The HIV-1 epidemic in sub-Saharan Africa is driven largely by heterosexual transmission of non-subtype B viruses, of which subtypes C and A are predominant. Previous studies of subtype B and subtype C transmission pairs have suggested that a single variant from the chronically infected partner can establish infection in their newly infected partner. However, in subtype A infected individuals from a sex worker cohort and subtype B individuals from STD clinics, infection was frequently established by multiple variants. This study examined over 1750 single-genome amplified viral sequences derived from epidemiologically linked subtype C and subtype A transmission pairs very early after infection. In 90% (18/20) of the pairs, HIV-1 infection is initiated by a single viral variant that is derived from the quasispecies of the transmitting partner. In addition, the virus initiating infection in individuals who were infected by someone other than their spouse was characterized to determine if genital infections mitigated the severe genetic bottleneck observed in a majority of epidemiologically linked heterosexual HIV-1 transmission events. In nearly 50% (3/7) of individuals infected by someone other than their spouse, multiple genetic variants from a single individual established infection. A statistically significant association was observed between infection by multiple genetic variants and an inflammatory genital infection in the newly infected individual. Thus, in the vast majority of HIV-1 transmission events in cohabiting heterosexual couples, a single genetic variant establishes infection. Nevertheless, this severe genetic bottleneck can be mitigated by the presence of inflammatory genital infections in the at risk partner, suggesting that this restriction on genetic diversity is imposed in large part by the mucosal barrier.

One aim for an HIV vaccine is to elicit neutralizing antibodies (Nab) that can limit replication of genetically diverse viruses and prevent establishment of a new infection. Thus, identifying the strengths and weaknesses of Nab during the early stages of natural infection could prove useful in achieving this goal. Here we demonstrate that viral escape readily occurred despite the development of high titer autologous Nab in two subjects with acute/early subtype C infection. To provide a detailed portrayal of the escape pathways, Nab resistant variants identified at multiple time points were used to create a series of envelope (Env) glycoprotein chimeras and mutants within the background of a corresponding newly transmitted Env. In one subject, Nab escape was driven predominantly by changes in the region of gp120 that extends from the beginning of the V3 domain to the end of the V5 domain (V3V5). However, Nab escape pathways in this subject oscillated and at times required cooperation between V1V2 and the gp41 ectodomain. In the second subject, escape was driven by changes in V1V2. This V1V2-dependent escape pathway was retained over time, and its utility was reflected in the virus's ability to escape from two distinct monoclonal antibodies (Mabs) derived from this same patient via introduction of a single potential N-linked glycosylation site in V2. Spatial representation of the sequence changes in gp120 suggested that selective pressure acted upon the same regions of Env in these two subjects, even though the Env domains that drove escape were different. Together the findings argue that a single mutational pathway is not sufficient to confer escape in early subtype C HIV-1 infection, and support a model in which multiple strategies, including potential glycan shifts, direct alteration of an epitope sequence, and cooperative Env domain conformational masking, are used to evade neutralization.

Context: Antiretroviral therapy (ART) to treat and pre-exposure prophylaxis (PrEP) to prevent HIV infection are effective tools to help end the HIV epidemic. However, their use could affect HIV transfusion-transmission risk. Objectives: Three different ART/PrEP prevalence analyses in blood donors were conducted. Methods: First, blood samples from HIV-positive and a comparison group of infection-nonreactive donors were tested under blind using liquid chromatography-tandem mass spectrometry for ART. Second, blood donor samples from infection-nonreactive, 18-45 year-old, male, first-time blood donors in six US locations were tested for emtricitabine and tenofovir. Third, in men who have sex with men (MSM) participating in the 2017 CDC National HIV Behavioral Surveillance (NHBS) from five US cities self-reported PrEP use proximate to donation was assessed. Findings: In blind testing, no ART was detected in 300 infection-nonreactive donor samples, but in 299 HIV-confirmed infected donor samples, 46 (15.4%, 95% CI 11.5 - 20.0%) had evidence of ART. Of the 1,494 samples tested from first-time, male donors, 9 (0.6%, 95% CI 0.03 - 1.1%) had tenofovir and emtricitabine. In the NHBS MSM survey, 27 of 591 respondents (4.8%, 95% CI 3.2 - 6.9%) reported donating blood in 2016 or 2017 and PrEP use within the same time frame as blood donation. Conclusions: Persons who are HIV-positive and taking ART and persons taking PrEP to prevent HIV infection are donating blood. Both situations could lead to increased risk of HIV transfusion transmission if blood screening assays are unable to detect HIV in donations from infected donors.

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The female genital tract (FGT) provides a means of entry to pathogens, including HIV, yet immune cell populations at this barrier between host and environment are not well defined. We initiated a study of healthy women to characterize resident T cell populations in the lower FGT from lavage and patient-matched peripheral blood to investigate potential mechanisms of HIV sexual transmission. Surprisingly, we observed FGT CD4 T cell populations were primarily CCR7hi, consistent with a central memory (TCM) or recirculating memory T cell phenotype. In addition, roughly half of these CCR7hi CD4 T cells expressed CD69, consistent with resident memory T cells (TRM), while the remaining CCR7hi CD4 T cells lacked CD69 expression, consistent with recirculating memory CD4 T cells that traffic between peripheral tissues and lymphoid sites. HIV susceptibility markers CCR5 and CD38 were increased on FGT CCR7hi CD4 T cells compared to blood, yet migration to the lymphoid homing chemokines CCL19 and CCL21 was maintained. Infection with GFP-HIV showed that FGT CCR7hi memory CD4 T cells are susceptible HIV targets, and productive infection of CCR7hi memory T cells did not alter chemotaxis to CCL19 and CCL21. Variations of resident CCR7hi FGT CD4 T cell populations were detected during the luteal phase of the menstrual cycle and longitudinal analysis showed the frequency of this population positively correlated to progesterone levels. These data provide evidence women may acquire HIV through local infection of migratory CCR7hi CD4 T cells and progesterone levels predict opportunities for HIV to access these novel target cells.

Increased association of 7SK snRNA with P-TEFb in activated lymphocytes correlates with increased global transcription. This suggests that 7SK snRNA is unlikely to promote transcriptional latency in lymphocytes through an association with P-TEFb; it also suggests that the proposal that the association of 7SK snRNA with P-TEFb acts to inhibit transcriptional elongation needs to be re-evaluated.

Plasma and rectal viral load were correlated, and rectal STIs did not increase the likelihood of detecting HIV in the rectal secretions in MSM, including those with low or undetectable plasma viral load. Suppressing plasma viral load is likely to reduce risk of HIV transmission to insertive partners.

P-TEFb is a general transcriptional elongation factor composed of Cdk9 and either cyclin T1, T2, or K. A substantial portion of P-TEFb is associated with the 7SK small nuclear RNA (7SK) and the HEXIM1 or HEXIM2 proteins; this complex has reduced kinase activity in vitro relative to free P-TEFb. Here we report that 7SK and HEXIM1 levels are induced in activated lymphocytes concomitantly with increased P-TEFb activity and global transcription. We used siRNA-mediated depletion to probe the function of 7SK in HeLa cells. Depletion of 7SK caused a large reduction in the association of HEXIM1 with Cdk9 and cyclin T1, and greatly reduced the amount of the cyclin T1 present in the 7SK/HEXIM1/P-TEFb complex. Similar to previous studies, siRNA-mediated depletion of 7SK resulted in increased expression of several reporter plasmids tested, including a plasmid lacking promoter elements. However, in contrast to previous studies, which did not examine the effects of 7SK depletion on endogenous gene expression, depletion of 7SK did not appear to affect the expression of the corresponding endogenous genes. Moreover, 7SK depletion had no effect on expression from the integrated HIV-1 provirus or the c-myc and MCL-1 genes, three transcription units known to be highly dependent upon P-TEFb. Importantly, depletion of 7SK was found to cause apoptosis by 72 h post-transfection in HeLa cells. These results suggest that 7SK may provide an essential cellular function whose relation to P-TEFb function is unclear.