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Abstract Background Cervical cancer is the leading cause of cancer death in Kenyan women. Integrating cervical cancer screening into family planning (FP) clinics is a promising strategy to improve health for reproductive-aged women. The objective of this cluster randomized trial was to test the efficacy of an implementation strategy, the Systems Analysis and Improvement Approach (SAIA), as a tool to increase cervical cancer screening in FP clinics in Mombasa County, Kenya. Methods Twenty FP clinics in Mombasa County were randomized 1:1 to SAIA versus usual procedures. SAIA has five steps: (1) cascade analysis tool to understand the cascade and identify inefficiencies, (2) sequential process flow mapping to identify bottlenecks, (3) develop and implement workflow modifications (micro-interventions) to address identified bottlenecks, (4) assess the micro-intervention in the cascade analysis tool, and (5) repeat the cycle. Prevalence ratios were calculated using Poisson regression with robust standard errors to compare the proportion of visits where women were screened for cervical cancer in SAIA clinics compared to control clinics. Results In the primary intent-to-treat analysis in the last quarter of the trial, 2.5% (37/1507) of visits with eligible FP clients at intervention facilities included cervical cancer screening compared to 3.7% (66/1793) in control clinics (prevalence ratio [PR] 0.67, 95% CI 0.45–1.00). When adjusted for having at least one provider trained to perform cervical cancer screening at baseline, there was no significant difference between screening in intervention clinics compared to control clinics (adjusted PR 1.14, 95% CI 0.74–1.75). Conclusions The primary analysis did not show an effect on cervical cancer screening. However, the COVID-19 pandemic and a healthcare worker strike likely impacted SAIA’s implementation with significant disruptions in FP care delivery during the trial. While SAIA’s data-informed decision-making and clinic-derived solutions are likely important, future work should directly study the mechanisms through which SAIA operates and the influence of contextual factors on implementation. Trial registration ClinicalTrials.gov, NCT03514459. Registered on April 19, 2018.

Abstract Background Epithelial trauma is a risk factor of HIV infection in men who have sex with men (MSM) and female sex workers (FSWs). Painful intercourse may be indicative of epithelial tissue disruption. Previous studies on a cohort of Kenyan FSWs established an association between prolonged sexual abstinence and late HIV seroconversion. Our research objective was to establish whether there is a relationship between HIV serostatus and signs of epithelial disruption and between HIV serostatus and sexual abstinence behaviour. Methods Participants were selected from a Nairobi health facility. A structured questionnaire was administered to 322 FSWs, who provided data on HIV status, sexual behaviour, abstinence intervals and the level of sexual dysfunction. Sexual dysfunction scores were created using parts of the Female Sexual Function Index (FSFI-19). Additional questions addressed epithelial trauma signs. Descriptive data analysis, bivariate and multivariate logistic regression were used to describe the study population and determine factors associated with living with HIV. Potential factors influencing sexual dysfunction were assessed by FSWs via self-rating. Results 36% of FSWs reported discomfort or pain during vaginal penetration half the time. 44% noticed genital bleeding half the time. Vaginal tenderness was experienced by 70.6% half the time during or after intercourse. Variables predictive of living with HIV on multivariate analysis included a medium and high score of discomfort or pain during and following vaginal penetration (medium: AOR 2.288, p-value 0.032, 95% CI 1.075–4.871; high: AOR 3.044, p-value 0.031, 95% CI 1.110–8.348). No significant association of HIV status with past abstinence durations as reported by participants could be established in the multivariate analysis. A majority of FSWs agreed that steady partnerships (81% agreement), regularity of intercourse (74%), foreplay (72%) and lubricants (65%) alleviated dyspareunia. Conclusions Recurrent exposure to blood during sex was highly prevalent in FSWs, as was sexual dysfunction. Complaint levels were associated with living with HIV, providing evidence that reducing sexual dysfunctions may prevent HIV transmission. Preventive initiatives may be created that address sexual dysfunction in key populations and general populations with a high HIV prevalence. Subjective assessments indicate that prevention may include the promotion of sexual intercourse regularity, foreplay, and lubricant use.

Abstract Background Mobile Health (“mHealth”) interventions have shown promise in improving HIV treatment outcomes for stigmatized populations. This paper presents the findings from a randomized controlled trial to assess the efficacy, participant-level feasibility and acceptability of a theory-informed mHealth intervention, Motivation Matters!, designed to improve viral suppression and ART adherence among HIV-seropositive women who engage in sex work in Mombasa, Kenya. Methods A total of 119 women were randomized between the intervention and standard of care control. The primary outcome examined viral suppression (≤ 30 copies/mL) six months following ART initiation. ART adherence was assessed monthly using a visual analogue scale. Participant-level feasibility was measured through response rates to study text messages. Acceptability was assessed through qualitative exit interviews. Results Six months following treatment initiation, 69% of intervention and 63% of control participants were virally suppressed (Risk Ratio [RR] = 1.09, 95% Confidence Interval [95% CI] (0.83, 1.44). Among women who were viremic at baseline and endorsed engagement in sex work, 74% of women in the intervention arm compared with 46% of women in the control arm achieved viral suppression at month six RR = 1.61, 95% CI (1.02, 2.55). Adherence was higher in intervention versus control participants every month. All participants responded to at least one message, and there was a 55% overall response rate to intervention text messages. Qualitative exit interviews suggested high acceptability and perceived impact of the intervention. Conclusion The improvements in ART adherence and viral suppression, combined with encouraging data on feasibility and acceptability, provides preliminary evidence that Motivation Matters! could support ART adherence and viral suppression in women who engage in sex work. Trial registration This trial was registered with ClinicalTrials.gov (NCT02627365, 10/12/2015; http://clinicaltrials.gov ).

Abstract Background Current advances in biomedical research have introduced new ethical challenges in obtaining informed consent in low and middle-income settings. For example, there are controversies about the use of broad consent in the collection of biological samples for use in future biomedical research. However, few studies have explored preferred informed consent models for future use of biological samples in Malawi and South Africa. Therefore, we conducted an empirical study to understand preferred consent models among key stakeholders in biomedical studies that involve collection of biological samples in Malawi and South Africa. The main objective of the study was to explore views of key stakeholders on current policies on informed consent in Malawi and South Africa. Methods This was a qualitative study involving in-depth interviews and focus group discussions. Thirty-four in-depth interviews and 6 focus group discussions were conducted with REC members, Funders, Policymakers, CAB members and Research Participants in Malawi and South Africa to gather their views on models of informed consent. The study was conducted in Cape Town, South Africa, and Blantyre and Lilongwe in Malawi. Results Most key stakeholders preferred broad consent and tiered consent to specific consent. Some participants expressed a strong preference for specific consent to other models of informed consent in biomedical research. Few participants did not have any preference for a consent model, opting for any consent model which provides adequate information about the proposed research and what their national consent regulations require. Finally, very few participants preferred blanket consent to other informed consent models. Conclusions This study aimed to help fill the gap in the scientific literature on key stakeholder views on consent models for future use of biological samples in Malawi and South Africa. The findings of the study have provided some evidence that may support policies on permissible consent models for future use of biological samples in sub-Saharan Africa considering the differences in informed consent regulations and guidelines. Finally, the findings can inform ongoing discussions on permissible consent models to be used for future use of biological samples.

Abstract Background Cervical cancer is the most common cancer in sub-Saharan Africa. With appropriate screening and treatment, cervical cancer can be prevented. In Kenya, cervical cancer screening is recommended for all women of reproductive age who visit a health facility. In particular, the Kenyan Ministry of Health has tasked family planning clinics and HIV clinics with implementing cervical cancer screening as part of the overall cervical cancer screening strategy. A cross-sectional survey was conducted to understand cervical cancer screening practices and explore clinic-level barriers and facilitators to screening in family planning clinics (FP) in Mombasa County, Kenya. Methods Structured interviews were conducted with randomly sampled FP clinic managers to collect information about clinic size, location, type, management support, infrastructure, screening practices, and availability of screening commodities. Data were abstracted from FP registers for a 15-month period from October 1, 2017 until December 31, 2018 to understand cervical cancer screening prevalence. Generalized linear models were used to calculate prevalence ratios (PR) and identify clinic-level correlates of reporting any cervical cancer screening. Results A total of 70 clinics were sampled, 54% (38) were urban and 27% (19) were public facilities. The median number of staff in a clinic was 4 (interquartile range [IQR] 2–6) with a median of 1 provider trained to perform screening (IQR 0–3). Fifty-four percent (38/70) of clinic managers reported that their clinics performed cervical cancer screening. Of these, only 87% (33) and 71% (27) had dependable access to speculums and acetic acid, respectively. Being a public FP clinic was associated with higher prevalence of reported screening (14/38 [37%] vs 6/32 [16%]; prevalence rate ratio [PR] 1.57, 95%CI 1.05–2.33). Clinics that reported cervical cancer screening were much more likely to have at least one provider trained to perform cervical cancer screening (84%, 32/38) compared to clinics that did not report screening (28%, 9/32; PR 3.77, 95%CI 1.82–7.83). Conclusion Integration of cervical cancer screening into FP clinics offers great potential to reach large numbers of reproductive-aged women. Increasing training of healthcare providers and ensuring adequate commodity supplies in FP clinics offer concrete solutions to increase screening in a largely unscreened population.

Abstract Background Although HIV testing in family planning (FP) clinics is a promising approach for engaging women in HIV treatment and prevention services, HIV testing rates are low in FP clinics in Kenya. In 2018, a cluster randomized trial was implemented in Mombasa, Kenya applying the Systems Analysis and Improvement Approach (SAIA) to integrate HIV testing into FP services (1K24HD088229-01). We estimated the incremental costs and explored cost drivers of the FP HIV SAIA implementation in Mombasa, Kenya. Methods We conducted a costing evaluation from the payer perspective for the FP HIV SAIA randomized control trial. We identified relevant activities for the intervention including start-up, training, research and FP HIV SAIA. We estimated activity time burden using a time-and motion study. We derived unit costs through staff interviews and programmatic budgets. We present cost estimates for two different scenarios: as-implemented including research and projected costs for a Ministry of Health-supported intervention. All costs are reported in 2018 USD. Results For an annual program output of 36,086 HIV tests administered to new FP clients, we estimated the total annual program cost to be $91,994 with an average cost per new FP client served of $2.55. Personnel and HIV rapid testing kits comprised 55% and 21% of programmatic costs, respectively. Assuming no changes to program outputs and with efficiency gains under the MOH scenario, the estimated cost per new FP client served decreased to $1.30 with a programmatic cost reduction of 49%. Conclusion FP HIV SAIA is a low-cost and flexible implementation strategy for facilitating integrated delivery of HIV testing alongside FP services. Although cost implications of the FP HIV SAIA intervention must continue to be evaluated over time, these findings provide context-specific cost data useful for budget planning and decision-making regarding intervention delivery and expansion. Trial registration The trial was registered on December 15, 2016, with clinicaltrials.gov (NCT02994355).

Abstract Background In Kenya, HIV incidence is highest among reproductive-age women. A key HIV mitigation strategy is the integration of HIV testing and counseling (HTC) into family planning services, but successful integration remains problematic. We conducted a cluster-randomized trial using the Systems Analysis and Improvement Approach (SAIA) to identify and address bottlenecks in HTC integration in family planning clinics in Mombasa County, Kenya. This trial (1) assessed the efficacy of this approach and (2) examined if SAIA could be sustainably incorporated into the Department of Health Services (DOHS) programmatic activities. In Stage 1, SAIA was effective at increasing HTC uptake. Here, we present Stage 2, which assessed if SAIA delivery would be sustained when implemented by the Mombasa County DOHS and if high HTC performance would continue to be observed. Methods Twenty-four family planning clinics in Mombasa County were randomized to either the SAIA implementation strategy or standard care. In Stage 1, the study staff conducted all study activities. In Stage 2, we transitioned SAIA implementation to DOHS staff and compared HTC in the intervention versus control clinics 1-year post-transition. Study staff provided training and minimal support to DOHS implementers and collected quarterly HTC outcome data. Interviews were conducted with family planning clinic staff to assess barriers and facilitators to sustaining HTC delivery. Results Only 39% (56/144) of planned SAIA visits were completed, largely due to the COVID-19 pandemic and a prolonged healthcare worker strike. In the final study quarter, 81.6% (160/196) of new clients at intervention facilities received HIV counseling, compared to 22.4% (55/245) in control facilities (prevalence rate ratio [PRR]=3.64, 95% confidence interval [CI]=2.68–4.94). HIV testing was conducted with 60.5% (118/195) of new family planning clients in intervention clinics, compared to 18.8% (45/240) in control clinics (PRR=3.23, 95% CI=2.29–4.55). Interviews with family planning clinic staff suggested institutionalization contributed to sustained HTC delivery, facilitated by low implementation strategy complexity and continued oversight. Conclusions Intervention clinics demonstrated sustained improvement in HTC after SAIA was transitioned to DOHS leadership despite wide-scale healthcare disruptions and incomplete delivery of the implementation strategy. These findings suggest that system interventions may be sustained when integrated into DOHS programmatic activities. Trial registration ClinicalTrials.gov (NCT02994355) registered on 16 December 2016.

Abstract Background Significant gaps remain in HIV testing and counseling (HTC) in family planning (FP) clinics. To address these gaps, our group tested an implementation strategy called the Systems Analysis and Improvement Approach (SAIA), an evidenced-based multi-component implementation strategy focused on improving entire care cascades. In a cluster randomized trial of 24 FP clinics in Mombasa County, Kenya, SAIA led to a significant increase in HTC in intervention clinics compared to control clinics. The objective of this manuscript was to evaluate SAIA using the Consolidated Framework for Implementation Research (CFIR) and assess the Implementation Outcomes Framework outcomes of acceptability, appropriateness, and feasibility. Methods This qualitative assessment was nested within the cluster-randomized trial. Data collection included questionnaires to assess modifiable and non-modifiable health system factors related to HTC and in-depth interviews to query clinic norms, priorities, communication strategies, and readiness for change. The primary outcomes of interest were feasibility, appropriateness, and acceptability of SAIA. Data on inner setting and structural characteristics of FP clinics were collected to inform how context may impact outcomes. All interviews were recorded and analyzed using a rapid assessment approach. Results Of the 12 intervention clinics, 6 (50%) were public facilities. Availability of resources varied by clinic. Most clinics had a positive implementation climate, engaged leadership, and access to resources and information. While not all clinics identified HTC as a clinic priority, most reported a strong culture of embracing change and recognition of the importance of HIV testing within FP clinics. Interviews highlighted very high acceptability, appropriateness, and feasibility of SAIA. The implementation strategy was not complicated and fit well into existing clinic processes. In particular, staff appreciated that SAIA allowed clinic staff to generate contextually relevant solutions that they implemented. Conclusions SAIA was implemented in FP clinics of varying sizes, capacity, and management support and was found to be acceptable, appropriate, and feasible. The agency that clinic staff felt in proposing and implementing their own solutions was likely part of SAIA’s success. We anticipate this will continue to be a mechanism of SAIA’s success when it is scaled up to more clinics in future trials. Trial registration ClinicalTrials.gov (NCT02994355) registered 16 December 2016.

The movements of humans have a significant impact on population health. While studies of such movements are as old as public health itself, the COVID-19 pandemic has raised the profile of mobility research using digital technologies to track transmission routes and calculate the effects of health policies, such as lockdowns. In sub-Saharan Africa, the high prevalence of cell phone and smartphone use is a source of potentially valuable mobility data for public health purposes. Researchers can access call data records, passively collected in real time from millions of clients by cell phone companies, and associate these records with other data sets to generate insights, make predictions or draw possible policy implications. The use of mobility data from this source could have a range of significant benefits for society, from better control of infectious diseases, improved city planning, more efficient transportation systems and the optimisation of health resources. We discuss key ethical issues raised by public health studies using mobility data from cell phones in sub-Saharan Africa and identify six key ethical challenge areas: autonomy, including consent and individual or group privacy; bias and representativeness; community awareness, engagement and trust; function creep and accountability; stakeholder relationships and power dynamics; and the translation of mobility analyses into health policy. We emphasise the ethical importance of narrowing knowledge gaps between researchers, policymakers and the general public. Given that individuals do not really provide valid consent for the research use of phone data tracking their movements, community understanding and input will be crucial to the maintenance of public trust. Significance: • Mobility data derived from cell phones are being increasingly used for health research and public health purposes in sub-Saharan Africa, with minimal individual consent and largely without public awareness. • While such data can have significant potential public health benefits, risks and concerns related to their collection and use in sub-Saharan African contexts have not been widely discussed. • Innovative community engagement initiatives, which are appropriate and responsive to sub-Saharan African contexts, need to be developed to address ethical challenge areas and help warrant public trust in mobility research.

Abstract Background Periodontitis has been associated with adverse pregnancy outcomes. Little is known about the burden and risk factors for periodontitis among reproductive age women in sub-Saharan Africa. This analysis aimed to determine the prevalence and correlates of periodontitis among Kenyan women planning to conceive. Methods HIV-seronegative, reproductive-age women who were planning to conceive were enrolled and underwent a periodontal examination. Following the US Centers for Disease Control and Prevention clinical case definitions, the presence and severity of periodontitis was determined by establishing the level of clinical periodontal attachment loss and graded in three categories: no/mild, moderate, and severe. Secondary outcomes included the scores on the Gingival Index and Decayed, Missing, and Filled Teeth (DMFT) Index. Correlates of periodontitis were examined using univariable and multivariable logistic regression. Results Of the 647 women in the study, 84% (n = 541) had no/mild periodontitis, 15% (n = 97) had moderate periodontitis, and 1% (n = 9) had severe periodontitis. Mild gingivitis was present in 61% (n = 396) of women, while 27% (n = 176) had moderate gingivitis, and 1% (n = 9) had severe gingivitis. The majority (75%, n = 487) of women had a DMFT index in the very low range (score

Abstract Background The number of older women living with HIV in Africa is growing, and their health outcomes may be adversely impacted by social frailty, which reflects deficits in social resources that accumulate over the lifespan. Our objective was to adapt a Social Vulnerability Index (SVI) originally developed in Canada for use in a study of older women living with or without HIV infection in Mombasa, Kenya. Methods We adapted the SVI using a five-step process: formative qualitative work, translation into Kiswahili, a Delphi procedure, exploration of potential SVI items in qualitative work, and a rating and ranking exercise. Four focus group discussions (FGD) were conducted (three with women living with HIV and one with HIV-negative women), and two expert panels were constituted for this process. Results Themes that emerged in the qualitative work were physical impairment with aging, decreased family support, a turn to religion and social groups, lack of a financial safety net, mixed support from healthcare providers, and stigma as an added burden for women living with HIV. Based on the formative FGD, the expert panel expanded the original 19-item SVI to include 34 items. The exploratory FGD and rating and ranking exercise led to a final 16-item Kenyan version of the SVI (SVI-Kenya) with six domains: physical safety, support from family, group participation, instrumental support, emotional support, and financial security. Conclusions The SVI-Kenya is a holistic index to measure social frailty among older women in Kenya, incorporating questions in multiple domains. Further research is needed to validate this adapted instrument.

Most cervicovaginal microbiome-immunology studies to date have relied on 16S rDNA microbial profiling which does not resolve the molecular subgroups of Gardnerella, believed to be central to the pathogenesis of bacterial vaginosis (BV) and subsequent risk of HIV acquisition. Here we used the cpn60 universal target which in addition to other microbial taxa, resolves four Gardnerella subgroups, for cervicovaginal microbial profiling in a longitudinal cohort of Kenyan women to examine associations with cellular and soluble markers of inflammation and HIV susceptibility. Participants (N = 41) were sampled, contributing 362 samples for microbiome analysis. All non-Lactobacillus dominant microbial communities were associated with high pro-inflammatory cytokine levels. Divergent associations were observed among different Gardnerella subgroup dominated communities with respect to the chemokine IP-10. Specifically, Gardnerella subgroup A dominant and polymicrobial communities were associated with reduced concentrations of IP-10 in adjusted linear mixed models (p

Introduction Prevalence of lifetime-induced abortion in female sex workers (FSWs) in Kenya was previously estimated between 43% and 86%. Our analysis aimed at assessing lifetime prevalence and correlates, and incidence and predictors of induced abortions among FSWs in Kenya.Methods This is a secondary prospective cohort analysis using data collected as part of the WHISPER or SHOUT cluster-randomised trial in Mombasa, assessing effectiveness of an SMS-intervention to reduce incidence of unintended pregnancy. Eligible participants were current FSWs, 16–34 years and not pregnant or planning pregnancy. Baseline data on self-reported lifetime abortion, correlates and predictors were collected between September 2016 and May 2017. Abortion incidence was measured at 6-month and 12-month follow-up. A multivariable logistic regression model was used to assess correlates of lifetime abortion and discrete-time survival analysis was used to assess predictors of abortions during follow-up.Results Among 866 eligible participants, lifetime abortion prevalence was 11.9%, while lifetime unintended pregnancy prevalence was 51.2%. Correlates of lifetime abortions were currently not using a highly effective contraceptive (adjusted OR (AOR)=1.76 (95% CI=1.11 to 2.79), p=0.017) and having ever-experienced intimate partner violence (IPV) (AOR=2.61 (95% CI=1.35 to 5.06), p=0.005). Incidence of unintended pregnancy and induced abortion were 15.5 and 3.9 per 100 women-years, respectively. No statistically significant associations were found between hazard of abortion and age, sex work duration, partner status, contraceptive use and IPV experience.Conclusion Although experience of unintended pregnancy remains high, lifetime prevalence of abortion may have decreased among FSW in Kenya. Addressing IPV could further decrease induced abortions in this population.Trial registration number ACTRN12616000852459.

This study presents qualitative results from a mixed-method investigation conducted between May and August 2012 into the prevalence and consequences of four forms of intimate partner violence among women living with HIV who attended the Comprehensive Care Clinic at the Kenyatta National Hospital in Nairobi. As a part of the research, a quantitative survey found that among 600 sexually active women living with HIV aged 18–69, all reported experiencing emotional abuse; 20%, 17%, and 15% experienced controlling behavior, physical violence, and sexual violence, respectively. Qualitative research using focus group discussions with 19 women from the quantitative survey sought to contextualize these experiences and place them within a larger social structure where institutionalized gender inequality sets the tone for intimate partner violence against women in households. Participants reported that intimate partner violence led to their exposure to the virus and made them leery of disclosing their positive status or seeking support from a male partner for fear of a violent reaction. This fear and the socio-structural conditions in Kenya limit their ability to actively pursue comprehensive care, the stress of which can exacerbate symptoms and make managing the disease more difficult.

Methods: A priority-setting process (PSP) was launched to define priorities for patient-centered antimicrobial resistance (AMR) surveillance and research in low- and middle-income countries (LMICs). A list of uncertainties related to AMR surveillance in human health was generated using an online survey of stakeholders in LMICs, which asked for unanswered questions about diagnosis, treatment, or prevention of antibiotic resistance. Results: A total of 445 respondents generated 1076 questions that were mapped to a final shortlist of 107 questions. The most common theme was the treatment of drug-resistant infections, followed by diagnosis, then prevention, and requests for local AMR data. The most asked question was a request for local AMR data, revealing the lack of basic information in many LMICs to guide actions to tackle AMR. The steering group recommended three research areas to be prioritized for funding in the next five years: infection prevention and control in LMICs, improved electronic patient records, starting with laboratory information management systems, and sustainable behavior change among doctors and other health care professionals with a focus on diagnostic stewardship.

BackgroundEmerging evidence suggests that after completion of treatment for tuberculosis (TB) a significant proportion of patients experience sequelae. However, there is limited synthesized evidence on this from low-income countries, from Sub-Saharan Africa, and in HIV infected individuals. We seek to provide an updated comprehensive systematic review and meta-analysis on the magnitude and factors associated with post-TB lung disease (PTLD) in low- and middle-income countries (LMICs).MethodsWe searched PubMed, Embase and CINAHL for studies from LMICs with data on post-TB lung health in patients who had previously completed treatment for pulmonary TB. Data on study characteristics, prevalence of PTLD-specifically abnormal lung function (spirometry), persisting respiratory symptoms and radiologic abnormalities were abstracted. Statistical analysis was performed using Microsoft Excel and R version 4.1 software, and random effects meta-analysis conducted to compute pooled prevalence of PTLD, evaluate heterogeneity, and assess factors associated with PTLD.ResultsWe identified 32 eligible studies with 6225 participants. Twenty-one studies were from Africa, 16 included HIV infected participants, spirometry was conducted in 20 studies, symptom assessment in 16 and chest imaging in eight. Pooled prevalence of abnormal lung function was 46.7%, persistent respiratory symptoms 41.0%, and radiologic abnormalities 64.6%. Magnitude of any type of PTLD varied by HIV status (HIV- 66.9%, HIV+ 32.8%, p = 0.0013), across geographic setting (SE Asia 57.5%, Southern America 50.8%, and Africa 38.2%, p = 0.0118), and across urban-rural settings (symptom prevalence: rural 68.8%, urban 39.1%, mixed settings 27.9%, p = 0.0035), but not by income settings, sex or age-group.ConclusionsThere is high burden of post-TB persistent respiratory symptoms, functional lung impairment and radiologic structural abnormalities in individuals living in LMICs. Burden varies across settings and by HIV status. This evidence may be valuable to advocate for and inform implementation of structured health care specific to the needs of this vulnerable population of individuals.

BackgroundThe microbiota of the lower female genital tract plays an important role in women's health. Microbial profiling using the chaperonin60 (cpn60) universal target (UT) improves resolution of vaginal species associated with negative health outcomes compared to the more commonly used 16S ribosomal DNA target. However, the choice of DNA extraction and PCR product purification methods may bias sequencing-based microbial studies and should be optimized for the sample type and molecular target used. In this study, we compared two commercial DNA extraction kits and two commercial PCR product purification kits for the microbial profiling of cervicovaginal samples using the cpn60 UT.MethodsDNA from cervicovaginal secretions and vaginal lavage samples as well as mock community standards were extracted using either the specialized QIAamp DNA Microbiome Kit, or the standard DNeasy Blood & Tissue kit with enzymatic pre-treatment for enhanced lysis of gram-positive bacteria. Extracts were PCR amplified using well-established cpn60 primer sets and conditions. Products were then purified using a column-based method (QIAquick PCR Purification Kit) or a gel-based PCR clean-up method using the QIAEX II Gel Extraction Kit. Purified amplicons were sequenced with the MiSeq platform using standard procedures. The overall quality of each method was evaluated by measuring DNA yield, alpha diversity, and microbial composition.ResultsDNA extracted from cervicovaginal samples using the DNeasy Blood and Tissue kit, pre-treated with lysozyme and mutanolysin, resulted in increased DNA yield, bacterial diversity, and species representation compared to the QIAamp DNA Microbiome kit. The column-based PCR product purification approach also resulted in greater average DNA yield and wider species representation compared to a gel-based clean-up method. In conclusion, this study presents a fast, effective sample preparation method for high resolution cpn60 based microbial profiling of cervicovaginal samples.

Background. Active case finding (ACF) for tuberculosis (TB) is a key strategy to reduce diagnostic delays, expedite treatment, and prevent transmission. Objective. Our objective was to identify the populations, settings, screening and diagnostic approaches that optimize coverage (proportion of those targeted who were screened) and yield (proportion of those screened who had active TB) in ACF programs. Methods. We performed a comprehensive search to identify studies published from 1980-2016 that reported the coverage and yield of different ACF approaches. For each outcome, we conducted meta-analyses of single proportions to produce estimates across studies, followed by meta-regression to identify predictors. Findings. Of 3,972 publications identified, 224 met criteria after full-text review. Most individuals who were targeted successfully completed screening, for a pooled coverage estimate of 93.5%. The pooled yield of active TB across studies was 3.2%. Settings with the highest yield were internally-displaced persons camps (15.6%) and healthcare facilities (6.9%). When compared to symptom screening as the reference standard, studies that screened individuals regardless of symptoms using microscopy, culture, or GeneXpert®MTB/RIF (Xpert) had 3.7% higher case yield. In particular, microbiological screening (usually microscopy) as the initial test, followed by culture or Xpert for diagnosis had 3.6% higher yield than symptom screening followed by microscopy for diagnosis. In a model adjusted for use of Xpert testing, approaches targeting persons living with HIV (PLWH) had a 4.9% higher yield than those targeting the general population. In all models, studies targeting children had higher yield (4.8%-5.7%) than those targeting adults. Conclusion. ACF activities can be implemented successfully in various populations and settings. Screening yield was highest in internally-displaced person and healthcare settings, and among PLWH and children. In high-prevalence settings, ACF approaches that screen individuals with laboratory tests regardless of symptoms have higher yield than approaches focused on symptomatic individuals.

Abstract Background A high proportion of African women utilize family planning (FP) services. Accordingly, incorporating HIV testing into FP services may strategically target the first WHO 90–90-90 goal of 90% of people living with HIV knowing their status. Methods The objective of this analysis was to determine the proportion of new FP clients counseled and tested for HIV, as well as correlates of HIV testing, in a random sample of 58 FP clinics in Mombasa County, Kenya. Structured interviews of FP clinic managers collected data on characteristics of FP clinics and staff. Study staff performed a 3-month review of FP registers, summarizing new client HIV testing and counseling (HTC). Because overall rates of HTC were quite low, a binary variable was created comparing clinics performing any HIV counseling and/or testing to clinics performing none. Generalized linear models were used to calculate prevalence ratios (PR) and identify correlates of HTC. Factors associated with any HTC with a p-value

The majority of Kenya’s > 3 million camels have antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV), although human infection in Africa is rare. We enrolled 243 camels aged 0–24 months from 33 homesteads in Northern Kenya and followed them between April 2018 to March 2020. We collected and tested camel nasal swabs for MERS-CoV RNA by RT-PCR followed by virus isolation and whole genome sequencing of positive samples. We also documented illnesses (respiratory or other) among the camels. Human camel handlers were also swabbed, screened for respiratory signs, and samples were tested for MERS-CoV by RT-PCR. We recorded 68 illnesses among 58 camels, of which 76.5% (52/68) were respiratory signs and the majority of illnesses (73.5% or 50/68) were recorded in 2019. Overall, 124/4692 (2.6%) camel swabs collected from 83 (34.2%) calves in 15 (45.5%) homesteads between April–September 2019 screened positive, while 22 calves (26.5%) recorded reinfections (second positive swab following ≥ 2 consecutive negative tests). Sequencing revealed a distinct Clade C2 virus that lacked the signature ORF4b deletions of other Clade C viruses. Three previously reported human PCR positive cases clustered with the camel infections in time and place, strongly suggesting sporadic transmission to humans during intense camel outbreaks in Northern Kenya.

Abstract With expanded HIV treatment and prevention programmes, most infants born to HIV‐positive women are uninfected, but the patterns and determinants of their growth are not well described. This study aimed to assess growth patterns in a cohort of HIV‐exposed uninfected (HEU) infants who participated in an experimental HIV vaccine trial and to test for associations with maternal and infant factors, including in‐utero exposure to antiretroviral therapy (ART), mode of delivery, exclusive breastfeeding, mother's education and receipt of the vaccine. Infants in the trial were seen at regular clinic visits from birth to 48 weeks of age. From the anthropometric measurements at these visits, weight‐for‐age z‐scores (WAZ), weight‐for‐length z‐scores (WLZ) and length‐for‐age z‐scores (LAZ) were computed using World Health Organization (WHO) software and reference tables. Growth patterns were investigated with respect to maternal and infant factors, using linear mixed regression models. From 94 infants included at birth, growth data were available for 75.5% at 48 weeks. The determinants of infant growth in this population are multifactorial: infant LAZ during the first year was significantly lower among infants delivered by caesarean section (p = 0.043); both WAZ and LAZ were depressed among infants with longer exposure to maternal ART (WAZ: p = 0.015; LAZ: p < 0.0001) and among infants of mothers with lower educational level (WAZ: p = 0.038; LAZ: p < 0.0001); the effect of maternal education was modified by breastfeeding practice, with no differences seen in exclusively breastfed infants. These findings inform intervention strategies to preserve growth in this vulnerable infant population.

INTRODUCTION: Opportunistic fungal infections due to immunosuppression coupled with antifungal drug resistance are an emerging challenge globally. The present study examined the antifungal susceptibility of yeasts and molds from sputum of tuberculosis retreatment and relapse patients at selected reference facilities in Kenya. METHODS: a total of 340 sputa samples from patients who gave written informed consent were examined. Fungal culture was done on sabouraud dextrose agar (SDA). Molds were identified by macroscopic and microscopic features while yeasts were inoculated on CHROMTMagar Candida and confirmed using API 20C AUXTM. Itraconazole (ICZ), voriconazole (VCZ), fluconazole (FCZ) and amphotericin B (AMB) were tested using broth micro-dilution methods according to Clinical and Laboratory Standards Institute (CLSI). RESULTS: out of the 340 samples, 14.4% (n=49) and 15.6% (n=53) were positive for yeasts and molds respectively. Candida albicans and C. krusei were the most predominant isolates constituting 49.0% (n=24) and 20.4% (n=10) of the total yeasts respectively. Aspergillus spp. were the most frequent (22.6%) molds and isolates with MICs 4μg/ml on the antifungal agents were noted. All the molds except two (n=2) isolates of Scedosporium aspiopermum exhibited MICs 4μg/ml for fluconazole. Overall, molds were more sensitive to AMB and VCZ.Candida albicans had MIC50 0.06μg/ml, and MIC 904μg/ml. There was a statistically significant difference (F=3.7, P=0.004=0.05) in the overall sensitivity pattern of molds for the four antifungal agents while there was no significant difference (F=1.7, P=0.154=0.05) in sensitivity exhibited by the yeasts. CONCLUSION: the study demonstrates the significance of fungal colonization in presumptive tuberculosis retreatment or relapse with evidence of triazole resistance. There is need to strengthen fungal diagnostic and clinical management capabilities in susceptible populations.

IntroductionThe postpartum period can be challenging for women living with HIV. Understanding how the postpartum period impacts ART adherence and condomless sex could inform the development of comprehensive sexual and reproductive health and HIV services tailored to the needs of women living with HIV during this critical interval.MethodsIn a longitudinal cohort study of HIV-seropositive Kenyan women, late ART refills and self-reported condomless sex were compared between the woman's pregnancy and the postpartum period. Analyses were conducted using generalized estimating equations and adjusted for alcohol use, depressive symptoms, intimate partner violence (IPV), and having a recent regular partner. Effect modification was explored for selected variables.Results and discussion151 women contributed visits. Late ART refills occurred at 7% (32/439) of pregnancy visits compared to 18% (178/1016) during the postpartum period (adjusted relative risk [aRR] 2.44, 95% confidence interval [CI] 1.62-3.67). This association differed by women's education level. Women with ≥8 years of education had late ART refills more during the postpartum period than pregnancy (aRR 3.00, 95%CI 1.95-4.62). In contrast, in women with ConclusionImproved support for ART adherence during the postpartum period and addressing IPV to limit condomless sex could improve HIV treatment and prevention outcomes for HIV-seropositive women as well as their infants and sexual partners.

A prerequisite for the design of an HIV vaccine that elicits protective antibodies is understanding the developmental pathways that result in desirable antibody features. The development of antibodies that mediate antibody-dependent cellular cytotoxicity (ADCC) is particularly relevant because such antibodies have been associated with HIV protection in humans. We reconstructed the developmental pathways of six human HIV-specific ADCC antibodies using longitudinal antibody sequencing data. Most of the inferred naive antibodies did not mediate detectable ADCC. Gain of antigen binding and ADCC function typically required mutations in complementarity determining regions of one or both chains. Enhancement of ADCC potency often required additional mutations in framework regions. Antigen binding affinity and ADCC activity were correlated, but affinity alone was not sufficient to predict ADCC potency. Thus, elicitation of broadly active ADCC antibodies may require mutations that enable high-affinity antigen recognition along with mutations that optimize factors contributing to functional ADCC activity.

IntroductionBacterial vaginosis (BV) and vaginal microbiota disruption during pregnancy are associated with increased risk of spontaneous preterm birth (SPTB), but clinical trials of BV treatment during pregnancy have shown little or no benefit. An alternative hypothesis is that vaginal bacteria present around conception may lead to SPTB by compromising the protective effects of cervical mucus, colonising the endometrial surface before fetal membrane development, and causing low-level inflammation in the decidua, placenta and fetal membranes. This protocol describes a prospective case-cohort study addressing this hypothesis.Methods and analysisHIV-seronegative Kenyan women with fertility intent are followed from preconception through pregnancy, delivery and early postpartum. Participants provide monthly vaginal specimens during the preconception period for vaginal microbiota assessment. Estimated date of delivery is determined by last menstrual period and first trimester obstetrical ultrasound. After delivery, a swab is collected from between the fetal membranes. Placenta and umbilical cord samples are collected for histopathology. Broad-range 16S rRNA gene PCR and deep sequencing of preconception vaginal specimens will assess species richness and diversity in women with SPTB versus term delivery. Concentrations of key bacterial species will be compared using quantitative PCR (qPCR). Taxon-directed qPCR will also be used to quantify bacteria from fetal membrane samples and evaluate the association between bacterial concentrations and histopathological evidence of inflammation in the fetal membranes, placenta and umbilical cord.Ethics and disseminationThis study was approved by ethics committees at Kenyatta National Hospital and the University of Washington. Results will be disseminated to clinicians at study sites and partner institutions, presented at conferences and published in peer-reviewed journals. The findings of this study could shift the paradigm for thinking about the mechanisms linking vaginal microbiota and prematurity by focusing attention on the preconception vaginal microbiota as a mediator of SPTB.

A reservoir of HIV-infected cells that persists despite suppressive antiretroviral therapy (ART) is the source of viral rebound upon ART cessation and the major barrier to a cure. Understanding reservoir seeding dynamics will help identify the best timing for HIV cure strategies. Here we characterize reservoir seeding using longitudinal samples from before and after ART initiation in individuals who sequentially became infected with genetically distinct HIV variants (superinfected). We previously identified cases of superinfection in a cohort of Kenyan women, and the dates of both initial infection and superinfection were determined. Six women, superinfected 0.2-5.2 years after initial infection, were subsequently treated with ART 5.4-18.0 years after initial infection. We performed next-generation sequencing of HIV gag and env RNA from plasma collected during acute infection as well as every ~2 years thereafter until ART initiation, and of HIV DNA from PBMCs collected 0.9-4.8 years after viral suppression on ART. We assessed phylogenetic relationships between HIV DNA reservoir sequences and longitudinal plasma RNA sequences prior to ART, to determine proportions of initial and superinfecting variants in the reservoir. The proportions of initial and superinfection lineage variants present in the HIV DNA reservoir were most similar to the proportions present in HIV RNA immediately prior to ART initiation. Phylogenetic analysis confirmed that the majority of HIV DNA reservoir sequences had the smallest pairwise distance to RNA sequences from timepoints closest to ART initiation. Our data suggest that while reservoir cells are created throughout pre-ART infection, the majority of HIV-infected cells that persist during ART entered the reservoir near the time of ART initiation. We estimate the half-life of pre-ART DNA reservoir sequences to be ~25 months, which is shorter than estimated reservoir decay rates during suppressive ART, implying continual decay and reseeding of the reservoir up to the point of ART initiation.

BackgroundExcessive alcohol intake has been associated with poor adherence to antiretroviral therapy (ART). The impact of alcohol on viral suppression is particularly important among groups at high risk of HIV transmission, such as female sex workers (FSWs). Few studies have directly evaluated the association between alcohol use and HIV viral load. We hypothesized that hazardous or harmful alcohol use is associated with detectable plasma viral load among HIV-positive FSWs.MethodsA prospective cohort study was conducted among HIV-positive FSWs in Mombasa, Kenya. Hazardous or harmful alcohol use was assessed yearly and defined as an Alcohol Use Disorders Identification Test (AUDIT) score ≥7. Detectable viral load was assessed every six months and defined as ≥180 c/mL. Adherence measures were collected monthly and included late ART refill (>48 hours) and self-reported adherence, using both a validated self-rating scale of ability to take medication and visual analog scale (VAS) of ART use in the last month. Generalized estimating equations were used to estimate adjusted relative risks (aRR) and 95% confidence intervals (CI).ResultsThis analysis included 366 participants followed monthly between October 2012 and March 2018. At baseline, AUDIT scores indicated hazardous alcohol use (AUDIT 7-15) in 14.3%, harmful alcohol use (AUDIT 16-19) in 1.4%, and alcohol dependency (AUDIT ≥20) in 1.4% of participants. After adjusting for potential confounders, a combined exposure including hazardous, harmful, and dependent alcohol use was not associated with detectable viral load (aRR 1.10, 95%CI 0.63-1.92) or late ART refill (aRR 1.13, 95%CI 0.82-1.56), but was associated with lower self-rated ability to take medication (aRR 2.38, 95%CI 1.42-3.99) and a lower rate of self-reported perfect ART adherence by VAS (aRR 2.62, 95%CI 1.84-3.71).ConclusionsIn this FSW cohort, while participants reporting hazardous, harmful, or dependent alcohol use were not more likely to have a detectable viral load, they were more likely to report lower ART adherence. These results suggest that interventions targeting alcohol use among this population of FSWs may not have a large impact on viral suppression.

Abstract Background Male circumcision provides men with approximately 60% protection from acquiring HIV infection via heterosexual sex, and has become a key component of HIV prevention efforts in sub-Saharan Africa. Possible mechanisms for this protection include removal of the inflammatory anaerobic sub-preputial environment and the high concentration of Langerhans cells on the inside of the foreskin, both believed to promote local vulnerability to HIV infection. In people who do acquire HIV, viral load is partially determined by infecting partner viral load, potentially mediated by size of infecting inoculum. By removing a portal for virion entry, prior male circumcision could decrease infecting inoculum and thus viral load in men who become HIV-infected, conferring the known associated benefits of slower progression to disease and decreased infectiousness. Methods We performed an as-treated analysis of plasma samples collected under a randomized controlled trial of male circumcision for HIV prevention, comparing men based on their circumcision status at the time of HIV acquisition, to determine whether circumcision is associated with lower viral load. Eligible men were seroconverters who had at least one plasma sample available drawn at least 6 months after infection, reported no potential exposures other than vaginal sex and, for those who were circumcised, were infected more than 6 weeks after circumcision, to eliminate the open wound as a confounder. Initial viral load testing indicated that quality of pre-2007 samples might have been compromised during storage and they were excluded, as were those with undetectable or unquantifiable results. Log viral loads were compared between groups using univariable and multivariable linear regression, adjusting for sample age and sexually transmitted infection diagnosis with 3.5 months of seroconversion, with a random effect for intra-individual clustering for samples from the same man. A per-protocol analysis was also performed. Results There were no viral load differences between men who were circumcised and uncircumcised at the time of HIV infection (means 4.00 and 4.03 log10 copies/mL respectively, p = .88) in any analysis. Conclusion Circumcision status at the time of HIV infection does not affect viral load in men. Trial registration The original RCT which provided the samples was ClinicalTrials.gov trial NCT00059371.

HIV-1 superinfection, in which an infected individual acquires a second HIV-1 infection from a different partner, is one of the only settings in which HIV acquisition occurs in the context of a pre-existing immune response to natural HIV infection. There is evidence that initial infection provides some protection from superinfection, particularly after 6 months of initial infection, when development of broad immunity occurs. Comparison of the immune response of superinfected individuals at the time of superinfection acquisition to that of individuals who remain singly infected despite continued exposure can shed light on immune correlates of HIV acquisition to inform prophylactic vaccine design. We evaluated a panel of humoral immune responses in the largest published group of superinfected individuals (n = 21), compared to a set of 3:1 matched singly infected controls from the same cohort. The immune functions studied included plasma neutralization, plasma and cervical antibody-dependent cellular cytotoxicity, and plasma IgG and IgA binding to a panel of 18 envelope antigens, including correlates of HIV acquisition in the RV144 vaccine trial, IgG binding to V1V2 and IgA binding to gp140. Association between each immune function and HIV superinfection was evaluated using conditional logistic regression. No significant associations were detected between any of the immune functions and superinfection acquisition. This study constitutes the most comprehensive and detailed characterization of multiple immune correlates of superinfection to date. The results suggest that immune responses not commonly measured in current HIV studies may be important in protection from HIV infection, and these or a more robust humoral response than that seen in naturally infected women may be needed for a protective vaccine.

ObjectivesFemale sex workers (FSWs) in sub-Saharan Africa are a key population for HIV prevention and treatment interventions, but less attention is given to their family planning needs. We evaluated the prevalence and predictors of unmet contraceptive need in HIV-positive FSWs.Study designThis cross-sectional analysis used data from an existing longitudinal study of FSWs in Mombasa, Kenya. This analysis included women who were HIV positive, age ≥18 years, pre-menopausal, not currently pregnant or desiring pregnancy, and reported exchanging sex for cash or in-kind payment at the time of enrollment. Unmet contraceptive need was defined as non-use of modern non-barrier contraceptives and not currently trying to become pregnant. Poisson regression was used to identify factors independently associated with unmet contraceptive need.ResultsAmong 346 HIV-positive FSWs, 125 (36.1%) reported modern non-barrier contraceptive use, leaving 221 (63.9%, 95%CI 58.8-68.9%) with unmet contraceptive need. Condom use was the only form of contraception for 129 (37.3%) participants. In unadjusted analyses, unmet contraceptive need was associated with physical abuse in the past year by someone other than a regular partner (PR 1.2, 95%CI 1.0-1.5), desire for (more) children (PR 1.3, 95%CI 1.1-1.5), and having 2-3 previous pregnancies compared to 0-1 prior pregnancies (PR 0.8, 95%CI 0.6-0.9). In adjusted analyses, lower number of previous pregnancies and having desire for future children remained significantly associated with a higher prevalence of unmet contraceptive need.ConclusionsUnmet need for modern non-barrier contraception was found in two-thirds of HIV-positive FSWs who reported that they were not currently trying to become pregnant, and was higher in women with the lowest number of prior pregnancies (0-1 prior pregnancies) and in those reporting desire for (more) children in the future. These findings highlight the need for concerted efforts to identify and eliminate barriers to contraceptive use in FSWs living with HIV.

Sub-Saharan Africa carries the biggest burden of the human immunodeficiency virus type 1 (HIV-1)/AIDS epidemic and is in an urgent need of an effective vaccine. CD8+ T cells are an important component of the host immune response to HIV-1 and may need to be harnessed if a vaccine is to be effective. CD8+ T cells recognize human leukocyte antigen (HLA)-associated viral epitopes and the HLA alleles vary significantly among different ethnic groups. It follows that definition of HIV-1-derived peptides recognized by CD8+ T cells in the geographically relevant regions will critically guide vaccine development. Here, we study fine details of CD8+ T-cell responses elicited in HIV-1/2-uninfected individuals in Nairobi, Kenya, who received a candidate vaccine delivering conserved regions of HIV-1 proteins called HIVconsv. Using 10-day cell lines established by in vitro peptide restimulation of cryopreserved PBMC and stably HLA-transfected 721.221/C1R cell lines, we confirm experimentally many already defined epitopes, for a number of epitopes we define the restricting HLA molecule(s) and describe four novel HLA-epitope pairs. We also identify specific dominance patterns, a promiscuous T-cell epitope and a rescue of suboptimal T-cell epitope induction in vivo by its functional variant, which all together inform vaccine design.

Cell surface expression of α4β7, α4β1 and αEβ7 integrins play a key role in T cell distribution. Understanding the contribution of integrins to the density and ratios of CD4+: CD4negT cell at the portals of entry for HIV is of fundamental importance for the advance of more effective HIV prevention strategies. We therefore set out to characterize and compare the expression of α4β7, α4β1 and αEβ7 integrins on systemic, cervical and rectal CD4+ and CD4negT cells isolated from a cohort of healthy Kenyan women at low risk for sexually transmitted infections (STI) (n = 45). Here we show that blood and cervix were enriched in α4+β1+CD4+T cells and α4+β7hiCD4+T cells, whereas the rectum had an equal frequency of α4+β7hiCD4+T cells and αE+β7hiCD4+T cells. Most cervical and rectal αE+β7hiCD4+T cells expressed CCR5 as well as CD69. Interestingly, αEβ7 was the predominant integrin expressed by CD4negT cells in both mucosal sites, outnumbering αE+β7hiCD4+T cells approximately 2-fold in the cervix and 7-fold in the rectum. The majority of αE+β7hiCD4negT cells expressed CD69 at the mucosa. Taken together, our results show unique tissue-specific patterns of integrin expression. These results can help in guiding vaccine design and also the use of therapeutically targeting integrin adhesion as a means to preventing HIV.

As countries scale up adult voluntary medical male circumcision (VMMC) for HIV prevention, they are looking ahead to long term sustainable strategies, including introduction of early infant male circumcision (EIMC). To address the lack of evidence regarding introduction of EIMC services in sub-Saharan African settings, we conducted a simultaneous, prospective comparison of two models of EIMC service delivery in Homa Bay County, Kenya. In one division a standard delivery package (SDP) was introduced and included health facility-based provision of EIMC services with community engagement for client referral versus in a different division a standard package plus (SDPplus) that included community-delivered EIMC services. Babies 1-60 days old were eligible for EIMC. A representative sample of mothers and fathers of baby boys at 16 health facilities was surveyed. We examined differences between mothers and fathers in the SDP and SDPplus divisions and identified factors associated with EIMC uptake. We report adjusted prevalence ratios (aPR). Of 1660 mothers interviewed, 1501 (89%) gave approval to contact the father, and 1259 fathers (84%) were interviewed. The proportion of babies circumcised was slightly greater in the SDPplus division than the SDP division (27.3% vs 23.7%), but the difference was not significant (p = 0.08). In adjusted analyses, however, the prevalence of babies being circumcised was greater in the SDPplus division (aPR = 1.23, 95% CI:1.04-1.45) and the factors associated with a baby being circumcised were the mother having received information about EIMC (during pregnancy, aPR = 4.81, 95% CI: 2.21-3.42), having discussed circumcision with the father if married or cohabiting (aPR = 5.39, 95% CI: 3.31-8.80) or being single (aPR = 5.67, 95% CI: 3.31-9.69), perceiving herself to be living with HIV (aPR = 1.39, 95% CI: 1.15-1.67), or having a post-secondary education (aPR = 1.33, 95% CI: 1.04-1.69), and the father being Muslim (aPR = 1.85, 95% CI: 1.29-2.65) or circumcised (aPR = 1.34, 95% CI: 1.13-1.59). The median age of 2117 babies circumcised was 8 days (IQR: 1-36), and the median weight was 3.6 kg (IQR: 3.2-4.4). There were 6 moderate adverse events (AEs) (0.28%); 5 severe AEs (0.24%), all involving an injury to the glans penis, requiring hospitalization and corrective surgery; and one death probably related to the procedure. There were no AEs among the 365 procedures performed outside health facilities. Information and education campaigns must reach members of the general population, especially men and fathers, who are influential to the EIMC decision. Serious AEs using the Mogen clamp are rare, but do occur and require efficient, reliable emergency back-up. Our results can assist countries considering scale-up of EIMC services for HIV prevention as their adult VMMC programs mature.

As access to antiretroviral therapy in sub-Saharan Africa continues to expand, more women with HIV can expect to survive through their reproductive years. Modern contraceptives can help women choose the timing and spacing of childbearing. However, concerns remain that women with HIV who use non-barrier forms of modern contraception may engage in more condomless sex because of their decreased risk of unintended pregnancy. We examined whether non-barrier modern contraceptive use by HIV-positive female sex workers was associated with increased frequency of recent condomless sex, measured by detection of prostate-specific antigen (PSA) in vaginal secretions.Women who were HIV-positive and reported transactional sex were included in this analysis. Pregnant and post-menopausal follow-up time was excluded, as were visits at which women reported trying to get pregnant. At enrollment and quarterly follow-up visits, a pelvic speculum examination with collection of vaginal secretions was conducted for detection of PSA. In addition, women completed a structured face-to-face interview about their current contraceptive methods and sexual risk behavior at enrollment and monthly follow-up visits. Log-binomial generalized estimating equations regression was used to test for associations between non-barrier modern contraceptive use and detection of PSA in vaginal secretions and self-reported condomless sex. Data from October 2012 through September 2014 were included in this analysis.Overall, 314 women contributed 1,583 quarterly examination visits. There was minimal difference in PSA detection at contraceptive-exposed versus contraceptive-unexposed visits (adjusted relative risk [aRR] 1.28, 95% confidence interval [95% CI] 0.93-1.76). There was a higher rate of self-reported condomless sex at visits where women reported using modern contraceptives, but this difference was not statistically significant after adjustment for potential confounding factors (aRR 1.59, 95% CI 0.98-2.58).Non-barrier methods of modern contraception were not associated with increased risk of objective evidence of condomless sex.

Penile coital injuries are one of the suggested mechanisms behind the increased risk of HIV among uncircumcised men. We evaluated the prevalence and correlates of self-reported penile coital injuries in a longitudinal community-based cohort of young (18-24 years old), newly circumcised and uncircumcised men in Western Kenya.Self-reported penile coital injuries were assessed at baseline, 6, 12, 18 and 24 months of follow-up, and were defined as scratches, cuts or abrasions during sex, penile soreness during sex, and skin of the penis bleeding during sex. Associations between penile coital injuries, circumcision, sexual satisfaction, and other covariates were estimated with mixed effect models.Between November 2008 and April 2010 3,186 participants were enrolled (1,588 into circumcision group and 1,598 as age-matched controls). Among 2,106 (66%) participants sexually active at baseline, 53% reported any penile injury, including 44% scratches, cuts or abrasions; 32% penile pain/soreness; and 22% penile bleeding. In multivariable modeling, risk was lower for circumcised men than uncircumcised men for scratches, cuts and abrasions (aOR = 0.39; 95% CI 0.34-0.44); penile pain/soreness (aOR = 0.58; 95% CI 0.51-0.65), penile bleeding (aOR = 0.53; 95% CI 0.46-0.62), and any penile coital injuries (aOR = 0.47; 95%CI 0.42-0.53). Other significant risk factors included increasing age, history of STIs and genital sores, and multiple sex partners, while condom use was protective. Coital injuries were significantly associated with lower levels of sexual satisfaction in longitudinal analyses (scratches, cuts or abrasions: aOR = 0.87, 95% CI: 0.76-0.98; penile pain/soreness: aOR = 0.82, 95% CI: 0.72-0.93; and penile bleeding: aOR = 0.65, 95% CI: 0.55-0.76).Self-reported penile coital injuries were common and decreased significantly following circumcision. Improving sexual experience through the removal of a potential source of sexual discomfort may resonate with many men targeted for circumcision services. The role of penile coital injuries in sexual satisfaction, HIV, HSV-2, and as a motivator for seeking circumcision services should be explored further.

INTRODUCTION:Optimal tuberculosis contact investigation impacts TB prevention, timely case finding and linkage to care, however data on routine implementation in high burden contexts is limited. MATERIALS AND METHODS:In a multi-method qualitative study based on individual interviews with TB patients, facility observations and focus group discussions with health workers (HWs) in 13 public health facilities, and key informant interviews with governmental and non-governmental experts, we describe TB contact investigation in the context of an urban setting in Kenya and identify opportunities for optimization. RESULTS:Invitation of TB patients to bring close contacts by HWs was key for all patient decisions that led to contact screening in addition to patients' understanding of TB transmission and desire to avoid contacts suffering from TB. Sub-optimal HW enquiry of TB patients and contacts presenting at the facility were missed opportunities which stemmed from lack of standardized operational procedures, documentation tools and HW training. Stakeholders proposed provision of fast tracked and holistic health packages for contacts seeking TB screening, and sustainable government led funding for the requisite infrastructure and workforce. CONCLUSION:TB contact invitation by HWs leading to contact screening occurs in this context. Stakeholder perspectives inform the design of an operational framework for optimized delivery.

Background. The increased number of clinical trials taking place in developing countries and the complexity of trial protocols mandate that local ethics review committees (ERCs) reviewing them have the capacity to ensure that they are conducted to the highest ethical standards.Methods. The Kenya AIDS Vaccine Initiative (KAVI) Institute of Clinical Research (ICR) (KAVI-ICR) and the Kenyan National Council for Science and Technology (NCST) embarked on an exercise to enhance the capacity of ERCs in Kenya to review such protocols. This process involved conducting an audit of all ERCs in the country, and performing training needs assessments to identify knowledge and capacity gaps. Information obtained was used to develop training materials for ERC members at workshops conducted in different parts of the country.Results. Five accredited and 13 non-accredited ERCs were identified. Four of the accredited ERCs were located in the capital city of Kenya, Nairobi. The most common challenges cited by participants during the needs assessments were excess workload, and a lack of co-ordination and/or communication between the ERCs. Subsequently, 140 ERC members from 17 institutions across the country were trained as follows: 36 from institutions in the western part of Kenya, 38 from institutions in the south-eastern coastal region, 38 from the eastern region and 44 from Nairobi.Conclusion. The KAVI-ICR and the NCST have developed training modules for training ERC members in Kenya and are in the process of developing a manual to train members. The Kenyan experience may be used to enhance the capacity of ERCs in the East African region.

We are developing a pan-clade HIV-1 T-cell vaccine HIVconsv, which could complement Env vaccines for prophylaxis and be a key to HIV cure. Our strategy focuses vaccine-elicited effector T-cells on functionally and structurally conserved regions (not full-length proteins and not only epitopes) of the HIV-1 proteome, which are common to most global variants and which, if mutated, cause a replicative fitness loss. Our first clinical trial in low risk HIV-1-negative adults in Oxford demonstrated the principle that naturally mostly subdominant epitopes, when taken out of the context of full-length proteins/virus and delivered by potent regimens involving combinations of simian adenovirus and poxvirus modified vaccinia virus Ankara, can induce robust CD8+ T cells of broad specificities and functions capable of inhibiting in vitro HIV-1 replication. Here and for the first time, we tested this strategy in low risk HIV-1-negative adults in Africa. We showed that the vaccines were well tolerated and induced high frequencies of broadly HIVconsv-specific plurifunctional T cells, which inhibited in vitro viruses from four major clades A, B, C, and D. Because sub-Saharan Africa is globally the region most affected by HIV-1/AIDS, trial HIV-CORE 004 represents an important stage in the path toward efficacy evaluation of this highly rational and promising vaccine strategy.

Cells from women who are epidemiologically deemed resistant to HIV infection exhibit a 40–60% reduction in endogenous IRF-1 (interferon regulatory factor-1), an essential regulator of host antiviral immunity and the early HIV replication. This study examined the functional consequences of reducing endogenous IRF-1 on HIV-1 replication and immune response to HIV in natural HIV target cells. IRF-1 knockdown was achieved in ex vivo CD4+ T cells and monocytes with siRNA. IRF-1 level was assessed using flow cytometry, prior to infection with HIV-Bal, HIV-IIIB, or HIV-VSV-G. Transactivation of HIV long terminal repeats was assessed by p24 secretion (ELISA) and Gag expression (reverse transcription–polymerase chain reaction (RT–PCR)). The expression of IRF-1–regulated antiviral genes was quantitated with RT–PCR. A modest 20–40% reduction in endogenous IRF-1 was achieved in >87% of ex vivo–derived peripheral CD4+ T cells and monocytes, resulted in >90% reduction in the transactivation of the HIV-1 genes (Gag, p24) and, hence, HIV replication. Curiously, these HIV-resistant women demonstrated normal immune responses, nor an increased susceptibility to other infection. Similarly, modest IRF-1 knockdown had limited impact on the magnitude of HIV-1–elicited activation of IRF-1–regulated host immunologic genes but resulted in lessened duration of these responses. These data suggest that early expression of HIV-1 genes requires a higher IRF-1 level, compared to the host antiviral genes. Together, these provide one key mechanism underlying the natural resistance against HIV infection and further suggest that modest IRF-1 reduction could effectively limit productive HIV infection yet remain sufficient to activate a robust but transient immune response.

The Mombasa Cohort is an open cohort study following HIV-seronegative women reporting transactional sex. Established in 1993, the cohort provides regular HIV counseling and testing at monthly visits. Over time, HIV acquisition risk has declined steadily in this cohort. To evaluate whether this decline may reflect changes in sexual risk behavior, we investigated trends in condom use and partner numbers among women who participated in the Mombasa Cohort between 1993 and 2007. Multinomial logistic regression and generalized estimating equations were used to evaluate the association of calendar time and follow-up time with key risk behaviors, after adjustment for potential confounding factors. At enrollment visits by 1,844 women, the adjusted probability of never using condoms decreased over time, from 34.2% to 18.9%. Over 23,911 follow-up visits, the adjusted probabilities of reporting >2 partners decreased from 9.9% to 4.9% and inconsistent condom use decreased from 7.9% to 5.3% after ≥12 cohort visits. Important predictors of risk behavior were work venue, charging low fees for sex, and substance abuse. Women with a later sexual debut had less risky behavior. Although sexual risk has declined among women participating in the Mombasa Cohort, HIV acquisition continues to occur and interventions to promote and reinforce safer sex are clearly needed.

HIV superinfection (reinfection) has been reported in several settings, but no study has been designed and powered to rigorously compare its incidence to that of initial infection. Determining whether HIV infection reduces the risk of superinfection is critical to understanding whether an immune response to natural HIV infection is protective. This study compares the incidence of initial infection and superinfection in a prospective seroincident cohort of high-risk women in Mombasa, Kenya. A next-generation sequencing-based pipeline was developed to screen 129 women for superinfection. Longitudinal plasma samples at 2 years and one intervening time after initial HIV infection were analyzed. Amplicons in three genome regions were sequenced and a median of 901 sequences obtained per gene per timepoint. Phylogenetic evidence of polyphyly, confirmed by pairwise distance analysis, defined superinfection. Superinfection timing was determined by sequencing virus from intervening timepoints. These data were combined with published data from 17 additional women in the same cohort, totaling 146 women screened. Twenty-one cases of superinfection were identified for an estimated incidence rate of 2.61 per 100 person-years (pys). The incidence rate of initial infection among 1910 women in the same cohort was 5.75 per 100 pys. Andersen-Gill proportional hazards models were used to compare incidences, adjusting for covariates known to influence HIV susceptibility in this cohort. Superinfection incidence was significantly lower than initial infection incidence, with a hazard ratio of 0.47 (CI 0.29-0.75, p = 0.0019). This lower incidence of superinfection was only observed >6 months after initial infection. This is the first adequately powered study to report that HIV infection reduces the risk of reinfection, raising the possibility that immune responses to natural infection are partially protective. The observation that superinfection risk changes with time implies a window of protection that coincides with the maturation of HIV-specific immunity.

Conventional survival estimates may be biased if loss to follow-up (LTF) is associated with the outcome of interest. Our goal was to assess whether the association between sexual risk behavior and HIV-1 acquisition changed after accounting for LTF with competing risks regression.HIV-1-seronegative women who enrolled in a Kenyan sex worker cohort from 1993-2007 were followed prospectively and tested for HIV at monthly clinic visits. Our primary predictor was self-reported sexual risk behavior in the past week, analyzed as a time-dependent covariate. Outcomes included HIV-1 acquisition and LTF. We analyzed the data using Cox proportional hazards regression and competing risks regression, in which LTF was treated as a competing event.A total of 1,513 women contributed 4,150 person-years (py), during which 198 (13.1%) acquired HIV-1 infection (incidence, 4.5 per 100 py) and 969 (64.0%) were LTF (incidence, 23.4 per 100 py). After adjusting for potential confounders, women reporting unprotected sex with multiple partners were less likely to be lost to follow-up (adjusted sub-hazard ratio (aSHR) 0.50, 95% confidence interval (CI) 0.32-0.76, relative to no sexual activity). The risk of HIV-1 acquisition after reporting unprotected sex with multiple partners was similar with Cox regression (adjusted hazard ratio (aHR) 2.41, 95% CI 1.36-4.27) and competing risks regression (aSHR 2.47, 95% CI 1.33-4.58).Unprotected sex with multiple partners was associated with higher HIV-1 acquisition risk, but lower attrition. This differential attrition did not substantially bias Cox regression estimates when compared to competing risks regression results.

While voluntary medical male circumcision (VMMC) has been shown to be protective against HIV-acquisition, the procedure may place men and their partners at risk of HIV infection in the period following circumcision if sex is resumed before the wound is healed. This prospective cohort study evaluates post-circumcision wound healing to determine whether the 42-day post-circumcision abstinence period, recommended by the World Health Organization and adopted by VMMC programs, is optimal.Men were circumcised by forceps-guided method and their post-circumcision wounds examined weekly for seven weeks and at 12 weeks. Time to complete healing was recorded in completed weeks since circumcision, and its associations with baseline covariates were assessed by Kaplan-Meier methods and Cox Proportional Hazard Models. A total of 215 HIV-negative and 108 HIV-positive men aged 18-35 years (median 26, IQR 23-30) were enrolled. 97.1% of scheduled follow-up visits were completed. At week 4, 59.3% of HIV-positive men and 70.4% of age-matched HIV-negative men were healed. At week 6, these percentages rose to 93.4% in HIV-positive men and 92.6% in age-matched HIV-negative men. There was no difference in the hazard of healing between 108 HIV-positive and 108 age-matched HIV-negative men (HR 0.91 95% CI 0.70-1.20). Early post-operative infection was associated with delayed healing in both HIV-positive and HIV-negative men (HR 0.48 95% CI 0.23-1.00).Our results indicate that the WHO recommendation for 42-days post-circumcision sexual abstinence should be maintained for both HIV-positive and HIV-negative men. It is important to stress condom use upon resumption of sex in all men undergoing circumcision.

Interferon regulatory factor 1 (IRF1) is induced by HIV early in the infection process and serves two functions: transactivation of the HIV-1 genome and thus replication, and eliciting antiviral innate immune responses. We previously described three IRF1 polymorphisms that correlate with reduced IRF1 expression and reduced HIV susceptibility.To determine whether IRF1 polymorphisms previously associated with reduced HIV susceptibility play a role in HIV pathogenesis and disease progression in HIV-infected ART-naïve individuals.IRF1 genotyping for polymorphisms (619, MS and 6516) was performed by PCR in 847 HIV positive participants from a sex worker cohort in Nairobi, Kenya. Rates of CD4+ T cell decline and viral loads (VL) were analyzed using linear mixed models.Three polymorphisms in the IRF1, located at 619, microsatellite region and 6516 of the gene, previously associated with decreased susceptibility to HIV infection show no effect on disease progression, either measured by HIV-1 RNA levels or the slopes of CD4 decline before treatment initiation.Whereas these three polymorphisms in the IRF1 gene protect against HIV-1 acquisition, they appear to exert no discernable effects once infection is established.

Identifying naturally-occurring neutralizing antibodies (NAb) that are cross-reactive against all global subtypes of HIV-1 is an important step toward the development of a vaccine. Establishing the host and viral determinants for eliciting such broadly NAbs is also critical for immunogen design. NAb breadth has previously been shown to be positively associated with viral diversity. Therefore, we hypothesized that superinfected individuals develop a broad NAb response as a result of increased antigenic stimulation by two distinct viruses. To test this hypothesis, plasma samples from 12 superinfected women each assigned to three singly infected women were tested against a panel of eight viruses representing four different HIV-1 subtypes at matched time points post-superinfection (~5 years post-initial infection). Here we show superinfected individuals develop significantly broader NAb responses post-superinfection when compared to singly infected individuals (RR = 1.68, CI: 1.23-2.30, p = 0.001). This was true even after controlling for NAb breadth developed prior to superinfection, contemporaneous CD4+ T cell count and viral load. Similarly, both unadjusted and adjusted analyses showed significantly greater potency in superinfected cases compared to controls. Notably, two superinfected individuals were able to neutralize variants from four different subtypes at plasma dilutions >1∶300, suggesting that their NAbs exhibit elite activity. Cross-subtype breadth was detected within a year of superinfection in both of these individuals, which was within 1.5 years of their initial infection. These data suggest that sequential infections lead to augmentation of the NAb response, a process that may provide insight into potential mechanisms that contribute to the development of antibody breadth. Therefore, a successful vaccination strategy that mimics superinfection may lead to the development of broad NAbs in immunized individuals.

The common but poorly understood condition known as bacterial vaginosis (BV) increases vulnerability to HIV infection and is associated with the absence of H(2)O(2)-producing Lactobacillus. Vaginal lactic acid bacteria (LAB) produce anti-HIV factors such as organic acids and hydrogen peroxide (H(2)O(2)), and may bind and inactivate HIV particles during scavenging of mannose. These factors define potential criteria for initial selection of candidate probiotics to block heterosexual transmission of HIV. Therefore, the primary goal of this study was to characterize acid production on mannose and H(2)O(2) production in vaginal isolates from Canadian adolescents (192 isolates, 16 individuals) and commercial sex workers in Nairobi, Kenya (576 isolates, 96 individuals). Selection of isolates from H(2)O(2)-detecting media suggested an idiosyncratic individual-level profile and extensive phenotypic diversity, including the identification of a subset of "double-strong" acid- and H(2)O(2)-producers with phenotypes similar to well-characterized probiotic strains. Molecular fingerprinting of all isolates by capillary electrophoresis of 16S-23S rRNA interspacer amplicons was coupled with chaperonin-60 universal target (cpn60 UT) sequencing in a subset, tentatively identifying 96% of isolates although only 19% were sequenced. Most isolates belonged to Lactobacillus, Streptococcus, Bifidobacterium or Gardnerella, with a total of 37 species in 15 genera, as well as 5 potentially novel organisms, identified in this study. This sensitivity was likely enhanced by phenotype-based selection on two chromogenic media formulations. Identification of double-strong isolates may provide a rational basis for selection and further characterization of vaginal probiotics, with potential application as part of HIV prevention initiatives in western Canada and East Africa.

HIV-1 is grouped phylogenetically into clades, which may impact rates of HIV-1 disease progression. Clade D infection in particular has been shown to be more pathogenic. Here we confirm in a Nairobi-based prospective female sex worker cohort (1985-2004) that Clade D (n = 54) is associated with a more rapid CD4 decline than clade A1 (n = 150, 20.6% vs 13.4% decline per year, 1.53-fold increase, p = 0.015). This was independent of "protective" HLA and country of origin (p = 0.053), which in turn were also independent predictors of the rate of CD4 decline (p = 0.026 and 0.005, respectively). These data confirm that clade D is more pathogenic than clade A1. The precise reason for this difference is currently unclear, and requires further study. This is first study to demonstrate difference in HIV-1 disease progression between clades while controlling for protective HLA alleles.

Identifying the immune correlates of reduced susceptibility to HIV remains a key goal for the HIV vaccine field, and individuals who are HIV-exposed, seronegative (HESN) may offer important clues. Reduced systemic immune activation has been described in HESN individuals. Conversely, pro-inflammatory T cell subsets, particularly CD4+ T cells producing the cytokine IL17 (Th17 cells), may represent a highly susceptible target for HIV infection after sexual exposure. Therefore, we characterized the cellular pro-inflammatory and IL17/IL22 cytokine immune milieu in the genital mucosa and blood of HESN female sex workers (FSWs).Blinded lab personnel characterized basal and mitogen-induced gene and cytokine immune responses in the cervix and blood of HESN FSWs (n = 116) and non-FSW controls (n = 17) using qPCR and ELISA. IL17 and IL22 production was significantly reduced in both the cervix and blood of HESNs, both in resting cells and after mitogen stimulation. In addition, HESN participants demonstrated blunted production of both pro-inflammatory cytokines and β-chemokines.We conclude that HIV exposure without infection was associated with blunted IL17/IL22 and pro-inflammatory responses, both systemically and at the site of mucosal HIV exposure. It will be important for further studies to examine the causal nature of the association and to define the cell subsets responsible for these differences.

With the persistent challenges towards controlling the HIV epidemic, there is an ongoing need for research into HIV vaccines and drugs. Sub-Saharan African countries--worst affected by the HIV pandemic--have participated in the conduct of clinical trials for HIV vaccines. In Kenya, the Kenya AIDS Vaccine Initiative (KAVI) at the University of Nairobi has conducted HIV vaccine clinical trials since 2001.Participants were recruited after an extensive informed consent process followed by screening to determine eligibility. Screening included an assessment of risk behavior, medical history and physical examination, and if clinically healthy, laboratory testing. In the absence of locally derived laboratory reference ranges, the ranges used in these trials were derived from populations in the West.Two hundred eighty-one participants were screened between 2003 and 2006 for two clinical trials. Of these, 167 (59.4%) met the inclusion/exclusion criteria. Overall, laboratory abnormalities based on the non-indigenous laboratory references used were the most frequent reasons (61.4%) for ineligibility. Medical abnormalities contributed 30.7% of the total reasons for ineligibility. Based on the laboratory reference intervals now developed from East and Southern Africa, those ineligible due to laboratory abnormalities would have been 46.3%. Of the eligible participants, 18.6% declined enrollment.Participant recruitment for HIV vaccine clinical trials is a rigorous and time-consuming exercise. Over 61% of the screening exclusions in clinically healthy people were due to laboratory abnormalities. It is essential that laboratory reference ranges generated from local populations for laboratory values be used in the conduct of clinical trials to avoid unnecessary exclusion of willing participants and to avoid over-reporting of adverse events for enrolled participants.Protocol IAVI VRC V001 [1]. ClinicalTrials.gov NCT00124007 Protocol IAVI 010 [2](registration with ClincalTrials.gov is in progress) Protocols IAVI 002 and IAVI 004 are Phase 1 trials only mentioned in introductory paragraphs; details will not be reported. Registration was not required when they were conducted.

Several candidate HIV vaccines aim to induce virus-specific cellular immunity particularly in the genital tract, typically the initial site of HIV acquisition. However, standardized and sensitive methods for evaluating HIV-specific immune responses at the genital level are lacking. Therefore we evaluated real-time quantitative PCR (qPCR) as a potential platform to measure these responses. β-Actin and GAPDH were identified as the most stable housekeeping reference genes in peripheral blood mononuclear cells (PBMCs) and cervical mononuclear cells (CMCs) respectively and were used for normalizing transcript mRNA expression. HIV-specific cellular T cell immune responses to a pool of optimized CD8+ HIV epitopes (HIV epitope pool) and Staphylococcal enterotoxin B (SEB) superantigen control were assayed in HIV infected PBMC by qPCR, with parallel assessment of cytokine protein production. Peak HIV-specific mRNA expression of IFNγ, IL-2 and TNFα occurred after 3, 5 and 12 hours respectively. PBMCs were titrated to cervical appropriate cell numbers to determine minimum required assay input cell numbers; qPCR retained sensitivity with input of at least 2.5×10(4) PBMCs. This optimized qPCR assay was then used to assess HIV-specific cellular T cell responses in cytobrush-derived cervical T cells from HIV positive individuals. SEB induced IFNγ mRNA transcription was detected in CMCs and correlated positively with IFNγ protein production. However, qPCR was unable to detect HIV-induced cytokine mRNA production in the cervix of HIV-infected women despite robust detection of gene induction in PBMCs. In conclusion, although qPCR can be used to measure ex vivo cellular immune responses to HIV in blood, HIV-specific responses in the cervix may fall below the threshold of qPCR detection. Nonetheless, this platform may have a potential role in measuring mitogen-induced immune responses in the genital tract.