Universal Testing, Expanded Treatment, and Incidence of HIV Infection in Botswana.

BACKGROUND: The feasibility of reducing the population-level incidence of human immunodeficiency virus (HIV) infection by increasing community coverage of antiretroviral therapy (ART) and male circumcision is unknown. METHODS: We conducted a pair-matched, community-randomized trial in 30 rural or periurban communities in Botswana from 2013 to 2018. Participants in 15 villages in the intervention group received HIV testing and counseling, linkage to care, ART (started at a higher CD4 count than in standard care), and increased access to male circumcision services. The standard-care group also consisted of 15 villages. Universal ART became available in both groups in mid-2016. We enrolled a random sample of participants from approximately 20% of households in each community and measured the incidence of HIV infection through testing performed approximately once per year. The prespecified primary analysis was a permutation test of HIV incidence ratios. Pair-stratified Cox models were used to calculate 95% confidence intervals. RESULTS: Of 12,610 enrollees (81% of eligible household members), 29% were HIV-positive. Of the 8974 HIV-negative persons (4487 per group), 95% were retested for HIV infection over a median of 29 months. A total of 57 participants in the intervention group and 90 participants in the standard-care group acquired HIV infection (annualized HIV incidence, 0.59% and 0.92%, respectively). The unadjusted HIV incidence ratio in the intervention group as compared with the standard-care group was 0.69 (P = 0.09) by permutation test (95% confidence interval [CI], 0.46 to 0.90 by pair-stratified Cox model). An end-of-trial survey in six communities (three per group) showed a significantly greater increase in the percentage of HIV-positive participants with an HIV-1 RNA level of 400 copies per milliliter or less in the intervention group (18 percentage points, from 70% to 88%) than in the standard-care group (8 percentage points, from 75% to 83%) (relative risk, 1.12; 95% CI, 1.09 to 1.16). The percentage of men who underwent circumcision increased by 10 percentage points in the intervention group and 2 percentage points in the standard-care group (relative risk, 1.26; 95% CI, 1.17 to 1.35). CONCLUSIONS: Expanded HIV testing, linkage to care, and ART coverage were associated with increased population viral suppression. (Funded by the President's Emergency Plan for AIDS Relief and others; Ya Tsie ClinicalTrials.gov number, NCT01965470.).

QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data.

Motivation: Genomic analysis has become one of the major tools for disease outbreak investigations. However, existing computational frameworks for inference of transmission history from viral genomic data often do not consider intra-host diversity of pathogens and heavily rely on additional epidemiological data, such as sampling times and exposure intervals. This impedes genomic analysis of outbreaks of highly mutable viruses associated with chronic infections, such as human immunodeficiency virus and hepatitis C virus, whose transmissions are often carried out through minor intra-host variants, while the additional epidemiological information often is either unavailable or has a limited use. Results: The proposed framework QUasispecies Evolution, Network-based Transmission INference (QUENTIN) addresses the above challenges by evolutionary analysis of intra-host viral populations sampled by deep sequencing and Bayesian inference using general properties of social networks relevant to infection dissemination. This method allows inference of transmission direction even without the supporting case-specific epidemiological information, identify transmission clusters and reconstruct transmission history. QUENTIN was validated on experimental and simulated data, and applied to investigate HCV transmission within a community of hosts with high-risk behavior. It is available at https://github.com/skumsp/QUENTIN. Contact: pskums@gsu.edu or alexz@cs.gsu.edu or rahul@sfsu.edu or yek0@cdc.gov. Supplementary information: Supplementary data are available at Bioinformatics online.

Accuracy of point-of-care HIV and CD4 field testing by lay healthcare workers in the Botswana Combination Prevention Project.

Accurate HIV and CD4 testing are critical in program implementation, with HIV misdiagnosis having serious consequences at both the client and/or community level. We implemented a comprehensive training and Quality Assurance (QA) program to ensure accuracy of point-of-care HIV and CD4 count testing by lay counsellors during the Botswana Combination Prevention Project (BCPP). We compared the performance of field testing by lay counsellors to results from an accredited laboratory to ascertain accuracy of testing. All trained lay counsellors passed competency assessments and performed satisfactorily in proficiency testing panel evaluations in 2013, 2014, and 2015. There was excellent agreement (99.6 %) between field and laboratory-based HIV test results; of the 3002 samples tested, 960 and 2030 were concordantly positive and negative respectively, with 12 misclassifications (kappa score 0.99, p < 0.0001). Of the 149 HIV-positive samples enumerated for CD4 count in the field using PIMA at a threshold of ≤ 350 cells/µl; there was 86 % agreement with laboratory testing, with only 21 misclassified. The mean difference between field and lab CD4 testing was - 16.16 cells/µl (95 % CI -5.4 to 26.9). Overall, there was excellent agreement between field and laboratory results for both HIV rapid test and PIMA CD4 results. A standard training package to train lay counsellors to accurately perform HIV and CD4 point-of-care testing in field settings was feasible, with point-of-care results obtained by lay counsellors comparable to laboratory-based testing.

Finding, treating and retaining persons with HIV in a high HIV prevalence and high treatment coverage country: Results from the Botswana Combination Prevention Project.

INTRODUCTION: The scale-up of Universal Test and Treat has resulted in reductions in HIV morbidity, mortality and incidence. However, healthcare system and personal challenges have impacted the levels of treatment coverage achieved. We implemented interventions to improve linkage to care, retention, viral load (VL) coverage and service delivery, and describe the HIV care cascade over the course of the Botswana Combination Prevention Project (BCPP) study. METHODS: BCPP was designed to evaluate the impact of prevention interventions on HIV incidence in 30 communities in Botswana. We followed a longitudinal cohort of newly identified and known HIV-positive persons not on antiretroviral therapy (ART) identified through community-based testing activities through BCPP and referred with appointments to local HIV clinics in 15 intervention communities. Those who did not keep the first or follow-up appointments were tracked and traced through phone and home contacts. Improvements to service delivery models in the intervention clinics were also implemented. RESULTS: A total of 3,657 newly identified or HIV-positive persons not on ART were identified and referred to their local HIV clinic; 90% (3,282/3,657) linked to care and of those, 93% (3,066/3,282) initiated treatment. Near the end of the study, 221 persons remained >90 days late for appointments or missing. Tracing efforts identified 54/3,066 (2%) persons who initiated treatment but died, and 106/3,066 (3%) persons were located and returned to treatment. At study end, 61/3,066 (2%) persons remained missing and were never reached. Overall, 2,951 (98%) persons living with HIV (PLHIV) who initiated treatment were still alive, retained in care and still receiving ART out of the 3,001 persons alive at the end of the study. Of those on ART, 2,854 (97%) had current VL results and 2,784 (98%) of those were virally suppressed at study end. CONCLUSIONS: This study achieved high rates of linkage, treatment initiation, retention and VL coverage and suppression in a cohort of newly identified and known PLHIV not on ART. Tracking and tracing interventions effectively identified those persons who needed more resource intensive follow-up. The interventions implemented to improve service delivery and data quality may have also contributed to high linkage and retention rates. Clinical trial number: NCT01965470.

Population uptake of HIV testing, treatment, viral suppression, and male circumcision following a community-based intervention in Botswana (Ya Tsie/BCPP): a cluster-randomised trial.

BACKGROUND: In settings with high HIV prevalence and treatment coverage, such as Botswana, it is unknown whether uptake of HIV prevention and treatment interventions can be increased further. We sought to determine whether a community-based intervention to identify and rapidly treat people living with HIV, and support male circumcision could increase population levels of HIV diagnosis, treatment, viral suppression, and male circumcision in Botswana. METHODS: The Ya Tsie Botswana Combination Prevention Project study was a pair-matched cluster-randomised trial done in 30 communities across Botswana done from Oct 30, 2013, to June 30, 2018. 15 communities were randomly assigned to receive HIV prevention and treatment interventions, including enhanced HIV testing, earlier antiretroviral therapy (ART), and strengthened male circumcision services, and 15 received standard of care. The first primary endpoint of HIV incidence has already been reported. In this Article, we report findings for the second primary endpoint of population uptake of HIV prevention services, as measured by proportion of people known to be HIV-positive or tested HIV-negative in the preceding 12 months; proportion of people living with HIV diagnosed and on ART; proportion of people living with HIV on ART with viral suppression; and proportion of HIV-negative men circumcised. A longitudinal cohort of residents aged 16-64 years from a random, approximately 20% sample of households across the 15 communities was enrolled to assess baseline uptake of study outcomes; we also administered an end-of-study survey to all residents not previously enrolled in the longitudinal cohort to provide study end coverage estimates. Differences in intervention uptake over time by randomisation group were tested via paired Student's t test. The study has been completed and is registered with ClinicalTrials.gov (NCT01965470). FINDINGS: In the six communities participating in the end-of-study survey, 2625 residents (n=1304 from standard-of-care communities, n=1321 from intervention communities) were enrolled into the 20% longitudinal cohort at baseline from Oct 30, 2013, to Nov 24, 2015. In the same communities, 10 791 (86%) of 12 489 eligible enumerated residents not previously enrolled in the longitudinal cohort participated in the end-of-study survey from March 30, 2017, to Feb 25, 2018 (5896 in intervention and 4895 in standard-of-care communities). At study end, in intervention communities, 1228 people living with HIV (91% of 1353) were on ART; 1166 people living with HIV (88% of 1321 with available viral load) were virally suppressed, and 673 HIV-negative men (40% of 1673) were circumcised in intervention communities. After accounting for baseline differences, at study end the proportion of people living with HIV who were diagnosed was significantly higher in intervention communities (absolute increase of 9% to 93%) compared with standard-of-care communities (absolute increase of 2% to 88%; prevalence ratio [PR] 1·08 [95% CI 1·02-1·14], p=0·032). Population levels of ART, viral suppression, and male circumcision increased from baseline in both groups, with greater increases in intervention communities (ART PR 1·12 [95% CI 1·07-1·17], p=0·018; viral suppression 1·13 [1·09-1·17], p=0·017; male circumcision 1·26 [1·17-1·35], p=0·029). INTERPRETATION: It is possible to achieve very high population levels of HIV testing and treatment in a high-prevalence setting. Maintaining these coverage levels over the next decade could substantially reduce HIV transmission and potentially eliminate the epidemic in these areas. FUNDING: US President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention.

Design and synthesis of human immunodeficiency virus entry inhibitors: sulfonamide as an isostere for the alpha-ketoamide group.

The crystal structures of many tertiary alpha-ketoamides reveal an orthogonal arrangement of the two carbonyl groups. Based on the hypothesis that the alpha-ketoamide HIV attachment inhibitor BMS 806 (formally BMS378806, 26) might bind to its gp120 target via a similar conformation, we designed and synthesized a series of analogs in which the ketoamide group is replaced by an isosteric sulfonamide group. The most potent of these analogs, 14i, demonstrated antiviral potency comparable to 26 in the M33 pseudotyped antiviral assay. Flexible overlay calculations of a ketoamide inhibitor with a sulfonamide inhibitor revealed a single conformation of each that gave significantly better overlap of key pharmacophore features than other conformations and thus suggest a possible binding conformation for each class.

Evaluation of SMARTube to Detect HIV Infection Before Seroconversion Using Standard Methods.

The acute phase of HIV infection carries substantial risk of transmission; identification of acute-phase infections may offer opportunities to reduce that risk. SMARTube incubation of blood specimens is designed to stimulate in vivo-primed HIV-specific lymphocytes to produce HIV antibodies in vitro. The resulting supernatant (S-plasma) can be tested to identify acute infections with commercially available HIV assays. We assessed the performance of the SMARTube to identify acute HIV infections in studies at three developing country sites. We conducted HIV incidence studies in Ho Chi Minh City, Vietnam, and Bloemfontein and Rustenburg, South Africa. We estimated HIV incidence in cross-sectional samples and measured prospective incidence in uninfected women followed for up to 12 months. We incorporated SMARTube into the HIV testing algorithm at cross-sectional screening and monthly follow-up visits. We tested 1,384 persons in Vietnam, 1,145 women in Bloemfontein, and 538 persons in Rustenburg. Cross-sectional samples from 11 participants that tested positive with SMARTube after an initial unincubated negative test result (11 of 2,472; 0.4% of all specimens) were considered "potential acute" infections. Matching samples from 3 of the 11 (27.3%) were confirmed by polymerase chain reaction (PCR) testing. In follow-up of 355, 401, and 223 uninfected women in Vietnam, Bloemfontein, and Rustenburg, respectively, 11 seroconversions occurred in Bloemfontein and Rustenburg. In four of these incident infections (36.4%), SMARTube testing had resulted in earlier detection of HIV infection than the eventual seroconversion visits. In our field studies, pretreatment with SMARTube allowed the identification of acute HIV-1 infection in some new infections, but with a positive predictive value of 27%. Larger studies are needed to evaluate SMARTube as an alternative to technically challenging and costly enzyme immunoassay and PCR testing to detect acute HIV infection.

Progressing beyond SLMTA: Are internal audits and corrective action the key drivers of quality improvement?

BACKGROUND: Kenya has implemented the Strengthening Laboratory Management Toward Accreditation (SLMTA) programme to facilitate quality improvement in medical laboratories and to support national accreditation goals. Continuous quality improvement after SLMTA completion is needed to ensure sustainability and continue progress toward accreditation. METHODS: Audits were conducted by qualified, independent auditors to assess the performance of five enrolled laboratories using the Stepwise Laboratory Quality Improvement Process Towards Accreditation (SLIPTA) checklist. End-of-programme (exit) and one year post-programme (surveillance) audits were compared for overall score, star level (from zero to five, based on scores) and scores for each of the 12 Quality System Essential (QSE) areas that make up the SLIPTA checklist. RESULTS: All laboratories improved from exit to surveillance audit (median improvement 38 percentage points, range 5-45 percentage points). Two laboratories improved from zero to one star, two improved from zero to three stars and one laboratory improved from three to four stars. The lowest median QSE scores at exit were: internal audit; corrective action; and occurrence management and process improvement (< 20%). Each of the 12 QSEs improved substantially at surveillance audit, with the greatest improvement in client management and customer service, internal audit and information management (≥ 50 percentage points). The two laboratories with the greatest overall improvement focused heavily on the internal audit and corrective action QSEs. CONCLUSION: Whilst all laboratories improved from exit to surveillance audit, those that focused on the internal audit and corrective action QSEs improved substantially more than those that did not; internal audits and corrective actions may have acted as catalysts, leading to improvements in other QSEs. Systematic identification of core areas and best practices to address them is a critical step toward strengthening public medical laboratories.

HIV incidence and prevalence among cohorts of women with higher risk behaviour in Bloemfontein and Rustenburg, South Africa: a prospective study.

OBJECTIVES: The primary objective was to measure HIV incidence in two prospective cohorts of HIV-negative women. Secondary objectives included measuring pregnancy rates and participant retention rates. DESIGN: Cross-sectional HIV screening of women selected for higher risk behaviours, with a subsequent prospective study of uninfected women, followed monthly for up to 6 months. SETTING: Clinics established for research purposes in Bloemfontein and Rustenburg, South Africa. PARTICIPANTS: The authors enrolled women 18-35 years old and presumed at higher risk of sexual acquisition of HIV as indicated by self-reported sexual behaviour or recent sexually transmitted infection symptoms. In Bloemfontein, 1364 women were screened, 1154 were eligible for HIV testing and 1145 agreed to be tested. The prospective study enrolled 401 HIV-negative women. In Rustenburg, 946 women were screened, 540 were eligible and underwent HIV testing and 223 HIV-negative women entered the prospective study. PRIMARY AND SECONDARY OUTCOMES: Baseline prevalences of HIV infection and HIV incidence rates in the prospective cohorts, according to a double rapid test algorithm with a third rapid test for discrepant or indeterminate results. Pregnancy prevalences and pregnancy incidence rate in Bloemfontein. Participant retention rates in the prospective cohort until the study end. RESULTS: In Bloemfontein, 1145 women were tested, 391 entered follow-up and 92.3% of participants completed six study visits. In Rustenburg, 540 women were tested, 194 entered follow-up and retention up to the point of early study termination was 88.6%. Overall HIV prevalence was 21.2% (95% CI 18.9% to 23.6%) in Bloemfontein and 23.5% (95% CI 19.9% to 27.1%) in Rustenburg. Overall HIV incidence was 5.5/100 person-years (95% CI 2.5 to 10.4) in Bloemfontein and 3.0/100 person-years (95% CI 0.4 to 10.8) in Rustenburg. Cross-sectional pregnancy prevalences were 6.5% in Bloemfontein and 8.6% in Rustenburg. CONCLUSIONS: The authors observed substantial HIV incidence rates in both cohorts. Vigorous prevention efforts are needed in these smaller cities.

Correlation of prospective and cross-sectional measures of HIV type 1 incidence in a higher-risk cohort in Ho Chi Minh City, Vietnam.

The primary aim of this study was to estimate HIV incidence within a high-risk population in Ho Chi Minh City (HCMC), Vietnam using both cross-sectional and prospective methodologies. A secondary aim was to develop a local correction factor for the BED and avidity index incidence assays. The research study design consisted of three phases: (1) cross-sectional, (2) prospective, and (3) BED false recent (BED FR). A total of 1619 high-risk, sexually active individuals were enrolled in the cross-sectional phase and 355 of the opiate-negative, HIV-negative women were subsequently enrolled in the prospective phase. Four-hundred and three men and women with known HIV infection duration of greater than 12 months were enrolled in the BED FR phase. The HIV prevalence for all participants in the cross-sectional phase was 15.8%. HIV incidence in the cross-sectional group was estimated using the BED IgG capture assay and AxSYM avidity index assay for recent HIV infection and incidence within the prospective cohort was determined by observations of HIV seroconversion. HIV incidence in opiate-negative women was estimated using the BED assay to be 0.8% unadjusted and 0.5% after applying the locally derived BED false recent rate of 1.7%; no seroconversions were observed in the prospective cohort. We also screened the cross-sectional samples for evidence of acute infection using nucleic acid testing, 4th generation HIV EIA, and SMARTube coupled with Genscreen and Determine diagnostic tests; no confirmed acute infections were identified by any method. HIV incidence within this opiate-negative study population was low and incidence estimates from the two methods compared favorably with each other. Incidence estimates and false recent rates using the AxSYM assay were higher: AI FRR of 2.7% and adjusted incidence of 1.7% per year (95% CI, 0.6, 2.8). By comparison, both HIV prevalence and incidence estimates for the opiate-positive group were higher.

Reduced community access to a key contraceptive: public health consequence from false suspicion of HIV-contaminated injectables.

BACKGROUND: This study was conducted to investigate a report of positive test results with DMPA on an HIV rapid test. Suspecting HIV contamination, the Zambian Ministry of Health initiated a product withdrawal pending full evaluation. STUDY DESIGN: DMPA was evaluated for compliance to product specifications. Contamination with HIV and blood components was investigated with PCR and human IgG ELISA. The performance of Genie II, Unigold and Determine HIV rapid tests was evaluated using DMPA. RESULTS: DMPA was found compliant with product specifications and negative for HIV and human IgG. DMPA impaired the performance of HIV rapid tests resulting in false-positive/indeterminant results. Rapid test results using polysorbate 80 (formulation component of DMPA) mimicked results obtained with DMPA. CONCLUSIONS: The DMPA sample was negative for HIV and human IgG. Formulation components may have led to the interpretation of false-positive results, reinforcing the need to validate the sample type used in any test. DMPA use was reinstated in Zambia, minimizing the public health impact that resulted from the initial rapid test results.

Heterobiaryl human immunodeficiency virus entry inhibitors.

Previously disclosed HIV (human immunodeficiency virus) attachment inhibitors, exemplified by BMS 806 (formally BMS378806, 1), are characterized by a substituted indole or azaindole ring linked to a benzoylpiperazine via a ketoamide or sulfonamide group. In the present report, we describe the discovery of a novel series of potent HIV entry inhibitors in which the indole or azaindole ring of previous inhibitors is replaced by a heterobiaryl group. Several of these analogues exhibited IC(50) values of less than 5 nM in a pseudotyped antiviral assay, and compound 13k was demonstrated to exhibit potency and selectivity similar to those of 1 against a panel of clinical viral isolates. Moreover, current structure-activity relationship studies of these novel biaryl gp120 inhibitors revealed that around the biaryl, a fine crevice might exist in the gp120 binding site. Taken in sum, these data reveal a hitherto unsuspected flexibility in the structure-activity relationships for these inhibitors and suggest new avenues for exploration and gp120 inhibitor design.

Synthesis of C-6 substituted pyrazolo[1,5-a]pyridines with potent activity against herpesviruses.

A novel series of potent C-6 substituted pyrazolo[1,5-a]pyridine inhibitors of herpes simplex viruses has been identified. A synthetic methodology was developed involving functionalization of a C-6 trifluoromethyl pyrazolo[1,5-a]pyridine to allow facile access to a diverse set of analogues from common late stage intermediates. The expansion of the SAR of this series at the 6 position allows for modifications to developability parameters such as clogP, while maintaining potency comparable to acyclovir.

Pyrazolopyridine antiherpetics: SAR of C2' and C7 amine substituents.

A novel series of potent pyrazolo[1,5-a]pyridine inhibitors of herpes simplex virus 1 replication have been identified. Several complimentary synthetic methods were developed to allow facile access to a diverse set of analogs from common late stage intermediates. Detailed examination of the amine substituents at the C2' position of the pyrimidine and C7 position of the core pyrazolopyridine is described. The antiviral data suggests that non-polar amines are preferred for optimal activity. Additionally, the 2' position has been shown to require an NH group to retain activity levels similar to that of the gold standard acyclovir.

Synthesis of novel substituted 2-phenylpyrazolopyridines with potent activity against herpesviruses.

Herpesviruses are a significant source of human disease; amongst these herpes simplex virus 1 (HSV-1) and HSV-2 are very prevalent and cause recurrent infections. We recently identified a pyrazolo[1,5-a]pyridine scaffold that showed promising activity against HSV-1 and HSV-2 in Vero cell antiviral assays. Here, we describe the synthesis and anti-herpetic activity of several 3-pyrimidinyl-2-phenylpyrazolo[1,5-a]pyridines with differing 2-phenyl substitution patterns. Approaches to rapidly access a number of analogs with different 2-phenyl substitution patterns are outlined. Several of the compounds described have comparable activity to acyclovir against HSV-1 and HSV-2.