Heterogeneity in Neutralization Sensitivities of Viruses Comprising the Simian Immunodeficiency Virus SIVsmE660 Isolate and Vaccine Challenge Stock

Abstract

The sooty mangabey-derived simian immunodeficiency virus (SIV) strain E660 (SIVsmE660) is a genetically heterogeneous, pathogenic isolate that is commonly used as a vaccine challenge strain in the nonhuman primate (NHP) model of human immunodeficiency virus type 1 (HIV-1) infection. Though it is often employed to assess antibody-based vaccine strategies, its sensitivity to antibody-mediated neutralization has not been well characterized. Here, we utilize single-genome sequencing and infectivity assays to analyze the neutralization sensitivity of the uncloned SIVsmE660 isolate, individual viruses comprising the isolate, and transmitted/founder (T/F) viruses arising from low-dose mucosal inoculation of macaques with the isolate. We found that the SIVsmE660 isolate overall was highly sensitive to neutralization by SIV-infected macaque plasma samples (50% inhibitory concentration [IC 50 ] < 10 ؊5 ) and monoclonal antibodies targeting V3 (IC 50 < 0.01 g/ml), CD4-induced (IC 50 < 0.1 g/ml), CD4 binding site (IC 50 ϳ 1 g/ml), and V4 (IC 50 , ϳ5 g/ml) epitopes. In comparison, SIVmac251 and SIVmac239 were highly resistant to neutralization by these same antibodies. Differences in neutralization sensitivity between SIVsmE660 and SIVmac251/239 were not dependent on the cell type in which virus was produced or tested. These findings indicate that in comparison to SIVmac251/239 and primary HIV-1 viruses, SIVsmE660 generally exhibits substantially less masking of antigenically conserved Env epitopes. Interestingly, we identified a minor population of viruses (ϳ10%) in both the SIVsmE660 isolate and T/F viruses arising from it that were substantially more resistant (>1,000-fold) to antibody neutralization and another fraction (ϳ20%) that was intermediate in neutralization resistance. These findings may explain the variable natural history and variable protection afforded by heterologous Env-based vaccines in rhesus macaques challenged by high-dose versus low-dose SIVsmE660 inoculation regimens.

Breakthrough of SIV strain smE660 challenge in SIV strain mac239-vaccinated rhesus macaques despite potent autologous neutralizing antibody responses

“…The prechallenge serum from vaccinated breakthrough animals neutralized the sensitive reference Env SIVsmE660.11 to varying degrees, whereas neutralizing activity against the resistant reference Env SIVsmE660.300-16 was uniformly low (Fig. 3B) (27). These data collectively demonstrate that all but one vaccinated animal produced prechallenge serum antibodies capable of neutralizing the autologous breakthrough T/F Env, yet this did not protect against infection.…”

“…Cell-to-cell transmission could play a more prominent role in intrarectal SIV infection than is currently recognized (48)(49)(50)(51), and higher concentrations of antibodies with certain specificities could then be necessary to prevent establishment of infection (52,53). It is similarly possible that the atypically high neutralization sensitivity of SIVsmE660 Env variants involves antibody specificities that are greatly enhanced in the TZM-bl assay and have limited relevance to those that neutralize HIV-1 (27). Finally, we were not able to directly assess the neutralizing activity in rectal secretions or in serum on the day of challenge.…”

“…3A demonstrates that the breakthrough T/F Env variants on the whole were highly susceptible to neutralization by antibodies in pooled serum. The majority of the T/F Envs from vaccinated animals were neutralized at an IC 50 titer of more than 1:1,000,000 by the serum antibody pool, typical of the extreme neutralization sensitivity of tier 1 SIVsmE660 variants such as E660.11 (27,28). In contrast, the T/F Envs from the control infections were less susceptible to neutralization (Fig.…”

Characterization and Implementation of a Diverse Simian Immunodeficiency Virus SIVsm Envelope Panel in the Assessment of Neutralizing Antibody Breadth Elicited in Rhesus Macaques by Multimodal Vaccines Expressing the SIVmac239 Envelope

“…SIVsmE660 is a viral quasispecies that mainly consists of neutralization-sensitive tier 1 Env variants and a minor population of resistant variants (17,18). SIVsmE660 exhibits phenotypic variability not only in neutralization sensitivity but also in pathogenicity and sensitivity to TRIM5␣-mediated restriction (17)(18)(19)(20). Because SIVsmE660 is largely susceptible to neutralization and its Env is substantially genetically distant from the SIVmac239 Env, this virus has become the most widely used heterologous challenge virus following SIVmac239 immunization.…”

“…Letvin et al demonstrated that an SIVmac239 Env-containing vaccine did not mediate protection against intrarectal challenge with the closely related, neutralization-resistant viral quasispecies SIVmac251 but the same vaccine provided protection against heterologous intrarectal SIVsmE660 challenge (16). SIVsmE660 is a viral quasispecies that mainly consists of neutralization-sensitive tier 1 Env variants and a minor population of resistant variants (17,18). SIVsmE660 exhibits phenotypic variability not only in neutralization sensitivity but also in pathogenicity and sensitivity to TRIM5␣-mediated restriction (17)(18)(19)(20).…”