Genotypic and phenotypic characteristics of CXCR4-using transmitted/founder HIV-1 envelope glycoproteins.

The characteristics of HIV-1 envelope glycoproteins (Env) that initiate infection remain incompletely understood. In the primary HIV infection (PHI) stage, Envs using CCR5 as entry coreceptor (R5-tropic Envs) are much more frequent than those using CXCR4, alone or in addition to CCR5 (X4 or R5X4 Envs). However, a comprehensive analysis of the genetic identity and functional properties of CXCR4-using Envs during PHI is lacking to attest whether they are less transmissible than R5 Envs. Here, Env populations in the plasma of 22 recently infected individuals with R5 or CXCR4-using viruses were characterized by single-genome amplification. Mathematical modeling of HIV evolution, phylogenetic analyses, and viral quasi-species complexity indices showed that infection with CXCR4-using viruses is most often initiated by one, occasionally two variants, similar to R5 viruses. After transmission, the diversity and complexity of CXCR4-using and R5 Env populations increase similarly during PHI, with mutations accumulating in preferential regions of the gp120 portion of Env, but not in gp41. Both Env types also shared similar traits influencing viral transmission (variable loop length, N-glycosylations) and T-cell- but non-macrophage-tropism. However, CXCR4-using Envs exhibited specific sensitivity profiles to neutralization by soluble CD4 and broadly neutralizing antibodies (bNAbs), suggesting differences in epitope exposure and conformational dynamics compared to R5 Envs. These results, therefore, indicate that CXCR4-using viruses are equipped to initiate infection and, like R5 viruses, undergo a genetic bottleneck during transmission. The specific antigenicity of transmitted CXCR4-using Envs could help improve protocols using bNAbs for passive immunization and HIV vaccine development. IMPORTANCE: Transmitted/founder (T/F) viruses are predominantly R5-tropic, and only on rare occasions have T/F viruses that use CXCR4 been reported in the literature. Consistently, R5 viruses account for over 90% of the viruses present during primary HIV infection (PHI). However, it remains unclear whether CXCR4-using Envs, unlike R5 Envs, lack key properties for virus transmission and/or persistence in the new host. Here, we found that transmitted CXCR4-using Envs shared with R5 Envs common genetic and functional determinants, demonstrating their potential to transmit infection. So, the low prevalence of CXCR4-using viruses among donors probably explains why they are infrequently transmitted. As with R5 viruses, a genetic bottleneck occurs during transmission of CXCR4-using viruses, suggesting that the barriers determining this bottleneck are independent of viral tropism. Remarkably, transmitted CXCR4-using Envs exhibit distinct antigenic properties compared to R5 Envs, which could be leveraged to improve broadly neutralizing antibody-based preventive and therapeutic vaccine strategies.