal and unavoidable.

    Even though this situation is, in fact, disappointing and could have been avoided with basic safety measures. 🙃

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  • COVID source callout: Spread at a CDC conference

    This past week, the CDC hosted a conference of about 2,000 people in the agency’s epidemic intelligence service. It was the first time this conference was held in-person since the pandemic started, and it appeared to take place with fairly limited (if any) COVID-19 precautions.

    And at least a few of the conference’s attendees tested positive for COVID-19 afterward, according to reporting by Dan Diamond at the Washington Post. While a CDC spokesperson told Diamond that the cases are “reflective of general spread in the community” and “should not be referred to as an outbreak,” it’s obviously not a great look for the agency to have virus spread at a conference intended to celebrate progress over COVID-19.

    These cases—and the CDC’s communication around them—add to a growing pattern of downplaying continued coronavirus transmission. The CDC is essentially saying it’s normal to risk COVID-19 at any large event going forward, even if that event is run by people who should, theoretically, have a good understanding of how to keep its attendees safe.

    Epidemiologist Ellie Murray elaborates on this idea in a Twitter thread about the situation:

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  • COVID source callout: Montana ends its dashboard

    Last week, I wrote about the Iowa health department’s move to end COVID-19 case reporting requirements for labs, and in turn stop reporting these data to the CDC. Well, Montana just became the next state to follow this trend.

    The state’s public health agency announced that it will stop updating its COVID-19 dashboard on May 5, the week before the federal public health emergency ends, in a note on the dashboard and a statement to local media outlets.

    Unlike Iowa, Montana will continue reporting COVID-19 numbers to the CDC; so residents of that state will still be able to find information on the CDC’s dashboard. But the discontinuation of Monatana’s own dashboard shows how the state is taking resources out of pandemic response and treating COVID-19 as an endemic virus—even though it’s not.

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  • COVID source callout: Iowa ends COVID-19 case reporting

    As of April 1, Iowa’s state health department is no longer requiring public health laboratories to report positive COVID-19 test results—and no longer reporting statewide data to the CDC. This decision, announced in late February, is part of a growing trend away from relying on case data as people use at-home tests instead of PCR tests.

    Iowa’s health department “will continue to review and analyze COVID-19 and other health data from several sources,” including hospitalization metrics and syndromic surveillance, according to the agency. It’s essentially treating COVID-19 similarly to the flu and other common respiratory viruses.

    As a result of this change, Iowa is now no longer reporting COVID-19 case data to the CDC, the national agency said in this week’s data update. National, regional, state, and county-level CDC data exclude the state of Iowa, starting on April 1.

    This move seems like a natural extension of the state health reporting changes that we’ve seen across the country since last spring. I wouldn’t be surprised if more state health departments similarly stop reporting every COVID-19 case when the federal health emergency ends in May. Unfortuantely, this will become another driver of increasingly-less-reliable COVID-19 data in the U.S.

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  • COVID source callout: GISAID in danger of losing trust

    GISAID, the global database of virus sequences, has faced a lot of criticism recently from the virologists and bioinformaticians who rely on it—potentially hindering responses to future virus outbreaks.

    First, there was controversy around genetic information from environmental samples taken at the Huanan Seafood Wholesale Market in Wuhan, China, which Chinese researchers posted to GISAID. An outside group of scientists found the sequences and analyzed them, finding the samples supported the hypothesis that SARS-CoV-2 originated in animals and jumped to humans at the seafood market. And then, GISAID revoked those scientists’ access to the database. (The original Chinese research group eventually published their findings.)

    Last week, another controversy came to light: GISAID is claiming that the first SARS-CoV-2 sequence to be publicly shared was posted on its platform, back in January 2020. Even though plenty of evidence suggests the first sequence was shared days earlier at virological.org, a virology forum. Reporting in Science Magazine and evidence shared on Twitter shows the true story of these early days of info-sharing, as well as how GISAID has tried to retroactively revise the narrative.

    While these issues might seem inconsequential outside of a small circle of experts, the controversies could lead some of the world’s top virologists and epidemiologists to stop using a major source for outbreak information. It doesn’t really matter who posted a SARS-CoV-2 sequence first. But it does matter that experts have trusted places to share data and collaborate on vital research.

    Without open data-sharing platforms like GISAID, the world may be less prepared for coming novel disease outbreaks. These recent controversies (and the broader debate over COVID-19’s origins) also speak to larger gaps in trust that could hinder future collaborations.

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  • COVID source shout-out: WastewaterSCAN’s newsletter

    COVID source shout-out: WastewaterSCAN’s newsletter

    Map of WastewaterSCAN sites, from the project’s March 24 newsletter.

    A few weeks ago, I learned that the WastewaterSCAN project has a newsletter, which shares updates about COVID-19 and other diseases nationally and for the Bay Area in California. It’s a helpful resource for following infectious disease trends.

    WastewaterSCAN, for any readers who might be unfamiliar, is a wastewater surveillance project founded by researchers at Stanford and Emory Universities. The project started in 2020 by monitoring wastewater in the Bay Area for SARS-CoV-2, but has since expanded to about 150 sites nationwide and six testing targets: the coronavirus, flu, RSV, mpox, norovirus, and human metapneumovirus (HMPV).

    In the newsletter, the SCAN team shares summary data about all of these diseases, as well as some variant analysis for SARS-CoV-2. The language is sometimes a bit technical (as its primary audience is the team’s academic and public health partners), but still very useful for seeing where diseases are rising or falling. SCAN’s local updates are especially helpful for anyone living in the Bay Area.

    Also, the SCAN team recently had a paper published in the Lancet discussing their work monitoring wastewater for diseases beyond COVID-19. The new article shows this technology’s potential for broader public health surveillance.

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