3 We begin…
In the bustling city of Fuchsia, a mysterious illness began spreading in the late winter of 2031. What started as an isolated flu-like sickness among trainers soon spiraled into a full-blown outbreak, baffling doctors and scientists alike. But the real mystery? The source of the infection remained completely unknown. As scientists scrambled to sequence the pathogen’s genome, an unsettling possibility emerged: Could this virus have been silently lurking among the Safari Zone in the city long before anyone could have even gotten sick?
We begin our outbreak mystery with the city’s history:
The fictional city of Fuchsia City is home to a population of about a million people and rests amid a Safari Zone. The Safari Zone, constructed many hundreds of years ago, is home to many docile wildlife that have adapted to coexist with humans. Living in the forests of the Safari Zone are many different species of friendly canines, always running playfully amuck in groups, different feline species, some of which are cunning, curious, and mischievous, and small bears, known for their soft fur and sheer laziness. The canines, felines, and small bears only make up a portion of the animal population; you can also find deer, bulls, kangaroos, a variety of bird species, both small and large, (including the famous ducklings!), pikas of varying sizes, and many diverse insects, of which includes the many diverse species of butterflies.
Due to the docile nature of the animals, many tourists from all over would come visit the Fuchsia City Safari Zone to interact with the animals. From time-to-time animals with potential docile natures are introduced to the Safari Zone but are fully trained by expert animal trainers before being integrated into the wild.
3.1 The newest attraction:
The Safari Zone is also home to many fruit bat species that you can find hanging about in the fruit trees and caves hidden within the mountains. The newest attraction of fruits bats includes the muubat, one of the friendliest and meek bat species to interact with. In December of 2030, Fuchsia City brought in a four muubats to be trained and then integrated into the Safari Zone. Many of the residents and tourists alike were very excited to meet the muubats. To garner attention to the newest attraction, Fuchsia City advertised that the muubats should be fully integrated into the Safari Zone by the summertime.
3.2 Standard Protocol:
Any new animal introduced into the Safari Zone must undergo a series of examinations, testing, and training before release into the wild. This is especially critical for muubats, as bat species are known to harbor a variety of viral pathogens that can occasionally spill over into humans or other animals. To reduce this risk, all candidate species are tested for known bacterial and viral agents capable of causing illness.
One of the most transformative technologies in pathogen detection is whole genome sequencing (WGS). Unlike traditional diagnostic tests that are designed to detect specific pathogens, WGS sequences the complete genetic material present in a sample and can identify a wide variety of microbes, including bacteria, viruses, fungi, and others, in a single analysis. This broad scope is what makes WGS such a powerful tool for clinical testing and routine surveillance.
From an epidemiological standpoint, WGS offers far greater resolution than conventional tests. Traditional methods may only reveal that two cases are infected with the same species or virus, but WGS allows investigators to examine genetic subtypes, genotypes, or even specific mutations. This is particularly useful for identifying whether two individuals are infected by the same strain or by genetically distinct lineages, which may indicate that the cases are not linked. In outbreak investigations, WGS can therefore be used to rule out cases that are not epidemiologically connected. Conversely, sequences that are genetically similar, especially when linked across space and time, may suggest a common source or chain of transmission.
However, WGS still depends on the quality of the underlying databases used for taxonomic identification. If a pathogen is completely novel, or if only limited genomic data exist for that organism, the system may fail to identify it. In addition, low-abundance pathogens or technical biases in sequencing can lead to false negatives. These limitations are important when interpreting negative results, particularly in surveillance contexts where early detection is crucial.
3.3 Testing the muubats:
Upon arrival, each of the four muubats underwent a full physical examination and sample collection. Blood and swab samples were collected from each bat. Blood samples were cultured for bacterial growth over 48 to 72 hours, yielding no viable colonies. Remaining samples were archived for potential future use.
Swab samples, collected from oral and cloacal sites, were analyzed using a pathogen-agnostic sequencing panel, which is a specific application of WGS. A pathogen-agnostic panel is typically used for clinical or single-host samples where the goal is to sequence all microbial nucleic acids in the specimen without targeting a particular species. In this case, the panel was used to detect any known microbial genomic material present in the bat swabs by comparing the sequencing output to reference databases.
While this approach is broad in scope, it is limited to organisms that already have validated reference sequences. If a novel virus is present in the sample but not represented in the database, the test may return a negative result, even if the pathogen is there.
Following nucleic acid extraction, the samples were prepped for sequencing, with a turnaround time of approximately ten days. During this time, the muubats remained in isolation and interacted only with their trainers. Swab extracts were also archived at minus 80 degrees Celsius in accordance with facility protocol.
When the sequencing results returned, they showed no evidence of any known pathogens associated with illness. With culture and sequencing data both suggesting the muubats were healthy, they were relocated to a designated training facility within the Safari Zone to begin acclimatization.
4 The winter season of respiratory illnesses begin:
The muubats arrived in the Safari Zone facilities in mid-December of 2030. Come January of 2031, the fruits bats were doing well adapting to the new humans and environments. At the beginning of January many of the trainers for the muubats went to a week-long conference to present on how well the bats were doing with training and adapting to the environment. However, on the third day, a mystery flu-like illness started to sweep through the conference. This illness was accompanied with symptoms like fever, chills, cough, sore throat, runny or stuffy nose, muscle and body aches, headaches, and fatigue. Some individuals even experienced diarrhea. Five of the eight Muubats trainers started to come down with the illness as well. On the fourth day of the conference, three people were confirmed to have an influenza virus infection and may have been the source of the outbreak. At this point in time many people have come down with an illness and so the final days of the conference were cancelled.
The muubat trainers believed it was in their best interest to fly back to Fuchsia City, so despite most of them being sick, they all masked up and traveled back home. Upon arrival, three of the trainers decided to isolate under the assumption that they had an influenza virus infection but opted out on getting any tests done. The three seemingly healthy trainers returned to work immediately. Two of the trainers said that they felt so ill that they decided to go up to the lab to get tested.
The two trainers went to the Safari Zone lab to get tested, but to their surprise the tests came back negative for the influenza virus. Doctors assumed it was probably some other respiratory pathogen not included in the testing panel and archived their swab samples for future investigation. The diagnostic panel used included a limited set of common respiratory viruses typically seen during seasonal respiratory illness season, but was not designed to detect every possible respiratory pathogen. The doctor mentioned that there wasn’t much they could do besides manage the symptoms, and provided medicine to alleviate them. The doctor told them to isolate for the time being and to come back in a couple of weeks if they’re still feeling unwell.
Unlike the flu caused by an influenza virus infection, which typically resolves in a week or two, this illness lingered. The two trainers who had been tested continued to experience fatigue, cough, and body aches for several weeks. Once the worst of their symptoms had subsided, they returned to work—however, they remained sluggish. They decided to go in for follow-up testing. Since the pathogen remained unidentified, the doctor opted to test for host immune response markers. The results showed elevated levels of interferons and pro-inflammatory cytokines, suggesting that the trainers might still be fighting the infection—and could potentially be contagious still.
Given the possibility of ongoing transmission, the trainers chose to continue quarantining until their fatigue and lethargy fully resolved. The three trainers who had not been tested also remained in isolation as a precaution. After a little over a month, all five trainers were feeling well again and returned to work.
5 The flu-like illness continues to spread into late winter:
As winter progressed, reports of a growing flu-like illness began to stream across regional news outlets. Doctors feared it might be the worst flu season in years. However, as patients began to seek testing and treatment, clinicians noticed something unusual. While many individuals tested positive for influenza virus, a substantial number of patients with similar symptoms were negative for both influenza virus and other common respiratory pathogens.
In response to the escalating situation, and out of concern that the illness could potentially affect wildlife, Fuchsia City decided to temporarily close the Safari Zone to outside tourists at the end of January. The goal was to reduce the possibility of human-to-animal transmission while allowing the park to remain open to staff and local residents. This intervention helped reduce the spread of influenza viral infections. Across a population of roughly one million, only about 100 influenza viral infection cases were confirmed among residents, trainers, workers, and medical personnel.
Despite curbing transmission of influenza viral infections, the unexplained illness continued to spread. By late January, more individuals were seeking care with respiratory symptoms, but their tests for known pathogens continued to return negative. These cases were not confined to a single setting, and some Safari Zone workers were also among those affected. Health officials were beginning to suspect that something atypical was happening.
At this stage, the cause of illness had not been identified. Clinicians began to question whether diagnostic tools were failing to detect a known pathogen, or whether something unfamiliar was circulating. The symptoms resembled influenza viral infection, but tests to detect the influenza virus were often negative. Some speculated that it could be a bacterial infection with flu-like symptoms, while others considered the possibility of a novel agent not captured by existing diagnostic panels. Although many leaned toward a viral explanation because of the seasonal timing and clinical presentation, there was not yet sufficient evidence to determine the nature of the pathogen.
Initially, animal testing had not been pursued, since no signs of illness had been reported among Safari Zone wildlife. But that changed soon after several of the trainers returned to work. A number of canine species began exhibiting signs of illness, followed by several feline species and a growing number of ducklings. The animals showed symptoms similar to those reported by human cases, including lethargy, appetite loss, and respiratory distress.
Shortly afterward, additional local residents who had recently visited or worked in the Safari Zone began reporting similar symptoms. This growing overlap in timing, symptoms, and potential exposures prompted public health authorities to expand their investigation. In early February, officials initiated testing in animals to determine whether the same illness might be spreading across species.
