Okay, I'm going to try and give a thorough review here.
What should I be looking at?
The logo could be better. I'd pay someone here or at digital point to come up with something that resembles a microbe (germ, of course) or a disease symbol.
To focus the design I would move the navigation above the logo. I would also have just one map without the fading, or make the fade slower. It's kind of hard to see what's being offered when the front keeps changing.
Overall I think the design could be more dramatic/bold given the kind of topic it's on. Maybe use bolder colors or have a background other than white for the map section on the homepage.
The site is pretty cool, otherwise