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Selected Publications of Dr. Shannon L. Abbey

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Shen, CP; Xu, SM; Lopez-Fernandez, AM; Anderson, SL; Esper, TA. "Autoimmune reactions and endothelial targeting of RhoA/Rho-kinase pathway for generation of recombinant Marburg virus derived from a bat isolate.” Viral Immun, 2014;27:261–273. 

 

 

For the first time in almost five years, Shannon feels like she made a good life decision in choosing to research developmental immunology in grad school. She could have picked something in cancer. Cancer was popular, cancer got generous research grants (compared to those her friends studying autoimmune disease mechanisms complained about, over cheap beer), and cancer, that year, was tentatively declared to be a declining health problem (or COMPLETELY CURED, depending on what level of scientific journalistic nuance you chose to read) once the engineered oncolytic filovirus, Marburg Amberlee, showed marvelous progress in Phase III trials. Labs all over the country were scrambling to re-orient their scope of work to incorporate the new development, and the evolutionary potential of it would add, once Dr. Daniel Wells’ treatment was more readily available for further study.

Then the Kellis flu was released before preclinical trials were complete, viral evolution did what it did best, and then the Rising happened. Cancer or the lack thereof was less of a research concern because there were fresh corpses stumbling around and biting people; the survivors in most labs were the students who spent more time watching horror movies on Netflix than pipetting. 

It was terrible, yes; that was a given. But it was also an opportunity Shannon had never expected to find. 

 Within fifteen months, she’s defended her dissertation to the two remaining members of her committee and gotten a post-doc fellowship at the CDC headquarters in Atlanta. (There’s so much clean-up work to be done there that some days, she’s not sure if she’s not one of the walking dead herself.)

 

 

Shoji, J; Abbey, S; Zhao, X. "A theoretical assessment of in situ vector-virus transmission mechanisms and pack behavior in Kellis-Amberlee viral development.” Brain Behav Immun, 2023;89:186–199.

 

 

The Rising had turned the world of scientific publishing upside down, which, admittedly, had not taken much effort. Journal editors are not generally a fast-moving breed when it comes to outrunning zombies, and  the whole development of open-access journals online already had people asking if traditional publishing was dying; with the dead actually showing quite a bit of animation, the metaphor was suddenly apt in a completely different way. The journal Cancer Journal for Clinicians, which had had an impact factor of approximately five million (give or take a few million) in 2014, plummeted to a status below that of Nature Reviews Urology in 2017.

 Dr. Shannon Abbey had become an associate editor on two journals since joining the faculty at Duke University in North Carolina: Developmental and Comparative Immunology (a pre-Rising publication), and a post-Rising open access journal, KA Treatment Communications. The latter had modeled itself after the blogging structure of disseminating information during the Rising, and prioritized publishing rigorous peer-reviewed research and facilitate a constructive discourse in what would normally be the dreaded comments section, at the greatest possible speed. 

 She likes working at Duke, and suspects she likes it better than she would have when it still had a football program. It’s close enough to the CDC headquarters that she can use their resources anytime she needs to, but it gives her some space for her own ideas, which are starting to become less about finding a cure for Kellis-Amberlee, and more about how to live with it as a fact of existence. Viruses are far better at evolving than they are at being completely wiped out. And there have to be better ways of coping with worldwide epidemic than the daily increase of amplification-prevention measures; her hair falls out regularly in the decontamination showers, breaking off where it’s most brittle.

 But her husband doesn’t mind when her hair isn’t pretty; he works in the computer science department and is developing apps to more accurately analyze big data and map KA outbreaks in real time. Joseph Abbey loves her, and on their first date took her to the aquarium, one of the few places left where animals could safely be observed by regular people, not scientists working with animal models. They’d gotten in trouble at the tank where they could touch an octopus; the aquarium staff wasn’t swayed by their explanations that they were conducting tests to discover its reaction time to a food source. Taunting octopi creates an overly stressful environment, the staff insisted. 

 He surprised her, on their first anniversary, with a bright orange shirt that said “Don’t taunt the octopus,” and she had laughed, long and hard, and decided right then that she was going to start seeing what contrasts octopi had with KA disease pattern in mammals, and also that she was going to love her husband forever.

 Later that year, a visiting scholar from another lab, with whom she’s published two papers, tells her he’s returning to Japan, ahead of schedule. He’s distraught when he tells her, and he won’t tell her why without making sure no one listens in.

 “The cross-infection tests. They showed good results in vivo, we really thought they were the answer to the strain causing the transmission behavior where those with amplified virus gather in packs. It worked, with the experimental strains of KA,” Dr. Joseph Shoji tells her.

 “That’s good news, so now I’m getting worried,” Shannon says.

 “They all died, Shannon. All of them. They were prisoners, they were given the option of having their sentences commuted if the treatment worked, who was going to turn that down? What about that makes them true volunteers? So when the cross-infection was administered, they were all ready to start new lives, right up til when the introduced virus latched onto other viral types that we hadn’t had the means to detect when selecting the cohort, and—"

 “—and they all amplified with an all-new type of KA, and they’re dead,” Shannon concludes.

 “The CDC is going to sit on this. They’ve put a moratorium on publishing the results."

 Shannon sets her coffee mug down with force, nearly splashing coffee onto her desk. “Are you fucking kidding me? What happens to the next lab that decides cross-infection is workable? What about— about— fucking scientific discourse and, I don’t know, the open exchange of ideas?"

 But they both know protesting the policy is futile; they both depend too much on CDC resources to run the risk of pissing them off, and even if they did, the CDC has the best legal team of any government organization, and could probably get them locked up for espionage or treason. Injudicious release of information about both viruses was what had brought the zombie apocalypse in the first place; people were afraid enough that they’d never question a scientist locked up for ethics-based whistleblowing. Even before the Rising, people were well-prepared to look the other way when people who leaked information got punished. 

 Joey drops a three-inch binder of results and a flash drive on her desk. “Lock this up, see if you can get anything out of it, if you want to risk publishing. I’m leaving and cutting my ties with the CDC. There have to be better ways than this."

 She does publish, and makes him first author, when she takes his results and reproduces them in a model that doesn’t involve killing “volunteer” prisoners and covering up the evidence. And then she accepts a job in the British Columbia CDC office, hoping for better legal restraints in Canada, and her husband gets a job at Simon Fraser University. 

 Shannon has always had a curious mind, wanting to know things that other people don’t know; now that she does, she feels the burden of knowledge weighing heavy on her shoulders. Sometimes she wishes she could have just been boring, and left well enough alone. 

 

 


Abbey, Joe. “Not Just Aiming For the Head: Big Data, Outbreak Mapping, and the Future of Popular Epidemiology.” Wired, August 29, 2031.  

 

 

The last words her husband says to her are unworried; outbreaks happen, they’ve seen them happen for more than fifteen years, and they can be contained. He’ll just wait out the panic somewhere secure on campus, and he’ll be home soon enough. 

 It’s that fact that leaves a bitter taste in her mouth: he never knew, not even when the planes flew overhead carpet-bombing the campus, that he would be one of the eleven thousand killed in minutes that day. 

 Shannon posts his name to The Wall, summarizing his work with crowd-sourced outbreak data analytics and the lives it saved, though his was not among them. He may not have been a journalist in the usual sense, not a Newsie or Stewart or Irwin, but he had aggregated mass amounts of data, collecting all the terms people used when talking about a new outbreak (whether they knew it was zombies or not) and pinning down the location based on where people were calling from, or sending texts or tweets or photos. She had heard about when Google had been a few steps ahead of the CDC in 2012, tracking flu outbreaks; she was not an epidemiologist, but she knew enough to be seriously impressed when Joe described his work to her. 

 She knows enough about containment and control of disease spread to know how it should have been conducted at SFU. It would be expensive, and it would be a stain on the university’s closed-campus reputation for safety, but it could have been done. But instead, the entire campus and everyone in it had been incinerated. There’s nothing she can do to stand up and say it was wrong, but when she accesses the CDC surveillance database to see, all the folders where the video files from SFU are empty. When she checks again, hours later, the folders don’t exist at all. She downloads a few from blogs across the internet; those videos are taken down and threatening legal jargon is left in their place, not long after. 

 They’ve done it again, Shannon knows. The cross-infection prisoner trials, the destruction of a whole university. They’re sweeping their failures under the rug, because it’s cheaper to keep going than to repair damage.

 Shannon also wonders if it’s paranoid to think that she’ll be next: she’s seen too much, she keeps applying for research grants to study how KA can be incorporated into human immune response, rather than studying how to eradicate the virus. The CDC knows enough about her to know she’s not a very tame scientist and they know what she’s seen.

 She takes three extensions of bereavement leave from work, trying to quit each time, and having her resignation rejected each time. It isn’t surprising. She packs up the apartment she shared with Joe, and fits everything that matters into her car; on the way out of town she stops by her office, ostensibly to hand her boss a paper copy of her resignation, and really to download every bit of research she can onto a portable drive. 

 Then she drives west until she reaches the ocean.

 

 

Abbey, SL; Smith, AC. “Developed immunities in a canine model prior to Kellis-Amberlee threshold amplification weight.” Int J KA Virology, 2036;20:568–580.

 

 

Setting up and working in a lab that she has to build from scratch, recruiting researchers on the qualification of if they can bring equipment with them and trading on the black market for biomedical research for anything else, is a challenge. There is no ready supply of virus-specific wild-type animal models and so her assistants also serve as wildlife trappers and fishermen. 

They bring her back a puppy.

“We’ve already tried this, trying to induce reservoir conditions before they hit threshold. Dogs aren't really the best animal model to work with,” she says to her lab assistant, Ashley. “I know we’re a little short on finding macaques around here, but we can probably at least find mice to breed. I want to at least have some decent results before we start bringing in zombies to work on."

“Wait, what?” says Ashley. “That was not in the interview. I prefer my research below the amplification threshold." 

“Then why did you bring me a mastiff, or whatever the hell this dog is? Look at its paws, it’s going to be the size of a horse." 

“Oh, hell." 

“And besides,” Shannon amends, “the zombies will be dead. More dead. Neutralized. I need them for tissue samples."

 Ashley backs out of Shannon’s tiny office nervously, muttering her own eulogy: “Ashley died doing what she loved: not listening when her mother questioned her career choices, like ones that involved being eaten alive."

Shannon strokes the puppy’s head, and contemplates what to do with it. It will reach the amplification threshold in less than a few months. That’s not very much time, to get results from it for the before-and-after comparisons. She could always just kill it now, to see what genetic factors are involved in restricting the activation of the virus prior to the threshold weight. She’s not really sure where to go next, with finding a dependable way to make effective antibody growth happen. It might be time to start looking at other methods of non-lethally integrating KA with the body’s immune system. 

 “Raw-ooooh-arr-mmm,” the puppy tells her, through a giant yawn, and drowsily slumps against her chest. It has such a tiny round head, and she can see its ribs. “Alright, let’s get you some food, and maybe a pillow. I’ll have to keep you in here, since the kennels are full." 

 Dogs are, unfortunately for her research, easy to find: when their owners died in the Rising, if their dogs didn’t die, they ran off, and found each other, and bred in the wild. The only pets people usually had by 2036 were bred so tiny they were basically genetic trash, but enough domestic dogs gone wild did survive to produce a very heterogeneous range of feral dogs. That heterogeneity makes them mostly unsuitable for research of any significance. 

Maybe a long time ago, she would have thought of dogs as pets, but she doesn’t have a lot of feeling or sympathy left for loving things. That part of her heart was firebombed years before.

Three weeks later, the puppy has been infected with and overcome two strains of KA, and has confirmed reservoir conditions for both when he crosses the forty-pound threshold and doesn’t amplify fully. Shannon gets a bigger dog bed for her office and names him Joe. 

 

 

Abbey, SL. “Case study: Kellis-Amberlee resistance in bite-infected patient.” Devel KA Res, 2042;20:5–12.

 


Joey— You owe me fifty bucks and bottle of Scotch, Shannon emails Joseph Shoji, after she sends Shaun Mason, the hallucination of his dead sister, and their news team off to Portland to talk to the CDC. The CDC and some bloggers finally came to my door, looking for answers. One was that kid who was on the presidential campaign last year, the one whose sister got killed. Maybe we’re not fucked after all. Or maybe we are, and we’ll all go out with just a few more people knowing that this disease didn’t have to wipe us out. 

 Shoji responds, You win the bet, but I still think we’re heading for the latter option.

  A while later, after Fiona hits and the mosquito vector dooms most of Florida and the Gulf Coast to certain death, the journalists come back, without their CDC scientist. However, they more than make up for it by toting along an infected Shaun Mason, who she had her suspicions about before. It’s a good day for science. And if Shaun doesn’t represent the immunology breakthrough she suspects he does, then somebody will just have to shoot him, which shouldn’t bother him unduly: she knows what it looks like when you lose the only person who ever truly, wholly, sees past whatever face you show everyone else, and how a life that can’t be shared is one that you don’t want to live at all. 

 Shaun acts like a man who knows how fast his friends will pull the trigger when he finally pushes himself too far. 

 Shaun also hears his sister’s voice in his head, and something about that sticks with Shannon after his first visit. KA was a unique predator, taking control of its host’s nervous system and making a million, a billion copies of its signaling patterns. That was how it kept a body going after functional brain death, and how it influenced zombies to cluster together in packs. 

The thought niggles at her until she thinks about the CDC scientist who had left a dead clone behind, because totally unethical human cloning was what the CDC was doing nowadays. It could actually be a fruitful line of research, if they were willing to pursue understanding of the KA viral structure, which they weren’t, because— perhaps, probably, KA created a virtual clone out of the brain’s electrical activity. 

And Shaun had a voice in his head, the voice of his dead sister with the reservoir condition who would have recovered from amplification if she hadn’t been shot, and that voice seemed to operate on different thought patterns than Shaun’s own mind. 

However, she hadn’t thought she’d get lucky enough to verify if Georgia Mason’s reservoir condition, and the virtual clone carried in it, had been passed to Shaun. Even if it had, there was no way to test if he was immune without doing things that might, in some lights, look like attempted murder. Besides, this was more of a curiosity than a legitimate hypothesis to work with.

 So Shaun did her an enormous favor by returning already zombie-bitten and right in time to go into full amplification. Truly, the gods of useful data shone down upon her.

Shannon watches him locked in a room, talking to his sister and waiting for death, and checks the blood results again. He’s not going to amplify. He was infected, and his body fought it off, and he isn’t infected anymore. She has a solid set of results demonstrating that the human body is capable of developing real immunity to Kellis-Amberlee. She has more questions than ever before, but they are questions she’d rather be able to ask than the answers that had been assumed for decades. 

“Holy fucknuts,” she says out loud. This is for real.

She grabs a can of Coke, and goes to tell the kid the first good news she’s had to give anyone in years. 

 

 

Abbey, SL; Lanier, LA; Chandrasekhar, AR; Shoji, JE. “Mucosal immune system possibilities for vaccine development in murine models.”Antiviral Res, 2042;140:35–46.

 

 

Shaun and Georgia Mason visit Shannon, on their trip through Canada to some destination only they know. Somewhere a zombie moose can be poked with a stick, if Shaun gets his wish, and there is a great deal of Canada where that is a possibility. 

 “We, uh, wanted to tell you something. About how I got the immunity from Georgia,” Shaun starts, once they sit down with drinks, and express condolences over the losses in Abbey’s research group. 

 “It’s kind of sensitive information, and we didn’t really want it to be part of the files the EIS has on us,” George says, less awkwardly, but not by much. “I have a pretty good idea of how I originally shared the immunity developed by my reservoir condition with him.” 

 Shannon has had a while to think it over, and she has a pretty good idea too. “Kellis-Amberlee is transmitted by blood or through mucus membranes,” she replies. “So either you had a blood transfusion or shared needles in some way, which is not recorded in your medical history, or it was sexually transmitted. There are other possibilities, but those stand out as most likely."

Silence fills the room in response to that. “Yeah,” Georgia finally says, “yeah, that’s it. We’re not genetically related in any way, you know. But it’s the kind of thing people will think is weird, and that derails more important information."

 Shannon shrugs. Out of all the terrible things happening in the world, it’s cute what people think is outrageous. Wipe out entire populations of disease carriers just to attempt to keep viruses from evolving, and nobody can be bothered to look at the data, but two adults with a private life who happen to have been raised together, and all the gossip blogs would take over the news cycle. “I wouldn’t give a shit even if you were related,” she says. “It would only matter if you wanted to lower your chances of having a baby with genetic issues, and I know you’re both smart enough to use birth control. So is that what you came out here to tell me?"

 “It was on our way,” Georgia assures her, though she doesn’t say to where. “It just seemed like something that would be relevant to whatever you study next about inducing reservoir conditions."

“We could make up health information sites, fuck your way to zombie immunity,” Shaun offers. 

“I think I’ll actually work on verifying that in animal models before starting the PSAs, but thanks for confirming my suspicions,” Shannon says dryly. 

She sends them off in their van, and watches til it disappears from view down the road. They’re off to a new life, built out of the ashes of their past. Then she heads back into the lab. 

There’s some metaphor in that, about life after death and zombies, but she doesn’t have time to dwell on that, or on all she’s lost to get here. There’s work to be done.