Powered by huge databases of exomes, various groups (in particular Daniel MacArthur's at the Broad Institute) have been finding all sorts of amazing population genetics information for humans -- genes we thought were critical that perhaps can be lived without, alleles which may provide beneficial phenotypes, genes that appear intolerant of non-synonymous substitutions and so much more. Search PubMed for "ExAC" and you'll already pull in about 3 dozen citations, and the list seems to be growing on a steady pace. This treasure trove of human biology, revealing on a grand scale how human evolution and the genome have interacted.
Certain mosquitoes, such as from the genus Aedes and Anopheles, carry a witches' brew of nasty diseases which cause great misery and death across the world, particularly in tropical regions. Zika is in a long line of such diseases. Zika is unusual among such diseases in threatening large swaths of the U.S.. It should be remembered that once "tropical diseases" were also endemic in the U.S. -- much of the southeast was a hotbed of malaria, and a yellow fever epidemic decimated Philadelphia (I grew up near there!) in 1793.
Now, for this project the phenotype of interest is the collection of diseases the individual mosquito is bearing. So, this would be the general idea. Design the necessary capture reagents for each species of mosquito, with capture probes also to target the DNA-based disease organisms. For RNA viruses (such as Zika and yellow fever), a separate reverse transcription would be needed, followed either by capture or simply scoring by PCR. Then sequence the captured DNA and identify polymorphisms. It would be essential to collect large numbers of mosquitoes from a diverse number of geographical regions.
From this, a huge database of mosquito exomes with vector status would be assembled. The hope would be to identify alleles that correlate (positively or negatively) with specific diseases being carried (or not carried). The existence of such a database would also be a valuable resource for engaging and training researchers around the world, particularly in developing countries in which these diseases greatly tax the health systems.
I found one large mosquito exome study in PubMed, which was looking at resistance to carrying a nematode disease agent (Brugia malayi -- is there no end to the awful payloads for mosquitoes?). And this study indeed found clues to interactions that may determine whether a mosquito will carray or kill Brugia. So something much like that -- but far more grandiose and with the potential to inform future disease or mosquito eradication efforts.