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Mistaken for Disease

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In cases where multiple people are found to be undergoing similar experiences with unpleasant physical effects, it's not unreasonable for medical professionals, journalists, and other observers to assume that this is the result of a known disease, or some new pathogen — even the start of an epidemic.
However, in this case, the source of these symptoms is usually a lot more complicated than that. Under comparatively mundane circumstances, anything from chemical spills to attacks by heretofore unknown animals may be to blame; in more overtly fantastical works, the "disease" could be the result of magic, alien weaponry, or maybe something even more exotic.
Long story short, it's not a disease.
Depending on the story, this can be played for mystery, horror or even comedy — especially if the "disease" turns out to be completely harmless despite all appearances. By the end of the story, the explanation might remain in place, either out of ignorance or as part of a cover-up... or the doctors might eventually realize that this is quite clearly not any form of recognizable infection and reveal the truth.
Can lead into You Don't Want to Catch This if the characters are intentionally exploiting the mistake.
Compare Hypochondria where someone mistakenly thinks they are sick, and Jumping-to-Conclusions Diagnosis where someone assumes someone is sick based on a trivial symptom like an itch or a sneeze. Contrast Definitely Just a Cold in which a troubling condition is dismissed as harmless.
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Among the many disasters afflicting Empire City in inFAMOUS is a lethal plague — one of the many reasons why the city is quarantined in the wake of the Ray Sphere explosion. However, though it's treated as a pathogen-spread disease, the sequel reveals that it most definitely isn't: it's actually a variant on radiation sickness caused by exposure to the Ray Sphere. Conduits are immune to its effects once they've been activated, but everyone else exposed to it is as good as dead.
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Phantoms. After the entire population of a small mountain town is either killed by unknown means or completely disappears, a doctor investigating the situation considers the possibility that the cause of the disaster is a disease unknown to science. However, it actually turns out to have been caused by an Eldritch Abomination feeding on the minds of living beings.
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In The Addams Family episode "Uncle Fester's Illness", Fester and Thing behave lethargically, and Morticia and Gomez believe they have a disease. As it turns out, Fester, with his Bizarre Human Biology, simply had a "mercury deficiency" and Thing was just sad because a picnic had been cancelled.
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In the Runaways short story "It's Not Lupus", Molly suddenly falls violently ill, and Nico's initial theory is that she caught some sort of old disease from Klara, who hails from the 19th century and thus is unvaccinated. Except that then Chase falls ill, too, despite Nico putting Molly and Klara in quarantine. The actual culprit is Nico herself, who accidentally cast a spell on Molly and Chase after losing her temper.
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Hayate's paralysis in Magical Girl Lyrical Nanoha A's is the result of an Artifact of Death feeding on her magic, though her doctors mistake it for some sort of ordinary (if unknown) malady since the number of earthlings aware of the existence of magic at this point in the franchise can literally be counted on one hand with fingers left over.
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The Fringe episode "The No-Brainer" begins with a teenager's brain being melted and pouring out of his nose. Walter Bishop, prone as always to thinking outside the box, initially suspects it might be the result of a super-strain of syphilis, but it eventually turns out to be caused by a Brown Note video transmitted over the Internet.
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My Left Nut: The premise of the story has The Protagonist Mick believing he has testicular cancer after his left nut becomes incredibly swollen, leading him to freak out because he thinks he might die. In the end, it's revealed to be a case of hydrocele, which is a fairly harmless ailment.
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The Perfection: Lizzie becomes convinced she's been infected by a terrible mystery disease in the middle of rural China when she gets sick on a bus and sees bugs spreading out of her arm, and she ends up cutting off her hand in a desperate attempt to stop it. Lizzie's lover Charlotte had actually poisoned her in order to make her sever her hand and free her from the poisonous environment of their music academy.
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By the end of In the Mouth of Madness, the outbreaks of violence and madness across the world have yet to be explained by health officials, as none of them believe John Trent's warning that the books of popular horror novelist Sutter Cane are driving readers insane. Even when readers begin to suffer hideous mutations, the Old Ones return to rule the world, and society itself collapses into a post-apocalyptic nightmare, authorities are still calling it an epidemic and advising people to distance themselves to prevent the spread of infection. Needless to say, it doesn't work: the film ends with Cane victorious and the human race completely overtaken by his masterpiece.
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In the Wicked fanfic The Land of What Might-Have-Been, the alternate Oz experiences a bizarre epidemic of people suddenly transforming into animals at random — sometimes causing them to permanently retain animal traits afterwards. With no spells detected in action at the scenes of the transformations, people assume it's a disease and call it "The Plague of Transformations", even believing it to be a Mystical Plague unleashed by an enemy of Oz. However, it's actually a chemical weapon created by Elphaba's Alternate Self, both to engineer her rise to power and to get Madame Morrible out of the picture by framing her for the crime.
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Spy X Family: In this fan comic, Anya looks at Damian, and rather than seeing the goofy looking kid with a stream of snot coming out of his nose (as she normaly pictures him in her imagination) she now sees that he has a "cool" looking face, and when he gets too close to her, her heart starts racing. When she gets home, Anya tells Yor about how "the boy" she thought she knew has suddenly started looking "cool" and makes her heart beat faster, and Loid, who overheard what they were saying, decides to eavesdrop on their conversation when he becomes concerned that his sixteen-year old daughter is now old enough to develop a physical attraction to a boy her age, and wants to know who this boy is. While Yor becomes alarmed and concludes that Anya needs to go to the hospital because she has a heart and eye condition, Loid becomes disappointed at the fact that his wife completely misidentified the fact that their daughter has a crush on a boy.
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In the Big Finish Doctor Who episode "Enemy of the Daleks", a research facility has been struck by a mysterious disease, infecting almost the entire staff population and forcing medical droid Sistermatic to quarantine them in a sealed ward of the infirmary while they slowly die. The only survivor is Professor Shimura, who claims to possess natural immunity. Upon catching a glimpse of all this, Hex at first believes the infection might be necrotising faciitis... but after sneaking into the ward for a closer look, he immediately confirms that this isn't the result of a disease. It's a parasitic infestation: Shimura is using the staff as incubators for the larvae of his genetically-engineered Kiseibya, which are now literally eating the researchers alive. For good measure, Sistermatic has been sabotaged so as not to recognize this fact, being unable to explain the condition of the patients even when Hex points out that infections don't leave bite marks.
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The Farscape episode "They've Got a Secret" features Moya demonstrating increasingly unusual symptoms after D'Argo impulsively breaks one of her internal components; among other things, her biochemistry surges in baffling ways, machinery around the ship begins malfunctioning, Pilot passes out, and DRDs become aggressive towards members of the crew found trespassing in certain areas. Crichton initially believes that Moya has been infected by a biomechanoid virus left behind by the Peacekeepers and accidentally released by D'Argo, and the ship's increasingly violent responses towards their investigations seem to bear that out. However, the truth turns out to be infinitely stranger: Moya is pregnant. The component D'Argo broke was a contraceptive shield; the malfunctions and biochemical weirdness were natural side-effects of the pregnancy; the aggression was due to a stressed-out Moya turning Mama Bear. Thankfully, the situation is resolved amicably before anyone's hurt.
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In one of the My Little Pony: Friends Forever comics, Spike and Zecora believe a disease has hit Ponyville because ponies have been breaking out in spots, acting lethargic, sneezing, and, in some cases, lisping, speaking nonsense, and having hypno-swirls in their eyes. As it turns out, though, they're just allergic to some mould that was on their hay.
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Avatar: The Last Airbender: Played for Laughs and subverted in "Return to Omashu" when Aang, Katara, and Sokka sneak back into the titular city only to get caught by some Fire Nation guards (as the Fire Nation had recently conquered the city), until one of the guards spots some strange marks along Sokka's neck, which the Gaang plays up as the result of a disease called "pentapox". Too afraid of catching "pentapox", the guards just let the kids go. As it happens, "pentapox" is actually just the result of the harmlessly adorable pentapus latching on to whatever it's swimming near, with the suckers on its tentacles leaving behind a few purplish marks, and the kids later use this to far greater effect when aiding every non-Fire Nation citizen in Omashu to escape the city by turning it into a false epidemic, then convince the guards into opening the city gates to let them all out.
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In Everybody's Gone to the Rapture, the effects of the Pattern on human beings are initially mistaken for an outbreak of flu, thanks in part to the military's pretext for the quarantine of Yaughton — which is really in place to prevent the Pattern from spreading to the rest of the world. Dr Wade soon recognizes that this explanation is nonsense, but still believes his symptoms to be the result of a disease, interpreting his crippling headaches and nosebleeds as the result of a rapidly-expanding tumour in his brain... until he notices the "liquid light" in the blood.
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Star Trek:
Star Trek: The Next Generation:
Downplayed in "Symbiosis". At first, it appears as though some aliens are suffering from a plague and have medicine to treat it. Then, it turns out that the "medicine" is a narcotic and the symptoms are withdrawal symptoms. However, it then turns out that there was a disease, but the drug cured it, only for the aliens to believe they still had the disease when they started experiencing withdrawal symptoms.
In "Unnatural Selection", some people suffer Rapid Aging. They initially think it's an infection, but it turns out that antibodies from some artificially created kids are attacking their DNA.
In "Thine Own Self", an amnesiac Data arrives on a planet with a village full of aliens with a Middle Ages-type level of technological advancement. Soon afterwards, villagers begin losing their hair, feeling weak, and developing fevers and burn-like lesions. They assume Data asymptomatically spread a disease to them, but it's actually radiation poisoning from the metal he had in his briefcase. He then makes a cure for the poisoning.
In the Star Trek: Voyager episode "Course: Oblivion", people begin to develop necrotic lesions, food decays, and B'Elanna in particular becomes lethargic and feels cold all the time. The EMH thinks it's due to an epidemic, but it's actually because they're not even the real Voyager crew: they're the "silver blood" copies of the crew made back in "Demon"; radiation from the warp drive is causing them to revert back to goop.
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In an episode of The Office (US), Michael believes he has herpes and goes around telling all the women he's had sex with that they may have it too. But at the end, its implied, and later confirmed in a future episode, that it was just an ingrown hair.
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In the Junji Ito Kyoufu Manga Collection story "Shiver", characters suffer inexplicable chills that are initially misdiagnosed as mundane illness. However, it turns out this is actually a precursor to holes opening up across the skin of the victims; contrary to the suspicions of the doctors, is not a disease, but the result of a cursed jade statuette passed from victim to victim.
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In Slither, upon hearing of Grant's ongoing transformation into an alien monster, the mayor attempts to dismiss it by claiming it must be the result of Llyme disease. The police officers on the scene — who actually saw the partly-transformed Grant in person — laugh uproariously at this, much to the mayor's annoyance.
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The Bay features several people in the small town of Claridge being admitted to hospital with lesions, boils, vomiting fits, and apparent necrosis. While in contact with the CDC, Dr. Abrams initially believes that this may be some kind of infection, but after seeing roughly half the town turn up in the hospital waiting room and witnessing the symptoms advancing too quickly to be treated even with amputation, he begins accepting wilder possibilities. Eventually, the CDC discover the truth: it's actually a parasitic infestation; Cymothoa exigua have been mutated by exposure to chemical waste from a factory farm, and are now capable of preying on humans. The "necrosis" is actually the parasites literally eating their victims alive from the inside. Worse still, their larvae are small and hardy enough to make it through filtration systems, meaning that people who drank local water or took a dip in a swimming pool are getting just as sick as the people who swam in the Bay or ate parasite-infested seafood. Unfortunately, by the time this information turns up, there's very little that can be done with it...
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The A Song of Ice and Fire novel A Game of Thrones, Jon Arryn is believed to have died from a chill of the stomach, having lapsed into a deadly fever and succumbed quickly due to old age. However, it soon becomes clear from the testimonies of both Jon's widow and the Master of Whispers that Jon was poisoned with the Tears of Lys — a rare poison that attacks the bowels in a way that will not seem unusual in old or sickly victims — presumably in order to prevent him from investigating the Lannisters' family secrets. A Storm of Swords reveals that the real killer was Lysa, Jon's widow, working on behalf of Petyr "Littlefinger" Baelish in order to start a war between the Starks and the Lannisters.
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Zigzagged in the Rugrats episode "All's Well That Pretends Well". Angelica really is sick, but it's not some crazy new disease; it's only a cold. She tries to hide her cold by making the babies come off as sick. First, she puts baby powder on Phil and Lil's faces and paints lipstick spots on them, intending to make them look as though they have the disease mentioned in Didi's medical book, but Chas thinks it's a strange, tropical illness instead. Betty quickly discovers that it's only makeup.
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The first story in Dissolving Classroom eventually features characters beginning to suffer chronic runny noses and advancing disorientation, initially believed to be caused by a cold or flu infection. It's actually a side-effect of hearing Yuuma Azawa's obsessive apologies. For good measure, they're wrong about the symptoms as well: the victims' brains are beginning to melt and pour out of their nostrils.
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In Deltora Quest: Sister of the South, this was done as a deliberate Evil Plan to destroy the city of Del. After Lief's mother Sharn returned from Tora, she was poisoned with a toxin giving symptoms of swollen scarlet botches. This illness would become known as the "Toran Plague" and was spread through a Blob Monster creature sent out in the night by the villain who would kill its victims by suffocating them, creating the illusion of a plague spreading.
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An inverted case in Zombieland: Double Tap. When Madison undergoes an allergic reaction to having eaten some peanuts, the gang ends up thinking that she's been bitten and is undergoing a zombification. It is only thanks to Columbus being ultimately unable to actually shoot her and choosing to instead shoot right above her head to scare her off that she is able to survive to later explain what was actually going on.
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SpongeBob SquarePants: In the episode "Once Bitten", Gary goes rabid and starts biting anyone he comes across. The result is that nearly everyone in Bikini Bottom contracts "Mad Snail Disease" where they turn into zombies, triggering a Zombie Apocalypse. However, once an actual doctor takes a look at Gary, he concludes that the so-called "disease" doesn't actually exist, and that the reason everyone is going all zombie-like is simply because of mass paranoia out of being bitten. As for Gary himself, he just has a really large thorn embedded in his tail.
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Late in Indiana Jones and the Fate of Atlantis, Indy begins encountering hideously-deformed bones scattered throughout the corridors of Atlantis, and briefly wonders if this the result of some kind of ancient disease — up until he notices that some of the skulls sport half-grown horns. They're actually failed experiments from the Colossus, victims of the Atlanteans' botched efforts to become gods. Klaus Kerner ends up becoming one such mutant in the finale.
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In the Doctor Who episode "The Empty Child", it's found that anyone making skin contact with the eponymous Undead Child soon manifest the same injuries as him — right down to the gas mask fused to the face. During his time at the Albion Hospital, doctors believed this was the result of some heretofore unknown disease, especially once his victims began spreading the plague to other patients. It's not until the following episode, "The Doctor Dances", that the truth is revealed: the Child was killed in the Blitz, only be brought back to life by a swarm of alien nanogenes; having never seen humans before, the nanogenes assumed that the Child was the acceptable template for a healthy human being and set out to "repair" any other humans they encountered by remaking them in the child's image.
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Henry Danger: Midway through Season 3, Henry gets a new superpower which enhances his reflexes allowing him to react more quickly. However, people began assuming Henry had some type of illness, given that the name they chose for the power was "Hyper Motility", and it took until the beginning of Season 4 to let them know. In the end, Henry decides to rename the power "Super-Fast Reflexes" to avoid any future consequences.
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The opening issue of The Sandman (1989) applies this trope to a real-life pandemic: Dream is imprisoned by a mortal occultist in 1915 during a botched attempt to capture his sister, Death; while he remains under lock and key, the disruption to the Dreaming results in random people around the world either suffering permanent insomnia or (more commonly) gradually lapsing into coma-like states. Not knowing what to make of it, doctors believe this pandemic to be the result of a disease, eventually labelling the condition Encephalitis lethargica or "Sleepy Sickness". As it did in the real world, the disease subsides just as quickly as it appeared with no explanation or cure — coinciding with Dream's escape from captivity.
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The opening issue of Hellblazer features random people across New York gorging themselves on the objects of their obsession — only to starve to death moments later, instantly reduced to Nothing but Skin and Bones despite being in perfect health beforehand. One talk show suggests that both symptoms are the result of a virus, but by this stage, Constantine already knows that this is the work of Mnemoth the famine demon.
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In Perdido Street Station, when people across New Crobuzon start turning up as brain-dead Empty Shells, people initially believe that this is the result of some kind of new epidemic. However, observers soon report glimpses of shadowy figures attacking the victims just before the bodies are discovered, and though the exact cause remains unknown to all but a select few, the epidemic is no longer accepted as an explanation - especially once a vampire is also found catatonic. It's actually the result of five Slake Moths being accidentally released from containment and going on a feeding frenzy across the city.
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In the Star Trek: Voyager episode "Course: Oblivion", people begin to develop necrotic lesions, food decays, and B'Elanna in particular becomes lethargic and feels cold all the time. The EMH thinks it's due to an epidemic, but it's actually because they're not even the real Voyager crew: they're the "silver blood" copies of the crew made back in "Demon"; radiation from the warp drive is causing them to revert back to goop.
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In The Mask episode "Little Big Mask," the eponymous character ends up uncontrollably regressing thanks to an experimental anti-aging cream. With a potential Death by De-aging on the horizon, Peggy Brandt is soon forced to take the toddler-aged Mask to the hospital where he first developed the anti-aging cream in the hopes of making a cure there, but because of his green face and demented behavior, well-meaning doctors immediately assume he's suffering from some kind of rare illness and put him in isolation, not knowing that these "symptoms" are quite normal for the Mask.
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The End of the World:
In Zombie Apocalypse, the scenario "Night of the Comet" begins with a series of animal attacks that are initially blamed on rabies. However, the scenario eventually makes it clear that freak radioactivity from a comet is actually reanimating the dead around the world as violently-hostile zombies, beginning with smaller animals and progressing gradually to humans.
Another scenario from the same book, "Under the Skin", features an ancient fungal parasite being accidentally unearthed by a mining operation and infesting all forms of life it encounters, compelling them to feed on the brains of others. Though the hosts initially retain a human appearance and intelligence, but eventually decompose as the parasite continues to feed on them, gradually reducing them to mindless zombies. Five days after the initial release of the parasite, doctors are left baffled by a plague of what appears to be necrosis and cannibalism... up until they finally discover the parasite infesting one of their patients.
In Wrath of the Gods, the crux of scenario "Gaea's Revenge" involves Mother Nature herself declaring war on humanity, resulting in animals all over the world spontaneously attacking humans — from wild animals to household pets. Baffled experts initially believe this to be the result of a mutant strain of rabies... up until plants begin growing out of control and earthquakes start leveling human cities en mass.
In the final scenario of Revolt of the Machines, "Nanopocalypse," the initial stages of a Grey Goo incident are met with confusion at first, and one of the many theories claims that the disaster is the result of a biological weapon - supposedly the reason for people suddenly withering into desiccated husks. Four days after the crisis begins, the government comes clean to the public, but with the nanobot swarms almost unstoppable, revealing the truth does very little to help apart from providing some basic safety guidelines.
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Vampire: The Masquerade - Bloodlines:
Primogen Alistair Grout seems to believe that vampirism is just a disease he can analyse and cure like any other illness, despite being a vampire himself for decades: as anyone who knows the setting and lore can tell you, vampirism is a biblical curse, and can't be cured by anything short of truly incredible circumstances. Then again, Grout is a Malkavian...
Also, thanks to the epidemic spreading throughout downtown Los Angeles, it's possible for a Nosferatu PC to be mistaken for a plague victim by a horrified desk clerk at the Empire Hotel. Of course, Nosferatu aren't diseased — just really, really ugly.
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Star Trek: The Next Generation:
Downplayed in "Symbiosis". At first, it appears as though some aliens are suffering from a plague and have medicine to treat it. Then, it turns out that the "medicine" is a narcotic and the symptoms are withdrawal symptoms. However, it then turns out that there was a disease, but the drug cured it, only for the aliens to believe they still had the disease when they started experiencing withdrawal symptoms.
In "Unnatural Selection", some people suffer Rapid Aging. They initially think it's an infection, but it turns out that antibodies from some artificially created kids are attacking their DNA.
In "Thine Own Self", an amnesiac Data arrives on a planet with a village full of aliens with a Middle Ages-type level of technological advancement. Soon afterwards, villagers begin losing their hair, feeling weak, and developing fevers and burn-like lesions. They assume Data asymptomatically spread a disease to them, but it's actually radiation poisoning from the metal he had in his briefcase. He then makes a cure for the poisoning.
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