i needed an avian influenza reference document so i wrote one for myself (but it's for you, too)

welcome to A Teetering Vulture! a newsletter about various science stuff as well as the life happenings of its author, Taylor.

On Monday, March 9, 2020, I stood in front of a class of undergraduate physics students and gave a presentation. The presentation’s title was “Modeling Mechanisms of Disease Spreading: COVID-19 & Society” – I was 22, an undergraduate student myself at the time, and I had begun to get more than an inkling that the world was about to change. Drastically.

Three days prior, the Grand Princess cruise ship had been stranded off the California coast because one of its passengers had died of a new and intimidating disease. Three days prior to that, the CDC reported 60 confirmed cases of the novel coronavirus in the United States. 

Instinctually, and as a biology student, I wanted to make sense of what was happening. I also wanted desperately to know what was going to happen. It was not just the disease that worried me, but people and their reaction to it. I, being somewhat of a hypochondriac with quite a lot of anxiety around contracting transmissible diseases, wanted reassurance that society could respond rationally and effectively to an impending pandemic. 

...

So I did what I felt I could do, at the time. I learned about COVID-19 and I learned what people were saying about it, and I turned what I learned into something I could share with other people. I sat aside plans to create a physics presentation about carbon nanotubes (an area of interest for me at the time as an inchoate scholar of genetic engineering) and turned to something I’d never paid attention to before: mathematical models of disease spreading patterns.

And then I spoke to my classmates about two things. One, about how multiple diseases can interact with one another and complicate our ability to predict, through nevertheless expert-driven modeling efforts, how contagions will spread. Because I still have my script write up from that presentation, I can tell you exactly how I explained this.

In the case of diseases, maybe you get the flu, which weakens your body’s defenses, and pneumonic infection moves into your lungs. Suddenly pneumonia is in the equation because you contracted the flu. Without the flu, you may have been completely fine, but now there’s the chance you will get sicker and infect others. It throws the whole thing out of whack.

It throws the whole thing out of whack. Meaning, other diseases make it a lot harder to predict how one disease will spread, because diseases sometimes create opportunities for other diseases to move in, or otherwise complicate illness duration and the period during which a person is infectious. 

And then I explained how social media and social reinforcement can play almost the exact same, complicating role as multiple diseases interacting with one another. Take the anti-vax movement, for example. By not getting vacccinated, a person may be creating an opportunity to become ill. Suddenly an illness is in the equation because you didn’t get vaccinated. Through this lens, one can view the anti-vax movement as equivalent to, or at least rather comparable to, something like the flu. Just, a social contagion rather than an epidemiological one.

Epidemiologists and disease modeling researchers have to confront the challenge of knowing to what extent a virus is being reinforced by other pathogens, social trends, or both. If online trends perpetuate irresponsible or unsafe behavior, it can worsen epidemics; in this way, pathogens can spread almost like memes. Except instead of appearing harmlessly and without warning all over our social media feeds, they invade our homes and harm ourselves and our loved ones. 

My script ended like this:

Most importantly, I think it is important to consider how your own actions and words online and in reality can influence who gets sick in your community. Even just last week, I overheard people in the library talking about how it isn’t worth it to get the flu vaccine. So we should all be considering these things right now. 

Two days later, the World Health Organization (WHO) declared COVID-19 a pandemic.

Five years later and here I am, thinking about a different virus but doing the same things: learning more about a concerning disease – one increasingly in the news – and feeling compelled to talk with people about it. To do whatever infinitesimal thing I can to be the antidote to social contagion. 

The current Highly Pathogenic Avian Influenza A (HPAI A(H5N1)) situation is very different from the initial COVID-19 situation, however. For one, it’s a virus that’s still primarily infecting birds. And it’s not circulating at all amongst humans. Only 70 human cases in the US have been reported by the CDC as of this writing, and all of them contracted the virus from animal sources. Dairy cows and chickens, mostly. 

But that doesn’t mean that it’s not critical that we pay attention to H5N1 and take steps and precautions now. Despite the remnant fatigue many still feel as a result of the COVID-19 pandemic, and despite the deeply troubling and exhausting societal and political moment we're contending with, there inevitably will be future pandemics, whether soon and whether the cause is H5N1, or whether later and some other pathogen, and so we should, in some ways, muster the strength to prepare now. Because it will take immense knowledge and collaborative effort to ensure as few of us are harmed as possible.

Over 100 million wild birds have been affected by H5N1 since February 2022. Mass die-offs of Sandhill Cranes (some estimates being 1,500 birds) in southern-central Indiana occurred as recently as January of this year. And, as is standard precautionary procedure, the US killed 11.4 million poultry birds in February over concerns of spreading infections on farms.

The worst case scenario, for us, would be that this virus evolves the ability to consistently spread between humans. “This is the nastiest virus that we’ve seen in terms of ability to cause disease,” said Dr. Richard Webby, Director of the WHO Collaborating Center for Studies on the Ecology of Influenza in Animals and Birds, and a researcher in the department of Infectious Diseases at St. Jude’s Children’s Research Hospital in Memphis, Tennessee, in a podcast episode of Science Friday back in January. Of 912 anomalous instances of humans confirmed to have contracted H5N1 from 1997-2024, 51.5% of them have resulted in death. This is compared to the case fatality rate of COVID-19, which in the US was estimated to be around 1-3% from 2020-2022.

Fortunately, if H5N1 did begin infecting and transmitting between people, it would certainly become less deadly. Communicable diseases in humans are generally naturally pressured towards a genetic trade-off, one between ability to infect a host and ability to cause severe or fatal disease. A virus that kills its hosts too rapidly, or too often, runs the risk of not being able to pass its viral progeny to other hosts and therefore continue its existence. A corpse is not going to be walking around coughing on other people, after all. 

Still, an H5N1 pandemic would be catastrophic. And recent genome sequencing of H5N1 viruses has suggested that alarming genetic changes might already be occurring, changes that may be precursors to the virus evolving to spread between people. 

Influenza A viruses of the HxNy subtype (of which H5N1 is one of 131 others) have an evolutionary history that has honed them into adeptly adaptable and changeable little packets of organic molecules. They are single-stranded, negative-sense RNA viruses with segmented genomes that are capable of rapid mutation and reassortment inside of (primarily) human, avian, and swine hosts. And they are classified based on the serotype (or subtype) of two viral surface molecules, hemagglutinin (HA) and neuraminidase (NA). 

Hemagglutinin is the protein responsible for granting a virus entry into a host cell; it possesses a receptor-binding site that allows it to bind to molecules on host cells called sialic acid receptors – and this binding activity is the first step required for virus entry. There are 18 known hemagglutinin serotypes, some of which preferentially bind to avian-specific sialic acid receptors, and some of which preferentially bind to human receptors. Changes to a virus’s hemagglutinin subtype is one of the central mechanisms by which a flu virus can make the switch from circulating in birds to circulating in mammals, including humans. 

Neuraminidase has 11 known subtypes, and it’s an enzyme that catalyzes the cleavage of sialic acid from glycans on the surface of the cell, which in effect means: it frees newly made viral progeny from a cell and permits them to go and infect other cells, or leave the body and infect other hosts. Antiviral flu medications such as oseltamivir (Tamiflu), though not always as effective as we want them to be and sometimes causing undesirable side effects, work by inhibiting the action of neuraminidase. These medicines introduce a competitor molecule that binds to the same place (sialic acid) that neuraminidase normally binds on the cell surface. Said simply, antiviral flu medicines physically block the neuraminidase enzyme from doing its job. 

If different strains of flu viruses co-infect the same cell in the same host, they may be given opportunities to mix and reassemble themselves into new versions of flu virus. Sometimes, these new versions find themselves better capable of infecting or spreading between certain hosts. Sometimes these new versions find themselves capable of causing more severe disease. At the same time, genetic mutations can occur in any virus that may also increase viral fitness in certain environments. This constant shifting and changing is why seasonal flu vaccinations are administered. And this is also what happened in 2021, when a lineage of H5N1 (referred to as Clade 2.3.4.4b) circulating in Europe suddenly became better adapted to spread and cause illness among wild birds.

The novelist and dedicated birdwatcher Amy Tan once wrote: When I see a bird that has died, I don’t accept the sanguine saying, “It’s the circle of life.” It is good to mourn and wish it weren’t so. 

It is remarkable what birds can endure. It is tragic what they cannot. This is from her book The Backyard Bird Chronicles, which contains a trove of obsession-driven, nonfiction accounts of the birds she feeds in her backyard, and drawings of them as well. 

Even if the risk of this virus ever affecting humans directly was zero, it wouldn’t change the reality that HPAI A(H5N1) being so widespread in the wild is already a tragedy. It is sad that so many birds are suffering and dying. There will be ecological consequences to the losses of huge numbers of birds – primarily though not exclusively waterfowl, the natural reservoir for this virus – that we naturally cannot yet gauge the extent of.

H5N1 reached bird populations in Antarctica during the 2023-24 austral summer. Migratory birds ferried the disease to the continent, and researchers there now fear what a disease that has decimated bird populations in other parts of the world will do to Antarctic bird colonies. In December of 2024, the SCAR Antarctic Wildlife Health Network released new safety recommendations for its scientists that include closing some research sites to limit potential spread of virus to humans or among birds, as well as not touching birds or bird carcasses unless wearing special suits, because feathers can harbor high viral loads for up to 100 days post-infection.

The Ventana Wildlife Society based in Monterey, California, has taken on the extremely complicated, time-intensive challenge of vaccinating the entire wild flock of California Condors in the central region of the state against H5N1. So far, 70% of these endangered birds have been successfully vaccinated. 

And countless wildlife rescue and rehabilitation centers around the globe are being increasingly faced with tough decisions about which sick or injured birds to take into their care and which to abandon, in order to protect workers, volunteers, and resident education or ambassador animals. 

A huge tragedy, even despite efforts to do what can be done to save as many birds as possible.  

More and more sick wild birds moreover means more opportunities for H5N1 to incidentally make its way onto high-density dairy and chicken farms. These farms are places replete with opportunity for the virus to mutate and rearrange. In a single milliliter of infected cow’s milk, for instance, there can thrive millions of virus particles. And yet, historically it has been difficult to convince farm workers to preventatively vaccinate against such threats, especially when they hardly appear, in the moment, as threats at all. Sometimes farm workers don’t even wear protective gear such as face masks and gloves when threats like these emerge. 

Mammal-to-mammal H5N1 transmission has only been recorded in sea lion populations in South America in 2023 – but it has been recorded. Thousands of sea lions died because a version of H5N1 in the region evolved to reliably invade mammal host cells. Other pinnipeds like elephant seals and crabeater seals have also died rapidly and en-masse in the last two years, the cause confirmed to be H5N1.

Which indicates that this virus can find ways to pass between mammals. If such evolution happens again, in a manner that allows human-to-human transmission, we’ll all be in trouble. 

What it will take to have a shot at controlling this virus includes global cooperative surveillance of its movements in humans as well as in animal populations, avian and non-avian, in addition to rapid data sharing between countries and ongoing study of the virus’ architecture and evolution. Current H5 vaccines require 2-doses and are not as protective as some of our other flu vaccines, so research into more effective vaccines is also a priority. 

On a local scale, people can use caution and protective equipment when coming into close contact with wild birds (or their feathers), they can keep their cats – which are susceptible to the disease – indoors, and they can also check the websites of local wildlife rehabilitation centers or their state’s Department of Natural Resources for information or links to helpful data on H5N1 in their area. 

One Health is the term given to the approach to public health that operates under a comprehension of how human health is inextricably linked to the health of the rest of the planet – all of its organisms, its ecosystems. We cannot neglect one to focus on another; it doesn’t help anyone to remain insular. If we all failed to pay attention to a serious pandemic happening in the world of our birds, such inaction could be, ultimately, tantamount to a human pandemic. 

Thankfully, many of us are paying attention. Thankfully scientists already understand more about the evolution and ecology of flu viruses than almost any other pathogen, and are working to come to know this one better. And thankfully every bird conservation organization around the world has its eyes trained warily on the spread of this disease. And thankfully, when political figures like Secretary of Health and Human Services Robert F. Kennedy, Jr. suggest letting H5N1 run rampant on poultry farms, so that workers can “identify the birds, and preserve the birds, that are immune to it,” approximately every expert on the disease is instantaneously at hand to explain why such a plan would be, frankly, insane. 

If I were to be given the chance to speak with my twenty-two-year-old-on-the-cusp-of-a-pandemic self, I would tell her that what she is doing is valuable. I would tell her that no matter how irrational the world around her seems, she must continue to learn and to hone her ability to talk with other people and seek ways to gain knowledge and communicate it. No matter how small her audience, no matter how scary or impossible things seem. It is worth it to tell people how diseases can spread. It is worth it to care. And it is worth it to hope that one day the world will understand.

Information for this article was obtained from:

✼ SciShow: Bird Flu is Here (+ Linked Sources) ✼ An Update on Highly Pathogenic Avian Influenza A(H5N1) Virus, Clade 2.3.4.4b ✼ The Ecology and Evolution of Influenza Viruses ✼ Emerging HxNy Influenza A Viruses ✼ First U.S. Bird Flu Death Raises Concerns About Preparedness ✼ CDC: Bird Flu Situation Summary ✼ USGS: Avian Influenza Surveillance ✼ World Animal Health Information System ✼ Sub-Antarctic and Antarctic Highly Pathogenic Avian Influenza H5N1 Monitoring Project ✼ Ohio Department of Natural Resources: Avian Flu ✼ Nature: Disease Primers - Influenza ✼ Mortality Risk of COVID-19 ✼ Ventana Wildlife - Condor Threats ✼ Deadly avian flu strain is spreading rapidly in Antarctica ✼ RFK, Jr. Wants to Let Bird Flu Spread on Poultry Farms. Why Experts Are Concerned ✼ The episodic resurgence of highly pathogenic avian influenza H5 virus ✼ Mass Mortality of Sea Lions Caused by Highly Pathogenic Avian Influenza A(H5N1) Virus ✼ More Than 1,500 Sandhill Cranes Killed by Bird Flu in Indiana, Raising Concerns Among Biologists ✼ The Backyard Bird Chronicles by Amy Tan ✼