Pie and Spike are on the border of Ponyville and Canterlot, they write letters to Twilight, Rarity and Applejack. Pinkie Pie regularly goes outside and helps to get rid of infected
Some of the healthy ones are hiding in the laboratory. While Twilight is looking for a vaccine, Rarity and her children are sewing bandages for the wounded
Applejack regularly goes out for new supplies, but sometimes protects the girls
Twilight works at a local lab while Rarity and Applejack look after the kids. so, Applejack went out to look for supplies, but did she close the door behind her?
Cadence and Armor are among the first to learn about the infection, and Shining Armor leads the knights and protects the empire, and hides the pregnant Cadence that is about to give birth in the castle