Reservoirs of infectious HIV-1 persist despite years of combination antiretroviral therapy and make curing HIV-1 infections a major challenge. Most of the proviral DNA resides in CD4+T cells. Some of these CD4+T cells are clonally expanded; most of the proviruses are defective. It is not known if any of the clonally expanded cells carry replication-competent proviruses. We report that a highly expanded CD4+ T-cell clone contains an intact provirus. The highly expanded clone produced infectious virus that was detected as persistent plasma viremia during cART in an HIV-1–infected patient who had squamous cell cancer. Cells containing the intact provirus were widely distributed and significantly enriched in cancer metastases. These results show that clonally expanded CD4+T cells can be a reservoir of infectious HIV-1.

Decay of HIV-1 DNA in blood is rapid in the first year after ART initiation (86% decline), slows during years 1-4 (23% decline/year), and subsequently plateaus. HIV-1 DNA decay is not associated with the levels of CD8+ T-cell activation or persistent viremia. The determinants of stable HIV-1 DNA persistence require further elucidation. Clinical Trials Registration. NCT00001137.

c Although a number of PCR-based quantitative assays for measuring HIV-1 persistence during suppressive antiretroviral therapy (ART) have been reported, a simple, sensitive, reproducible method is needed for application to large clinical trials. We developed novel quantitative PCR assays for cell-associated (CA) HIV-1 DNA and RNA, targeting a highly conserved region in HIV-1 pol, with sensitivities of 3 to 5 copies/1 million cells. We evaluated the performance characteristics of the assays using peripheral blood mononuclear cells (PBMCs) from 5 viremic patients and 20 patients receiving effective ART. Total and resting CD4 ؉ T cells were isolated from a subset of patients and tested for comparison with PBMCs. The estimated standard deviations including interassay variability and intra-assay variability of the assays were modest, i.e., 0.15 and 0.10 log 10 copies/10 6 PBMCs, respectively, for CA HIV-1 DNA and 0.40 and 0.19 log 10 copies/10 6 PBMCs for CA HIV-1 RNA. Testing of longitudinally obtained PBMC samples showed little variation for either viremic patients (median fold differences of 0.80 and 0.88 for CA HIV-1 DNA and RNA, respectively) or virologically suppressed patients (median fold differences of 1.14 and 0.97, respectively). CA HIV-1 DNA and RNA levels were strongly correlated (r ‫؍‬ 0.77 to 1; P ‫؍‬ 0.0001 to 0.037) for assays performed using PBMCs from different sources (phlebotomy versus leukapheresis) or using total or resting CD4 ؉ T cells purified by either bead selection or flow cytometric sorting. Their sensitivity, reproducibility, and broad applicability to small numbers of mononuclear cells make these assays useful for observational and interventional studies that examine longitudinal changes in the numbers of HIV-1-infected cells and their levels of transcription.

To test the significance of human papillomavirus (HPV) type 16 and HPV16 E6 variants as risk factors for viral persistence and progression to high-grade lesion, we did a nested case-control study within a cohort study of >15,000 Caucasian French women. Three groups infected with highrisk HPV were compared: (a) women with cleared infection (controls, n = 201), (b) women with persistent infection (cases, n = 87), and (c) women who progressed into highgrade lesion (cases, n = 58 A subgroup of human papillomaviruses (HPV), referred to as high-risk types, are the etiologic agents of cervical cancer (1). Among the high-risk types HPV16 is the most prevalent type in premalignant and malignant cervical lesions worldwide (2, 3). Persistence of viral infection has a key role in cervical cancer development (4, 5). HPV16 is likelier to persist (6) and to cause progression into cervical intraepithelial neoplasia (CIN) than other high-risk HPV types (7,8). Nucleic acid sequencing of HPV16 genomes has revealed the existence of numerous natural variants that differ from the original European prototype sequence (9) up to 2% in the coding region and/or up to 5% in the noncoding region (10). HPV16 variants have been classified as five major phylogenetic clusters (or lineages): European, Asian, Asian American, African, and North American. For each lineage, several subclasses have been identified (summarized in ref. 11). Interestingly, three codon sites in the HPV16 E6 open reading frame coding for amino acids 10, 14, and 83 were shown to be under selective pressure (12). Variants at these residues lead to changes from arginine to glycine or isoleucine (R10G or R10I) at codon 10, from glutamine to histidine or aspartic acid (Q14H or Q14D) at codon 14, and from leucine to valine (L83V) at codon 83. Recent studies suggest that HPV16 E6 variants are involved in determining persistence of the viral infection and the development of cervical lesions (13-20). Some of these have shown that non-European HPV16 variants are more associated with disease progression than the European variants (21, 22).By using cross-sectional analyses of several European populations, we have previously shown that within the European lineage, the L83V E6 variant harboring a nucleotide substitution at position 350 (HPV16 350G) alone or in combination with other polymorphisms is more prevalent in cervical cancer than in . This phenomenon may be explained by the fact that natural variants alter the immunogenic and/or carcinogenic properties of the virus. In this study, we have used a large French cohort to elucidate further whether HPV16 and HPV16-specific variants are predictors for persistence of infection and progression into high-grade lesion.We did a nested case-control study within a large cohort study of >15,000 Caucasian French women ages between 18 and 76 years (median = 34 years). They had been recruited between 1997 and 2003 among women who underwent their biennial or triennial routine screening in the Department of Obstetrics and Gynaecology at t...

BackgroundThe epidemiological and molecular characteristics of hepatitis C virus (HCV) infection in the general population have been poorly investigated in Africa. The aim of this study was to determine the prevalence, genotype distribution and epidemic history of HCV in the Gabonese general population.Methods/Principal FindingsA total of 4042 sera collected from adults in 220 villages in all nine administrative areas of the country were screened for antibodies to HCV. HCV NS5B region sequencing was performed for molecular characterization and population genetic analyses. Of 4042 tested sera, 455 (11.2%) were positive. The seroprevalence of HCV varied significantly by administrative area, with the highest rate in Ogooué-Lolo province (20.4%) and the lowest in Ogooué-Maritine province (3.7%). History of parenteral injections, past hospital admission and age over 55 years were independent risk factors for HCV infection (p<0.0001). Phylogenetic analyses showed that 91.9% of the strains were genotype 4 (HCV-4), 5.7% genotype 1 and 2.2% genotype 2. HCV-4 strains were highly heterogeneous, with more than eight subtypes; subtype 4e predominated (57.3%). Coalescence analyses indicated that subtype 4e was the oldest, with an estimated most recent common ancestor of 1702 [95% CI, 1418–1884]. The epidemic profile indicated that it spread exponentially during the first part of the 20th century, probably by iatrogenic transmission.Conclusions/SignificanceThese results confirm the endemicity of HCV subtype 4e in Gabon and show that its spread is due to a cohort effect, with previous, possibly iatrogenic events. More extensive epidemiological studies are needed to better characterize the route of transmission and the dissemination of HCV in Gabon.