APOBEC3G expression is dysregulated in primary HIV-1 infection and polymorphic variants influence CD4+ T-cell counts and plasma viral load

OBJECTIVES: In the absence of HIV-1 virion infectivity factor (Vif), cellular cytosine deaminases such as apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G) inhibit the virus by inducing hypermutations on viral DNA, among other mechanisms of action. We investigated the association of APOBEC3G mRNA levels and genetic variants on HIV-1 susceptibility, and early disease pathogenesis using viral load and CD4 T-cell counts as outcomes. METHODS: Study participants were 250 South African women at high risk for HIV-1 subtype C infection. We used real-time PCR to measure the expression of APOBEC3G in HIV-negative and HIV-positive primary infection samples. APOBEC3G variants were identified by DNA re-sequencing and TaqMan genotyping. RESULTS: We found no correlation between APOBEC3G expression levels and plasma viral loads (r = 0.053, P = 0.596) or CD4 T-cell counts (r = 0.030, P = 0.762) in 32 seroconverters. APOBEC3G expression levels were higher in HIV-negative individuals as compared with HIV-positive individuals (P < 0.0001), including matched pre and postinfection samples from the same individuals (n = 13, P < 0.0001). Twenty-four single nucleotide polymorphisms, including eight novel, were identified within APOBEC3G by re-sequencing and genotyping. The H186R mutation, a codon-changing variant in exon 4, and a 3' extragenic mutation (rs35228531) were associated with high viral loads (P = 0.0097 and P < 0.0001) and decreased CD4 T-cell levels (P = 0.0081 and P < 0.0001), respectively. CONCLUSION: These data suggest that APOBEC3G transcription is rapidly downregulated upon HIV-1 infection. During primary infection, APOBEC3G expression levels in peripheral blood mononuclear cells do not correlate with viral loads or CD4 T-cell counts. Genetic variation of APOBEC3G may significantly affect early HIV-1 pathogenesis, although the mechanism remains unclear and warrants further investigation

Relationship between levels of inflammatory cytokines in the genital tract and CD4+ cell counts in women with acute HIV-1 infection.

Inflammatory responses at mucosal surfaces after human immunodeficiency virus type 1 (HIV-1) transmission may influence disease outcome. We evaluated levels of interleukin (IL)-1beta, IL-6, tumor necrosis factor-alpha, IL-8, IL-10, and IL-12 in genital tract and plasma specimens from 44 women with acute HIV infection and 29 HIV-negative control women (13 of whom were women in the acute HIV infection cohort who had preinfection samples available for analysis). Women with acute HIV infection had significantly elevated levels of IL-6, IL-10, and IL-12 in genital tract specimens and elevated levels of IL-1beta, IL-8, and IL-10 in plasma specimens, compared with HIV-negative control women. Levels of IL-1beta, IL-6, and IL-8 in cervicovaginal specimens from women with acute HIV infection showed a significant inverse correlation with systemic CD4(+) cell counts, suggesting that mucosal inflammation is associated with low CD4(+) cell counts during acute HIV infection

Virological and Immunological Factors Associated with HIV-1 Differential Disease Progression in HLA-B*58:01-Positive Individuals

Molecular epidemiology studies have identified HLA-B*58:01 as a protective HIV allele. However, not all B*58:01-expressing persons exhibit slow HIV disease progression. We followed six HLA-B*58:01-positive, HIV subtype C-infected individuals for up to 31 months from the onset of infection and observed substantial variability in their clinical progression despite comparable total breadths of T cell responses. We therefore investigated additional immunological and virological factors that could explain their different disease trajectories. Cytotoxic T-lymphocyte (CTL) responses during acute infection predominantly targeted the TW10 and KF9 epitopes in p24Gag and Nef, respectively. Failure to target the TW10 epitope in one B*58:01-positive individual was associated with low CD4+ counts and rapid disease progression. Among those targeting TW10, escape mutations arose within 2 to 15 weeks of infection. Rapid escape was associated with preexisting compensatory mutations in the transmitted viruses, which were present at a high frequency (69%) in the study population. At 1 year postinfection, B*58:01-positive individuals who targeted and developed escape mutations in the TW10 epitope (n = 5) retained significantly higher CD4+ counts (P = 0.04), but not lower viral loads, than non-B*58:01-positive individuals (n = 17). The high population-level frequency of these compensatory mutations may be limiting the protective effect of the B*58:01 allele

Association of polymorphisms in the LEDGF/p75 gene (PSIP1) with susceptibility to HIV-1 infection and disease progression

OBJECTIVE: LEDGF/p75, encoded by the PSIP1 gene, interacts with HIV-1 integrase and targets HIV-1 integration into active genes. We investigated the influence of polymorphisms in PSIP1 on HIV-1 acquisition and disease progression in black South Africans. METHODS: Integrase binding domain of LEDGF/p75 was sequenced in 126 participants. Four haplotype tagging SNPs rs2277191, rs1033056, rs12339417 and rs10283923 referred to as SNP1, SNP2, SNP3 and SNP4, respectively, and one exonic SNP rs61744944 (SNP5, Q472L) were genotyped in 195 HIV-1 seronegative, 52 primary and 403 chronically infected individuals using TaqMan assays. LEDGF/p75 expression was quantified by real-time RT-PCR. The impact of Q472L mutation on the interaction with HIV_1 IN was measured by AlphaScreen. RESULTS: rs2277191 (SNP1) A was more frequent among seropositives (P = 0.06, Fisher's exact test). Among individuals followed longitudinally SNP1A trended towards association with higher likelihood of HIV-1 acquisition [relative hazard (RH) = 2.21, P = 0.08; Cox model] and it was also associated with rapid disease progression (RH = 5.98, P = 0.04; Cox model) in the recently infected (primary infection) cohort. rs12339417 (SNP3)C was associated with slower decline of CD4(+) T cells (P = 0.02) and lower messenger RNA (mRNA) levels of LEDGF/p75 (P < 0.01). Seroconverters had higher preinfection mRNA levels of LEDGF/p75 (P < 0.01) and these levels decreased after HIV-1 infection (P = 0.02). CONCLUSIONS: Genetic variants of PSIP1 may affect HIV-1 outcomes. Further studies are needed to confirm the effect of genetic variation of PSIP1 on HIV-1 pathogenesis in different cohorts

Co-enrollment in multiple HIV prevention trials — Experiences from the CAPRISA 004 Tenofovir gel trial

Background: In settings where multiple HIV prevention trials are conducted in close proximity, trial participants may attempt to enroll in more than one trial simultaneously. Co-enrollment impacts on participant's safety and validity of trial results. We describe our experience, remedial action taken, inter-organizational collaboration and lessons learnt following the identification of co-enrolled participants. Experiences: Between February and April 2008, we identified 185 of the 398 enrolled participants as ineligible. In violation of the study protocol exclusion criteria, there was simultaneous enrollment in another HIV prevention trial (ineligible co-enrolled, n = 135), and enrollment of women who had participated in a microbicide trial within the past 12 months (ineligible not co-enrolled, n = 50). Following a complete audit of all enrolled participants, ineligible participants were discontinued via study exit visits from trial follow-up. Custom-designed education program on co-enrollment impacting on participants' safety and validity of the trial results was implemented. Shared electronic database between research units was established to enable verification of each volunteer's trial participation and to prevent future co-enrollments. Lessons learnt: Interviews with ineligible enrolled women revealed that high-quality care, financial incentives, altruistic motives, preference for sex with gel, wanting to increase their likelihood of receiving active gel, perceived low risk of discovery and peer pressure are the reasons for their enrollment in the CAPRISA 004 trial. Conclusion: Instituting education programs based on the reasons reported by women for seeking enrollment in more than one trial and using a shared central database system to identify co-enrollments have effectively prevented further co-enrollments

Towards elimination of mother-to-child transmission of HIV: performance of different models of care for initiating lifelong antiretroviral therapy for pregnant women in Malawi (Option B+).

INTRODUCTION: Malawi introduced a new strategy to improve the effectiveness of prevention of mother-to-child HIV transmission (PMTCT), the Option B+ strategy. We aimed to (i) describe how Option B+ is provided in health facilities in the South East Zone in Malawi, identifying the diverse approaches to service organization (the "model of care") and (ii) explore associations between the "model of care" and health facility-level uptake and retention rates for pregnant women identified as HIV-positive at antenatal (ANC) clinics. METHODS: A health facility survey was conducted in all facilities providing PMTCT/antiretroviral therapy (ART) services in six of Malawi's 28 districts to describe and compare Option B+ service delivery models. Associations of identified models with program performance were explored using facility cohort reports. RESULTS: Among 141 health facilities, four "models of care" were identified: A) facilities where newly identified HIV-positive women are initiated and followed on ART at the ANC clinic until delivery; B) facilities where newly identified HIV-positive women receive only the first dose of ART at the ANC clinic, and are referred to the ART clinic for follow-up; C) facilities where newly identified HIV-positive women are referred from ANC to the ART clinic for initiation and follow-up of ART; and D) facilities serving as ART referral sites (not providing ANC). The proportion of women tested for HIV during ANC was highest in facilities applying Model A and lowest in facilities applying Model B. The highest retention rates were reported in Model C and D facilities and lowest in Model B facilities. In multivariable analyses, health facility factors independently associated with uptake of HIV testing and counselling (HTC) in ANC were number of women per HTC counsellor, HIV test kit availability, and the "model of care" applied; factors independently associated with ART retention were district location, patient volume and the "model of care" applied. CONCLUSIONS: A large variety exists in the way health facilities have integrated PMTCT Option B+ care into routine service delivery. This study showed that the "model of care" chosen is associated with uptake of HIV testing in ANC and retention in care on ART. Further patient-level research is needed to guide policy recommendations

Plasma cytokine levels during acute HIV-1 infection predict HIV disease progression

BACKGROUND: Both T-cell activation during early HIV-1 infection and soluble markers of immune activation during chronic infection are predictive of HIV disease progression. Although the acute phase of HIV infection is associated with increased pro-inflammatory cytokine production, the relationship between cytokine concentrations and HIV pathogenesis is unknown. OBJECTIVES: To identify cytokine biomarkers measurable in plasma during acute HIV-1 infection that predict HIV disease progression. DESIGN: Study including 40 South African women who became infected with HIV-1 and were followed longitudinally from the time of infection. METHODS: The concentrations of 30 cytokines in plasma from women with acute HIV-1 infection were measured and associations between cytokine levels and both viral load set point 12 months postinfection and time taken for CD4 cell counts to fall below 350 cells/microl were determined using multivariate and Cox proportional hazards regression. RESULTS: We found that the concentrations of five plasma cytokines, IL-12p40, IL-12p70, IFN-gamma, IL-7 and IL-15 in women with acute infection predicted 66% of the variation in viral load set point 12 months postinfection. IL-12p40, IL-12p70 and IFN-gamma were significantly associated with lower viral load, whereas IL-7 and IL-15 were associated with higher viral load. Plasma concentrations of IL-12p40 and granulocyte-macrophage colony-stimulating factor during acute infection were associated with maintenance of CD4 cell counts above 350 cells/microl, whereas IL-1alpha, eotaxin and IL-7 were associated with more rapid CD4 loss. CONCLUSION: A small panel of plasma cytokines during acute HIV-1 infection was predictive of long-term HIV disease prognosis in this group of South African women

Evolution of epidemiologic methods and concepts in selected textbooks of the 20th century

Summary: Textbooks are an expression of the state of development of a discipline at a given moment in time. By reviewing eight epidemiology textbooks published over the course of a century, we have attempted to trace the evolution of five epidemiologic concepts and methods: study design (cohort studies and case-control studies), confounding, bias, interaction and causal inference. Overall, these eight textbooks can be grouped into three generations. Greenwood (1935) and Hill (first edition 1937; version reviewed 1961)'s textbooks belong to the first generation, "early epidemiology”, which comprise early definitions of bias and confounding. The second generation, "classic epidemiology”, represented by the textbooks of Morris (first edition 1957; version reviewed 1964), MacMahon & Pugh (first edition 1960; version reviewed 1970), Susser (1973), and Lilienfeld & Lilienfeld (first edition 1976; version reviewed 1980), clarifies the properties of cohort and case-control study designs and the theory of disease causation. Miettinen (1985) and Rothman (1986)'s textbooks belong to a third generation, "modern epidemiology”, presenting an integrated perspective on study designs and their measures of outcome, as well as distinguishing and formalizing the concepts of confounding and interaction. Our review demonstrates that epidemiology, as a scientific discipline, is in constant evolution and transformation. It is likely that new methodological tools, able to assess the complexity of the causes of human health, will be proposed in future generations of textbook

The impact of sexually transmitted infections (STI) and genital tract inflammation on HIV-1 acquisition and rate of disease progression in subtype C infected women.

Ph. D. University of KwaZulu-Natal, Durban 2014.Introduction: Women carry more than half the burden of HIV disease globally and this burden is even higher in sub-Saharan Africa (SSA). Young women, in particular, are at disproportionate risk of HIV infection in South Africa. Understanding risk behaviours and factors associated with ability to negotiate safe sex and condom use is one of the key elements in curbing the spread of HIV. Sexually transmitted infections (STI) and bacterial vaginosis (BV), which cause female genital tract inflammation, have been identified as key drivers of the HIV epidemic. This inflammation, which is also present in the absence of symptoms, is associated with increased susceptibility to HIV infection. Although syndromic management of symptomatic STIs or BV at the first encounter with a health care provider is an important public health measure, its effectiveness is minimised because a substantial proportion of individuals have either asymptomatic infections or fail to recognise signs and symptoms of STI and are therefore excluded. Most new HIV infections in SSA occur among young people and particularly among young girls. Prompt diagnosis of acute HIV infection (AHI) is critical and benefits the individual as well as providing opportunities for public health intervention. In South Africa, the majority of HIV infections are due to infection with HIV-1 subtype C for which there is limited data compared to subtype-B HIV-1 infections. The overall aim of this study was to assess the impact of BV, STIs, and associated genital tract inflammation on acquisition of HIV-1 subtype C infections; and evaluate the rate of subsequent disease progression in women. The objectives were: i. to investigate STIs and genital tract inflammation as risk factors for HIV infection in high risk women and adequacy of syndromic management; ii. to evaluate the challenges associated with diagnosing recently acquired (acute) HIV infection in a subtype C prevalent population; iii. and to evaluate the relationship between clinical disease progression and genital and or systemic inflammation in high-risk women who became infected with HIV. We assessed the adequacy of syndromic diagnosis of STIs, compared with laboratory diagnosis of STIs, and evaluated the association between STI diagnosis and the risk of HIV acquisition in a cohort of high-risk women. Genital cytokine profiles and the degree of inflammation associated with common STIs and bacterial vaginosis were assessed. The most common signs and symptoms of acute HIV infection (AHI) were described and a clinical algorithm to identify acute HIV cases was developed. We investigated rates of HIV disease progression of subtype C–infected South African women. Methods: The CAPRISA 002 study was a prospective cohort study established to examine the pathogenesis and natural history of HIV-1 subtype C infection and to describe the immunologic, virologic and clinical characteristics of acute and early infection in KwaZulu Natal, South Africa. A total of 775 high-risk women were screened for HIV infection, and 245 HIV-uninfected women were enrolled into the study. At each monthly visit for a total of 24 months behavioural and clinical data were collected. Cervico-vaginal lavage (CVL) samples were collected at enrolment and at each six month follow-up visits and were tested for STI pathogens (including Chlamydia trachomatis, Neisseria gonorrhoeae, herpes simplex virus type 2 (HSV-2) and Trichomonas vaginalis) and bacterial vaginosis. Forty-two cytokines were measured from the CVL and 13 from the plasma samples at enrolment. All women received monthly HIV-1 antibody and RNA testing and were assessed for AHI. Signs and symptoms at the visit with HIV-1 antibody or HIV-1 RNA positive test were compared to HIV negative visits. Logistic regression identified clinical predictors of AHI and a model-based score was assigned to each predictor to create a risk score for every woman. All women who seroconverted were followed up for more than five years and monitored for HIV disease progression. Rapid disease progression was defined as CD4+ T cell count decline to <350 cells/μl within two years post-infection. Serial clinical and laboratory assessments were compared using survival analysis and logistic regression models. CAPRISA had established several cohorts of HIV negative women to determine the feasibility of establishing cohorts and sites for HIV biomedical prevention trials. Women seroconverting in these studies were referred to the CAPRISA 002 study for longitudinal follow-up for HIV post seroconversion. Results: In this study, the HIV-1 prevalence at screening was 59.6% (95% CI: 55.9% to 62.8%). During a total of 390 person-years of follow-up, 28 new infections occurred, yielding a seroincidence rate of 7.2 (95% CI: 4.5 to 9.8) per 100 person-years. A total of 62 participants, including seroconvertors from other CAPRISA cohorts, were enrolled into the acute HIV infection Women from the HIV-1 negative cohort generally demonstrated a high level of knowledge on HIV/AIDS, and 60.3% reported use of condoms. Reported condom use at last sexual encounter varied slightly by partner type (57.0% with steady versus 64.4% with casual partners; p = 0.36), whilst self-perceived ability to choose to use a condom was significantly lower with steady partners compared to casual partners (20.8% versus 53.9%; p=0.01). An important finding was that vaginal discharge was a poor predictor of laboratory-diagnosed STIs, as only 12.3% of women (25/204) who had a laboratory-confirmed discharge causing pathogen had clinical evidence of a discharge (yielding a sensitivity of 12.3% and a specificity of 93.8%). CVL cytokine concentrations did not differ between women with asymptomatic or symptomatic STIs; and were elevated in women with either asymptomatic or symptomatic STIs compared to women with no STIs or BV. Women with chlamydia or gonorrhoea had the highest genital cytokine concentrations, with 17/42 and 14/42 of the cytokines measured in CVL being up-regulated compared with women with no infections, respectively. While BV was associated with elevated pro-inflammatory cytokine concentrations in CVL, women with BV had lower levels of chemokines and haematopoietic cytokines than women with no infections or BV. HSV-2 reactivation was inflammatory, but yielded a comparatively lower level of inflammation than Chlamydia or gonnorhoea. Trichomoniasis, despite being relatively common in this cohort, did not cause significant changes in genital tract cytokine concentrations compared to women with no infections or BV. Genital infections did not influence plasma cytokine concentrations, suggesting that the compartments were not linked with respect to cytokine responses. Although laboratorydiagnosed STIs were associated with increased risk of HIV infection [hazard ratio, 3.3 (95% confidence interval, 1.5 – 7.2)], clinical symptoms were not. Of the women who became infected, factors predictive of AHI included age, 25 years (OR = 3.2; 1.4 – 7.1), rash (OR = 6.1; 2.4 –15.4), sore throat (OR = 2.7; 1.0 – 7.6), weight loss (OR = 4.4; 1.5 – 13.4), genital ulcers (OR = 8.0; 1.6 – 39.5) and vaginal discharge (OR = 5.4; 1.6 – 18.4). A risk score of 2 correctly predicted AHI in 50.0% of cases. The number of signs and symptoms correlated with higher HIV-1 RNA at diagnosis (r = 0.63; p = 0.001). The 62 acutely infected women were identified at a median of 42 days post-infection (IQR = 34 – 59). Mean CD4 count dropped by 39.6% at 3 months and 46.7% at 6 months post-infection in women with pre-infection measurements. CD4 decline to <350 cells/μL occurred in 31%, 44%, and 55% of women at 1, 2, and 3 years post-infection, respectively, and to <500 cells/μL in 69%, 79%, and 81% at equivalent time-points. Predictors of rapid progression were CD4 count at 3 months post-infection (hazard ratio [HR], 2.07; 95% confidence interval [CI], 1.31–3.28; P = .002), setpoint viral load (HR, 3.82; 95% CI, 1.51–9.67; P = .005), and hepatitis B coinfection (HR, 4.54; 95% CI, 1.31–15.69; P = .017). Conversely, presence of any of HLAB*1302, B*27, B*57, B*5801, or B*8101 alleles predicted non–rapid progression (HR, 0.19; 95% CI, .05–.74; P = .016). Discussion/Conclusion: This study showed that syndromic STI diagnosis, which is dependent on clinical signs of vaginal discharge, was poorly predictive of laboratory-diagnosed STIs or BV and missed a significant proportion of women with asymptomatic infections. However, the level of genital inflammation, as measured by cytokine concentrations in CVL, was similar in women with symptomatic and asymptomatic infections and therefore place women at increased risk for HIV infection. While laboratory-diagnosed STIs and the presence of inflammatory cytokines in the genital tract were associated with increased susceptibility to HIV acquisition, vaginal discharge was not. Chlamydial infection was associated with the highest genital cytokine concentrations, followed by gonorrhoea, HSV-2, trichomoniasis, and BV. In regions where HIV is prevalent and STIs are managed syndromically, targeted screening of populations at risk for STIs is critical and urgently needed. Recognition of signs and symptoms of AHI is important for early diagnosis of HIV infection. The proposed algorithm of risk-stratifying individuals for AHI provides a useful clinical tool especially in resource-limited settings where there are limited or no routinely available tests for AHI. However, validation of the algorithm on another cohort is needed to assess its utility further. Point-of-care HIV antigen or viral load testing is needed, to detect asymptomatic, antibody negative cases enabling early interventions and prevention of transmission. This cohort showed high rates of rapid disease progression, with nearly half of these subtype C–infected women progressing to a CD4+ T cell count of below 350 cells/μL within 2 years of infection. Implementing 2013 World Health Organization treatment guidelines (CD4+ T cell counts less than 500cells/μL) would require most individuals to start antiretroviral therapy within 1 year of HIV infection. The economic and health systems planning implicated by these findings need to be explored and addressed to guide policy makers as countries adopt the current WHO guidelines

Empirical antimicrobial therapy for probable v. directed therapy for possible ventilator-associated pneumonia in critically injured patients

Background. Ventilator-associated pneumonia (VAP) has recently been classified as possible or probable. Although direct attributable mortality has been difficult to prove, delay in instituting appropriate therapy has been reported to increase morbidity and mortality. Recent literature suggests that in possible VAP, instituting directed therapy while awaiting microbiological culture does not prejudice outcome compared with best-guess empirical therapy.Objectives. To ascertain outcomes of directed v. empirical therapy in possible and probable VAP, respectively. Methods. Endotracheal aspirates were obtained from patients with suspected VAP. Those considered to have possible VAP were given directed therapy following culture results, whereas patients with more convincing evidence of VAP were classed as having probable VAP and commenced on empirical antimicrobials based on microbiological surveillance.Results. Pneumonia was suspected in 106 (36.8%) of 288 patients admitted during January - December 2014. Of these, 13 did not fulfil the criteria for VAP. Of the remaining 93 (32.2%), 31 (33.3%) were considered to have probable and 62 (66.7%) possible VAP. The former were commenced on empirical antimicrobials, with 28 (90.3%) receiving appropriate therapy. Of those with possible VAP, 34 (54.8%) were given directed therapy and in 28 (45.2%) no antimicrobials were prescribed. Of the latter, 24 recovered without antimicrobials and 4 died, 3 from severe traumatic brain injury and 1 due to overwhelming intra-abdominal sepsis. No death was directly attributable to failure to treat VAP. No significant difference in mortality was found between the 34 patients with possible VAP who were commenced on directed therapy and the 31 with probable VAP who were commenced on empirical antimicrobials (p=0.75).Conclusions. Delaying antimicrobial therapy for VAP where clinical doubt exists does not adversely affect outcome. Furthermore, this policy limits the use of antimicrobials in patients with possible VAP following improvement in their clinical condition despite no therapy