If something radically altered your DNA, the first place the changes would show up would be at the site of a wound, where cells are dividing rapidly and new tissue is being produced. What's the first part of William Birkin to mutate dramatically? His right arm, which was riddled with bullets during the laboratory break-in. In addition, Birkin only changes forms after you fight him; he gets more alien every time he heals.
If you watched the cutscene where mutated William attacked the soldiers, you can see that we saw three of them getting killed, but there were four of them. The one who escape was Hunk.
Watch the opening cutscene as Claire rides into town. The first living residents of the city in the cutscene are...some rats crawling along the top of some crates. Later in the cutscene where Annete Birkin describes her husband's death, it's shown that the rats, as the initial carriers, helped spread the infection around the city.
Why does Wesker have a picture of Rebecca Chambers? In Resident Evil 0, he apparently recognizes her as one of the newest members of S.T.A.R.S while searching that picture, and leading an investigation of the first game.
It seems a bit odd that, when trying to start up the train in the B Scenarios, the game requires you to pick up two Joint Plugs and then immediately use them one room later, with nothing in between. Even more odd is that you only have to use one of the plugs on the generator - it automatically places the second one in with the first - when every other part of the game has you use items individually. Odd until you realize that what the game is doing is forcing you to have two inventory slots open, so that you can pick up the two-slot rocket launcher Ada throws to you during the Mr. X/Tyrant fight that starts immediately afterwards.
As pointed out in a fan FAQ, the reason why HUNK's team attacked Birkin's lab in the first place was revenge for Wesker and Birkin stealing credit on the Nemesis project from the French branch of Umbrella by producing a viable sample in Lisa Trevor. With Wesker gone, Birkin was vulnerable and he had a shiny new virus that was ripe for the taking. This is proven by HUNK's CO being the R&D chief of the French branch, as well as certain details from the Wesker Report.