Search

During 2006-2007, transmitted human immunodeficiency virus (HIV) drug resistance (TDR) among drug-naive women with newly diagnosed HIV infection and likely to be recently infected when attending antenatal clinics in Entebbe was found to be <5% with use of the World Health Organization (WHO) survey method. Using the same method, we attempted to classify TDR among women who seroconverted during 2008-2010 and who were identified from a cohort of recently infected sex workers in Kampala, Uganda. TDR mutations were identified using the 2009 WHO TDR mutations list. The WHO survey method could not be used to classify TDR because the necessary sample size was not reached during the survey period. However, a point prevalence estimate of 2.6% (95% confidence interval, 0.07%-13.8%) nonnucleoside reverse-transcriptase inhibitor TDR was determined.

Introduction: HIV pre-exposure prophylaxis (PrEP) significantly reduces the risk of HIV acquisition. However, studies have demonstrated discordance between self-reported measures and biomedical benchmarks of PrEP adherence. We estimated the correlation between self-reported PrEP adherence and PrEP biomarkers and explored factors associated with adherence among men who have sex with men (MSM) in Nigeria. Methods: TRUST-PrEP, an open-label, prospective study; conducted in Abuja between April 2018 and May 2019. MSM ≥ 18 years with substantial HIV risk were enrolled. Participants reported PrEP adherence in the last month using a 4-point scale from "poor" to "perfect" and serum samples for PrEP biomarkers were collected at months 3 and 9. Serum tenofovir concentration was measured by liquid chromatography-tandem mass spectrometry and considered protective for adherence if ≥ 4.2 ng/ml. Spearman's rank correlation was used to estimate correlation between self-reported adherence and measured tenofovir levels. Generalized estimating equations with a logit link was used to estimate adjusted odds ratios (aORs) and 95% confidence intervals (CIs) for associations between self-reported adherence and laboratory-measured adherence. Results: A total of 219 MSM with median age 23 (interquartile range 20–27) years had at least one PrEP biomarker assay. Only 66/219 (30%) had at least one record of protective tenofovir concentration. Correlation between tenofovir and self-reported adherence at 3 and 9 months were 0.1 and 0.02 respectively. Furthermore, 17/219 (8%,) and 49/219 (22%) had serum tenofovir of 4.2–35.4 ng/mL and ≥ 35.5 ng/mL, corresponding to at least 4 and 7 days' PrEP use in a week, respectively. PrEP adherence was higher among participants introduced to PrEP in the clinics compared with communities (aOR: 8.35, 95%CI: [3.24, 21.5]) and those with same-sex practices family disclosure (aOR: 3.60 95% CI: [1.73, 7.51]). Conclusion: Self-reported PrEP adherence poorly correlated with biomarkers. Facilitating clinic-based PrEP introduction and disclosure of same-sex practices to family among MSM may improve PrEP adherence. [ABSTRACT FROM AUTHOR]

Background: Deep sequencing could improve understanding of HIV treatment failure and viral population dynamics. However, this tool is often inaccessible in low- and middle-income countries.Objectives: To determine the genetic patterns of resistance emerging in West African HIV-1 subtypes during first-line virological failure, and the implications for future antiretroviral options.Patients and Methods: Participants were selected from a Nigerian cohort of people living with HIV who had failed first-line ART and subsequently switched to second-line therapy. Whole HIV-1 genome sequences were generated from first-line virological failure samples with Illumina MiSeq. Mutations detected at ≥2% frequency were analysed and compared by subtype.Results: HIV-1 sequences were obtained from 101 participants (65% female, median age 30 years, median 32.9 months of nevirapine- or efavirenz-based ART). Thymidine analogue mutations (TAMs) were detected in 61%, other core NRTI mutations in 92% and NNRTI mutations in 99%. Minority variants (<20% frequency) comprised 18% of all mutations. K65R was more prevalent in CRF02_AG than G subtypes (33% versus 7%; P = 0.002), and ≥3 TAMs were more common in G than CRF02_AG (52% versus 24%; P = 0.004). Subtype G viruses also contained more RT cleavage site mutations. Cross-resistance to at least one of the newer NNRTIs, doravirine, etravirine or rilpivirine, was predicted in 81% of participants.Conclusions: Extensive drug resistance had accumulated in people with West African HIV-1 subtypes, prior to second-line ART. Deep sequencing significantly increased the detection of resistance-associated mutations. Caution should be used if considering newer-generation NNRTI agents in this setting. [ABSTRACT FROM AUTHOR]

Introduction: Men who have sex with men (MSM), and transgender women (TGW), face specific obstacles to retention in care, particularly in settings with stigmatization such as sub‐Saharan Africa. We evaluated the impacts of HIV status and other factors on loss‐to‐follow‐up (LTFU) and visit adherence among MSM and TGW in Abuja and Lagos, Nigeria. Methods: TRUST/RV368 is an open cohort that provides comprehensive and integrated prevention and treatment services for HIV and sexually transmitted infections (STIs) at community venues supportive of sexual and gender minorities. Recruitment began in March 2013 and participants were followed every three months for up to 18 months. LTFU was defined as not presenting for an expected visit in the past 180 days. Visit adherence was calculated as a rate of completed visits adjusted by the number of three‐month intervals elapsed since enrolment. HIV and other factors predictive of LTFU and visit adherence were evaluated using Cox proportional hazards and Poisson regression models, respectively. Results: A total of 1447 participants who completed enrolment evaluations over two visits as of November 2018 were included in these analyses. Their median age was 24 years (interquartile range [IQR]: 21 to 28) and 53% (n = 766) were living with HIV. LTFU occurred in 56% (n = 808) and visit adherence was 0.62 (95% confidence interval: 0.61 to 0.64) visits per three‐month interval. Participants at risk and living with HIV had median follow‐up times of 12 months (IQR: 6 to 22), and 21 months (IQR: 12 to 30), respectively (p < 0.01). After controlling for other factors, LTFU was less common among participants living with HIV or other STIs and more common among those who did not own a cell phone, sold sex and had never undergone HIV testing prior to enrolment. These factors had parallel associations with visit adherence. Conclusions: Retention was suboptimal in Nigerian clinics designed to serve MSM and TGW. Particularly high LTFU and low visit adherence among participants at risk for HIV could complicate deployment of HIV prevention interventions. Marketing the benefits of testing, improving access to cell phones and nurturing more trust with clients may improve retention among marginalized communities in Nigeria. [ABSTRACT FROM AUTHOR]

Background: Many lines of evidence point to HIV-1 subtype-specific differences in the development of drug resistance mutations. While variation between subtype C and others has been extensively explored, there has been less emphasis on subtypes common to West Africa. We examined a previously described national survey of pretreatment drug resistance in HIV-1-infected Nigerian children aged <18 months, to explore the association between subtypes and patterns of resistance.Methods: Five hundred and forty-nine dried blood spots, from 15 early infant diagnostic facilities in Nigeria, were amplified and HIV-1 polymerase was sequenced. Four hundred and twenty-four were analysed for surveillance drug resistance mutations (SDRMs). Associations between subtype and SDRMs were evaluated by Fisher's exact test and logistic regression analysis, controlling for geographical region and exposure.Results: Using the sub-subtypes of HIV-1 G defined by Delatorre et al. (PLoS One 2014.9: e98908) the most common subtypes were CRF02_AG (174, 41.0%), GWA-I (128, 30.2%), GWA-II (24, 5.7%), GCA (11, 2.6%), A (21, 5.0%) and CRF06_cpx (18, 4.2%). One hundred and ninety infants (44.8%) had ≥1 NNRTI mutation, 92 infants (21.7%) had ≥1 NRTI mutation and 6 infants (1.4%) had ≥1 PI mutation. By logistic regression, 67N was more common in GWA-II/GCA than CRF02_AG (OR 12.0, P = 0.006), as was 70R (OR 23.1, P = 0.007), 184I/V (OR 2.92, P = 0.020), the presence of ≥1 thymidine analogue mutation (TAM) (OR 3.87, P = 0.014), ≥1 type 2 TAM (OR 7.61, P = 0.001) and ≥1 NRTI mutation (OR 3.26, P = 0.005).Conclusions: This dataset reveals differences among SDRMs by subtype; in particular, between the GWA-II and GCA subclades, compared with CRF02_AG and GWA-I. [ABSTRACT FROM AUTHOR]

Background: Global surveillance of viral sequence diversity is needed to keep pace with the constant evolution of HIV. Recent next generation sequencing (NGS) methods have realized the goal of sequencing circulating virus directly from patient specimens. Yet, a simple, universal approach that maximizes sensitivity and sequencing capacity remains elusive. Here we present a novel HIV enrichment strategy to yield near complete genomes from low viral load specimens. Methodology: A non-redundant biotin-labeled probe set (HIV-xGen; n = 652) was synthesized to tile all HIV-1 (groups M, N, O, and P) and HIV-2 (A and B) strains. Illumina Nextera barcoded libraries of either gene-specific or randomly primed cDNA derived from infected plasma were hybridized to probes in a single pool and unbound sequences were washed away. Captured viral cDNA was amplified by Illumina adaptor primers, sequenced on a MiSeq, and NGS reads were demultiplexed for alignment with CLC Bio software. Results: HIV-xGen probes selectively captured and amplified reads spanning the entirety of the HIV phylogenetic tree. HIV sequences clearly present in unenriched libraries of specimens but previously not observed due to high host background levels, insufficient sequencing depth or the extent of multiplexing, were now enriched by >1,000-fold. Thus, xGen selection not only substantially increased the depth of existing sequence, but also extended overall genome coverage by an average of 40%. We characterized 50 new, diverse HIV strains from clinical specimens and demonstrated a viral load cutoff of approximately log 3.5 copies/ml for full length coverage. Genome coverage was <20% for 5/10 samples with viral loads 90% for 35/40 samples with higher viral loads. Conclusions: Characterization of >20 complete genomes at a time is now possible from a single probe hybridization and MiSeq run. With the versatility to capture all HIV strains and the sensitivity to detect low titer specimens, HIV-xGen will serve as an important tool for monitoring HIV sequence diversity. [ABSTRACT FROM AUTHOR]

Background. Human immunodeficiency virus type 1 (HIV-1) subtype has been shown to be associated with disease progression. We compared cognitive function between individuals infected with HIV-1 subtype G and CRF02_AG in Nigeria. Methods. For this cross-sectional study, samples were analyzed from 146 antiretroviral-naive participants. Genotypic analysis of plasma HIV RNA was performed by nested polymerase chain reaction of protease and reverse transcriptase genes, and sequences were aligned with curated HIV-1 subtype references. Cognitive status was determined using demographically adjusted T scores and global deficit score (GDS) obtained from a comprehensive neuropsychological test battery. Results. A total of 76 (52.1%) participants were infected with CRF02_AG, 48 (32.8%) with subtype G, and 22 (15.1%) with other HIV-1 strains. In a multivariable linear regression adjusting for plasma HIV RNA, CD4 count, and depression score, mean global T score was lower among subtype G–infected compared with CRF02_AG-infected participants (mean difference, -3.0 [95% confidence interval {CI}, -5.2, to -.7]; P = .011). Also, T scores were significantly lower among subtype G- than CRF02_AG-infected participants for the speed of information processing, executive function, and verbal fluency ability domains. Adjusting for similar variables in a logistic regression, the odds of global cognitive impairment (GDS ⩾0.5) were 2.2 times higher among subtype G compared with CRF02_AG-infected participants (odds ratio, 2.2 [95% CI, .9-5.4]; P = .078). Conclusions. Cognitive performance was significantly worse among antiretroviral-naive individuals with HIV-1 subtype G vs CRF02_AG infection. Further studies are required to characterize the mechanistic basis for these differences. [ABSTRACT FROM AUTHOR]

Background: Serum albumin may be used to stratify human immunodeficiency virus (HIV)-infected persons with high CD4 count according to their risk of serious non-AIDS endpoints.Methods: Cox proportional hazards models were used to analyze the risk of serious non-AIDS events in the Strategic Timing of Antiretroviral Treatment (START) study (NCT00867048) with serum albumin as a fixed and time-updated predictor. Models with exclusion of events during initial follow-up years were built to assess the ability of serum albumin to predict beyond shorter periods of time. Secondarily, we considered hospitalizations and AIDS events.Results: Among 4576 participants, 71 developed a serious non-AIDS event, 788 were hospitalized, and 63 experienced an AIDS event. After adjusting for a range of variables associated with hypoalbuminemia, higher baseline serum albumin (per 1 g/dL) was associated with a decreased risk of serious non-AIDS events (hazard ratio, 0.37 [95% confidence interval, .20-.71]; P = .002). Similar results were obtained in a time-updated model, after controlling for interleukin 6, and after excluding initial follow-up years. Serum albumin was independently associated with hospitalization but not with risk of AIDS.Conclusions: A low serum albumin level is a predictor for short- and long-term serious non-AIDS events, and may be a useful marker of risk of noncommunicable diseases, particularly in resource-limited settings. [ABSTRACT FROM AUTHOR]

Background: Fishing communities around Lake Victoria in sub-Saharan Africa have been characterised as a population at high risk of HIV-infection. Methods: Using data from a cohort of HIV-positive individuals aged 13–49 years, enrolled from 5 fishing communities on Lake Victoria between 2009–2011, we sought to identify factors contributing to the epidemic and to understand the underlying structure of HIV transmission networks. Clinical and socio-demographic data were combined with HIV-1 phylogenetic analyses. HIV-1 gag-p24 and env-gp-41 sub-genomic fragments were amplified and sequenced from 283 HIV-1-infected participants. Phylogenetic clusters with ≥2 highly related sequences were defined as transmission clusters. Logistic regression models were used to determine factors associated with clustering. Results: Altogether, 24% (n = 67/283) of HIV positive individuals with sequences fell within 34 phylogenetically distinct clusters in at least one gene region (either gag or env). Of these, 83% occurred either within households or within community; 8/34 (24%) occurred within household partnerships, and 20/34 (59%) within community. 7/12 couples (58%) within households clustered together. Individuals in clusters with potential recent transmission (11/34) were more likely to be younger 71% (15/21) versus 46% (21/46) in un-clustered individuals and had recently become resident in the community 67% (14/21) vs 48% (22/46). Four of 11 (36%) potential transmission clusters included incident-incident transmissions. Independently, clustering was less likely in HIV subtype D (adjusted Odds Ratio, aOR = 0.51 [95% CI 0.26–1.00]) than A and more likely in those living with an HIV-infected individual in the household (aOR = 6.30 [95% CI 3.40–11.68]). Conclusions: A large proportion of HIV sexual transmissions occur within house-holds and within communities even in this key mobile population. The findings suggest localized HIV transmissions and hence a potential benefit for the test and treat approach even at a community level, coupled with intensified HIV counselling to identify early infections. [ABSTRACT FROM AUTHOR]

Abstract: A rapid one-step reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay targeting the pol-integrase gene was developed to detect human immunodeficiency virus type 1 (HIV-1) group M. This HIV-1 RT-LAMP assay is simple and rapid, and amplification can be completed within 35min under isothermal conditions at 60°C. The 100% detection limit of HIV-1 RT-LAMP was determined using a standard strain (WHO HIV-1 [97/656]) in octuplicate and found to be 120 copies/ml. The RT-LAMP assay was evaluated for use for clinical diagnosis using plasma samples collected from 57 HIV-1-infected and 40 uninfected individuals in Cameroon, where highly divergent HIV-1 strains are prevalent. Of the 57 samples from infected individuals, 56 harbored group-M HIV-1 strains, such as subtypes A, B, G, F2, and circulating recombinant forms (CRFs) _01, _02, _09, _11, _13; all were RT-LAMP positive. One sample harboring group-O HIV-1 and the 40 HIV-1-uninfected samples were RT-LAMP negative. These findings indicate that HIV-1 RT-LAMP can detect HIV-1 group-M RNA from plasma samples rapidly and with high sensitivity and specificity. These data also suggest that this RT-LAMP assay can be useful for confirming HIV diagnosis, particularly in resource-limited settings. [Copyright &y& Elsevier]

The article focuses on the study of the prevalence of antiretrovial therapy resistance-associated primary mutations among HIV-1-infected individuals in western Cameroon. The research involves an evaluation and analysis of strains isolated from drug-naive individuals wherein DNA is extracted from 54 blood samples and amplified by polymerase chain reaction of protease, integrase, reverse transcriptase and envelope genes.

Supplemental Digital Content is Available in the Text. Background: To date, HIV incidence studies among men who have sex with men (MSM) across sub-Saharan Africa have focused on studying sexual risk practices with less focus on sexual networks. Setting: TRUST/RV368 conducted in Abuja and Lagos, Nigeria, recruited MSM using respondent-driven sampling and followed HIV-negative men for incident infection over 4 years. Methods: Four-hundred forty-one HIV-uninfected MSM underwent a parallel rapid HIV testing algorithm every 3 months for up to 18 months. HIV incidence per 100 person-years (PY) and 95% confidence intervals (CIs) were estimated using Poisson regression. Individual and network characteristics were examined using multivariable Cox-proportional hazards regression adjusted and unadjusted for respondent-driven sampling weights. Results: Among cohort members with a median age of 23 years [interquartile range (IQR): 20–27], 81 HIV infections occurred over 527 PY (incidence 15.4/100 PY; 95% CI: 12.3 to 19.0). The incidence rate was highest among 16–19 year olds as compared to those 25 years or older (30.9/100 PY; 95% CI: 22.1 to 45.3 vs. 6.9/100 PY; 95% CI: 4.2 to 10.9, respectively). Individual determinants included receptive partnerships, condomless sex, no history of testing for HIV, and rectal gonorrhea. Sexual networks were larger and consisted of an older sexual partner, although there was no clustering by recruitment networks. Conclusions: These HIV incidence data reinforce the unmet HIV prevention needs among young MSM in Nigeria. Even in the context of emerging HIV diagnostic and prevention strategies, structural challenges including stigma and criminalization of same-sex practices highlight the need for novel implementation approaches in the context of MSM-friendly services. [ABSTRACT FROM AUTHOR]

Objective(s) We evaluated relationships between critical Gag T-cell escape mutations and concomitant T-cell responses to determine whether HLA-restricted Gag mutations that confer protection, occur at similar rates in a population infected with mixed HIV-1 clades A1 and D viruses. Methods Assessment of Gag selective pressure, and adaptive T-cell functions to KAFSPEVIPMF (KF11), ISPRTLNAW (ISW9) and TSTLQEQIGW (TW10) Gag epitopes were combined with host HLA to assess correlations with rates of critical epitope escape mutations in clades A1- ( n = 23) and D- ( n = 21) infected, untreated subjects. Infecting clades and selection pressure were determined from the gag sequences. Results Overall, Gag escape mutations A163X in KF11 were detected in 61% (14/23) A1- infected compared to 5% (1/21) in D-infected subjects ( p = 0.00015). Gag mutations I147X in the ISW9 epitope were seen in 43%: (10/23) clade A compared to 5%: (1/21) clade D infected subjects, p = 0.007, Fisher's Exact test. Both mutations were more frequent in clade A1 infection. Frequencies of the measured epitope-specific T-cell responses were comparable across clades. Peptide binding affinities for the restricting HLA alleles did not differ across clades. Overall, selection pressure on the Gag protein was significantly greater in clade A than in clade D sequences. Conclusions These findings imply that HIV-1 vaccine strategies designed to target structurally constrained T-cell epitopes may be further challenged by clade-driven outcomes in specific HLA-restricted Gag epitopes. Equally, the data are line with slower HIV-1 disease progression in clade A infection; and raise hope that increased selective pressure on Gag may be protective irrespective of host HLA alleles. [ABSTRACT FROM AUTHOR]

Evolutionary analyses have revealed an origin of pandemic HIV-1 group M in the Congo River basin in the first part of the XX century, but the patterns of historical viral spread in or around its epicentre remain largely unexplored. Here, we combine epidemiologic and molecular sequence data to investigate the spatiotemporal patterns of the CRF02_AG clade. By explicitly integrating prevalence counts and genetic population size estimates we date the epidemic emergence of CRF02_AG at 1973.1 (1972.1, 1975.3, 95% CI). To infer the phylogeographic signature of this clade at a regional scale, we analyze pol and env time-stamped sequence data from 10 countries using a Bayesian phylogeographic approach based on an asymmetric discretized diffusion model. Our data confirms a spatial origin of CRF02_AG in the Democratic Republic of Congo (DRC) and suggests that viral dissemination to Cameroon occurred at an early stage of the evolutionary history of CRF02_AG. We find considerable support for epidemiological linkage between neighbour countries. Compilation of ethnographic data suggested that well-supported viral migration did not reflect sustained human migratory flows. Finally, using sequence data from 15 locations in Cameroon, we use relaxed random walk models to explore the spatiotemporal dynamics of CRF02_AG at a finer geographical detail. Phylogeographic dispersal in continuous space reveals that at least two distinct CRF02_AG lineages are circulating in overlapping regions that are evolving at different evolutionary and diffusion rates. In conclusion, by combining molecular and epidemiological data, our results provide a time scale for CRF02_AG, early 70s, place its spatial root in the DRC within the putative root of group-M diversity and propose a scenario of chance-exportation events for the spatiotemporal patterns of a successful HIV-1 lineage both at a regional and country-scale. [ABSTRACT FROM AUTHOR]

In resource-limited settings, use of dried blood spots (DBS) could be a pragmatic alternative to plasma for VL monitoring in people living with HIV (PLWH). We compared results from DBS to standard plasma VL testing under field conditions in patients receiving antiretroviral therapy (ART). DBS cards were prepared from venous blood (V-DBS), finger-pricks using micro-capillary tubes (M-DBS), and direct spotting (D-DBS). DBS and matched EDTA plasma were tested on the Abbott m2000 platform using the appropriate RealTime HIV-1 quantitative CE protocol. Matched plasma samples were also tested on the Roche COBAS Ampliprep/COBAS TaqMan version 2.0. Diagnostic accuracy indicators (sensitivity, specificity, misclassification rate, and kappa coefficient) for viral failure (VF) based on different VL threshold levels and agreement of absolute VL were calculated. A total of 669 participants provided 2676 samples. V-DBS had a peak sensitivity for VF of 89.1 % [95 % CI: 85.5–92.7] at the 1000 copies/mL threshold and a peak specificity of 97.4 % [95 % CI: 95.9–99.0] at the 5000 copies/mL threshold. The lowest proportion of upward misclassification (patients classified with VF who actually had viral suppression) for V-DBS was 3.1 % [95 % CI: 1.4–4.8] at the 5000 copies/mL threshold, whereas the lowest proportion of downward misclassification (patients classified as undetectable who actually had VF) was 10.9 % [95 % CI: 7.2–14.5] at the 1000 copies/mL threshold. Abbott RealTime HIV-1 VL results from all 3 DBS types for adults and children showed strong correlation with the gold standard plasma-based assay. DBS could be useful for monitoring VL in resource limited settings such as Nigeria. [ABSTRACT FROM AUTHOR]

We report the second human immunodeficiency virus (HIV) belonging to the new HIV type 1 (HIV-1) group P lineage that is closely related to the simian immunodeficiency virus found in gorillas. This virus was identified in an HIV-seropositive male hospital patient in Cameroon, confirming that the group P virus is circulating in humans. Results from screening 1,736 HIV-seropositive specimens collected in Cameroon indicate that HIV-1 group P infections are rare, accounting for only 0.06% of HIV infections. Despite its rarity, group P shows evidence of adaptation to humans. [ABSTRACT FROM AUTHOR]