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Suppressing infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will probably require the rapid identification and isolation of individuals infected with the virus on an ongoing basis. Reverse-transcription polymerase chain reaction (RT–PCR) tests are accurate but costly, which makes the regular testing of every individual expensive. These costs are a challenge for all countries around the world, but particularly for low-to-middle-income countries. Cost reductions can be achieved by pooling (or combining) subsamples and testing them in groups 1 – 7 . A balance must be struck between increasing the group size and retaining test sensitivity, as sample dilution increases the likelihood of false-negative test results for individuals with a low viral load in the sampled region at the time of the test 8 . Similarly, minimizing the number of tests to reduce costs must be balanced against minimizing the time that testing takes, to reduce the spread of the infection. Here we propose an algorithm for pooling subsamples based on the geometry of a hypercube that, at low prevalence, accurately identifies individuals infected with SARS-CoV-2 in a small number of tests and few rounds of testing. We discuss the optimal group size and explain why, given the highly infectious nature of the disease, largely parallel searches are preferred. We report proof-of-concept experiments in which a positive subsample was detected even when diluted 100-fold with negative subsamples (compared with 30–48-fold dilutions described in previous studies 9 – 11 ). We quantify the loss of sensitivity due to dilution and discuss how it may be mitigated by the frequent re-testing of groups, for example. With the use of these methods, the cost of mass testing could be reduced by a large factor. At low prevalence, the costs decrease in rough proportion to the prevalence. Field trials of our approach are under way in Rwanda and South Africa. The use of group testing on a massive scale to monitor infection rates closely and continually in a population, along with the rapid and effective isolation of people with SARS-CoV-2 infections, provides a promising pathway towards the long-term control of coronavirus disease 2019 (COVID-19). A mathematical algorithm for population-wide screening of SARS-CoV-2 infections using pooled parallel RT–PCR tests requires considerably fewer tests than individual testing procedures and has minimal delays in the identification of individuals infected with SARS-CoV-2.

The bacterium Treponema pallidum pertenue causes yaws in humans and nonhuman primates. We describe 33% T. pallidum pertenue seropositivity in 9 species of nonhuman primates in Uganda and Rwanda, seroconversion during a lethal outbreak and a novel bacterial genomic lineage. Yaws may threaten both public health and conservation in the region.

Unsafe drinking water and household air pollution (HAP) are major causes of morbidity and mortality among children under 5 in low and middle-income countries. Household water filters and higher-efficiency biomass-burning cookstoves have been widely promoted to improve water quality and reduce fuel use, but there is limited evidence of their health effects when delivered programmatically at scale. In a large-scale program in Western Province, Rwanda, water filters and portable biomass-burning natural draft rocket-style cookstoves were distributed between September and December 2014 and promoted to over 101,000 households in the poorest economic quartile in 72 (of 96) randomly selected sectors in Western Province. To assess the effects of the intervention, between August and December, 2014, we enrolled 1,582 households that included a child under 4 years from 174 randomly selected village-sized clusters, half from intervention sectors and half from nonintervention sectors. At baseline, 76% of households relied primarily on an improved source for drinking water (piped, borehole, protected spring/well, or rainwater) and over 99% cooked primarily on traditional biomass-burning stoves. We conducted follow-up at 3 time-points between February 2015 and March 2016 to assess reported diarrhea and acute respiratory infections (ARIs) among children <5 years in the preceding 7 days (primary outcomes) and patterns of intervention use, drinking water quality, and air quality. The intervention reduced the prevalence of reported child diarrhea by 29% (prevalence ratio [PR] 0.71, 95% confidence interval [CI] 0.59-0.87, p = 0.001) and reported child ARI by 25% (PR 0.75, 95% CI 0.60-0.93, p = 0.009). Overall, more than 62% of households were observed to have water in their filters at follow-up, while 65% reported using the intervention stove every day, and 55% reported using it primarily outdoors. Use of both the intervention filter and intervention stove decreased throughout follow-up, while reported traditional stove use increased. The intervention reduced the prevalence of households with detectable fecal contamination in drinking water samples by 38% (PR 0.62, 95% CI 0.57-0.68, p < 0.0001) but had no significant impact on 48-hour personal exposure to log-transformed fine particulate matter (PM2.5) concentrations among cooks (β = -0.089, p = 0.486) or children (β = -0.228, p = 0.127). The main limitations of this trial include the unblinded nature of the intervention, limited PM2.5 exposure measurement, and a reliance on reported intervention use and reported health outcomes. Our findings indicate that the intervention improved household drinking water quality and reduced caregiver-reported diarrhea among children <5 years. It also reduced caregiver-reported ARI despite no evidence of improved air quality. Further research is necessary to ascertain longer-term intervention use and benefits and to explore the potential synergistic effects between diarrhea and ARI. Clinical Trials.gov NCT02239250.

Household air pollution (HAP) from biomass combustion in traditional cooking methods poses significant health risks, particularly in rural communities of low- and middle-income countries. Improved cookstoves (ICS), designed to enhance combustion efficiency and reduce emissions, have been promoted as a transitional alternative towards cleaner cooking. However, evidence of their benefits remains mixed and context-specific. A randomized controlled trial was conducted to evaluate the impact of introducing the Save80 ICS on the respiratory health of adults in rural settlements in Rwanda. The study comprised two assessment rounds, and participants ( n  = 1001) were divided into two groups: one using traditional cooking methods and one using improved cookstoves. Baseline and follow-up data were collected through structured questionnaires and lung function tests. Furthermore, HAP was measured in a field campaign at households cooking with the ICS or traditional methods. The primary outcomes included respiratory symptoms, spirometry (FVC, FEV 1 , and PEF), and exposure to particulate matter (PM 0.3−2.5 ) and its components (EC, OC, BC, BrC, and PAH). We found that households using the ICS spent, on average, 34% less time cooking and had 77% lower indoor PM 0.3−2.5 levels. BC and BrC exposure decreased by 50% and 78%, respectively; OC and TC concentrations were 58% and 45% lower. PAH concentrations showed inconsistent patterns, with most species presenting non-statistically significant changes, constraining objective conclusions. Over the study period (3 years), ICS users reported lower prevalence of cough (-11%) and mucus production (-9%), and showed better forced vital capacity than users of traditional methods. A comparison of lung function decline over time showed that the ICS users had lower deterioration of FVC over three years. This study documents the effects and benefits of introducing ICS. While limitations such as the lack of baseline HAP data during the first health assessment and inconclusive PAH concentrations constrain interpretations and quantified causality, the results contribute to the evidence on the health and indoor air pollution impacts of ICS adoption in rural East African areas.

COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the B.1.1.7 and B.1.351 variants of concern among incoming travelers tested at Kigali International Airport. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences were available. Our results highlight the importance of systematic genomic surveillance and regional collaborations for a durable response towards combating COVID-19. Genomic surveillance of SARS-CoV-2 can inform regional transmission dynamics and inform public health interventions. Here, the authors sequence ~200 samples from Rwanda, identify shifts in predominating strains from May 2020 to February 2021, and infer geographic origins.

Rift Valley fever (RVF), a mosquito-borne transboundary zoonosis, was first confirmed in Rwanda’s livestock in 2012 and since then sporadic cases have been reported almost every year. In 2018, the country experienced its first large outbreak, which was followed by a second one in 2022. To determine the circulating virus lineages and their ancestral origin, two genome sequences from the 2018 outbreak, and thirty-six, forty-one, and thirty-eight sequences of small (S), medium (M), and large (L) genome segments, respectively, from the 2022 outbreak were generated. All of the samples from the 2022 outbreak were collected from slaughterhouses. Both maximum likelihood and Bayesian-based phylogenetic analyses were performed. The findings showed that RVF viruses belonging to a single lineage, C, were circulating during the two outbreaks, and shared a recent common ancestor with RVF viruses isolated in Uganda between 2016 and 2019, and were also linked to the 2006/2007 largest East Africa RVF outbreak reported in Kenya, Tanzania, and Somalia. Alongside the wild-type viruses, genetic evidence of the RVFV Clone 13 vaccine strain was found in slaughterhouse animals, demonstrating a possible occupational risk of exposure with unknown outcome for people working in meat-related industry. These results provide additional evidence of the ongoing wide spread of RVFV lineage C in Africa and emphasize the need for an effective national and international One Health-based collaborative approach in responding to RVF emergencies.

The relationship between food insecurity and transactional sex is well recognized, but less is known about this relationship among adolescents. We analyzed cross-sectional baseline data from 3,130 female secondary students aged 12–19 enrolled in a three-arm, cluster randomized controlled trial to examine the association between food insecurity and transactional sex. The explanatory variable was food security and the outcome was ever engaging in transactional sex. Over one quarter (28.7%) reported any food insecurity and 1.9% of all participants (9.6% of sexually active participants) reported ever engaging in transactional sex. In adjusted models, ever experiencing any food insecurity was associated with a higher prevalence of ever transactional sex (PR: 1.60; 95% CI: 1.02, 2.49) compared to little to no food insecurity. These results provide insight into potential predictors of higher-risk sexual behavior in Rwanda; they also provide policy-makers with populations with whom to intervene on upstream determinants of transactional sex, notably poverty and food insecurity.ResumenLa inseguridad alimentaria y el sexo transaccional están poco estudiados entre las adolescentes ruandesas. Analizamos datos de referencia transversales de 3,130 estudiantes secundarias de 12 a 19 años de edad inscritas en un ensayo controlado aleatorio por grupos de tres brazos para examinar la asociación entre la inseguridad alimentaria y el sexo transaccional. La variable independiente fue la seguridad alimentaria y la variable dependiente fue participation en sexo transaccional por lo menos una vez. Más de una cuarta parte (28,7%) informó alguna inseguridad alimentaria y el 1,9% de todos los participantes (9,6% de los participantes sexualmente activos) informaron haber tenido relaciones sexuales transaccionales alguna vez. En modelos ajustados, experimentar alguna inseguridad alimentaria alguna vez se asoció con una mayor relación sexual transaccional (PR: 1,60; IC del 95%: 1,02, 2,49) en comparación con poca o ninguna inseguridad alimentaria. Estos resultados brindan información sobre posibles predictores de comportamiento sexual de mayor riesgo en Ruanda; también brindan a los formuladores de políticas poblaciones para intervenir en los determinantes anteriores del sexo transaccional, en particular la pobreza y la inseguridad alimentaria.

Cardiovascular disease (CVD) is a global health issue. Low- and middle-income countries (LMICs) are facing early CVD-related morbidity. Early diagnosis and treatment are an effective strategy to tackle CVD. The aim of this study was to assess the ability of community health workers (CHWs) to screen and identify persons with high risks of CVD in the communities, using a body mass index (BMI)-based CVD risk assessment tool, and to refer them to the health facility for care and follow-up. This was an action research study conducted in rural and urban communities, conveniently sampled in Rwanda. Five villages were randomly selected from each community, and one CHW per each selected village was identified and trained to conduct CVD risk screening using a BMI-based CVD risk screening tool. Each CHW was assigned to screen 100 fellow community members (CMs) for CVD risk and to refer those with CVD risk scores ≥10 (either moderate or high CVD risk) to a health facility for care and further management. Descriptive statistics with Pearson’s chi-square test were used to assess any differences between rural and urban study participants vis-à-vis the key studied variables. Spearman’s rank coefficient and Cohen’s Kappa coefficient were mainly used to compare the CVD risk scoring from the CHWs with the CVD risk scoring from the nurses. Community members aged 35 to 74 years were included in the study. The participation rates were 99.6% and 99.4% in rural and urban communities, respectively, with female predominance (57.8% vs. 55.3% for rural and urban, p-value: 0.426). Of the participants screened, 7.4% had a high CVD risk (≥20%), with predominance in the rural community compared to the urban community (8.0% vs. 6.8%, p-value: 0.111). Furthermore, the prevalence of moderate or high CVD risk (≥10%) was higher in the rural community than in the urban community (26.7% vs. 21.1%, p-value: 0.111). There was a strong positive correlation between CHW-based CVD risk scoring and nurse-based CVD risk scoring in both rural and urban communities, 0.6215 (p-value < 0.001) vs. 0.7308 (p-value = 0.005). In regard to CVD risk characterization, the observed agreement to both the CHW-generated 10-year CVD risk assessment and the nurse-generated 10-year CVD risk assessment was characterized as “fair” in both rural and urban areas at 41.6% with the kappa statistic of 0.3275 (p-value < 001) and 43.2% with kappa statistic of 0.3229 (p-value =0.057), respectively. In Rwanda, CHWs can screen their fellow CMs for CVD risk and link those with high CVD risk to the healthcare facility for care and follow-up. CHWs could contribute to the prevention of CVDs through early diagnosis and early treatment at the bottom of the health system.

HIV-related stigma in healthcare settings remains a key barrier to engaging people living with HIV (PLHIV) in care. This study investigated the association between clinical encounter frequency and HIV-related anticipated, enacted, and internalized stigma among newly-diagnosed PLHIV in Rwanda. From October 2020 to May 2022, we collected data from adult PLHIV on antiretroviral therapy (ART) in Kigali, Rwanda who were participating in a randomized, controlled trial testing early entry into differentiated care at 6 months after ART initiation. We measured anticipated HIV stigma with five-point Likert HIV Stigma Framework measures, enacted stigma with the four-point Likert HIV/AIDS Stigma Instrument, and internalized stigma with the four-point Likert HIV/AIDS Stigma Instrument. We used multivariable linear regression to test the associations between clinical encounter frequency (average inter-visit interval ≥ 50 days vs. < 50 days) and change in mean anticipated, enacted and internalized HIV stigma over the first 12 months in care. Among 93 individuals enrolled, 76 had complete data on encounter frequency and stigma measurements and were included in the present analysis. Mean internalized stigma scores of all participants decreased over the first 12 months in care. Anticipated and enacted stigma scores were low and did not change significantly over time. There was no association between encounter frequency and change in internalized stigma. In this pilot study of newly-diagnosed Rwandan PLHIV with relatively low levels of HIV-related stigma, clinical encounter frequency was not associated with change in stigma. Additional research in diverse settings and with larger samples is necessary to further explore this relationship.

The East Africa Preterm Birth Initiative-Rwanda began a cluster randomized controlled trial of group antenatal care (ANC) and postnatal care (PNC) in Rwanda in 2017. That trial will report its primary outcome, gestational length at birth, after data collection concludes in 2019. This nested study includes providers of ANC and/or PNC at the 18 health centers randomized to provide the group model of ANC/PNC and the 18 health centers randomized to continue providing ANC/PNC in the traditional, individual visit model. The objective of this study is to understand the experiences of providers of group ANC/PNC and compare their job satisfaction and perceived stress with individual ANC/PNC providers. We collected both quantitative and qualitative data from providers (nurses and midwives) who were recruited by health center directors to participate as group ANC and PNC facilitators at intervention sites and from a similar number of providers of standard ANC and PNC at control sites. Quantitative data was collected with questionnaires administered at baseline and approximately 9 months later (follow up). Qualitative data was collected in 3 focus groups of group ANC/PNC providers conducted one year after group care began. Eighty-six percent of nurses and midwives surveyed who implemented group ANC and PNC reported that they prefer group care to the traditional individual model of ANC and PNC. Perceived stress levels and job satisfaction results were similar between groups. Mixed focus group discussions among both nurses and midwives experienced in group ANC and PNC suggest that the group model of care has advantages for both service beneficiaries and providers. When providers described implementation challenges, their peers in the focus groups offered them suggestions to cope and improve service delivery. These results are consistent with studies of providers of group ANC and PNC in other LMIC contexts with respect to the perceived benefits of group care. This study adds new insights into the ways peer providers can help one another solve implementation problems. When given the opportunity to meet as a group, these study participants offered one another peer support and shared knowledge about best practices for successful implementation of group ANC/PNC. This trial is registered at clinicaltrials.gov as NCT03154177.