So I recently finished Metal Gear solid 3: Snake Eater, i know i am a bit late.
At the end you see The boss's scar transforming into a white snake. and big boss holds a red leaf.
So at the beginning of DP you see a white snake Moving along annas' body. And i didn't see any explanation for that snake.
So could it be some sort of tribute or something to Metal gear solid 3?
and thoughts/explanations?

I don't know but I believe Swery has said that Hideo Kojima's work was an inspiration for him so it seems possible. Although with Swery, who knows what it really means.

You're probably right actually. That snake never gets explained. With all the movie talk in that game, I expect SWERY would have an appreciation of the MGS series and their cinematic nature.
 
Or you could just ask him on twitter.