HIV-1 Rev-RRE Functional Activity in Primary Isolates is Highly Dependent on Minimal Context-Dependent Changes in Rev

During HIV infection, intron-containing viral mRNAs have to be exported efficiently from the host cell nucleus to the cytoplasm in order to complete the replication cycle. To overcome cellular restrictions to export incompletely spliced transcripts, HIV encodes a protein, Rev, that is constitutively expressed from a completely spliced transcript. Rev is then imported into the nucleus where it binds to an RNA structure on intron-containing viral mRNAs called the Rev Response Element (RRE). Bound Rev multimerizes and recruits cellular factors that permit the nuclear export of the resulting ribonucleoprotein complex. Primary HIV isolates display substantial variation in the functional activity of the Rev-RRE axis, which may permit viral adaptation to differing immune environments. We describe two subtype G primary isolates with disparate Rev activity. Rev activity was correlated with in vitro fitness of replication-competent viral constructs. Amino acid differences within the oligomerziation domain, but not within the arginine-rich motif or nuclear export signal, determined the different levels of Rev activity. Two specific amino acid substitutions were demonstrated to be able to alter the low-activity Rev to a high-activity phenotype. However, introducing the original amino acids from the the low activity Rev into high activity Rev in this position did not result in significant alterations in activity, highlighting the importance of the broader sequence context for functional activity. These results demonstrate that studies of Rev and RRE activity variation, which may have broader implications for HIV transmission and pathogenesis, should include sequences from primary isolates, as findings using only laboratory-adapted strains cannot be generalized.