A combined multilevel factor analysis and covariance regression model with mixed effects in the mean and variance structure.

Li et al developed a multilevel covariance regression (MCR) model as an extension of the covariance regression model of Hoff and Niu. This model assumes a hierarchical structure for the mean and the covariance matrix. Here, we propose the combined multilevel factor analysis and covariance regression model in a Bayesian framework, simultaneously modeling the MCR model and a multilevel factor analysis (MFA) model. The proposed model replaces the responses in the MCR part with the factor scores coming from an MFA model. Via a simulation study and the analysis of real data, we show that the proposed model is quite efficient when the responses of the MCR model are not measured directly but are latent variables such as the patient experience measurements in our motivating dataset.

Efficacy of a low-dose candidate malaria vaccine, R21 in adjuvant Matrix-M, with seasonal administration to children in Burkina Faso: a randomised controlled trial.

BACKGROUND: Stalled progress in controlling Plasmodium falciparum malaria highlights the need for an effective and deployable vaccine. RTS,S/AS01, the most effective malaria vaccine candidate to date, demonstrated 56% efficacy over 12 months in African children. We therefore assessed a new candidate vaccine for safety and efficacy. METHODS: In this double-blind, randomised, controlled, phase 2b trial, the low-dose circumsporozoite protein-based vaccine R21, with two different doses of adjuvant Matrix-M (MM), was given to children aged 5-17 months in Nanoro, Burkina Faso-a highly seasonal malaria transmission setting. Three vaccinations were administered at 4-week intervals before the malaria season, with a fourth dose 1 year later. All vaccines were administered intramuscularly into the thigh. Group 1 received 5 µg R21 plus 25 µg MM, group 2 received 5 µg R21 plus 50 µg MM, and group 3, the control group, received rabies vaccinations. Children were randomly assigned (1:1:1) to groups 1-3. An independent statistician generated a random allocation list, using block randomisation with variable block sizes, which was used to assign participants. Participants, their families, and the local study team were all masked to group allocation. Only the pharmacists preparing the vaccine were unmasked to group allocation. Vaccine safety, immunogenicity, and efficacy were evaluated over 1 year. The primary objective assessed protective efficacy of R21 plus MM (R21/MM) from 14 days after the third vaccination to 6 months. Primary analyses of vaccine efficacy were based on a modified intention-to-treat population, which included all participants who received three vaccinations, allowing for inclusion of participants who received the wrong vaccine at any timepoint. This trial is registered with ClinicalTrials.gov, NCT03896724. FINDINGS: From May 7 to June 13, 2019, 498 children aged 5-17 months were screened, and 48 were excluded. 450 children were enrolled and received at least one vaccination. 150 children were allocated to group 1, 150 children were allocated to group 2, and 150 children were allocated to group 3. The final vaccination of the primary series was administered on Aug 7, 2019. R21/MM had a favourable safety profile and was well tolerated. The majority of adverse events were mild, with the most common event being fever. None of the seven serious adverse events were attributed to the vaccine. At the 6-month primary efficacy analysis, 43 (29%) of 146 participants in group 1, 38 (26%) of 146 participants in group 2, and 105 (71%) of 147 participants in group 3 developed clinical malaria. Vaccine efficacy was 74% (95% CI 63-82) in group 1 and 77% (67-84) in group 2 at 6 months. At 1 year, vaccine efficacy remained high, at 77% (67-84) in group 1. Participants vaccinated with R21/MM showed high titres of malaria-specific anti-Asn-Ala-Asn-Pro (NANP) antibodies 28 days after the third vaccination, which were almost doubled with the higher adjuvant dose. Titres waned but were boosted to levels similar to peak titres after the primary series of vaccinations after a fourth dose administered 1 year later. INTERPRETATION: R21/MM appears safe and very immunogenic in African children, and shows promising high-level efficacy. FUNDING: The European & Developing Countries Clinical Trials Partnership, Wellcome Trust, and National Institute for Health Research Oxford Biomedical Research Centre.

Mouse experiments demonstrate differential pathogenicity and virulence of Trypanosoma brucei rhodesiense strains.

Trypanosoma brucei rhodesiense is the causative agent for Rhodesian human African trypanosomiasis. The disease is considered acute, but varying clinical outcomes including chronic infections have been observed. The basis for these different clinical manifestations is thought to be associated with a combination of parasite and host factors. In the current study, Trypanosoma brucei rhodesiense strains responsible for varying infection outcomes were sought using mouse model. Clinical rHAT parasite isolates were subjected to PCR tests to confirm presence of the serum resistance associated (SRA) gene. Thereafter, four T. b. rhodesiense isolates were subjected to a comparative pathogenicity study using female Swiss white mice; the parasite strains were compared on the basis of parasitaemia, host survival time, clinical and postmortem biomarkers of infection severity. Isolates identified to cause acute and chronic disease were compared for establishment in insect vector, tsetse fly. The mouse survival time was significantly different (Log-rankp = 0.0001). With mice infected with strain KETRI 3801 exhibiting the shortest survival time (20 days) as compared to those infected with KETRI 3928 that, as controls, survived past the 60 days study period. In addition, development of anaemia was rapid in KETRI 3801 and least in KETRI 3928 infections, and followed the magnitude of survival time. Notably, hepatosplenomegaly was pronounced with longer survival. Mouse weight and feed intake reduced (KETRI 3801 > KETRI 2636 > EATRO 1762) except in KETRI 3928 infections which remained similar to controls. Comparatively, acute to chronic infection outcomes is in the order of KETRI 3801 > KETRI 2636 > EATRO 1762 > KETRI 3928, indicative of predominant role of strain dependent factors. Further, KETRI 3928 strain established better in tsetse as compared to KETRI 3801, suggesting that transmission of strains causing chronic infections could be common. In sum, we have identified Trypanosoma brucei rhodesiense strains that cause acute and chronic infections in mice, that will be valuable in investigating pathogen - host interactions responsible for varying disease outcomes and transmission in African trypanosomiasis.

Reaching early adolescents with a complex intervention for HIV prevention: findings from a cohort study to evaluate DREAMS in two informal settlements in Nairobi, Kenya.

BACKGROUND: The DREAMS Partnership promotes combination HIV prevention among adolescent girls and young women. We examined the extent to which DREAMS interventions reached early adolescent girls (EAG; aged 10-14 years) in two informal settlements in Nairobi, and the characteristics of those reached, after 3 years of implementation. METHODS: We utilized three data rounds from a randomly-sampled cohort of EAG established in 2017 in Korogocho and Viwandani informal settlements where DREAMS interventions were implemented. Interventions were classified as individual or contextual-level, with individual interventions further categorised as primary (prioritised for this age group), or secondary. We summarised self-reported invitation to participate in DREAMS, and uptake of eight interventions that were supported by DREAMS, during 2017-2019. Multivariable logistic regression analysis was used to identify individual and household characteristics associated with invitation to DREAMS and uptake of primary interventions. RESULTS: Data were available for 606, 516 (retention rate of 85%) and 494 (82%) EAG in 2017, 2018 and 2019, respectively. Proportions invited to DREAMS increased from 49% in 2017, to 77% by 2018, and to 88% by 2019. School-based HIV and violence prevention, and HIV testing and counselling were the most accessed interventions (both at 82%). Cumulative uptake of interventions was higher among those invited to participate in DREAMS compared to those never invited, particularly for new interventions such as social asset building and financial capability training. Contextual-level interventions were accessed infrequently. Most of those invited both in 2017 and 2018 accessed ≥3 interventions (96%), and 55% received all three primary interventions by 2019. CONCLUSIONS: Uptake of DREAMS interventions among a representative sample of EAG was high and quickly increased over the implementation period. The majority accessed multiple interventions, indicating that it is feasible to integrate and deliver a package of interventions to EAG in a challenging informal context.

Depressive symptoms as predictors of sexual experiences among very young adolescent girls in slum communities in Nairobi, Kenya.

Mental health issues are a predisposing factor for HIV acquisition. We examined the association between depressive symptoms and patterns of sexual experience among girls aged 10-14 years living in Korogocho and Viwandani slums in Nairobi, Kenya. We analysed data collected in 2017 from a random sample of 606 girls. Using Latent Class Analysis, we modelled patterns of sexual experiences and used multivariable regression analysis to determine the association between self-reported depressive symptoms and sexual experiences. Seven in ten girls reported at least one symptom of self-reported depression in the past 12 months. About 13% of girls had had a sexual experience, resulting in two patterns of sexual experience - naïve and experienced. Girls reporting depressive symptoms were more likely to be sexually experienced. Sexual and reproductive health programs targeting adolescent girls should consider including intervention packages that address mental health conditions such as depression.

Contribution of HCAHPS Specific Care Experiences to Global Ratings Varies Across 7 Countries: What Can be Learned for Reporting These Global Ratings?

BACKGROUND: Given the increased international interest in improvement strategies for patient experiences with care, it is important to understand whether the same specific care experiences affect global ratings across countries. Moreover, reporting of these global ratings currently substantially varies in both research and public reporting. OBJECTIVES: The objectives of this study were to examine the differential magnitude of associations between Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) specific care experiences and global ratings, and to explore implications for reporting these global ratings. METHODS: HCAHPS data were collected from 11,289 patients across 7 European countries. We studied the association between 11 experience items and 2 global ratings (0-10 hospital rating, hospital recommendation) using multilevel ordered logistic regression analysis. Using interaction terms, we examined consistency of these associations across countries. Assuming homogeneous use and interpretations of response categories of these specific experiences across patients within and between countries, we investigated what the associations between specific experiences and global ratings imply for reporting global ratings across countries. RESULTS: All specific experiences were associated with both global ratings. "Being talked to about care after leaving the hospital" showed the strongest association. There were relatively little differential effects across countries. A reporting strategy with different cutpoints across countries might provide a more equitable comparison of global ratings. CONCLUSIONS: Our findings highlight a differential contribution of HCAHPS specific experiences to overall ratings across countries. Research and public reporting may consider examining in more detail within and across populations global rating cutpoints that represent the same true level of positive patient experiences.

Awareness and uptake of layered HIV prevention programming for young women: analysis of population-based surveys in three DREAMS settings in Kenya and South Africa.

BACKGROUND: The DREAMS Partnership is an ambitious effort to deliver combinations of biomedical, behavioural and structural interventions to reduce HIV incidence among adolescent girls and young women (AGYW). To inform multi-sectoral programming at scale, across diverse settings in Kenya and South Africa, we identified who the programme is reaching, with which interventions and in what combinations. METHODS: Randomly-selected cohorts of 606 AGYW aged 10-14 years and 1081 aged 15-22 years in Nairobi and 2184 AGYW aged 13-22 years in uMkhanyakude, KwaZulu-Natal, were enrolled in 2017, after ~ 1 year of DREAMS implementation. In Gem, western Kenya, population-wide cross-sectional survey data were collected during roll-out in 2016 (n = 1365 AGYW 15-22 years). We summarised awareness and invitation to participate in DREAMS, uptake of interventions categorised by the DREAMS core package, and uptake of a subset of 'primary' interventions. We stratified by age-group and setting, and compared across AGYW characteristics. RESULTS: Awareness of DREAMS was higher among younger women (Nairobi: 89%v78%, aged 15-17v18-22 years; uMkhanyakude: 56%v31%, aged 13-17v18-22; and Gem: 28%v25%, aged 15-17v18-22, respectively). HIV testing was the most accessed intervention in Nairobi and Gem (77% and 85%, respectively), and school-based HIV prevention in uMkhanyakude (60%). Among those invited, participation in social asset building was > 50%; > 60% accessed ≥2 core package categories, but few accessed all primary interventions intended for their age-group. Parenting programmes and community mobilisation, including those intended for male partners, were accessed infrequently. In Nairobi and uMkhanyakude, AGYW were more likely to be invited to participate and accessed more categories if they were: aged < 18 years, in school and experienced socio-economic vulnerabilities. Those who had had sex, or a pregnancy, were less likely to be invited to participate but accessed more categories. CONCLUSIONS: In representative population-based samples, awareness and uptake of DREAMS were high after 1 year of implementation. Evidence of 'layering' (receiving multiple interventions from the DREAMS core package), particularly among more socio-economically vulnerable AGYW, indicate that intervention packages can be implemented at scale, for intended recipients, in real-world contexts. Challenges remain for higher coverage and greater 'layering', including among older, out-of-school AGYW, and community-based programmes for families and men.

Impact of Cross-level Measurement Noninvariance on Hospital Rankings Based on Patient Experiences With Care in 7 European Countries.

BACKGROUND: Hospital-level findings on patient experiences with care are increasingly reported publicly. A critical aspect left unexamined is the commonality of composite measures of patient experiences across different groups of patients, nursing units, hospitals, and countries. Absence of commonality is termed measurement noninvariance and is hypothesized to have a strong impact on performance assessment. AIM: The aim of this study is to examine measurement invariance across groups and levels under study (patients, nursing units, hospitals, and countries) and illustrate the degree to which this method of analysis impacts hospital rankings. RESEARCH DESIGN: Data were collected from 11,289 patients in 7 European countries, 186 hospitals, and 824 nursing units. Multilevel factor analytic models were applied to evaluate measurement invariance across the hierarchical levels of the study and across groups at specific levels (self-perceived health at patient level; unit speciality at nursing unit level). Hospital rankings for the final multilevel model were compared with those from a single-level factor model that is unsuspecting of measurement invariance. RESULTS: Cross-group invariance was shown for levels of self-perceived health and to a large degree also for nursing unit speciality. Patient experience composite measures were, however, not invariant across patient, unit, and hospital levels. Hospital rankings were largely impacted when accounted for this cross-level invariance. The percentage of hospitals with discordant ranks by >10 percentile points varied from 26.7% in Spain to 70% in Poland. CONCLUSIONS: Leaving unexamined possible noninvariance across groups and hierarchical levels may have far reaching consequences for how the public perceives hospitals' position relative to other hospitals.

Erratum to: Composition of Anopheles mosquitoes, their blood-meal hosts, and Plasmodium falciparum infection rates in three islands with disparate bed net coverage in Lake Victoria, Kenya.

After publication of the article [1], it has been brought to our attention that a funding acknowledgement has been omitted from the original article. The authors would like to include the following, "The study was undertaken as part of the Target Malaria consortium, which receives core funding from the Bill & Melinda Gates Foundation & from the Open Philanthropy Project Fund, an advised fund of Silicon Valley Community Foundation."

Composition of Anopheles mosquitoes, their blood-meal hosts, and Plasmodium falciparum infection rates in three islands with disparate bed net coverage in Lake Victoria, Kenya.

BACKGROUND: Small islands serve as potential malaria reservoirs through which new infections might come to the mainland and may be important targets in malaria elimination efforts. This study investigated malaria vector species diversity, blood-meal hosts, Plasmodium infection rates, and long-lasting insecticidal net (LLIN) coverage on Mageta, Magare and Ngodhe Islands of Lake Victoria in western Kenya, a region where extensive vector control is implemented on the mainland. RESULTS: From trapping for six consecutive nights per month (November 2012 to March 2015) using CDC light traps, pyrethrum spray catches and backpack aspiration, 1868 Anopheles mosquitoes were collected. Based on their cytochrome oxidase I (COI) and intergenic spacer region PCR and sequencing, Anopheles gambiae s.l. (68.52%), Anopheles coustani (19.81%) and Anopheles funestus s.l. (11.67%) mosquitoes were differentiated. The mean abundance of Anopheles mosquitoes per building per trap was significantly higher (p < 0.001) in Mageta than in Magare and Ngodhe. Mageta was also the most populated island (n = 6487) with low LLIN coverage of 62.35% compared to Ngodhe (n = 484; 88.31%) and Magare (n = 250; 98.59%). Overall, 416 (22.27%) engorged Anopheles mosquitoes were analysed, of which 41 tested positive for Plasmodium falciparum infection by high-resolution melting (HRM) analysis of 18S rRNA and cytochrome b PCR products. Plasmodium falciparum infection rates were 10.00, 11.76, 0, and 18.75% among blood-fed An. gambiae s.s. (n = 320), Anopheles arabiensis (n = 51), An. funestus s.s. (n = 29), and An. coustani (n = 16), respectively. Based on HRM analysis of vertebrate cytochrome b, 16S rRNA and COI PCR products, humans (72.36%) were the prominent blood-meal hosts of malaria vectors, but 20.91% of blood-meals were from non-human vertebrate hosts. CONCLUSIONS: These findings demonstrate high Plasmodium infection rates among the primary malaria vectors An. gambiae s.s. and An. arabiensis, as well as in An. coustani for the first time in the region, and that non-human blood-meal sources play an important role in their ecology. Further, the higher Anopheles mosquito abundances on the only low LLIN coverage island of Mageta suggests that high LLIN coverage has been effective in reducing malaria vector populations on Magare and Ngodhe Islands.

Active aggregation among sexes in bean flower thrips (Megalurothrips sjostedti) on cowpea (Vigna unguiculata).

Male sexual aggregations are a common territorial, mating-related or resource-based, behaviour observed in diverse organisms, including insects such as thrips. The influence of factors such as plant substrate, time of day, and geographic location on aggregation of thrips is uncertain, therefore we monitored the dispersion of male and female bean flower thrips (BFT), Megalurothrips sjostedti (Trybom) (Thysanoptera: Thripidae), on cowpea, Vigna unguiculata (L.) Walp. (Fabaceae), over three cowpea growth stages and across three cowpea-growing areas of Kenya. Our results indicated that for all the crop growth stages, the density of BFTs varied over the time of day, with higher densities at 10:00, 13:00, and 16:00 hours than at 07:00 hours. Thrips densities did not differ among blocks at the budding stage, but they did at peak flowering and podding stages. Dispersion indices suggested that both male and female BFTs were aggregated. Active male aggregation occurred only on green plant parts and it varied across blocks, crop stages, and locations. Similarly, active female aggregation was observed in peak flowering and podding stages. Such active aggregation indicates a semiochemical or behaviour-mediated aggregation. Identification of such a semiochemical may offer new opportunities for refining monitoring and management strategies for BFT on cowpea, the most important grain legume in sub-Saharan Africa.

Analysing the oviposition behaviour of malaria mosquitoes: design considerations for improving two-choice egg count experiments.

BACKGROUND: Choice egg-count bioassays are a popular tool for analysing oviposition substrate preferences of gravid mosquitoes. This study aimed at improving the design of two-choice experiments for measuring oviposition substrates preferences of the malaria vector Anopheles gambiae senso lato, a mosquito that lays single eggs. METHODS: In order to achieve high egg-laying success of female An. gambiae sensu stricto (s.s.) and Anopheles arabiensis mosquitoes in experiments, four factors were evaluated: (1) the time provided for mating; (2) the impact of cage size, mosquito age and female body size on insemination; (3) the peak oviposition time; and, (4) the host sources of blood meal. Choice bioassays, with one mosquito released in each cage containing two oviposition cups both with the same oviposition substrate (100 ml water), were used to measure and adjust for egg-laying characteristics of the species. Based on these characteristics an improved design for the egg-count bioassay is proposed. RESULTS: High oviposition rates [84%, 95% confidence interval (CI) 77-89%] were achieved when 300 male and 300 blood-fed female An. gambiae s.s. were held together in a cage for 4 days. The chances for oviposition dropped (odds ratio 0.30; 95% CI 0.14-0.66) when human host source of blood meal was substituted with a rabbit but egg numbers per female were not affected. The number of eggs laid by individual mosquitoes was overdispersed (median = 52, eggs, interquartile range 1-214) and the numbers of eggs laid differed widely between replicates, leading to a highly heterogeneous variance between groups and/or rounds of experiments. Moreover, one-third of mosquitoes laid eggs unequally in both cups with similar substrates giving the illusion of choice. Sample size estimations illustrate that it takes 165 individual mosquitoes to power bioassays sufficiently (power = 0.8, p = 0.05) to detect a 15% shift in comparative preferences of two treatments. CONCLUSION: Two-choice egg count bioassays with Anopheles are best done with a two-tier design that (1) implements a parallel series of experiments with mosquitoes given a choice of two identical substrates choices and, (2) uses a single mosquito in each test cage rather than groups of mosquitoes to assess the preference of a test or control solution. This approach, with sufficient replication, lowers the risk detecting pseudopreferences.

Tungiasis among children in Kenya is associated with poor nutrition status, absenteeism, poor school performance and high impact on quality of life.

Tungiasis is a highly neglected tropical skin disease caused by the sand flea, Tunga penetrans. The flea burrows into the skin inducing a strong inflammatory response, leading to pain and mobility restrictions with potential impacts on quality of life. Few countries implement control efforts and there are few data on the impact of the disease to support policy decisions. We conducted a survey to determine the impact of tungiasis among primary school children across nine counties of Kenya. A total of 10,600 pupils aged 8 to 14 years were randomly selected from 97 primary schools and examined for tungiasis. For 81 cases and 578 randomly selected controls, anthropometric measurements were made, and school attendance and exam scores were collected from school records. Of those with tungiasis, 73 were interviewed regarding their quality of life using a tungiasis-specific instrument. Mixed effect ordered logistic and linear models were used to assess associations between disease status and impact variables. Compared to uninfected pupils, those with tungiasis had lower weight-for-age z-scores (adjusted ß -0.41, 95% CI: -0.75-0.06, p = 0.020), missed more days of school the previous term (adjusted Incidence Rate Ratio: 1.49, 95% CI: 1.01-2.21, p = 0.046) and were less likely to receive a high score in mathematics (aOR 0.18, 95% CI: 0.08-0.40, p<0.001) and other subjects. Pupils with severe disease (clinical score >10) were four times more likely to experience severe pain than those with mild disease (OR 3.96, 95% CI: 1.35-11.64, p = 0.012) and a higher impact on their quality of life than those with mild disease (aOR 3.57, 95% CI: 1.17-10.8, p = 0.025) when adjusted for covariates. This study has demonstrated tungiasis has a considerable impact on children's lives and academic achievement. This indicates the need for integrated disease management for school-aged children to protect their physical and cognitive development and their future prospects.

Age-dependent acquisition of IgG antibodies to Shigella serotypes-a retrospective analysis of seroprevalence in Kenyan children with implications for infant vaccination.

Background: Shigellosis mainly affects children under 5 years of age living in low- and middle-income countries, who are the target population for vaccination. There are, however, limited data available to define the appropriate timing for vaccine administration in this age group. Information on antibody responses following natural infection, proxy for exposure, could help guide vaccination strategies. Methods: We undertook a retrospective analysis of antibodies to five of the most prevalent Shigella serotypes among children aged <5 years in Kenya. Serum samples from a cross-sectional serosurvey in three Kenyan sites (Nairobi, Siaya, and Kilifi) were analyzed by standardized ELISA to measure IgG against Shigella sonnei and Shigella flexneri 1b, 2a, 3a, and 6. We identified factors associated with seropositivity to each Shigella serotype, including seropositivity to other Shigella serotypes. Results: A total of 474 samples, one for each participant, were analyzed: Nairobi (n = 169), Siaya (n = 185), and Kilifi (n = 120). The median age of the participants was 13.4 months (IQR 7.0-35.6), and the male:female ratio was 1:1. Geometric mean concentrations (GMCs) for each serotype increased with age, mostly in the second year of life. The overall seroprevalence of IgG antibodies increased with age except for S. flexneri 6 which was high across all age subgroups. In the second year of life, there was a statistically significant increase of antibody GMCs against all five serotypes (p = 0.01-0.0001) and a significant increase of seroprevalence for S. flexneri 2a (p = 0.006), S. flexneri 3a (p = 0.006), and S. sonnei (p = 0.05) compared with the second part of the first year of life. Among all possible pairwise comparisons of antibody seropositivity, there was a significant association between S. flexneri 1b and 2a (OR = 6.75, 95% CI 3-14, p < 0.001) and between S. flexneri 1b and 3a (OR = 23.85, 95% CI 11-54, p < 0.001). Conclusion: Children living in low- and middle-income settings such as Kenya are exposed to Shigella infection starting from the first year of life and acquire serotype-specific antibodies against multiple serotypes. The data from this study suggest that Shigella vaccination should be targeted to infants, ideally at 6 or at least 9 months of age, to ensure children are protected in the second year of life when exposure significantly increases.

Shifts in malaria vector species composition and transmission dynamics along the Kenyan coast over the past 20 years.

BACKGROUND: Over the past 20 years, numerous studies have investigated the ecology and behaviour of malaria vectors and Plasmodium falciparum malaria transmission on the coast of Kenya. Substantial progress has been made to control vector populations and reduce high malaria prevalence and severe disease. The goal of this paper was to examine trends over the past 20 years in Anopheles species composition, density, blood-feeding behaviour, and P. falciparum sporozoite transmission along the coast of Kenya. METHODS: Using data collected from 1990 to 2010, vector density, species composition, blood-feeding patterns, and malaria transmission intensity was examined along the Kenyan coast. Mosquitoes were identified to species, based on morphological characteristics and DNA extracted from Anopheles gambiae for amplification. Using negative binomial generalized estimating equations, mosquito abundance over the period were modelled while adjusting for season. A multiple logistic regression model was used to analyse the sporozoite rates. RESULTS: Results show that in some areas along the Kenyan coast, Anopheles arabiensis and Anopheles merus have replaced An. gambiae sensu stricto (s.s.) and Anopheles funestus as the major mosquito species. Further, there has been a shift from human to animal feeding for both An. gambiae sensu lato (s.l.) (99% to 16%) and An. funestus (100% to 3%), and P. falciparum sporozoite rates have significantly declined over the last 20 years, with the lowest sporozoite rates being observed in 2007 (0.19%) and 2008 (0.34%). There has been, on average, a significant reduction in the abundance of An. gambiae s.l. over the years (IRR = 0.94, 95% CI 0.90-0.98), with the density standing at low levels of an average 0.006 mosquitoes/house in the year 2010. CONCLUSION: Reductions in the densities of the major malaria vectors and a shift from human to animal feeding have contributed to the decreased burden of malaria along the Kenyan coast. Vector species composition remains heterogeneous but in many areas An. arabiensis has replaced An. gambiae as the major malaria vector. This has important implications for malaria epidemiology and control given that this vector predominately rests and feeds on humans outdoors. Strategies for vector control need to continue focusing on tools for protecting residents inside houses but additionally employ outdoor control tools because these are essential for further reducing the levels of malaria transmission.

A multivariate joint model to adjust for random measurement error while handling skewness and correlation in dietary data in an epidemiologic study of mortality.

PURPOSE: A substantial proportion of global deaths is attributed to unhealthy diets, which can be assessed at baseline or longitudinally. We demonstrated how to simultaneously correct for random measurement error, correlations, and skewness in the estimation of associations between dietary intake and all-cause mortality. METHODS: We applied a multivariate joint model (MJM) that simultaneously corrected for random measurement error, skewness, and correlation among longitudinally measured intake levels of cholesterol, total fat, dietary fiber, and energy with all-cause mortality using US National Health and Nutrition Examination Survey linked to the National Death Index mortality data. We compared MJM with the mean method that assessed intake levels as the mean of a person's intake. RESULTS: The estimates from MJM were larger than those from the mean method. For instance, the logarithm of hazard ratio for dietary fiber intake increased by 14 times (from -0.04 to -0.60) with the MJM method. This translated into a relative hazard of death of 0.55 (95% credible interval: 0.45, 0.65) with the MJM and 0.96 (95% credible interval: 0.95, 0.97) with the mean method. CONCLUSIONS: MJM adjusts for random measurement error and flexibly addresses correlations and skewness among longitudinal measures of dietary intake when estimating their associations with death.

Correlations between three ELISA protocols measurements of RTS,S/AS01-induced anti-CSP IgG antibodies.

BACKGROUND: RTS,S/AS01 induced anti-circumsporozoite protein (CSP) IgG antibodies are associated with the vaccine efficacy. There is currently no international standardisation of the assays used in the measurement of anti-CSP IgG antibody concentrations for use in evaluations of the vaccine's immunogenicity and/or efficacy. Here, we compared the levels of RTS,S/AS01 induced anti-CSP IgG antibodies measured using three different enzyme-Linked ImmunoSorbent Assays (ELISA). METHODS: 196 plasma samples were randomly selected from the 447 samples collected during the RTS,S/AS01 phase IIb trial in 2007 from Kenyan children aged between 5-17 months. The vaccine-induced anti-CSP IgG antibodies were then measured using two independently developed ELISA protocols ('Kilifi-RTS,S' and 'Oxford-R21') and compared to the results from the reference 'Ghent-RTS,S' protocol for the same participants. For each pair of protocols, a deming regression model was fitted. Linear equations were then derived to aid in conversions into equivalent ELISA units. The agreement was assessed using Bland and Altman method. FINDINGS: The anti-CSP IgG antibodies measured from the three ELISA protocols were in agreement, and were positively and linearly correlated; 'Oxford' and 'Kilifi' r = 0.93 (95% CI 0.91-0.95), 'Oxford' and 'Ghent' r = 0.94 (95% CI: 0.92-0.96), and 'Kilifi' and 'Ghent' r = 0.97 (95% CI: 0.96-0.98), p<0.0001 for all correlations. CONCLUSIONS: With the linearity, agreement and correlations established between the assays, conversion equations can be applied to convert results into equivalent units, enabling comparisons of immunogenicities across different vaccines of the same CSP antigens. This study highlights the need for the international harmonisation of anti-CSP antibody measurements.

Validation of saline, PBS and a locally produced VTM at varying storage conditions to detect the SARS-CoV-2 virus by qRT-PCR.

Coronavirus Disease-2019 tests require a Nasopharyngeal (NP) and/or Oropharyngeal (OP) specimen from the upper airway, from which virus RNA is extracted and detected through quantitative reverse transcription-Polymerase Chain Reaction (qRT-PCR). The viability of the virus is maintained after collection by storing the NP/OP swabs in Viral Transport Media (VTM). We evaluated the performance of four transport media: locally manufactured ("REVITAL") Viral Transport Media (RVTM), Standard Universal Transport Media (SUTM), PBS and 0.9% (w/v) NaCl (normal saline). We used laboratory cultured virus to evaluate: i) viral recovery and maintaining integrity at different time periods and temperatures; ii) stability in yielding detectable RNA consistently for all time points and conditions; and iii) their overall accuracy. Four vials of SARS-CoV-2 cultured virus (2 high and 2 low concentration samples) and 1 negative control sample were prepared for each media type (SUTM, RVTM, PBS and normal saline) and stored at the following temperatures, -80°C, 4°C, 25°C and 37°C for 7 days. Viral RNA extractions and qRT-PCR were performed at 1, 2, 3, 4 and 7 days after inoculation with the cultured virus to assess virus stability and viral recovery. Ct values fell over time at 25°C and 37°C, but normal saline, PBS, RVTM and SUTM all showed comparable performance in maintaining virus integrity and stability allowing for the detection of SARS-CoV-2 RNA. Overall, this study demonstrated that normal saline, PBS and the locally manufactured VTM can be used for COVID-19 sample collection and testing, thus expanding the range of SARS-CoV-2 viral collection media.

National prevalence and risk factors for tungiasis in Kenya.

BACKGROUND: Tungiasis is a highly neglected tropical skin disease caused by the sand flea, Tunga penetrans, the female of which burrows into the skin, causing pain and itching. The disease occurs throughout South America and sub-Saharan Africa but there are few systematic data on national disease burdens. The tungiasis research community is keen to develop survey methods to fill this gap. Here we used a school-based, thorough examination method to determine the prevalence and risk factors for tungiasis in Kenya. METHODS: We conducted the first nationally representative survey of tungiasis, including nine counties covering the major ecological zones of Kenya. A stratified multistage random sampling was used to select 22 primary schools from each of the nine counties and to select up to 114 pupils aged 8 to 14 years in each school. Pupils were examined thoroughly for tungiasis. Two surveys were conducted, the first between May and July 2021 and the second between October 2021 and April 2023 when pupils were also interviewed for risk factors. Mixed effect logistic regression models were used to test associations of independent variables with tungiasis using the school as a random effect. RESULTS: The overall prevalence of tungiasis in the first survey was 1.35% [95% confidence interval (CI): 1.15-1.59%], and 0.89% in the second survey. The prevalence ranged from 0.08% (95% CI: 0.01-0.59%) in Taita Taveta county to 3.24% (95% CI: 2.35-4.44%) in Kajiado county. Tungiasis infection was associated with county of residence, male sex [adjusted odds ratio (aOR) = 2.01, 95% CI: 1.52-2.67], and lower age (aOR = 0.81, 95% CI: 0.75-0.88). For the first time we demonstrate an association with attending public schools rather than private schools (aOR = 5.62, 95% CI: 1.20-26.22) and lower socioeconomic status (aOR = 0.10, 95% CI: 0.03-0.33). Using a rapid screening method of the top of feet only, would have missed 62.9% of all cases, 78.9% of mild cases and 20.0% of severe cases. CONCLUSIONS: Tungiasis is widely but heterogeneously distributed across Kenya. School-based surveys offer an efficient strategy for mapping tungiasis distribution.

Impact of DREAMS interventions on experiences of violence among adolescent girls and young women: Findings from population-based cohort studies in Kenya and South Africa.

DREAMS aims to reduce HIV incidence among adolescent girls and young women (AGYW) by tackling drivers of HIV risk including gender-based violence. We evaluate the impact of DREAMS on recent experiences of violence perpetuated by men against AGYW. AGYW cohorts were randomly selected from demographic platforms in South Africa (rural KwaZulu-Natal) and Kenya (Nairobi informal settlements and rural Gem sub-county). AGYW aged 13-22 years were enrolled in 2017 (Nairobi, KwaZulu-Natal) or 2018 (Gem), with annual follow-up to 2019. We described proportions of AGYW who self-reported experiences of violence perpetrated by males in the 12 months preceding the interview, overall and by form (physical, sexual, emotional). We investigated associations with DREAMS (invitation to participate during 2017-2018) through multivariable propensity score-adjusted logistic regression and estimated the causal effect of DREAMS on experiences of violence, under counter-factual scenarios in which all versus no AGYW were DREAMS beneficiaries. Among 852, 1018 and 1712 AGYW followed-up in 2019 in Nairobi, Gem and KZN, respectively, proportions reporting any violence in 2019 were higher in Nairobi (29%) than Gem (18%) and KwaZulu-Natal (19%). By sub-type, emotional and physical violence were more frequently reported than sexual violence. We found no evidence of an impact attributable to DREAMS on overall levels of violence, in any setting. Nor was there evidence of impact on sub-types of violence, with one exception: an increase in physical violence in Nairobi if all, versus no, AGYW were DREAMS beneficiaries (16% vs 11%; +5% difference [95% CI: +0.2%, +10.0%]). Experiences of gender-based violence were common among AGYW, especially in urban settings, and DREAMS had no measurable impact on reducing violence within three years of implementation. Violence prevention programming that reaches more men and the broader community, sustained for longer periods, may yield greater gains in violence reduction than AGYW-focused programming. Additionally, more investment in implementation research is needed to bridge trial-based study findings from efficacy to population-level effectiveness.