Genomic surveillance of severe acute respiratory syndrome coronavirus 2 in Burundi, from May 2021 to January 2022.

BACKGROUND: The emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants have challenged the control of the COVID-19 pandemic globally. Burundi was not spared by that pandemic, but the genetic diversity, evolution, and epidemiology of those variants in the country remained poorly understood. The present study sought to investigate the role of different SARS-COV-2 variants in the successive COVID-19 waves experienced in Burundi and the impact of their evolution on the course of that pandemic. We conducted a cross-sectional descriptive study using positive SARS-COV-2 samples for genomic sequencing. Subsequently, we performed statistical and bioinformatics analyses of the genome sequences in light of available metadata. RESULTS: In total, we documented 27 PANGO lineages of which BA.1, B.1.617.2, AY.46, AY.122, and BA.1.1, all VOCs, accounted for 83.15% of all the genomes isolated in Burundi from May 2021 to January 2022. Delta (B.1.617.2) and its descendants predominated the peak observed in July-October 2021. It replaced the previously predominant B.1.351 lineage. It was itself subsequently replaced by Omicron (B.1.1.529, BA.1, and BA.1.1). Furthermore, we identified amino acid mutations including E484K, D614G, and L452R known to increase infectivity and immune escape in the spike proteins of Delta and Omicron variants isolated in Burundi. The SARS-COV-2 genomes from imported and community-detected cases were genetically closely related. CONCLUSION: The global emergence of SARS-COV-2 VOCs and their subsequent introductions in Burundi was accompanied by new peaks (waves) of COVID-19. The relaxation of travel restrictions and the mutations occurring in the virus genome played an important role in the introduction and the spread of new SARS-COV-2 variants in the country. It is of utmost importance to strengthen the genomic surveillance of SARS-COV-2, enhance the protection by increasing the SARS-COV-2 vaccine coverage, and adjust the public health and social measures ahead of the emergence or introduction of new SARS-COV-2 VOCs in the country.

Developing and validating a risk algorithm to diagnose Neisseria gonorrhoeae and Chlamydia trachomatis in symptomatic Rwandan women.

BACKGROUND: Algorithms that bridge the gap between syndromic sexually transmitted infection (STI) management and treatment based in realistic diagnostic options and local epidemiology are urgently needed across Africa. Our objective was to develop and validate a risk algorithm for Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) diagnosis among symptomatic Rwandan women and to compare risk algorithm performance to the current Rwandan National Criteria for NG/CT diagnosis. METHODS: The risk algorithm was derived in a cohort (n = 468) comprised of symptomatic women in Kigali who sought free screening and treatment for sexually transmitted infections and vaginal dysbioses at our research site. We used logistic regression to derive a risk algorithm for prediction of NG/CT infection. Ten-fold cross-validation internally validated the risk algorithm. We applied the risk algorithm to an external validation cohort also comprised of symptomatic Rwandan women (n = 305). Measures of calibration, discrimination, and screening performance of our risk algorithm compared to the current Rwandan National Criteria are presented. RESULTS: The prevalence of NG/CT in the derivation cohort was 34.6%. The risk algorithm included: age < =25, having no/primary education, not having full-time employment, using condoms only sometimes, not reporting genital itching, testing negative for vaginal candida, and testing positive for bacterial vaginosis. The model was well calibrated (Hosmer-Lemeshow p = 0.831). Higher risk scores were significantly associated with increased prevalence of NG/CT infection (p < 0.001). Using a cut-point score of > = 5, the risk algorithm had a sensitivity of 81%, specificity of 54%, positive predictive value (PPV) of 48%, and negative predictive value (NPV) of 85%. Internal and external validation showed similar predictive ability of the risk algorithm, which outperformed the Rwandan National Criteria. Applying the Rwandan National Criteria cutoff of > = 2 (the current cutoff) to our derivation cohort had a sensitivity of 26%, specificity of 89%, PPV of 55%, and NPV of 69%. CONCLUSIONS: These data support use of a locally relevant, evidence-based risk algorithm to significantly reduce the number of untreated NG/CT cases in symptomatic Rwandan women. The risk algorithm could be a cost-effective way to target treatment to those at highest NG/CT risk. The algorithm could also aid in sexually transmitted infection risk and prevention communication between providers and clients.

The effect of nitrogen-fertilizer and optimal plant population on the profitability of maize plots in the Wami River sub-basin, Tanzania: A bio-economic simulation approach.

Maize (Zea mays L.) is the essential staple in sub-Saharan Africa (SSA) and Tanzania in particular; the crop accounts for over 30% of the food production, 20% of the agricultural gross domestic product (GDP) and over 75% of the cereal consumption. Maize is grown under a higher risk of failure due to the over-dependence rain-fed farming system resulting in low income and food insecurity among maize-based farmers. However, many practices, including conservation agriculture, soil and water conservation, resilient crop varieties, and soil fertility management, are suggested to increase cereal productivity in Tanzania. Improving planting density, and the use of fertilizers are the immediate options recommended by Tanzania's government. In this paper, we evaluate the economic feasibility of the improved planting density (optimized plant population) and N-fertilizer crop management practices on maize net returns in semi-arid and sub-humid agro-ecological zones in the Wami River sub-Basin, Tanzania. We introduce a bio-economic simulation model using Monte Carlo simulation procedures to evaluate the economic viability of risky crop management practices so that the decision-maker can make better management decisions. The study utilizes maize yield data sets from two biophysical cropping system models, namely the APSIM and DSSAT. A total of 83 plots for the semi-arid and 85 plots for the sub-humid agro-ecological zones consisted of this analysis. The crop management practices under study comprise the application of 40 kg N-fertilizer/ha and plant population of 3.3 plants/m2 . The study finds that the use of improved plant population had the lowest annual net return with fertilizer application fetching the highest return. The two crop models demonstrated a zero probability of negative net returns for farms using fertilizer rates of 40 kg N/ha except for DSSAT, which observed a small probability (0.4%) in the sub-humid area. The optimized plant population presented 16.4% to 26.6% probability of negatives net returns for semi-arid and 14.6% to 30.2% probability of negative net returns for sub-humid zones. The results suggest that the application of fertilizer practices reduces the risks associated with the mean returns, but increasing the plant population has a high probability of economic failure, particularly in the sub-humid zone. Maize sub-sector in Tanzania is projected to continue experiencing a significant decrease in yields and net returns, but there is a high chance that it will be better-off if proper alternatives are employed. Similar studies are needed to explore the potential of interventions highlighted in the ACRP for better decision-making.

First-in-Human Evaluation of the Safety and Immunogenicity of an Intranasally Administered Replication-Competent Sendai Virus-Vectored HIV Type 1 Gag Vaccine: Induction of Potent T-Cell or Antibody Responses in Prime-Boost Regimens.

BACKGROUND: We report the first-in-human safety and immunogenicity assessment of a prototype intranasally administered, replication-competent Sendai virus (SeV)-vectored, human immunodeficiency virus type 1 (HIV-1) vaccine. METHODS: Sixty-five HIV-1-uninfected adults in Kenya, Rwanda, and the United Kingdom were assigned to receive 1 of 4 prime-boost regimens (administered at 0 and 4 months, respectively; ratio of vaccine to placebo recipients, 12:4): priming with a lower-dose SeV-Gag given intranasally, followed by boosting with an adenovirus 35-vectored vaccine encoding HIV-1 Gag, reverse transcriptase, integrase, and Nef (Ad35-GRIN) given intramuscularly (SLA); priming with a higher-dose SeV-Gag given intranasally, followed by boosting with Ad35-GRIN given intramuscularly (SHA); priming with Ad35-GRIN given intramuscularly, followed by boosting with a higher-dose SeV-Gag given intranasally (ASH); and priming and boosting with a higher-dose SeV-Gag given intranasally (SHSH). RESULTS: All vaccine regimens were well tolerated. Gag-specific IFN-γ enzyme-linked immunospot-determined response rates and geometric mean responses were higher (96% and 248 spot-forming units, respectively) in groups primed with SeV-Gag and boosted with Ad35-GRIN (SLA and SHA) than those after a single dose of Ad35-GRIN (56% and 54 spot-forming units, respectively) or SeV-Gag (55% and 59 spot-forming units, respectively); responses persisted for ≥8 months after completion of the prime-boost regimen. Functional CD8+ T-cell responses with greater breadth, magnitude, and frequency in a viral inhibition assay were also seen in the SLA and SHA groups after Ad35-GRIN boost, compared with those who received either vaccine alone. SeV-Gag did not boost T-cell counts in the ASH group. In contrast, the highest Gag-specific antibody titers were seen in the ASH group. Mucosal antibody responses were sporadic. CONCLUSIONS: SeV-Gag primed functional, durable HIV-specific T-cell responses and boosted antibody responses. The prime-boost sequence appears to determine which arm of the immune response is stimulated. CLINICAL TRIALS REGISTRATION: NCT01705990.

Evaluation of new farming technologies in Ethiopia using the Integrated Decision Support System (IDSS).

This study investigates multi-dimensional impacts of adopting new technology in agriculture at the farm/village and watershed scale in sub-Saharan Africa using the Integrated Decision Support System (IDSS). Application of IDSS as an integrated modeling tool helps solve complex issues in agricultural systems by simultaneously assessing production, environmental, economic, and nutritional consequences of adopting agricultural technologies for sustainable increases in food production and use of scarce natural resources. The IDSS approach was applied to the Amhara region of Ethiopia, where the scarcity of resources and agro-environmental consequences are critical to agricultural productivity of small farm, to analyze the impacts of alternative agricultural technology interventions. Results show significant improvements in family income and nutrition, achieved through the adoption of irrigation technologies, proper use of fertilizer, and improved seed varieties while preserving environmental indicators in terms of soil erosion and sediment loadings. These pilot studies demonstrate the usefulness of the IDSS approach as a tool that can be used to predict and evaluate the economic and environmental consequences of adopting new agricultural technologies that aim to improve the livelihoods of subsistence farmers.

Assessing the social vulnerability to malaria in Rwanda.

BACKGROUND: Since 2004, malaria interventions in Rwanda have resulted in substantial decline of malaria incidence. However, this achievement is fragile as potentials for local malaria transmissions remain. The risk of getting malaria infection is partially explained by social conditions of vulnerable populations. Since vulnerability to malaria is both influenced by social and environmental factors, its complexity cannot be measured by a single value. The aim of this paper is, therefore, to apply a composite indicator approach for assessing social vulnerability to malaria in Rwanda. This assessment informs the decision-makers in targeting malaria interventions and allocating limited resources to reduce malaria burden in Rwanda. METHODS: A literature review was used to conceptualize the social vulnerability to malaria and to select the appropriate vulnerability indicators. Indicators used in the index creation were classified into susceptibility and lack of resilience vulnerability domains. The main steps followed include selection of indicators and datasets, imputation of missing values, descriptive statistics, normalization and weighting of indicators, local sensitivity analysis and indicators aggregation. Correlation analysis helped to empirically evidence the association between the indicators and malaria incidence. RESULTS: The high values of social vulnerability to malaria are found in Gicumbi, Rusizi, Nyaruguru and Gisagara, and low values in Muhanga, Nyarugenge, Kicukiro and Nyanza. The most influential susceptibility indicators to increase malaria are population change (r = 0.729), average number of persons per bedroom (r = 0.531), number of households affected by droughts and famines (r = 0.591), and area used for irrigation (r = 0.611). The bed net ownership (r = -0.398) and poor housing wall materials (0.378) are the lack of resilience indicators that significantly correlate with malaria incidence. CONCLUSIONS: The developed composite index social vulnerability to malaria indicates which indicators need to be addressed and in which districts. The results from this study are salient for public health policy- and decision makers in malaria control in Rwanda and timely support the national integrated malaria initiative. Future research development should focus on spatial explicit vulnerability assessment by combining environmental and social drivers to achieve an integrated and complete assessment of vulnerability to malaria.

Impact of implementing performance-based financing on childhood malnutrition in Rwanda.

BACKGROUND: Malnutrition remains a serious concern in Rwanda, particularly among children under-5 years. Performance-based financing (PBF), an innovative health systems financing strategy, has been implemented at the national level since 2008. This study aimed to assess the impact of PBF and other factors associated with the prevalence of three classifications of malnutrition (stunting, wasting and underweight) in children under-5 years in Rwanda. METHODS: The study is a cross-sectional study comprising of 713 children under five years old from 557 households, whose anthropometric measurements (height, weight and age) had been obtained as part of the 2008 Rwanda General Health and HIV household survey. Z-scores for height-for-age, weight-for-age, weight-for-height, and body mass index-for-age were analyzed according to the World Health Organization 2006 Child Growth Standards. Random intercept logistic regression models were used to regress each anthropometric measure (WAZ, HAZ and WHZ) against child, maternal and household characteristics. RESULTS: Child participants ranged in age from 0 to 60 months, 20.2% of children were under 12 months and 5.1% were HIV positive. The prevalence of wasting was 8.8%; of stunting was 58.4%; and of underweight status was 20.7%. Maternal emotional and social wellbeing was protective of wasting in children under-5 years of age. Living in districts implementing PBF was protective of wasting (Adjusted Odds Ratio: 0.43; 95% confidence interval: 0.19-0.97). Living in a district with PBF was not found to be associated with either stunting or underweight status among children under-5. CONCLUSIONS: PBF may have a protective association with particular forms of malnutrition among children under-5 years in Rwanda. These findings warrant further investigation in relation to the impact of implementing innovative financing schemes on health outcomes.

Spatial Machine Learning for Exploring the Variability in Low Height-For-Age From Socioeconomic, Agroecological, and Climate Features in the Northern Province of Rwanda.

Childhood stunting is a serious public health concern in Rwanda. Although stunting causes have been documented, we still lack a more in-depth understanding of their local factors at a more detailed geographic level. We cross-sectionally examined 615 height-for-age prevalence observations in the Northern Province of Rwanda, linked with their related covariates, to explore the spatial heterogeneity in the low height-for-age prevalence by fitting linear and non-linear spatial regression models and explainable machine learning. Specifically, complemented with generalized additive models, we fitted the ordinary least squares (OLS), a standard geographically weighted regression (GWR), and multiscale geographically weighted regression (MGWR) models to characterize the imbalanced distribution of stunting risk factors and uncover the nonlinear effect of significant predictors, explaining the height-for-age variations. The results reveal that 27% of the children measured were stunted, and that likelihood was found to be higher in the districts of Musanze, Gakenke, and Gicumbi. The local MGWR model outperformed the ordinary GWR and OLS, with coefficients of determination of 0.89, 0.84, and 0.25, respectively. At specific ranges, the study shows that height-for-age decreases with an increase in the number of days a child was left alone, elevation, and rainfall. In contrast, land surface temperature is positively associated with height-for-age. However, variables like the normalized difference vegetation index, slope, soil fertility, and urbanicity exhibited bell-shaped and U-shaped non-linear associations with the height-for-age prevalence. Identifying areas with the highest rates of stunting will help determine the most effective measures for reducing the burden of undernutrition.

False-negative qualitative human chorionic gonadotropin (hCG) test result ('hook effect') with classical ultrasound findings of complete molar pregnancy: an uncommon case.

False-negative qualitative Human Chorionic Gonadotropin (hCG) result is a phenomenon in which large amounts of ß-hCG are produced by molar pregnancy, oversaturating the test's assay system and leading to false-negative results known as the 'prozone phenomenon' or the 'hook effect'. This can lead to misdiagnosis and delay in management despite high suspicious clinical and ultrasound findings. We report a case of an 18-year-old female who presented to our health facility with amenorrhea of 16 weeks, lower abdominal pain, soft and large fundal height for gestational age, and cramping with slight per-vaginal bleeding, and a negative urinary pregnancy test (UPT). Based on clinical presentation, ultrasound findings and a positive UPT after urine dilution, molar pregnancy was diagnosed. Aspiration was performed under ultrasound guidance, and follow-up was done as per MSF guidelines. HCPs need to be familiar with some rare cases for which the possibility of finding false-negative UPT is likely.

Understanding the spatial non-stationarity in the relationships between malaria incidence and environmental risk factors using Geographically Weighted Random Forest: A case study in Rwanda.

As found in the health studies literature, the levels of climate association between epidemiological diseases have been found to vary across regions. Therefore, it seems reasonable to allow for the possibility that relationships might vary spatially within regions. We implemented the geographically weighted random forest (GWRF) machine learning method to analyze ecological disease patterns caused by spatially non-stationary processes using a malaria incidence dataset for Rwanda. We first compared the geographically weighted regression (WGR), the global random forest (GRF), and the geographically weighted random forest (GWRF) to examine the spatial non-stationarity in the non-linear relationships between malaria incidence and their risk factors. We used the Gaussian areal kriging model to disaggregate the malaria incidence at the local administrative cell level to understand the relationships at a fine scale since the model goodness of fit was not satisfactory to explain malaria incidence due to the limited number of sample values. Our results show that in terms of the coefficients of determination and prediction accuracy, the geographical random forest model performs better than the GWR and the global random forest model. The coefficients of determination of the geographically weighted regression (R2), the global RF (R2), and the GWRF (R2) were 4.74, 0.76, and 0.79, respectively. The GWRF algorithm achieves the best result and reveals that risk factors (rainfall, land surface temperature, elevation, and air temperature) have a strong non-linear relationship with the spatial distribution of malaria incidence rates, which could have implications for supporting local initiatives for malaria elimination in Rwanda.

Going beyond consensus genome sequences: An innovative SNP-based methodology reconstructs different Ugandan cassava brown streak virus haplotypes at a nationwide scale in Rwanda.

Cassava Brown Streak Disease (CBSD), which is caused by cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), represents one of the most devastating threats to cassava production in Africa, including in Rwanda where a dramatic epidemic in 2014 dropped cassava yield from 3.3 million to 900,000 tonnes (1). Studying viral genetic diversity at the genome level is essential in disease management, as it can provide valuable information on the origin and dynamics of epidemic events. To fill the current lack of genome-based diversity studies of UCBSV, we performed a nationwide survey of cassava ipomovirus genomic sequences in Rwanda by high-throughput sequencing (HTS) of pools of plants sampled from 130 cassava fields in thirteen cassava-producing districts, spanning seven agro-ecological zones with contrasting climatic conditions and different cassava cultivars. HTS allowed the assembly of a nearly complete consensus genome of UCBSV in twelve districts. The phylogenetic analysis revealed high homology between UCBSV genome sequences, with a maximum of 0.8 per cent divergence between genomes at the nucleotide level. An in-depth investigation based on Single Nucleotide Polymorphisms (SNPs) was conducted to explore the genome diversity beyond the consensus sequences. First, to ensure the validity of the result, a panel of SNPs was confirmed by independent reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing. Furthermore, the combination of fixation index (FST) calculation and Principal Component Analysis (PCA) based on SNP patterns identified three different UCBSV haplotypes geographically clustered. The haplotype 2 (H2) was restricted to the central regions, where the NAROCAS 1 cultivar is predominantly farmed. RT-PCR and Sanger sequencing of individual NAROCAS1 plants confirmed their association with H2. Haplotype 1 was widely spread, with a 100 per cent occurrence in the Eastern region, while Haplotype 3 was only found in the Western region. These haplotypes' associations with specific cultivars or regions would need further confirmation. Our results prove that a much more complex picture of genetic diversity can be deciphered beyond the consensus sequences, with practical implications on virus epidemiology, evolution, and disease management. Our methodology proposes a high-resolution analysis of genome diversity beyond the consensus between and within samples. It can be used at various scales, from individual plants to pooled samples of virus-infected plants. Our findings also showed how subtle genetic differences could be informative on the potential impact of agricultural practices, as the presence and frequency of a virus haplotype could be correlated with the dissemination and adoption of improved cultivars.

Clinical and Epidemiology Characteristics of COVID-19 Cases Detected During Mass Screening Campaign from July to October 2020 in Bujumbura, Burundi.

Background: Coronavirus disease of 2019 (COVID-19) is an infectious disease caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2 Virus). It was reported for the first time in Wuhan city, Hubei province of China. The first cases of COVID-19 in Burundi were identified on 31st March 2020. Several signs and symptoms, including mainly; fever, dry cough, fatigue, myalgia, and dyspnea are the most prominent characteristics of the disease. The aim of this study was to provide description of the clinical and epidemiological characteristics of COVID-19 cases identified during the mass screening campaign conducted between July and October, 2020 in Burundi. Methods: We conducted a retrospective secondary analysis of data of clients to the mass screening campaign in Bujumbura city that was run between July and October 2020. Clients with complete data and tested for COVID-19 with Reverse Transcription Polymerase Chain Reaction (RT-PCR) were included in the study. Epi-Info 7.2.2.6 was used to perform descriptive and analytical statistics and Quantum Geographic Information System (QGIS) was used for cases mapping. Association between positive cases and independent variables such as sex, history of contact with confirmed COVID-19 case was measured using chi-square statistical test at a p-value of .05. Results: The study included 20,114 participants. 243 (1.2%) were tested positive for COVID-19. The mean age for confirmed cases was 33 (±15) years. The majority of cases (72.8%) were between 20 and 59 years of age and they were predominantly males (67.9%). 164 (67.5%) were symptomatic and cough was the most frequent symptom observed 109 (66.5%), followed by rhinorrhea 69 (42.1%). Fever was present in only 18 (11.0%) of symptomatic patients. Participants with a history of contact with a COVID-19 confirmed case (aOR=2.2; 95%CI [1.6-3.0]; p-value <.001), were more likely to be positive for COVID-19. Also, those who were coughing (aOR=1.47; 95%CI [1.06-2.05]; p-value=.023) and having sore throat (aOR=2.4; 95%CI [1.1-4.9]; p-value=.02) were more likely to test positive for COVID-19. Conclusion: This study revealed that a significant proportion (32.5%) of COVID-19 patients were silent carriers of the virus. Data highlighted that high proportion of cases were among the active age group and contacts with confirmed cases, and noted high proportion of asymptomatic cases at diagnosis. Measures including routine testing of asymptomatic contacts could contribute to tackling corona virus in Burundi.

Risk factors associated with cassava brown streak disease dissemination through seed pathways in Eastern D.R. Congo.

Vegetatively propagated crops are particularly prone to disease dissemination through their seed systems. Strict phytosanitary measures are important to limit the impact of diseases as illustrated by the potato seed system in Europe. Cassava brown streak disease (CBSD) is a devastating disease caused by two viral species collectively named cassava brown streak viruses (CBSVs). CBSD can cause substantial root yield losses of up to 100% in the worst affected areas and is easily transmitted through stem cuttings. In Eastern and Central Africa, the epidemiology of CBSVs in the local socio-economical context of production remains poorly known while a better understanding would be an asset to properly manage the disease. This lack of information explains partially the limited efficiency of current regulatory schemes in increasing the availability of quality seed to smallholders and mitigating the spread of pests and diseases. This study surveyed the epidemiology of CBSVs in Uvira territory, Eastern D.R. Congo, and its drivers using a multivariate approach combining farmer's interview, field observation, sampling and molecular detection of CBSVs. Investigation on the epidemiology of CBSD revealed that three clusters in the study area could be identified using five most significant factors: (i) symptoms incidence, (ii) number of whiteflies, (iii) types of foliar symptoms, (iv) cutting's pathways and (v) plant age. Among the three clusters identified, one proved to be potentially interesting for seed multiplication activities since the disease pressure was the lowest. Through risk assessment, we also identified several key socio-economic determinants on disease epidemy: (i) factors related to farmer's knowledge and awareness (knowledge of cassava pests and diseases, knowledge of management practices, support from extension services and management strategies applied), (ii) factors related to the geographical location of farmer's fields (proximity to borders, proximity to town, distance to acquire cuttings), as well as (iii) the pathways used to acquire cuttings.

Etiologies of genital inflammation and ulceration in symptomatic Rwandan men and women responding to radio promotions of free screening and treatment services.

INTRODUCTION: The longstanding inadequacies of syndromic management for genital ulceration and inflammation are well-described. The Rwanda National Guidelines for sexually transmitted infection (STI) syndromic management are not yet informed by the local prevalence and correlates of STI etiologies, a component World Health Organization guidelines stress as critical to optimize locally relevant algorithms. METHODS: Radio announcements and pharmacists recruited symptomatic patients to seek free STI services in Kigali. Clients who sought services were asked to refer sexual partners and symptomatic friends. Demographic, behavioral risk factor, medical history, and symptom data were collected. Genital exams were performed by trained research nurses and physicians. We conducted phlebotomy for rapid HIV and rapid plasma reagin (RPR) serologies and vaginal pool swab for microscopy of wet preparation to diagnose Trichomonas vaginalis (TV), bacterial vaginosis (BV), and vaginal Candida albicans (VCA). GeneXpert testing for Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) were conducted. Here we assess factors associated with diagnosis of NG and CT in men and women. We also explore factors associated with TV, BV and VCA in women. Finally, we describe genital ulcer and RPR results by HIV status, gender, and circumcision in men. RESULTS: Among 974 men (with 1013 visits), 20% were positive for CT and 74% were positive for NG. Among 569 women (with 579 visits), 17% were positive for CT and 27% were positive for NG. In multivariate analyses, factors associated with CT in men included younger age, responding to radio advertisements, <17 days since suspected exposure, and not having dysuria. Factors associated with NG in men included not having higher education or full-time employment, <17 days since suspected exposure, not reporting a genital ulcer, and having urethral discharge on physical exam. Factors associated with CT in women included younger age and < = 10 days with symptoms. Factors associated with NG in women included younger age, lower education and lack of full-time employment, sometimes using condoms vs. never, using hormonal vs. non-hormonal contraception, not having genital ulcer or itching, having symptoms < = 10 days, HIV+ status, having BV, endocervical discharge noted on speculum exam, and negative vaginal wet mount for VCA. In multivariate analyses, only reporting >1 partner was associated with BV; being single and RPR+ was associated with TV; and having < = 1 partner in the last month, being pregnant, genital itching, discharge, and being HIV and RPR negative were associated with VCA. Genital ulcers and positive RPR were associated with being HIV+ and lack of circumcision among men. HIV+ women were more likely to be RPR+. In HIV+ men and women, ulcers were more likely to be herpetic rather than syphilitic compared with their HIV- counterparts. CONCLUSIONS: Syndromic management guidelines in Rwanda can be improved with consideration of the prevalence of confirmed infections from this study of symptomatic men and women representative of those who would seek care at government health centers. Inclusion of demographic and risk factor measures shown to be predictive of STI and non-STI dysbioses may also increase diagnostic accuracy.

Increased Frequency of Inter-Subtype HIV-1 Recombinants Identified by Near Full-Length Virus Sequencing in Rwandan Acute Transmission Cohorts.

Most studies of HIV-1 transmission have focused on subtypes B and C. In this study, we determined the genomic sequences of the transmitted founder (TF) viruses from acutely infected individuals enrolled between 2005 and 2011 into IAVI protocol C in Rwanda and have compared these isolates to viruses from more recent (2016-2019) acute/early infections in three at risk populations - MSM, high risk women (HRW), and discordant couples (DC). For the Protocol C samples, we utilized near full-length single genome (NFLG) amplification to generate 288 HIV-1 amplicons from 26 acutely infected seroconverters (SC), while for the 21 recent seroconverter samples (13 from HRW, two from DC, and six from MSM), we PCR amplified overlapping half-genomes. Using PacBio SMRT technology combined with the MDPseq workflow, we performed multiplex sequencing to obtain high accuracy sequences for each amplicon. Phylogenetic analyses indicated that the majority of recent transmitted viruses from DC and HRW clustered within those of the earlier Protocol C cohort. However, five of six sequences from the MSM cohort branched together and were greater than 97% identical. Recombination analyses revealed a high frequency (6/26; 23%) of unique inter-subtype recombination in Protocol C with 19% AC and 4% CD recombinant viruses, which contrasted with only 6.5% of recombinants defined by sequencing of the pol gene previously. The frequency of recombinants was significantly higher (12/21; 57%) in the more recent isolates, although, the five related viruses from the MSM cohort had identical recombination break points. While major drug resistance mutations were absent from Protocol C viruses, 4/21 of recent isolates exhibited transmitted nevirapine resistance. These results demonstrate the ongoing evolution and increased prevalence of recombinant and drug resistant transmitted viruses in Rwanda and highlight the importance of defining NFLG sequences to fully understand the nature of TF viruses and in particular the prevalence of unique recombinant forms (URFs) in transmission cohorts.

Performance of International AIDS Vaccine Initiative African clinical research laboratories in standardised ELISpot and peripheral blood mononuclear cell processing in support of HIV vaccine clinical trials.

BACKGROUND: Standardisation of procedures for performing cellular functional assays across laboratories participating in multicentre clinical trials is key for generating comparable and reliable data. OBJECTIVE: This article describes the performance of accredited laboratories in Africa and Europe on testing done in support of clinical trials. METHODS: For enzyme-linked immunospot assay (ELISpot) proficiency, characterised peripheral blood mononuclear cells (PBMCs) obtained from 48 HIV-negative blood donors in Johannesburg, South Africa, were sent to participating laboratories between February 2010 and February 2014. The PBMCs were tested for responses against cytomegalovirus, Epstein Barr and influenza peptide pools in a total of 1751 assays. In a separate study, a total of 1297 PBMC samples isolated from healthy HIV-negative participants in clinical trials of two prophylactic HIV vaccine candidates in Kenya, Uganda, Rwanda and Zambia were analysed for cell viability, cell yield and cell recovery from frozen PBMCs. RESULTS: Most (99%) of the 1751 ELISpot proficiency assays had data within acceptable ranges with low responses to mock stimuli. No significant statistical difference were observed in ELISpot responses at the five laboratories actively conducting immunological analyses. Of the 1297 clinical trial PBMCs processed, 94% had cell viability above 90% and 96% had cell yield above 0.7 million per mL of blood in freshly isolated cells. All parameters were within the predefined acceptance criteria. CONCLUSION: We demonstrate that multiple laboratories can generate reliable, accurate and comparable data by using standardised procedures, having regular training, having regular equipment maintenance and using centrally sourced reagents.

Female sex workers in Kigali, Rwanda: a key population at risk of HIV, sexually transmitted infections, and unplanned pregnancy.

Female sex workers (FSWs) were recruited from known hotspots in Kigali, Rwanda, and offered free, anonymous human immunodeficiency virus (HIV) counseling and testing, diagnosis and treatment of sexually transmitted infections (STIs) and long-acting reversible contraception (LARC). From September 2012 to March 2015, 1168 FSWs sought services, including 587 (50%) who were HIV-positive. More than 90% had previously tested for HIV, and 26% who reported previously testing negative had seroconverted. Of the 349 who already knew their HIV-positive status, 74% were on antiretroviral treatment. The prevalence of serologic syphilis was 43% in HIV-positive and 19% in HIV-negative FSWs (p < 0.0001), and Trichomonas vaginalis was found in vaginal wet mounts in 21% of HIV-positive and 13% of HIV-negative FSWs (p < 0.0001). Signs and symptoms of STIs were found in 35% of HIV-positive compared with 21% of HIV-negative FSWs (p < 0.0001). Only one-third reported consistent condom use in the last month. Modern contraceptive use was reported by 43% of HIV-positive and 56% of HIV-negative FSWs (p < 0.0001). Current pregnancy was reported by 4% of HIV-positive and 6% of HIV-negative FSWs (p = 0.0409). Despite Rwanda's successes with preventing 70% of new infections in the general population through nationwide couples' testing in antenatal clinics, prevention and timely treatment in key populations including FSWs are lacking. The prevalence of HIV - including many new cases - and STIs among FSWs in Kigali is high and condom and contraceptive use are low. Tailored and integrated HIV/STIs and family planning programs are urgently needed for FSWs.

Sustainable manufacture of insect repellents derived from Nepeta cataria.

Malaria devastates sub-Saharan Africa; the World Health Organization (WHO) estimates that 212 million people contract malaria annually and that the plasmodium virus will kill 419 000 in 2017. The disease affects rural populations who have the least economic means to fight it. Impregnated mosquito nets have reduced the mortality rate but the Anopheles mosquitoes are changing their feeding patterns and have become more active at dusk and early morning rather than after 22h00 as an adaptation to the nets. Everyone is susceptible to the Anopheles at these times but infants and pregnant women are the most vulnerable to the disease. Plant-based mosquito repellents are as effective as synthetic repellents that protect people from bites. They are sustainable preventative measures against malaria not only because of their efficacy but because the local population can produce and distribute them, which represents a source of economic growth for rural areas. Here, we extract and test the essential oil nepetalactone from Nepeta cataria via steam distillation. Families in endemic areas of Burundi found them effective against bites but commented that the odor was pungent. An epidemiological study is required to establish its clinical efficacy.

Modelling homogeneous regions of social vulnerability to malaria in Rwanda.

Despite the decline in malaria incidence due to intense interventions, potentials for malaria transmission persist in Rwanda. To eradicate malaria in Rwanda, strategies need to expand beyond approaches that focus solely on malaria epidemiology and also consider the socioeconomic, demographic and biological/disease-related factors that determine the vulnerability of potentially exposed populations. This paper analyses current levels of social vulnerability to malaria in Rwanda by integrating a set of weighted vulnerability indicators. The paper uses regionalisation techniques as a spatially explicit approach for delineating homogeneous regions of social vulnerability to malaria. This overcomes the limitations of administrative boundaries for modelling the trans-boundary social vulnerability to malaria. The utilised approach revealed high levels of social vulnerability to malaria in the highland areas of Rwanda, as well as in remote areas where populations are more susceptible. Susceptibility may be due to the populations' lacking the capacity to anticipate mosquito bites, or lacking resilience to cope with or recover from malaria infection. By highlighting the most influential indicators of social vulnerability to malaria, the applied approach indicates which vulnerability domains need to be addressed, and where appropriate interventions are most required. Interventions to improve the socioeconomic development in highly vulnerable areas could prove highly effective, and provide sustainable outcomes against malaria in Rwanda. This would ultimately increase the resilience of the population and their capacity to better anticipate, cope with, and recover from possible infection.