Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape

Abstract

Single genome sequencing of early HIV-1 genomes provides a sensitive, dynamic assessment of virus evolution and insight into the earliest anti-viral immune responses in vivo. By using this approach, together with deep sequencing, site-directed mutagenesis, antibody adsorptions and virus-entry assays, we found evidence in three subjects of neutralizing antibody (Nab) responses as early as 2 weeks post-seroconversion, with Nab titers as low as 1∶20 to 1∶50 (IC50) selecting for virus escape. In each of the subjects, Nabs targeted different regions of the HIV-1 envelope (Env) in a strain-specific, conformationally sensitive manner. In subject CH40, virus escape was first mediated by mutations in the V1 region of the Env, followed by V3. HIV-1 specific monoclonal antibodies from this subject mapped to an immunodominant region at the base of V3 and exhibited neutralizing patterns indistinguishable from polyclonal antibody responses, indicating V1–V3 interactions within the Env trimer. In subject CH77, escape mutations mapped to the V2 region of Env, several of which selected for alterations of glycosylation. And in subject CH58, escape mutations mapped to the Env outer domain. In all three subjects, initial Nab recognition was followed by sequential rounds of virus escape and Nab elicitation, with Nab escape variants exhibiting variable costs to replication fitness. Although delayed in comparison with autologous CD8 T-cell responses, our findings show that Nabs appear earlier in HIV-1 infection than previously recognized, target diverse sites on HIV-1 Env, and impede virus replication at surprisingly low titers. The unexpected in vivo sensitivity of early transmitted/founder virus to Nabs raises the possibility that similarly low concentrations of vaccine-induced Nabs could impair virus acquisition in natural HIV-1 transmission, where the risk of infection is low and the number of viruses responsible for transmission and productive clinical infection is typically one.

CD4 mimetics sensitize HIV-1-infected cells to ADCC

“…pNL43-ADA(Env)-GFP.IRES.Nef proviral vectors (deleted for vpu, nef, and nef and vpu or expressing the D368R Env variant) and the VSVG-encoding plasmid (pSVCMV-IN-VSV-G) were previously described (12,51). T/F and corresponding 6-mo consensus IMCs of patients CH58 and CH77 were inferred, constructed, and biologically characterized as described (36)(37)(38)(39).…”

“…To ensure that sensitization of HIV-1-infected cells by CD4 mimetics was also observed when using full-length clinically relevant primary HIV-1 isolates, we infected primary CD4 T cells with extensively characterized infectious molecular clones (IMCs) constructed from two transmitted/founder (T/F) and their corresponding 6-mo consensus sequences (36)(37)(38)(39). Primary viruses are known to exhibit low Env reactivity and, as such, have little or no intrinsic exposure of CD4i epitopes (40).…”

Resistance to type 1 interferons is a major determinant of HIV-1 transmission fitness

“…Molecular cloning of HIV-1 genomes is labor intensive and thus limits the number of IMCs that can reasonably be characterized. Moreover, predicting which viral genomes are functional in chronically infected individuals is challenging, because immune escape mutations frequently incur fitness costs (38)(39)(40)(41)(42)(43)(44)(45). Virus isolation represents an alternative to cloning, but bulk cultures cannot account for the biological variation of individual quasispecies members.…”

HIV-1 Conserved-Element Vaccines: Relationship between Sequence Conservation and Replicative Capacity

“…These studies were performed using a subject-derived gene integrated in a common HIV-1 backbone (9,(15)(16)(17)(18)(19)(20)(21)(22)(23)(24), and thus the results are contingent on mutations that are private to each subject's viruses and the replicative capacity of these viruses reflect a combination of mutations that differs from one subject to the next. More recently, infectious molecular clones have been developed from a number of subjects (25)(26)(27)(28)(29) and these infectious molecular clones provide the best opportunity to study interactions between different mutations and subject-specific mutational pathways that are evidenced during an HIV-1 infection.…”