[Turing_Machine]

"Maybe there's a stable region or set of regions you can target (in which case the high overall mutation rate doesn't matter). Or a cocktail of sequences, specific to the global HIV population (I doubt this, HIV mutates more in a single individual than Flu does in the global population)."

Hmm... I would bet that there is a cocktail of sequences such that if they are not conserved, the virus effectively becomes no longer HIV (no longer infectious, no longer capable of producing symptoms...).

HIV is obviously not a human being, right? Find every sequence where it differs, target them all. :-)

[new299]

I did a quick literature search, but couldn't find anything. It should be easy to answer that question.

There appears to be at least one conserved protein. However there's a lot of scope for different underlying sequences due to synonymous codons.

Depending on how long a fragment you need to target, that could end up being a lot of sequences, and unpractical.

[new299]

It's also possible that HIV could stick introns into the sequence too to avoid CRISPR...