Field Notes #14: Counterpoint

Counterpoint

On the pathogens that won't play along

Field Notes is where I take one idea from the episode—something that feels like a hinge point—and follow it to see what it reveals. If you want the full story, you can read or listen to the episode here.

In the Margins

In this week's episode, I described vaccines as rehearsals. I like that metaphor because rehearsals aren't about avoiding the performance. They're about arriving prepared when the moment finally comes. But not every pathogen agrees to the rehearsal.

History has a way of making vaccination feel inevitable. Jenner showed it could be done. Pasteur expanded the idea. One vaccine became many. Looking backward, it can seem as though medicine simply learned the trick and kept repeating it.

The biology tells a different story.

Some pathogens cooperate. They wear the same face every time we meet them. They announce themselves clearly. Once the immune system has learned their pattern, it remembers. Others not so much.

Some change so quickly that by the time the immune system has learned yesterday's version, today's looks different. Some disappear into our own cells and wait quietly for years. Others provoke immune responses that are surprisingly poor teachers, leaving little lasting protection even after natural infection. A few are so adept at manipulating the immune system that the response itself can become part of the problem.

Vaccines aren't difficult because scientists haven't worked hard enough. They're difficult because every pathogen plays a different song.

Smallpox happened to be an unusually cooperative opponent. It changed very little. Infection left strong immunity, and vaccination could imitate that lesson safely.  Most of the microbes we wrestle with today are far less accommodating.

The remarkable thing isn't that we still struggle to build vaccines for some diseases. It's that we've managed to build so many.

Underlined

Some of the different songs pathogens bring to the rehearsal:

• The Shape-Shifter

  Some pathogens, like influenza and HIV, change so rapidly that the immune system is always studying yesterday's sheet music. By the time immunity recognizes one version, the melody has already changed.

• The Ghost

  Some pathogens refuse to leave the composition. Herpesviruses establish lifelong residence inside our own cells, slipping quietly out of sight before the immune system can eliminate them completely. Like a rest in the middle of a measure, they seem absent—but they're still part of the piece, waiting for their next entrance.

• The Forgettable Stranger

  Some pathogens never leave a lasting impression. Gonorrhea, for example, often fails to generate strong protective immunity, allowing repeated infections throughout life. RSV behaves similarly, producing only partial or short-lived protection after natural infection. The melody fades almost as soon as it's heard.

• The Syncopation

  Sometimes the immune response lands just off the expected beat. Dengue virus is the classic example, where antibodies from one infection can complicate infection with another strain. Teaching the immune system safely requires understanding not just how to generate immunity, but how to keep it in rhythm.

• The Labyrinth

  Some pathogens don't present just one theme. The malaria parasite transforms repeatedly as it moves between mosquito and human, changing form throughout its life cycle. Rather than offering the immune system a single melody to learn, it becomes a fugue—multiple voices entering at different moments until the whole becomes difficult to follow.

What It Points To

There is no universal score for prevention. 

Outbreak Watch

Updates include active outbreaks and emerging signals I'm keeping an eye on. Information is verified through official public health agencies and credible reporting. 

As of mid-morning, July 15, 2026:

Active Outbreaks

EBOLA (Bundibugyo, DRC and Uganda)

According to the most recent DRC SitRep #60, the Bundibugyo Ebola outbreak in the Democratic Republic of the Congo continues to accelerate, with 2011 confirmed cases, 754 deaths, and 753 hospitalized patients. The outbreak has expanded into additional provinces, while WHO officials now warn that the true number of infections may be at least double—and potentially several times higher—than official case counts, reflecting the large number of infections occurring outside recognized chains of transmission. Roughly 80% of newly identified cases are not linked to known contacts, highlighting how much transmission is occurring beyond the reach of current surveillance and contact tracing efforts. Funding shortfalls, insecurity, healthcare worker strikes, and community mistrust continue to hamper response operations even as treatment capacity and clinical research expand.

The outbreak is also continuing to produce international exported cases. A second U.S. humanitarian worker has now been diagnosed with Bundibugyo Ebola after working in the DRC and was medically evacuated to Germany and admitted to the University Hospital in Frankfurt for treatment on July 13. Another American physician infected earlier in the outbreak was treated at Charité Hospital in Berlin. These cases do not indicate sustained transmission outside Central Africa, but they do highlight the ongoing risks faced by healthcare and humanitarian workers responding on the front lines. Uganda's associated outbreak remains comparatively small and appears stable, with no evidence that sustained transmission is occurring independently of imported cases from the DRC. The broader regional concern continues to center on containing the rapidly growing outbreak at its source.

New World Screwworm in Texas

New World screwworm remains one of the most closely watched agricultural outbreaks in North America. Reports indicate 37 cases in 13 TX counties and 1 NM county. Response efforts continue to focus on surveillance, movement restrictions, sterile fly releases, and rapid treatment of affected animals to prevent the parasite from becoming permanently reestablished in wildlife populations. While new detections continue to occur, the overall strategy remains unchanged: find infestations quickly, eliminate larvae before adult flies emerge, and overwhelm wild populations with sterile males until transmission collapses.

As I said before, the longer-term concern remains wildlife. Livestock can be inspected and treated. Free-ranging wildlife cannot. And illegal cattle movement makes the problem worse. If screwworm establishes a self-sustaining cycle outside managed animal populations, eradication becomes substantially more difficult. A recent study from the Wildlife Conservation Society, documents infestations deep within remote forest wildlife populations in Central America and echoes my warning. 

Cyclosporiasis (United States)The summer cyclosporiasis outbreak continues to expand rapidly. Michigan remains the epicenter, now reporting 3,762 confirmed cases, while CDC’s national dashboard continues to lag behind rapidly evolving state reporting. Investigators now say early evidence increasingly points toward lettuce or other salad greens as a likely source, although no specific grower, supplier, or product has been identified and the investigation remains ongoing.

Because Cyclospora has an incubation period of roughly one to two weeks and requires specialized laboratory testing, identifying outbreaks and tracing contaminated foods remains particularly challenging. Until investigators identify a definitive source (hard to do since surveillance of this was ended last year), officials continue recommending careful washing of fresh produce, recognizing that washing alone cannot reliably remove the parasite from leafy greens. Cooking remains the most effective way to eliminate Cyclospora on contaminated foods.

Marburg in Uganda

No significant changes this week. Available evidence continues to indicate that Uganda's Marburg outbreak remains contained. I'll continue monitoring for any change in transmission, but unless new cases emerge, this will be the final routine update.

Watching

H5 Avian Influenza

While human infections remain uncommon, H5 avian influenza viruses continue reshaping the wildlife landscape in ways that are difficult to ignore. Norway reported the first detection of H5N5 avian influenza in a polar bear in Europe in May, and we've seen spillover of H5N1 into elephant seals again....in California with a limited outbreak in the spring of this year and more recently on Australia's remote Heard Island there was catastrophic mortality from H5N1 in southern elephant seal pups—an estimated 13,000 deaths—as well as infections in multiple bird and marine mammal species. Although these are different influenza subtypes, both belong to the broader H5 lineage and illustrate the same pattern: highly pathogenic avian influenza viruses continue crossing into new mammalian hosts.

I'm watching less for human case counts than for what these mammalian infections represent. Every time an influenza virus successfully infects a mammal, it gains another opportunity to explore what works in a mammalian host. So, my attention is on these moments, when H5 infections don't remain confined to birds.

The Surveillance Gap

Michigan's Cyclospora outbreak is a reminder that outbreaks aren't just biological events—they're surveillance events. The longer it takes to identify a contaminated food source, the longer exposures can continue.

Recent reductions in federal foodborne disease surveillance, including programs that supported investigations of pathogens such as Cyclospora and Vibrio vulnificus (and many others), don't guarantee we'll see more outbreaks. But they do increase the possibility that outbreaks could take longer to recognize, investigate, and connect to their source. That's something I'll be watching closely over the coming months...especially Vibrio.

Postscript

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This week's issue wandered into music almost by accident, but maybe it wasn't an accident after all. Long before I studied virology, I started college as a music major. I still play guitar and write songs, and often find myself thinking about the world in musical terms. So somewhere along the way, pathogens stopped asking different questions and started playing different songs.

Maybe science and music aren't as different as they seem. Both reward careful listening. And both have a way of reminding us that sometimes the fastest way forward is to slow down first. 

So, until next week, I'll leave you with a piece of advice from my late jazz band director and saxophone teacher, Dick Harvey, who once played with Duke Ellington:

"Play it half-fast 'til you get it right."

— Heather