These are great links, and answer many of the questions that I had. But there must be something more to the story; PhyloD is from 2007 and the news article is from 2011. Tangentially related, the research article that you linked is cited by a paper in PNAS that describes extraordinarily constrained coevolving group of sites in HIV (which appears to be a site of protein-protein interaction in the Gag protein). Such a group is likely a good target for multiple simultaneous therapeutics, as multiple mutations there likely reduce HIV's intrinsic fitness: http://www.pnas.org/content/108/28/11530.full