Compartmentalization of HIV-1 has been observed in the cerebrospinal fluid (CSF) of patients with HIV-related neurocognitive disorders (HAND). Compartment specific modifications have been frequently described in the variable loops and the glycosylation sites of the envelope, a known mechanism to escape antibody neutralization. Considering the low permeability of the blood-brain barrier, we wondered if a lower selective pressure by neutralizing antibodies (NAb) could favor the evolution of NAb-sensitive viruses in the CSF.
Single genome amplification (SGA) was used to sequence near full-length HIV-1 envelope variants (453 sequences) from paired CSF and blood plasma samples of 9 subjects with HAND infected by HIV variants of 5 different clades. Dynamics of viral evolution were evaluated with a bayesian coalescent approach for individuals with longitudinal samples (n=4). For 6 subjects, pseudotyped viruses expressing envelope glycoproteins variants representative of the quasi-species present in each compartment were generated, and their sensitivity to autologous neutralization, broadly neutralizing antibodies (bNAbs) and sCD4 was assessed.
In cross-sectional analyses, significant compartmentalization of HIV populations between blood and CSF were detected in 5 out of 9 subjects by all tests (p < 0,001). Phylogenetic analysis confirmed the presence of monophyletic populations evolving independently within the CSF (aLRT > 0.9). Some of the previously described genetic determinants for neuroadaptation were observed regardless of the HIV-1 clade. There was no difference of sensitivity to autologous neutralization between blood- and CSF-variants, even using sera collected at different time-points. By contrast, in all cases, we observed major differences of sensitivity to sCD4 or to at least one bNAb targeting the N160-V1V2 site, the N332-V3 site or the CD4bs, between blood- and CSF-variants.
Our data show that selective pressure by autologous NAb is not the main driver of HIV evolution in the CSF. Given that each of the conserved neutralizing epitopes is linked to a specific property for cell entry, our data suggest that some functional properties of the envelope are responsible for compartmentalization. Considering the possible migration from CSF to blood, CSF could be a reservoir of bNAb resistant viruses, an observation that should be considered for future studies of immunotherapy.