Sorry for the wait, but here is the reference post I promised. This should provide enough information to all people to make side stories that fit the universe. I've also just created a new Submissions folder that anyone can post a story to.

Progression of the transformation

The transformation always begins with a bout of the flu with all its typical symptoms. For the initial round of transformations, the actual pony symptoms start about a week after the normal flu symptoms subside.

The initial generation of the virus induced a slow transformation. This is because the available pool of transformation magic is low. This is what we saw largely in Lazy Pines, where the virus was first unleashed. So the progression was:

Day 1 : Hair starts to change color
Day 3 : Hair color change complete
Day 4 : Eyes feel itchy
Day 5 : Eye color change, tailbone aches, mild aversion to meat
Day 6 : Tail appears, begin to lose height, stronger aversion to meat
Day 7 : Tail complete, mild pain in forehead (unicorns) or shoulders and upper back (pegasi) or signs of increased strength (earth ponies)
Day 8 : Ears migrate, height loss, meat unpalatable
Day 9 : Fur appears; night ponies-to-be will start to become nocturnal
Day 10 : Wings or horn appears
Day 11 : Feet turn into hooves, body starts to distort into equine form
Day 12 : Pony magical abilities begin to manifest
Day 13 : Muzzle appears, fingers begin to fuse
Day 14 : Transformation completed (sans cutie mark)

Further generations of the virus produced faster transformations, but the progression of changes is invariant. It's always hair -> eyes -> tail -> ears -> fur -> wings/horn/strength -> rear hooves -> magic -> muzzle -> complete. By the time Twilight cast the counterspell, transformations were taking only a few days to complete.

The transformation will tend to cure a person of most physical disorders, disease, and chronic conditions. Mental disorders depend on the nature of the disorder. If no actual brain damage is involved, then the person can expect to see improvement. Severe brain damage and mental impairment might see some improvement, but not a lot.

Where and how it spread

The virus started in Lazy Pines, a fictional town but with a real location. It spread from there to first the nearby towns, then further along the Front Range. Outbreaks then occured in Arizona and Florida (freeze frame bonus: how did Florida get infected? It was during the trip Sarah and Bob took to Breckinridge to get groceries).

From there it pretty much exploded, as this variant of the flu was intended to be almost 100% contagious (if you're into Stephen King, think Captain Trips from the novel The Stand and how rapidly it spread. So like that ... except ponies). This means nearly everyone in the US caught the flu component, but the counterspell stopped it from progressing to the transformation.

Heaviest hit was the US, mostly in the west and south. China and Russia also took big hits. Europe was not quite as severely impacted. I had not quite explored every possible nation as to what the impact would be, so there is some room for interpretation there. Suffice it to say, this had tremendous global impact.

Some places in the US, of course are much more severely impacted. Many smaller towns in the west are simply gone if their entire population transformed, or have been modified to better suit the needs of ponies. I called out Denver specifically as a city where about three quarters of the city are ponies.

Mental effects

The transformation incurs several noticeable mental effects as well. The first is a heightened herd instinct. This manifests as an increasing need to be close to others, both friends and families. This starts in the middle of the transformation, so it can be misinterpreted as simply a need for support while trying to figure out what's happening. Ths will cause those who are transforming to come together into groups for mutual support.

Speech patterns also start to change as the transformation progresses. The affected person will start to use "pony-pronouns" like "anypony" or "everypony."

As the transformation enters the last third or so, a sense of calm acceptance starts to come over the person. The pony features start to seem more natural, and there is an increasing sense of wanting to get the transformation over with. Pegasi-to-be will start to become anxious to use their wings, unicorns-to-be using their magic, and earth-ponies-to-be their strength and other abilities.

Once the transformation is completed, being a pony will seem natural and comfortable. There will be more of urge to get on with life, albeit as a pony. Then when Sunset's vision arrives, it will have a profound emotional impact on most as the dream will generally be tailored to the individual's concerns, worries, and challenges in life.

Finally, unless told about it by someone else, a pony will eventually discover the concept of cutie marks, and it will sound like something desirable.

Magic

People transforming start to come into their magical abilities near the end of the transformation. Only the earth ponies, however, realize a full potential -- their strength -- before the transformation is completed. Unicorns will be able to throw sparks with their horn but not much else. Pegasi wings won't carry them in flight until the transformation is completed.

Once fully pony, however, unicorns will be able to do simple levitation with a little practice, and pegasi will be capable of rudimentary flight until they practice it a bit more. Weather control is a bit different. All pegasi will have an instinctive feel for the weather in general, but actual ability to control will vary. Generally it will take one pegasus with a good deal of initial skill to take the lead and help the others bring out their abilities.

Earth ponies will come into their other abilities fairly quickly, which will allow them to grow food. Combined with the pegasi who have come into their weather control abilities, that will leave ponies for no want of food or water.

The night ponies (sometimes referred to as "bat ponies" or "thestrals", neither term I particularly cared for) are one of the rarer ones you will see. They are nocturnal and have enhanced night vision. They are also capable of the same dreamwalking ability as Princess Luna, though nowhere near her power level. Generally any sizeable pony community will have at least one.

The rarest of all are crystal ponies. They appear as they do in Equestria but have an additional ability. They can transform one magic type into another. I have yet to fully explore how this will work in future stories.

As of the end of the first story, some unicorns have puzzled out more complex spells, such as for healing. They may have additional abilities depending on their talents.

Cutie marks

The transformed earn cutie marks the same way other ponies do: by learning what their special talent is. Sometimes it's related to what they did as a human, or some latent talent they had that they never developed, and sometimes it's something completely new that opened up to them upon gaining pony magic.

A cutie mark is the end of the road. You can't transform back after that.

Alicorns

There are no alicorns among the transformed, period. Any alicorns appearing in a side story makes it non-canon. Feel free to write one if you want, it just will have to go in the non-canon folder.

Will alicorns eventually appear on Earth among the transformed? Perhaps. It certainly will not be in the immediate aftermath or the first sequel, and it will likely happen the way it did for Twilight, an Ascension after doing some feat of magic.

Timeline

For those wishing to write side stories that take place in the timeframe of the first story, below is a timeline of events. I try to indicate how much it has spread outside the initial area and how much the public would know, as well as conditions in the country in general.

WEEK 1

Monday - Tanner family starting to show the signs of the transformation, with Laura as the most advanced. Laura also sees Kevin this day, and he sends the first hair sample off for testing.

The rest of the world knows nothing of what is going on. All that would be noticed would be a new round of flu spreading largely through the western half of the country from people who visited or passed through Lazy Pines, likely on their way to or back from the skiiing resorts in Breckinridge.

Tuesday - More patients start showing up in Kevin's office with odd hair color.

Wednesday - By this time Kevin is getting back medical test results on hair samples. People in some areas outside of Lazy Pines have been getting the first discolored hair symptoms. The place mentioned specifically in the story was Arizona, but it wouldn't be the only area. Some may post on the internet about it, but not enough to generate a reaction.

Thursday - Laura gets the beginning of a tail, and Kevin notifies the Colorado Department of Health. The only thing making the general news is that cases of the flu have sharply increased.

People in Lazy Pines will likely be chatting more about this on the internet, so it will start to gain some traction. Laura posts a picture of her tail on the internet.

More people outside of Lazy Pines will start to see the first pony symptoms.

Friday - The intenet is abuzz with what's happening in Lazy Pines, and more incidents of discolored hair and eyes pop up from other locations. Rumors of "horse-man" Turner will start to spread as well.

The Colorado Department of Health is now fully involved, but no public announcements yet.

A reporter arrives in Lazy Pines and interviews some of the residents. It will be breaking news by next morning.

Saturday - People start sporting pony ears in Lazy Pines. The Colorado Department of Health declares a public health emergency covering Lazy Pines and the towns around it.

Social media explodes over this, and more people outside the area sport pony symptoms. The news media covers this story intensely, so pretty much the rest of the country knows by now that something is happening. A link with the flu is only speculation at this point, but flu cases are exploding as well across the country.

Sarah posts to her website about the pony-like petroglyphs that she found.

WEEK 2

Sunday - Isolation/quarantine formally imposed in the emergency zone area. A fully transformed Fred is taken into medical isolation, but the public is unaware of this.

The National Guard is called into assist in keeping order in the emergency zone. This causes most news outlets to cover this 24 by 7.

The "disease" is given its unofficial name: ETS, or Equine Transformation Syndrome.

Eileen tries to make her way to Lazy Pines from Denver, and we see the havoc that the emergency is causing with traffic through Colorado (the main east-west corridor through Colorado is I-70).

People in the areas covered by the emergency zone are encouraged to report to shelters.

Monday - Twilight and Starlight arrive, but no one knows about this yet.

People in Lazy Pines are sprouting wings and horns. When news of this breaks, it is likely to cause equal measures of disbelief and panic at first. The latter may cause some to take up arms to protect friends and family, especially in more rural areas.

The people in the shelters have not had their cellphones taken away, so many are broadcasting their plight to friends and relatives and on the internet.

Tuesday - The FBI formally step in. The government is treating this as biological warfare, but this is not public knowledge yet. The public, however, is considering it among all their other rampant speculation. There are a lot of implications of impending apocalypse.

A huge number of people across the country will be sick with flu. Some businesses will be without sufficient employees to handle day to day operations. Those who had recovered from the flu will be experiencing the first pony symptoms.

Twilight and Starlight make formal contact. While no details of this contact are formally released to the public, several people were in the church when Twilight and Starlight arrived, so likely something would get out to the public that something unusual happened.

Wednesday - The first full transformations complete within Lazy Pines and its immediate environs. Incidents of new pony symptoms outside of that arena will be ramping up sharply.

All airline flights in and out of the US have been grounded, and it is announced that the transporation grid will be shut down (no interstate travel allowed).

Thursday - Emergency zone staff discover that the hair of transforming humans is a vector by which the flu spreads. They discover the pocket of immunity among some Native American tribes.

People with pony symptoms outside the emergency zone will be coming together for mutual support. There will definitely be people advanced as far as the ears, and transformations in general will be accelerating. Terms like "ponify" or "ponification" will be making the rounds on the internet.

The government makes an official statement that part of what is behind the transformation is "a previously unknown force or energy that operates on matter in seemingly fantastic ways that have yet to be fully understood". One news reporter quips "that's the most long-winded definition of 'magic' I've ever heard."

Friday - The public learns about the hair vector, and this sparks panic and eruptions of violence against those who are transforming. There will be more who arefully pony and will start to tap into their magical abilities, however inexpertly at first.

This combined with rampant absenteeism from jobs first from people with the flu and later with people transforming will lead to breakdowns in infrastructure. Power outages will take longer to fix, for example.

Martial is declared, which means a lot more military presence in civilian areas.

Sunset's vision is propagaged overnight into Saturday morning to all those who have fully transformed. It will be repeated in subsequent nights to those who continue to reach the final phase, propagated by night ponies. ONLY full ponies get the vision, not those still transforming.

Saturday - Sunset is first taken into custody. The public knows only that ETS is an act of bioterrorism. After Sunset's vision, the fully transformed will start actively seeking to come together into tighter-knit communities along with those still transforming, who will be seeking protection.

The economy begins showing signs of imminent collapse. There will be shortages of food due to lack of deliveries. Rioting breaks in some areas. Banks will likely close to prevent a run on people withdrawing money.

WEEK 3

Sunday - The great western blackout starts early in the morning, affecting Colorado, Wyoming, Nevada, and Idaho. There is very little information on when power will be restored.

People who are newly transformed into full ponies will continue to experience Sunset's original vision as relayed by night ponies.

The number of fully transformed ramps up sharply. Those still with the flu see even that stage accelerating, people getting over it faster and the transformation starts right after.

Fully transformed ponies in urban settings will either migrate into the countryside or will rip up concrete and asphalt to expose soil. Pegasi will start using their abilities to affect the weather in these new communities.

News will leak that the government has apprehended the terrorist behind the transformations. Speculation abounds of a first contact scenario based on interviews with people who witnessed the arrival of Twilight and Starlight at the church. The government indicates that a formal statement is forthcoming.

Monday - An EAN (Emergency Action Notification) message is issued to the nation.Also, civilian communication networks will be partially inaccessible as they are taken over for emergency use, which means increasing isolation between communities.

Sunset briefly escapes but in the end was shot and killed, but this is not public knowledge yet.

Note that from this point on, no NEW transformations will start due to the thaumic pulse from the EAN and the later counterspell.

That night is the first time that ponies will start to receive the modified vision that encourages ponies to work with humans rather than remaining isolated from them.

Tuesday - The counterspell is cast. This is followed by the President addressing the nation where he starts to offer more details of what has happened. He states that ETS has been eliminated in those who have not yet started to show ETS symptoms, and that the remaining flu should run its course without incident. He does state however that this will not affect those who are already transformaing but states that there will be shelters set up for them.

NOTE: The more advanced the transformation, the more likely they will join pony communities and let the transformation run its course.

The timeline is a little more looser after this. Figure about a week for the remaining tranformation magic to be drained, which would cause transformations that had already started right before the counterspell to slow and stop in mid-transformation. Another week after that for Equestrian mages to attempt reversals of them (for those who are willing). There would be shelters set up by the government for this purpose.

An Ascension by a feat of magic implies that only unicorns can get it, so... only unicorns can ascend or any species of pony can?

6227096
Mud ponies and horseflies deserving to be Alicorns? Puh-lease!

(sarcasm)

6227096
Not necessarily. All the tribes have their own magic. For example, pegasi's magic is what allows them to fly when purely physically they shouldn't be able to. If you think about it, Rainbow Dash is actually one of the most powerful and proficient magic users in FiM. No, she's not casting spells the way a unicorn does, but she has so much pegasus magic and pushes it so hard that she's able to actually break the sound barrier. A feat we haven't seen from any other pegasus, and one that, really, I'd think would warrant an ascension if the order of events had been different in the show. So yeah, maybe a pegasus pull some really astounding weather feat, like wrangling a tornado. Or a night pony does some... uh, dream thing that's especially impressive (I've got nothing on that one). Or a crystal pony succeeds in transmuting one form of energy into another, more potent energy, say, a small amount of heat into a vast amount of electricity and in the process creates a means for free, plentiful power for the world. That could be worth ascension.

Still deep in my other project, but will get around to a story in this universe eventually. Likely something happening parallel to the events in Pandemic rather than later on.

As a transgender individual, I was wanting to explore a story about how this impacts a transgender person, since the transformation seems to take what is in the person's mind and character as the guide for what form they will eventually take, rather than biology. There had already been hints in your original story that the virus had fanned more contraversies about the nature of gender, even if what those were never were explained. I am an LGBT writer so I prefer to write LGBT characters.

Any hints about when we will be seeing the first sequel?

6227096
6227175
There is also the fact that Cadance was supposedly born a Pegasus.

6227096
Well Cadance was a pegasus who ascended after bouncing back some powerful love stealing spell, so we know ascendable feats of magic aren't limited to unicorns.

6227140
I always like to headcanon Luna and Celestia having been earth ponies before they ascended.

6227175

Rainbow Dash is actually one of the most powerful and proficient magic users in FiM. No, she's not casting spells the way a unicorn does, but she has so much pegasus magic and pushes it so hard that she's able to actually break the sound barrier. A feat we haven't seen from any other pegasus, and one that, really, I'd think would warrant an ascension if the order of events had been different in the show.

Ehh, there's more to being an alicorn than powerful magic. Alicorns always seem to symbolize something important Equestria needs. Day, night, love, friendship, each alicorn has their own domain and all it encompasses to watch over.

6227208
Yes, I'm aware of this, but my comment was in reply to

An Ascension by a feat of magic implies that only unicorns can get it, so... only unicorns can ascend or any species of pony can?

I was speaking purely of the magical aspect of it. Also, Flurry Heart is proof thart alicorns need not symbolize or preside over some aspect of the world.

6227321
Hmm, Flurry Heart is a complete exception to the rules though, being the only alicorn to be actually born an alicorn. And who knows? She might preside over her own domain once she gets her cutie mark.

6227197
I would love to see stories covering LGBT issues. As to whether I will tackle them myself, it depends on who I can draw on for help. I try to go by the maxim "write what you know, and for everything else, RESEARCH." However, LGBT issues are sensitive enough that I would much rather have close friends or family I can call on to share their experiences. While I have a few gay friends, I don't know anyone who is transgender.

Sunset likely would not have had a deep understanding of transgender issues, but where her directive concerning the transformation spell was that the resulting pony be as comfortable as possible in his or her body, it might mean that the spell would alter physical gender to match their identity. I hinted at this dilemma in the epilogue when Sarah spoke out against forced reversal of the transformation:

Then there are concepts we still debate vociferously among ourselves that the transformation 'solved' for them, such as gender identity, and thus you run the risk of someone with an agenda making a decision for them.

I tried to acknowledge here that even the scientific community is divided on the issue. There would be no easily solutions to deciding these sorts of things were they to go the route of forced transformation back to human. While that track is unlikely at this point, it does leave potential for friction within families were some remain completely transformed, while others had it reversed or never transformed at all.

6227391
We still don't know Cellestia and Luna's origin. For all we know, being born an alicorn may be the more common thing.

6227455

While that track is unlikely at this point, it does leave potential for friction within families were some remain completely transformed, while others had it reversed or never transformed at all.

Now there's a thought. A story about someone who, for whatever reason, never transformed but still wants to transform. Society and the government are unlikely to be supportive in that person's attempt to find a way to transform regardless, while the Equestrians... whoo boy, ethical and political concerns all around.

6227592
Hmm, maybe it's because I got into the fandom late and so didn't dive into the many six seasons worth of debates, comics and fiction about their origins, but when Celestia and Luna say that "the birth of an alicorn is something Equestria has never seen" and that it is "beyond even their understanding" that to me says that Flurry was the first born alicorn.

Granted though, this can easily go either way with just a bit of tweaking of the lines and fanworks don't have to stick to details like that even if it were that way.

6227664
it's also possible that that line simply meant that Flurry Heart is the first natural born alicorn since Equestria was founded and since Celestia and Luna are older then Equestria it is still possible for them to have been born as such and might even have been the last to be born as such which would likely explain why they don't it as they were to young to remember.

Does anyone have any idea when the sequel is going to start being published? And what the title is going to be?

6372038
I hope to start posting it this spring. I'm going to make a blog post about my progress later tonight. The working title right now is "Pandemic: Aftermath".

6374272
Are we allowed to recommend titles?

6374273
You're welcome to, but I would use them only if they line up with what the story will be about.

6374274
Thank you. And I’ve got a few ideas too:

“Pandemonium”.

“Brave New Worlds”.

“Compromises, Concessions and Conflicts”.

“Hoof in Hand, and Hand on Hoof”.

“Evolution”.

“Revolution”.

There is now a written up version of the (partially transformed) President's address to the country it can be found in Chapter 9 of the side story "Pandemic: What you are Meant to Be" by Halira it goes as follows...

"My fellow Americans, both human and pony, and all those tuning in around the world; today marks the official end to Equine Transformation Syndrome. I know many of you are confused, scared, and have questions. I am here to answer them to the best of my ability.

"There is no simple way of saying this, so I will say it straight out. Equine Transformation Syndrome was the result of a single alien invader from another world. That pony, Sunset Shimmer, had been living in secret on this planet for more than twenty years preparing to unleash this pandemic upon us. Her goal was nothing less than to forcibly change the entire population of Earth into her own species.

"Fortunately, we were contacted and assisted by the world that she was native to. With the combined efforts of Earth and Equestria we were able to eliminate the terrorist Sunset Shimmer and find a way to counteract what she had done.

"I am making sure I am clearly stating this now. This government and our allies put no blame on the ponies of Equestria for the actions of one mad terrorist. It has come to our attention she had been branded an outlaw before she ever arrived here by their government, and they were under the mistaken impression that she was deceased. It was pure luck that they were able to even determine that she had escaped to our world and have any time to try to stop her. They took action on our part with no personal gain for themselves, and they have our gratitude for that.

"We are now opening formal diplomatic relations with the first extraterrestrial species we have ever encountered. They plan to work with our world to develop a full cure for Equine Transformation Syndrome, but for now there will be no further outbreaks of it.

"Their government has concerns about the safety and security of the fully transformed and discussions regarding those ponies are ongoing. For now I wish to assure any pony that may be watching that this government will not tolerate any attack on its citizens by other citizens and that our pony citizens safety is a top concern. Until regular order can be restored any human attacking ponies will be punished in swift order. We are still under martial law and violence will not be tolerated.

"I will be dispatching all branches of the military, along with FEMA workers to the hardest hit areas. We will be maintaining order and bringing much needed relief supplies to both humans and ponies. We understand that while there are no new occurrences of Equine Transformation Syndrome there are many that are still in varying stages of it already. We will establish official government regulated shelters in all major metropolitan areas to meet the needs of these citizens. It is the Equestrian government's belief that those in the earlier stages of this may still have the changes reversed.

"In a few moments I will transfer this transmission to an undisclosed location where Princess Twilight Sparkle of Equestria will address the people of Earth as a whole for the first time. She has worked tirelessly and selflessly with our ground crews for some time now, and we would have lost all of humanity without her efforts. It is my sincerest hope that her continued work as official ambassador of her world will help bring us to a new era of peace and prosperity."

As for Twilight's speech it is incomplete but it start's with...

"Hello everyone and everypony. My name is Princess Twilight Sparkle, but you may all just call me Twilight as I hope to be seen as a friend to you all. In my short time here I have been very impressed by your culture, technology, and other achievements. I hope that both our worlds will have much to gain by working together in the years to come.

"It is unfortunate about the circumstances that brought about our first formal meeting. I want to reiterate that Sunset Shimmer was acting on her own without any cooperation with us. She tried this exact same thing before, and we had to take action about it then as well. We are sorry that we were slow in realizing she had escaped justice to here, and beg your forgiveness for that.

"I need to stress that she almost succeeded in her plans. If we had been any slower and without a few lucky breaks on our part we would not have been able to implement this counterspell. She was a brilliant mind and we are still trying to understand everything about her spell. There are some aspects of this transformation that are well beyond our current scope of knowledge. And the scale on which things have happened is mind boggling. There are now ten times more ponies living on this planet than there are on my own, and their wellbeing is a top priority to me personally and my world. Equestria will not tolerate the mistreatment of ponies, even newly transformed ones. If you are a pony watching this address let me assure you we will not allow any more to be done to you against your will."

"We will be sending ponies out to help with pony communities and helping the become more self sufficient. We understand a lot has changed in very little time and it isn't possible to just put things back the way they were. We have hope that the ponies of this world don't all choose to abandon the many great achievements they accomplished as humans and continue to work alongside humanity as they did before. This would be a tragedy, and one of the many horrible things that Sunset Shimmer would have caused had she been successful."

Sunset Blessing from Pandemic:What you are Meant to Be has art now for anyone who wants to use her.

6227175
On that note, Cadence is a pegasus in the cannon.

6738799
Holy necropost, Batman!

6738808
lol

ETS tribe sorting behavior:

So there are two factors at work for assigning a person to each tribe. There are their defining personality traits including interests--and then there are demographics. The spell constantly checks against the number of earth ponies. For instance if the number of pegasi is climbing and the number of earth ponies isn't high enough above their numbers it will be make the standards to become a pegasus more strict. The same for unicorns and night ponies. It's like a sliding standard scale of what sorts each person into each tribe.

If a tribe is no where near it's 'quota' versus earth ponies then the standards for sorting them into that tribe are more relaxed. So depending on what the quotas checked when a person started transforming each person may have had different levels of strictness applied for sorting them for each tribe.

The earth ponies always had to be the most numerous by a certain percentage of the population in comparison to each tribe.

Night ponies were instance were set to have a much lower critical mass number than the other tribes, making it hardest to be sorted into night pony. As you got closer to your critical mass of numbers the spell would have increasingly strict standards about sorting you into that tribe (and if critical mass has been reached it just won't put you into it no matter what until there are enough more earth ponies to allow for that tribe again).

It will check you against multiple tribes so it isn't a strict your either this type of pony or an earth pony. This is why you'll see ponies that are of one tribe that clearly demonstrate personality traits that you'd think would put them in a different tribe. An example would be Wildflower in Aftermath who shows strong night pony traits, but she was sorted into unicorn. The strictness for night pony was so high it went with the second most appropriate tribe.

If no clear appropriate tribe can be determined based on where they are in the various sliding scales then it will default to earth pony. Earth pony has it's own standards of course, but lack of clear tribal mindset in the sliding scale can also sort a person into this tribe.

Very young foals it treats with a more random demographic sorting method rather than personality unless a strong personality has been already established, which may be unlikely.

6227063

freeze frame bonus: how did Florida get infected? It was during the trip Sarah and Bob took to Breckinridge to get groceries

It was that girl Bob talked to, wasn't it...?