BACKGROUND: Measures of diagnostic test accuracy provide evidence of how well a test correctly identifies or rules-out disease. Commonly used diagnostic accuracy measures (DAMs) include sensitivity and specificity, predictive values, likelihood ratios, area under the receiver operator characteristic curve (AUROC), area under precision-recall curves (AUPRC), diagnostic effectiveness (accuracy), disease prevalence, and diagnostic odds ratio (DOR) etc. Most available analysis tools perform accuracy testing for a single diagnostic test using summarized data. We developed a SAS macro for evaluating multiple diagnostic tests using individual-level data that creates a 2 × 2 summary table, AUROC and AUPRC as part of output. METHODS: The SAS macro presented here is automated to reduce analysis time and transcription errors. It is simple to use as the user only needs to specify the input dataset, "standard" and "test" variables and threshold values. It creates a publication-quality output in Microsoft Word and Excel showing more than 15 different accuracy measures together with overlaid AUROC and AUPRC graphics to help the researcher in making decisions to adopt or reject diagnostic tests. Further, it provides for additional variance estimation methods other than the normal distribution approximation. RESULTS: We tested the macro for quality control purposes by reproducing results from published work on evaluation of multiple types of dried blood spots (DBS) as an alternative for human immunodeficiency virus (HIV) viral load (VL) monitoring in resource-limited settings compared to plasma, the gold-standard. Plasma viral load reagents are costly, and blood must be prepared in a reference laboratory setting by a qualified technician. On the other hand, DBS are easy to prepare without these restrictions. This study evaluated the suitability of DBS from venous, microcapillary and direct spotting DBS, hence multiple diagnostic tests which were compared to plasma specimen. We also used the macro to reproduce results of published work on evaluating performance of multiple classification machine learning algorithms for predicting coronary artery disease. CONCLUSION: The SAS macro presented here is a powerful analytic tool for analyzing data from multiple diagnostic tests. The SAS programmer can modify the source code to include other diagnostic measures and variance estimation methods. By automating analysis, the macro adds value by saving analysis time, reducing transcription errors, and producing publication-quality outputs.

BACKGROUND: Tanzania has made significant progress in improving access to HIV care and treatment. However, virologic suppression among people living with HIV (PLHIV) has not been fully realized. In March 2019, Tanzania introduced a World Health Organization (WHO)-recommended dolutegravir-based regimen as the default first-line regimen. Eighteen months later we investigated the HIV viral suppression rates and the factors associated with lack of viral suppression among PLHIV (children and adults) in Tanzania. METHODOLOGY: A cross-sectional survey was conducted from September to December 2020 among PLHIV on antiretroviral therapy (ART) in Tanzania. Whole blood samples, demographic data and clinical information were obtained from eligible adults (≥15 years) and children (< 15 years) attending thirty-six HIV care and treatment centres located in 22 regions of Tanzania mainland. A whole blood sample from each participant was processed into plasma and HIV viral load was estimated using real-time PCR. HIV viral suppression was defined at a cut-off of < 50 copies/mL as recommended by WHO. Analyses were conducted using descriptive statistics to establish the national representative prevalence of viral suppression, and logistic regression analyses to determine independent factors associated with non-suppression. RESULTS: A total of 2,039 PLHIV on ART were recruited; of these, adults and children were 57.5% (n = 1173) and 42.5% (n = 866), respectively. Among the adult population, the mean age and standard deviation (SD) was 42.1 ± 12.4 years, with 64.7% being female. Among children, the mean age and SD were 9.6 ± 3 years, and 53.2% were female. Overall viral suppression at < 50 copies/mL (undetectable) was achieved in 87.8% of adults and 74.4% of children. Adults and children on dolutegravir-based regimen recorded viral suppression rates of 89.7% and 85.1% respectively. Factors independently associated with lack of viral suppression status in the adult population were age and ART adherence while in the children population, the factors were sex, ART adherence, and current ART regimen (p<0.05). CONCLUSION: Dolutegravir-based regimens are promising to help attain epidemic control in Tanzania. More efforts especially on ART adherence are needed to attain optimal treatment outcomes for children and adults PLHIV in Tanzania.

Voluntary medical male circumcision (VMMC) reduces men's risk of acquiring Human immunodeficiency virus (HIV) through vaginal sex. However, VMMC uptake remains lowest among Kenyan men ages 25-39 years among whom the impact on reducing population-level HIV incidence was estimated to be greatest at the start of the study in 2014. We conducted a pre- and post-intervention survey as part of a cluster randomized controlled trial to determine the effect of two interventions (interpersonal communication (IPC) and dedicated service outlets (DSO), delivered individually or together) on improving VMMC uptake among men ages 25-39 years in western Kenya between 2014 and 2016. The study had three intervention arms and a control arm. In arm one, an IPC toolkit was used to address barriers to VMMC. In arm two, men were referred to DSO that were modified to address their preferences. Arm three combined the IPC and DSO. The control arm had standard of care. At baseline, uncircumcised men ranked the top three reasons for remaining uncircumcised. An IPC demand creation toolkit was used to address the identified barriers and men were referred for VMMC at study-designated facilities. At follow-up, those who remained uncircumcised were again asked to rank the top three reasons for not getting circumcised. There was inconsistency in ranking of reported barriers at pre- and post- intervention: 'time/venue not convenient' was ranked third at baseline and seventh at follow-up; 'too busy to go for circumcision' was tenth at baseline but second at follow-up, and concern about 'what I/family will eat' was ranked first at both baseline and follow-up, but the proportion reduced from 62% to 28%. Men ages 25-39 years cited a variety of logistical and psychosocial barriers to receiving VMMC. After exposure to IPC, most of these barriers shifted while some remained the same. Additional innovative interventions to address on-going and shifting barriers may help improve VMMC uptake among older men.

Antibodies are used to estimate prevalence of past infection. However, T cell responses against SARSCoV-2 may more accurately define prevalence because SARS-CoV-2-specific antibodies wane. In November-December 2021, we studied serological and cellular immune responses in residents of rural Kenya who had not experienced any respiratory symptom nor had contact with COVID-19 cases. Among participants we detected anti-spike antibodies in 41.0% and T cell responses against >=2 SARSCoV-2 proteins in 82.5%, which implies that serosurveys underestimate SARS-CoV-2 prevalence in settings where asymptomatic infections prevail. Distinct from cellular immunity in European and Asian COVID-19 convalescents, strong T cell immunogenicity was observed against viral accessory proteins in these asymptomatic Africans, as well as a higher IL-10/IFN-gamma ratio cytokine profile, suggesting that environmental or genetic factors modulate pro-inflammatory responses. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.

BACKGROUND: SARS-CoV-2 infection in Africa has been characterized by less severe disease than elsewhere but the profile of SARS-CoV-2 specific adaptive immunity in this largely asymptomatic spread has not been studied. METHODS: We collected blood and nasopharyngeal samples from rural Kenyans (n=80) without respiratory symptoms since 2019, had no contact with COVID-19 cases or received COVID-19 vaccines and were negative for current SARS-CoV-2 infection. We analyzed spike-specific antibodies and T cells specific for SARS-CoV-2 structural (membrane, nucleocapsid and spike) and accessory (ORF3a, ORF7, ORF8) proteins. Pre-pandemic samples collected in urban Nairobi, Kenya (n=13) between 2015-2016 and samples of mild-moderately symptomatic COVID-19 convalescents (n=36) living in the urban environment of Singapore were also studied. RESULTS: Among asymptomatic Kenyans, we detected anti-spike antibodies in 41.0% and T cell responses against ≥2 SARS-CoV-2 proteins in 82.5%. The pre-pandemic samples from Nairobi had low-level, monospecific responses. Furthermore, distinct from cellular immunity in European and Asian COVID-19 convalescents, strong T cell immunogenicity was observed against viral accessory proteins (ORF3a, ORF8) and not structural proteins, as well as a higher IL-10/IFN-γ ratio cytokine profile. CONCLUSIONS: The high incidence of T cell responses against different SARS-CoV-2 proteins in largely seronegative participants suggests that serosurveys underestimate SARS-CoV-2 prevalence in settings where asymptomatic infections prevail. Similar observations have been made with other coronavirus infections such as MERS and SARS-CoV-1. The functional and antigen-specific profile of SARS-CoV-2 specific T cells in these African individuals suggests that genetic or environmental factors play a role in the development of protective antiviral immunity. FUNDINGS: U.S. Centers for Disease Control and Prevention, Division of Global Health Protection; the Singapore Ministry of Health's National Medical Research Council.

BACKGROUND: The emergence of HIV drug resistance mutations (DRMs) is of significant threat to achieving viral suppression (VS) in the quest to achieve global elimination targets. We hereby report virologic outcomes and patterns of acquired DRMs and its associated factors among adolescents and young adults (AYA) from a broader HIV drug resistance surveillance conducted in Tanzania. METHODS: Data of AYA was extracted from a cross-sectional study conducted in 36 selected facilities using a two-stage cluster sampling design. Dried blood spot (DBS) samples were collected and samples with a viral load (VL) ≥1000 copies/mL underwent genotyping for the HIV-1 pol gene. Stanford HIV database algorithm predicted acquired DRMs, Fisher's exact test and multivariable logistic regression assessed factors associated with DRMs and VS, respectively. FINDINGS: We analyzed data of 578 AYA on antiretroviral therapy (ART) for 9-15 and ≥ 36 months; among them, 91.5% and 88.2% had VS (VL<1000copies/mL) at early and late time points, respectively. Genotyping of 64 participants (11.2%) who had VL ≥1000 copies/ml detected 71.9% of any DRM. Clinically relevant DRMs were K103N, M184V, M41L, T215Y/F, L210W/L, K70R, D67N, L89V/T, G118R, E138K, T66A, T97A and unexpectedly absent K65R. Participants on a protease inhibitor (PI) based regimen were twice as likely to not achieve VS compared to those on integrase strand transfer inhibitors (INSTI). The initial VL done 6 months after ART initiation of ≥1000copies/mL was the primary factor associated with detecting DRMs (p = .019). CONCLUSIONS: VS amongst AYA is lower than the third UNAIDs target. Additionally, a high prevalence of ADR and high levels of circulating clinically relevant DRMs may compromise the long-term VS in AYA. Furthermore, the first VL result of ≥1000copies/ml after ART initiation is a significant risk factor for developing DRMs. Thus, strict VL monitoring for early identification of treatment failure and genotypic testing during any ART switch is recommended to improve treatment outcomes for AYA.

The World Health Organization advocates a multimodal approach to improving infection prevention and control (IPC) measures, which Kenya adopted in response to the COVID-19 pandemic. The Kenya Ministry of Health formed a national IPC committee for policy and technical leadership, coordination, communication, and training. During March-November 2020, a total of 69,892 of 121,500 (57.5%) healthcare workers were trained on IPC. Facility readiness assessments were conducted in 777 health facilities using a standard tool assessing 16 domains. A mean score was calculated for each domain across all facilities. Only 3 domains met the minimum threshold of 80%. The Ministry of Health maintained a national list of all laboratory-confirmed SARS-CoV-2 infections. By December 2020, a total of 3,039 healthcare workers were confirmed to be SARS-CoV-2-positive, an infection rate (56/100,000 workers) 12 times higher than in the general population. Facility assessments and healthcare workers' infection data provided information to guide IPC improvements.

INTRODUCTION: Voluntary medical male circumcision (VMMC) for HIV prevention began in Nyanza Region, Kenya in 2008. By 2014, approximately 800,000 VMMCs had been conducted, and 84.9% were among males aged 15-24 years. We evaluated the impact of interpersonal communication (IPC) and dedicated service outlets (DSO) on VMMC uptake among men aged 25-39 years in Nyanza Region. MATERIALS AND METHODS: We conducted a cluster randomized controlled trial in 45 administrative Locations (clusters) in Nyanza Region between May 2014 and June 2016 among uncircumcised men aged 25-34 years. In arm one, an IPC toolkit was used to address barriers to VMMC. In the second arm, men were referred to DSO that were modified to address their preferences. Arm three combined the IPC and DSO arms, and arm four was standard of care (SOC). Randomization was done at Location level (11-12 per arm). The primary outcome was the proportion of enrolled men who received VMMC within three months. Generalized estimating equations were used to evaluate the effect of interventions on the outcome. RESULTS: At baseline, 9,238 households with men aged 25-39 years were enumerated, 9,679 men were assessed, and 2,792 (28.8%) were eligible. For enrollment, 577 enrolled in the IPC arm, 825 in DSO, 723 in combined IPC + DSO, and 667 in SOC. VMMC uptake among men in the SOC arm was 3.2%. In IPC, DSO, and combined IPC + DSO arms, uptake was 3.3%, 4.5%, and 4.4%, respectively. The adjusted odds ratio (aOR) of VMMC uptake in the study arms compared to SOC were IPC aOR = 1.03; 95% CI: 0.50-2.13, DSO aOR = 1.31; 95% CI: 0.67-2.57, and IPC + DSO combined aOR = 1.31, 95% CI: 0.65-2.67. DISCUSSION: Using these interventions among men aged 25-39 years did not significantly impact VMMC uptake. These findings suggest that alternative demand creation strategies for VMMC services are needed to reach men aged 25-39 years. TRIAL REGISTRATION: clinicaltrials.gov identifier: NCT02497989.

BACKGROUND: Despite the scale-up of ART and the rollout in Tanzania of dolutegravir, an integrase strand transfer inhibitor (INSTI), treatment success has not been fully realized. HIV drug resistance (HIVDR), including dolutegravir resistance, could be implicated in the notable suboptimal viral load (VL) suppression among HIV patients. OBJECTIVES: To determine the prevalence and patterns of acquired drug resistance mutations (DRMs) among children and adults in Tanzania. METHODS: A national cross-sectional HIVDR survey was conducted among 866 children and 1173 adults. Genotyping was done on dried blood spot and/or plasma of participants with high HIV VL (≥1000 copies/mL). HIV genes (reverse transcriptase, protease and integrase) were amplified by PCR and directly sequenced. The Stanford HIVDR Database was used for HIVDR interpretation. RESULTS: HIVDR genotyping was performed on blood samples from 137 participants (92 children and 45 adults) with VL ≥ 1000 copies/mL. The overall prevalence of HIV DRMs was 71.5%, with DRMs present in 78.3% of children and 57.8% of adults. Importantly, 5.8% of participants had INSTI DRMs including major DRMs: Q148K, E138K, G118R, G140A, T66A and R263K. NNRTI, NRTI and PI DRMs were also detected in 62.8%, 44.5% and 8% of participants, respectively. All the participants with major INSTI DRMs harboured DRMs targeting NRTI backbone drugs. CONCLUSIONS: More than 7 in 10 patients with high HIV viraemia in Tanzania have DRMs. The early emergence of dolutegravir resistance is of concern for the efficacy of the Tanzanian ART programme.

BACKGROUND: Estimating cause-related mortality among the dead is not common, yet for clinical and public health purposes, a lot can be learnt from the dead. HIV/AIDS accounted for the third most frequent cause of deaths in Kenya; 39.7 deaths per 100,000 population in 2019. OraQuick Rapid HIV-1/2 has previously been validated on oral fluid and implemented as a screening assay for HIV self-testing in Kenya among living subjects. We assessed the feasibility and diagnostic accuracy of OraQuick Rapid HIV-1/2 for HIV screening among decedents. METHODS: Trained morticians collected oral fluid from 132 preembalmed and postembalmed decedents aged >18 months at Jaramogi Oginga Odinga Teaching and Referral Hospital mortuary in western Kenya and tested for HIV using OraQuick Rapid HIV-1/2. Test results were compared with those obtained using the national HIV Testing Services algorithm on matched preembalming whole blood specimens as a gold standard (Determine HIV and First Response HIV 1-2-O). We calculated positive predictive values, negative predictive values, area under the curve, and sensitivity and specificity of OraQuick Rapid HIV-1/2 compared with the national HTS algorithm. RESULTS: OraQuick Rapid HIV-1/2 had similar sensitivity of 92.6% [95% confidence interval (CI): 75.7 to 99.1] on preembalmed and postembalmed samples compared with the gold standard. Specificity was 97.1% (95% CI: 91.9 to 99.4) and 95.2% (95% CI: 89.2 to 98.4) preembalming and postembalming, respectively. Preembalming and postembalming positive predictive value was 89.3% (95% CI: 71.8 to 97.7) and 83.3% (95% CI: 65.3 to 94.4), respectively. The area under the curve preembalming and postembalming was 94.9% (95% CI: 89.6 to 100) and 93.9% (95% CI: 88.5 to 99.4), respectively. CONCLUSIONS: The study showed a relatively high-performance sensitivity and specificity of OraQuick Rapid HIV-1/2 test among decedents, similar to those observed among living subjects. OraQuick Rapid HIV-1/2 presents a convenient and less invasive screening test for surveillance of HIV among decedents within a mortuary setting.

BACKGROUND: Self-reported male circumcision (MC) status is widely used to estimate community prevalence of circumcision, although its accuracy varies in different settings depending on the extent of misreporting. Despite this challenge, self-reported MC status remains essential because it is the most feasible method of collecting MC status data in community surveys. Therefore, its accuracy is an important determinant of the reliability of MC prevalence estimates based on such surveys. We measured the concurrence between self-reported and physically verified MC status among men aged 25-39 years during a baseline household survey for a study to test strategies for enhancing MC uptake by older men in Nyanza region of Kenya. The objective was to determine the accuracy of self-reported MC status in communities where MC for HIV prevention is being rolled out. METHODS: Agreement between self-reported and physically verified MC status was measured among 4,232 men. A structured questionnaire was used to collect data on MC status followed by physical examination to verify the actual MC status whose outcome was recorded as fully circumcised (no foreskin), partially circumcised (foreskin is past corona sulcus but covers less than half of the glans) or uncircumcised (foreskin covers half or more of the glans). The sensitivity and specificity of self-reported MC status were calculated using physically verified MC status as the gold standard. RESULTS: Out of 4,232 men, 2,197 (51.9%) reported being circumcised, of whom 99.0% were confirmed to be fully circumcised on physical examination. Among 2,035 men who reported being uncircumcised, 93.7% (1,907/2,035) were confirmed uncircumcised on physical examination. Agreement between self-reported and physically verified MC status was almost perfect, kappa (k) = 98.6% (95% CI, 98.1%-99.1%. The sensitivity of self-reporting being circumcised was 99.6% (95% CI, 99.2-99.8) while specificity of self-reporting uncircumcised was 99.0% (95% CI, 98.4-99.4) and did not differ significantly by age group based on chi-square test. Rate of consenting to physical verification of MC status differed by client characteristics; unemployed men were more likely to consent to physical verification (odds ratio [OR] = 1.48, (95% CI, 1.30-1.69) compared to employed men and those with post-secondary education were less likely to consent to physical verification than those with primary education or less (odds ratio [OR] = 0.61, (95% CI, 0.51-0.74). CONCLUSIONS: In this Kenyan context, both sensitivity and specificity of self-reported MC status was high; therefore, MC prevalence estimates based on self-reported MC status should be deemed accurate and applicable for planning. However MC programs should assess accuracy of self-reported MC status periodically for any secular changes that may undermine its usefulness for estimating community MC prevalence in their unique settings.

INTRODUCTION: Uptake of voluntary medical male circumcision (VMMC) as an intervention for prevention of HIV acquisition has been low among men aged ≥25 years in Nyanza region, western Kenya. We conducted a baseline survey of the prevalence and predictors of VMMC among men ages 25-39 years as part of the preparations for a cluster randomized controlled trial (cRCT) called the Target, Speed and Coverage (TASCO) Study. The TASCO Study aimed to assess the impact of two demand creation interventions-interpersonal communication (IPC) and dedicated service outlets (DSO), delivered separately and together (IPC + DSO)-on VMMC uptake. METHODS: As part of the preparatory work for implementation of the cRCT to evaluate tailored interventions to improve uptake of VMMC, we conducted a survey of men aged 25-39 years from a traditionally non-circumcising Kenyan ethnic community within non-contiguous locations selected as study sites. We determined their circumcision status, estimated the baseline circumcision prevalence and assessed predictors of being circumcised using univariate and multivariate logistic regression. RESULTS: A total of 5,639 men were enrolled of which 2,851 (50.6%) reported being circumcised. The odds of being circumcised were greater for men with secondary education (adjusted Odds Ratio (aOR) = 1.65; 95% CI: 1.45-1.86, p<0.001), post-secondary education (aOR = 1.72; 95% CI: 1.44-2.06, p <0.001), and those employed (aOR = 1.32; 95% CI: 1.18-1.47, p <0.001). However, the odds were lower for men with a history of being married (currently married, divorced, separated, or widowed). CONCLUSION: Among adult men in the rural Nyanza region of Kenya, men with post-primary education and employed were more likely to be circumcised. VMMC programs should focus on specific sub-groups of men, including those aged 25-39 years who are married, divorced/separated/ widowed, and of low socio-economic status (low education and unemployed).

OBJECTIVES: To evaluate excess mortality and risk factors for death during anti-tuberculosis treatment in Western Kenya. METHODS: We abstracted surveillance data and compared mortality rates during anti-tuberculosis treatment with all-cause mortality from a health and demographic surveillance population to obtain standardised mortality ratios (SMRs). Risk factors for excess mortality were obtained using a relative survival model, and for death during treatment using a proportional hazards regression model. RESULTS: The crude mortality rate during anti-tuberculosis treatment was 18.0 (95%CI 16.8-19.2) per 100 person-years. The age and sex SMR was 8.8 (95%CI 8.2-9.4). Excess mortality was greater in human immunodeficiency virus (HIV) positive TB patients (excess hazard ratio [eHR] 2.1, 95%CI 1.5-3.1), and lower in patients who were female or started treatment in a later year. Mortality was high in patients with unknown HIV status (HR 2.9, 95%CI 2.2-3.8) or, if HIV-positive, not on antiretroviral treatment (ART; HR 3.3, 95%CI 2.5-4.5) or not known to be on ART (HR 2.8, 95%CI 2.1-3.7). The attributable fraction of incomplete uptake of HIV testing and ART on mortality was 31% (95%CI 15-45) compared to HIV-positive patients on ART. CONCLUSION: Increasing the uptake of HIV testing and ART would further reduce mortality during anti-tuberculosis treatment by an estimated 31%.

SETTING: Francistown and Gaborone, Botswana. OBJECTIVE: Chest radiography is used to screen for tuberculosis (TB) in asymptomatic persons living with the human immunodeficiency virus (PLWH) seeking isoniazid preventive therapy (IPT). We describe radiographic features in PLWH in a TB-endemic setting and identify features associated with TB disease. DESIGN: Asymptomatic PLWH seeking IPT under program conditions for a clinical trial between 2004 and 2006 received chest radiographs (CXRs) that were read using the standardized Chest Radiograph Reading and Recording System (CRRS). Clinical characteristics, including TB disease, were compared with the radiographic findings. RESULTS: From 2732 screening CXRs, 183 had one or more abnormalities and were scored using CRRS, with 42% having infiltrates (36% upper lobes), 35% parenchymal fibrosis and 32% adenopathy. TB disease status was determined in 129 (70%) PLWH, of whom 22 (17%) had TB disease. TB disease was associated with upper lobe infiltrates (relative risk [RR] 3.0, 95%CI 1.5-6.2) and mediastinal adenopathy (RR 3.9, 95%CI 1.8-8.4). The sensitivity and specificity of either upper lobe infiltrates or mediastinal lymphadenopathy for TB disease were respectively 64% and 82%. CONCLUSION: A combination of CXR features was useful for predicting TB disease in asymptomatic PLWH. CRRS should be used more frequently in similar studies.