A 12-year old boy unwittingly sets off a deadly pandemic on an island and becomes the lone survivor. He must deal with grief and guilt, while trying to outrun the Army, and decide if he can trust his estranged mother.

That remind me of the French comic book "Le transperceneige". It has been adapted into a Korean movie "Snowpiercer". I have not seen the movie, but I gather they have changed quite a lot of the original story.
In the comic book, a perpetual snow storm engulf earth. Humanity survives on a train. A disease is spreading from the back coaches killing everybody. One poor from the relegated back coaches rebels. He tries to grap the power while trying to escape a deadly disease. He finally realises that he is the carrier of the disease. The entire train died because he was trying to reach the first coaches.

Back to your logline.
What is the end game of the kid? He is unlikely to always evade the army while stuck on an island.
Why is his mother estranged? Why does he need to trust her, does she offer help? How does she know how to contact him while the army does not?
Your logline throws a very interesting concept, however it also raises too many questions.