First of all, let's think about the scientific method, and its processes of how it works.
It all starts with observation, so we need to check all the data we have and all the information that can be collected to have a good thought on what's going on.
After gathering enough information, let's think about a hypothesis that could help solving this problem. Well, reading the question, we can check that that region passed through the wettest summer in 100 years, and that's the main problem here, because before this weather, was this disease a problem? I guess not, so this can be a reason, the change in the percentage of water in the air.
With that said, we need to test if this is true or not, and for that, we'll need mosquitoes with the West Nile virus, and we'll put them in different environments, one that it's wet, and another one that it's not that wet, just like the West Nile problem. This way we can check if this is the problem or not, if it's affecting their reproduction and etc.