Advanced HIV disease in Homa Bay County, Kenya:Characteristics of newly-diagnosed and antiretroviral therapy-experienced clients

Advanced HIV disease (AHD) remains a significant burden, despite the widespread use of antiretroviral therapy (ART) programs. Individuals with AHD are at a high risk of death even after starting ART. We characterized treatment naïve and treatment experienced clients presenting with AHD in western Kenya to inform service delivery and program improvement. We conducted a retrospective study using routinely collected program data from October 2016 to September 2019 for AHD clients in eight facilities in Homa Bay County, Kenya. Demographic and clinical data were abstracted from the medical records of AHD clients, defined as HIV-positive clients aged ≥ 5 years with documented CD4 count &lt; 200 cells/mm3 and/or WHO clinical stage II/IV. Associations were assessed using Pearson's chi-square and Mann-Whitney Rank-Sum tests at 5% level of significance. Of the 19,427 HIV clients at the eight facilities, 6649 (34%) had a CD4 count &lt; 200 cells/mm3 or a WHO III/IV stage. Of these, 1845 were randomly selected for analysis. Over half (991) of participants were aged 45 + years and 1040 (56%) were female. The median age was 46.0 years (interquartile range: 39.2-54.5); 1553 (84%) were in care at county and sub-county hospitals; and 1460 (79%) were WHO stage III/IV at enrollment. At ART initiation, 241 (13%) had tuberculosis, 192 (10%) had chronic diarrhea, and 94 (5%) had Pneumocystis jiroveci pneumonia. At the time of data collection, 89 (5%) participants had died and 140 (8%) were lost to follow-up. Eighteen percent (330) of participants were ART-experienced (on ART for ≥ 3 months). The proportions of ART-experienced and -naïve clients regarding age, sex and marital status were similar. However, a higher proportion of ART-experienced clients received care at primary care facilities, (93(28%) vs. 199 (13%); P &lt; .001); were WHO stage 3/4 at AHD diagnosis, 273 (84%) vs. 1187 (79%) (P = .041); and had died or been LTFU, (124 (38%) vs. 105 (7%); P &lt; .001). With increasing prevalence of patients on ART, the proportion of AHD treatment-experienced clients may increase without effective interventions to ensure that these patients remain in care.</p

Integrating pediatric TB services into child healthcare services in Africa: study protocol for the INPUT cluster-randomized stepped wedge trial

Background Tuberculosis is among the top-10 causes of mortality in children with more than 1 million children suffering from TB disease annually worldwide. The main challenge in young children is the difficulty in establishing an accurate diagnosis of active TB. The INPUT study is a stepped-wedge cluster-randomized intervention study aiming to assess the effectiveness of integrating TB services into child healthcare services on TB diagnosis capacities in children under 5 years of age. Methods Two strategies will be compared: i) The standard of care, offering pediatric TB services based on national standard of care; ii) The intervention, with pediatric TB services integrated into child healthcare services: it consists of a package of training, supportive supervision, job aids, and logistical support to the integration of TB screening and diagnosis activities into pediatric services. The design is a cluster-randomized stepped-wedge of 12 study clusters in Cameroon and Kenya. The sites start enrolling participants under standard-of-care and will transition to the intervention at randomly assigned time points. We enroll children aged less than 5 years with a presumptive diagnosis of TB after obtaining caregiver written informed consent. The participants are followed through TB diagnosis and treatment, with clinical information prospectively abstracted from their medical records. The primary outcome is the proportion of TB cases diagnosed among children < 5 years old attending the child healthcare services. Secondary outcomes include: number of children screened for presumptive active TB; diagnosed; initiated on TB treatment; and completing treatment. We will also assess the cost-effectiveness of the intervention, its acceptability among health care providers and users, and fidelity of implementation. Discussion Study enrolments started in May 2019, enrolments will be completed in October 2020 and follow up will be completed by June 2021. The study findings will be disseminated to national, regional and international audiences and will inform innovative approaches to integration of TB screening, diagnosis, and treatment initiation into child health care services.publishedVersio

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Advanced HIV disease in Homa Bay County, Kenya:Characteristics of newly-diagnosed and antiretroviral therapy-experienced clients

Advanced HIV disease (AHD) remains a significant burden, despite the widespread use of antiretroviral therapy (ART) programs. Individuals with AHD are at a high risk of death even after starting ART. We characterized treatment naïve and treatment experienced clients presenting with AHD in western Kenya to inform service delivery and program improvement. We conducted a retrospective study using routinely collected program data from October 2016 to September 2019 for AHD clients in eight facilities in Homa Bay County, Kenya. Demographic and clinical data were abstracted from the medical records of AHD clients, defined as HIV-positive clients aged ≥ 5 years with documented CD4 count &lt; 200 cells/mm3 and/or WHO clinical stage II/IV. Associations were assessed using Pearson's chi-square and Mann-Whitney Rank-Sum tests at 5% level of significance. Of the 19,427 HIV clients at the eight facilities, 6649 (34%) had a CD4 count &lt; 200 cells/mm3 or a WHO III/IV stage. Of these, 1845 were randomly selected for analysis. Over half (991) of participants were aged 45 + years and 1040 (56%) were female. The median age was 46.0 years (interquartile range: 39.2-54.5); 1553 (84%) were in care at county and sub-county hospitals; and 1460 (79%) were WHO stage III/IV at enrollment. At ART initiation, 241 (13%) had tuberculosis, 192 (10%) had chronic diarrhea, and 94 (5%) had Pneumocystis jiroveci pneumonia. At the time of data collection, 89 (5%) participants had died and 140 (8%) were lost to follow-up. Eighteen percent (330) of participants were ART-experienced (on ART for ≥ 3 months). The proportions of ART-experienced and -naïve clients regarding age, sex and marital status were similar. However, a higher proportion of ART-experienced clients received care at primary care facilities, (93(28%) vs. 199 (13%); P &lt; .001); were WHO stage 3/4 at AHD diagnosis, 273 (84%) vs. 1187 (79%) (P = .041); and had died or been LTFU, (124 (38%) vs. 105 (7%); P &lt; .001). With increasing prevalence of patients on ART, the proportion of AHD treatment-experienced clients may increase without effective interventions to ensure that these patients remain in care.</p

Active pediatric HIV case finding in Kenya and Uganda: A look at missed opportunities along the prevention of mother-to-child transmission of HIV (PMTCT) cascade.

BACKGROUND:Children living with HIV remain undiagnosed due to missed opportunities along the prevention of mother-to-child HIV transmission cascade. This study addresses programmatic gaps in the cascade by describing pregnancy and HIV-related services received by mothers of children newly identified as HIV-positive through active case finding. METHODS:This was a prospective observational cohort (2017-2018) of HIV-positive children <15 years of age newly diagnosed at study facilities and/or surrounding communities in Kenya and Uganda. At enrollment, caregivers were interviewed about maternal and child health and HIV history. Child medical and laboratory information was abstracted at two months post-diagnosis. Descriptive summary statistics were calculated; associations between selected factors and child age at HIV diagnosis were evaluated using generalized estimating equations. RESULTS:174 HIV-positive children (median age 2.4 years) were enrolled. Among maternal caregivers, 110/132 (83.3%) attended antenatal care and 60 (45.5%) reported testing HIV-negative in antenatal care. Of 41 and 56 women known to be HIV-positive during pregnancy and breastfeeding respectively, 17 (41.5%) and 15 (26.8%) did not receive antiretroviral drugs. Despite known maternal HIV-positive status during pregnancy, 39% of these children were not diagnosed until after two years of age; children were diagnosed at younger ages in Uganda (p = 0.0074) and if mother was the caregiver (p<0.0001). The most common HIV testing points identifying children were outpatient (44.3%) and maternal/child health departments (29.9%). Nearly all children initiated antiretroviral therapy within two weeks of diagnosis. CONCLUSIONS:Multiple missed opportunities for HIV prevention and delays in HIV testing of HIV-exposed children were identified in newly diagnosed children. Findings support critical prevention messaging and retesting of HIV-negative women during pregnancy and breastfeeding, strengthening HIV treatment initiation and follow-up systems and interventions to ensure HIV-positive women receive lifelong antiretroviral therapy throughout the cascade, and broader implementation of community case finding so children not engaged in care receive testing services

Antiretroviral treatment failure and associated factors among people living with HIV on therapy in Homa Bay, Kenya: A retrospective study.

Despite large numbers of patients accessing antiretroviral treatment (ART) in Kenya, few studies have explored factors associated with virologic failure in Western Kenya, specifically. We undertook a study in Homa Bay County, Kenya to assess the extent of virologic treatment failure and factors associated with it. This was an observational retrospective study conducted from September 2020 to January 2021. Data were abstracted from the records of patients who had been on ART for at least six months at the time of data collection after systematic sampling stratified by age group at ART initiation (0-14 and 15+ years), using probability proportion to the numbers of patients attending the facility. Confirmed viral treatment failure was defined as viral load ≥1000 copies/ml based on two consecutive viral load measurements after at least three months of enhanced adherence counseling. Data were analyzed using descriptive statistics and Cox regression modeling. Of the 2,007 patients sampled, 160 (8.0%) had confirmed virologic treatment failure. Significantly higher virologic treatment failure rates were identified among male patients 78/830 (9.4%) and children 115/782 (14.7%). Factors associated with virologic treatment failure (VTF), were age 0-14 years, adjusted hazard ratio (AHR) 4.42, (95% Confidence Interval [CI], 3.12, 6.32), experience of treatment side effects AHD: 2.43, (95% CI, 1.76, 3.37), attending level 2/3 health facility, AHR: 1.87, (95% CI: 1.29, 2,72), and history of opportunistic infections (OIs), AHR: 1.81, (95% CI, 1.76, 3.37). Children, attendees of level 2/3 health facilities, patients with a history of OIs, and those experiencing treatment side-effects are at risk of VTF. Increased focus on children and adolescents on screening for drug resistance, administration of and adherence to medication, and on effective information and education on side-effects is critical. Additionally, there is need for increased training and support for health care workers at primary level care facilities

Integrating pediatric TB services into child healthcare services in Africa: study protocol for the INPUT cluster-randomized stepped wedge trial

Background Tuberculosis is among the top-10 causes of mortality in children with more than 1 million children suffering from TB disease annually worldwide. The main challenge in young children is the difficulty in establishing an accurate diagnosis of active TB. The INPUT study is a stepped-wedge cluster-randomized intervention study aiming to assess the effectiveness of integrating TB services into child healthcare services on TB diagnosis capacities in children under 5 years of age. Methods Two strategies will be compared: i) The standard of care, offering pediatric TB services based on national standard of care; ii) The intervention, with pediatric TB services integrated into child healthcare services: it consists of a package of training, supportive supervision, job aids, and logistical support to the integration of TB screening and diagnosis activities into pediatric services. The design is a cluster-randomized stepped-wedge of 12 study clusters in Cameroon and Kenya. The sites start enrolling participants under standard-of-care and will transition to the intervention at randomly assigned time points. We enroll children aged less than 5 years with a presumptive diagnosis of TB after obtaining caregiver written informed consent. The participants are followed through TB diagnosis and treatment, with clinical information prospectively abstracted from their medical records. The primary outcome is the proportion of TB cases diagnosed among children < 5 years old attending the child healthcare services. Secondary outcomes include: number of children screened for presumptive active TB; diagnosed; initiated on TB treatment; and completing treatment. We will also assess the cost-effectiveness of the intervention, its acceptability among health care providers and users, and fidelity of implementation. Discussion Study enrolments started in May 2019, enrolments will be completed in October 2020 and follow up will be completed by June 2021. The study findings will be disseminated to national, regional and international audiences and will inform innovative approaches to integration of TB screening, diagnosis, and treatment initiation into child health care services

Expanded eligibility for HIV testing increases HIV diagnoses-A cross-sectional study in seven health facilities in western Kenya.

Homa Bay, Siaya, and Kisumu counties in western Kenya have the highest estimated HIV prevalence (16.3-21.0%) in the country, and struggle to meet program targets for HIV testing services (HTS). The Kenya Ministry of Health (MOH) recommends annual HIV testing for the general population. We assessed the degree to which reducing the interval for retesting to less than 12 months increased diagnosis of HIV in outpatient departments (OPD) in western Kenya. We conducted a retrospective analysis of routinely collected program data from seven high-volume (>800 monthlyOPD visits) health facilities in March-December, 2017. Data from persons ≥15 years of age seeking medical care (patients) in the OPD and non-care-seekers (non-patients) accompanying patients to the OPD were included. Outcomes were meeting MOH (routine) criteria versus criteria for a reduced retesting interval (RRI) of 12 months, and 5% (4,832) met other criteria. The remaining 80% (74,033) met criteria for a RRI of < 12 months. In total 1.3% (1,185) of clients had a positive test. Although the percent yield was over 2-fold higher among those meeting routine criteria (2.4% vs. 1.0%; p<0.001), 63% (750) of all HIV infections were found among clients tested less than 12 months ago, the majority (81%) of whom reported having a negative test in the past 3-12 months. Non-patients accounted for 45% (539) of all HIV-positive persons identified. Percent yield was higher among non-patients as compared to patients (1.5% vs. 1.2%; p-value = <0.001) overall and across eligibility criteria and age categories. The majority of HIV diagnoses in the OPD occurred among clients reporting a negative HIV test in the past 12 months, clients ineligible for testing under the current MOH guidelines. Nearly half of all HIV-positive individuals identified in the OPD were non-patients. Our findings suggest that in the setting of a generalized HIV epidemic, retesting persons reporting an HIV-negative test in the past 3-12 months, and routine testing of non-patients accessing the OPD are key strategies for timely diagnosis of persons living with HIV

Enhancing Malaria Research, Surveillance, and Control in Endemic Areas of Kenya and Ethiopia

Malaria control programs in Africa encounter daunting challenges that hinder progressive steps toward elimination of the disease. These challenges include widespread insecticide resistance in mosquito vectors, increasing outdoor malaria transmission, lack of vector surveillance and control tools suitable for outdoor biting vectors, weakness in malaria surveillance, and an inadequate number of skilled healthcare personnel. Ecological and epidemiological changes induced by environmental modifications resulting from water resource development projects pose additional barriers to malaria control. Cognizant of these challenges, our International Center of Excellence for Malaria Research (ICEMR) works in close collaboration with relevant government ministries and agencies to align its research efforts with the objectives and strategies of the national malaria control and elimination programs for the benefit of local communities. Our overall goal is to assess the impact of water resource development projects, shifting agricultural practices, and vector interventions on Plasmodium falciparum and P. vivax malaria in Kenya and Ethiopia. From 2017 to date, the ICEMR has advanced knowledge of malaria epidemiology, transmission, immunology, and pathogenesis, and developed tools to enhance vector surveillance and control, improved clinical malaria surveillance and diagnostic methods, and strengthened the capacity of local healthcare providers. Research findings from the ICEMR will inform health policy and strategic planning by ministries of health in their quest to sustain malaria control and achieve elimination goals

Novel FujiLAM assay to detect tuberculosis in HIV-positive ambulatory patients in four African countries: a diagnostic accuracy study

International audienceBackground: Development of rapid biomarker-based tests that can diagnose tuberculosis using non-sputum samples is a priority for tuberculosis control. We aimed to compare the diagnostic accuracy of the novel Fujifilm SILVAMP TB LAM (FujiLAM) assay with the WHO-recommended Alere Determine TB-LAM Ag test (AlereLAM) using urine samples from HIV-positive patients.Methods: We did a diagnostic accuracy study at five outpatient public health facilities in Uganda, Kenya, Mozambique, and South Africa. Eligible patients were ambulatory HIV-positive individuals (aged ≥15 years) with symptoms of tuberculosis irrespective of their CD4 T-cell count (group 1), and asymptomatic patients with advanced HIV disease (CD4 count <200 cells per μL, or HIV clinical stage 3 or 4; group 2). All participants underwent clinical examination, chest x-ray, and blood sampling, and were requested to provide a fresh urine sample, and two sputum samples. FujiLAM and AlereLAM urine assays, Xpert MTB/RIF Ultra assay on sputum or urine, sputum culture for Mycobacterium tuberculosis, and CD4 count were systematically carried out for all patients. Sensitivity and specificity of FujiLAM and AlereLAM were evaluated against microbiological and composite reference standards.Findings: Between Aug 24, 2020 and Sept 21, 2021, 1575 patients (823 [52·3%] women) were included in the study: 1031 patients in group 1 and 544 patients in group 2. Tuberculosis was microbiologically confirmed in 96 (9·4%) of 1022 patients in group 1 and 18 (3·3%) of 542 patients in group 2. Using the microbiological reference standard, FujiLAM sensitivity was 60% (95% CI 51-69) and AlereLAM sensitivity was 40% (31-49; p<0·001). Among patients with CD4 counts of less than 200 cells per μL, FujiLAM sensitivity was 69% (57-79) and AlereLAM sensitivity was 52% (40-64; p=0·0218). Among patients with CD4 counts of 200 cells per μL or higher, FujiLAM sensitivity was 47% (34-61) and AlereLAM sensitivity was 24% (14-38; p=0·0116). Using the microbiological reference standard, FujiLAM specificity was 87% (95% CI 85-89) and AlereLAM specificity was 86% (95 CI 84-88; p=0·941). FujiLAM sensitivity varied by lot number from 48% (34-62) to 76% (57-89) and specificity from 77% (72-81) to 98% (93-99).Interpretation: Next-generation, higher sensitivity urine-lipoarabinomannan assays are potentially promising tests that allow rapid tuberculosis diagnosis at the point of care for HIV-positive patients. However, the variability in accuracy between FujiLAM lot numbers needs to be addressed before clinical use