High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation.

Africa contains more human genetic variation than any other continent, but the majority of the population-scale analyses of the African peoples have focused on just two of the four major linguistic groups, the Niger-Congo and Afro-Asiatic, leaving the Nilo-Saharan and Khoisan populations under-represented. In order to assess genetic variation and signatures of selection within a Nilo-Saharan population and between the Nilo-Saharan and Niger-Congo and Afro-Asiatic, we sequenced 50 genomes from the Nilo-Saharan Lugbara population of North-West Uganda and 250 genomes from 6 previously unsequenced Niger-Congo populations. We compared these data to data from a further 16 Eurasian and African populations including the Gumuz, another putative Nilo-Saharan population from Ethiopia. Of the 21 million variants identified in the Nilo-Saharan population, 3.57 million (17%) were not represented in dbSNP and included predicted non-synonymous mutations with possible phenotypic effects. We found greater genetic differentiation between the Nilo-Saharan Lugbara and Gumuz populations than between any two Afro-Asiatic or Niger-Congo populations. F3 tests showed that Gumuz contributed a genetic component to most Niger-Congo B populations whereas Lugabara did not. We scanned the genomes of the Lugbara for evidence of selective sweeps. We found selective sweeps at four loci (SLC24A5, SNX13, TYRP1, and UVRAG) associated with skin pigmentation, three of which already have been reported to be under selection. These selective sweeps point toward adaptations to the intense UV radiation of the Sahel.

Target product profile: Trypanosoma brucei gambiense test to verify elimination.

Human African trypanosomiasis is a life-threatening parasitic infection transmitted by the tsetse fly in sub-Saharan Africa. The most common form is caused by Trypanosoma brucei gambiense, with humans as the main reservoir. Diagnosis in the field requires microscopic examination performed by specifically trained personnel. After over two decades of sustained efforts, the incidence of the disease is strongly declining, and some historically endemic countries are no longer detecting cases. The World Health Organization (WHO) has targeted the elimination of transmission of gambiense human African trypanosomiasis by 2030, defined as zero autochthonous cases for at least five consecutive years. Endemic countries reaching this goal must maintain dedicated surveillance to detect re-emergence or re-introduction. With this new agenda, new tools are needed for verification of the absence of transmission. WHO has therefore developed a target product profile calling for development of a method for population-level cross-cutting surveillance of T. b. gambiense transmission. The method needs to be performed in national or sub-national reference laboratories, and to test in parallel numerous samples shipped from remote rural areas. Among other characteristics the product profile specifies: (i) a simple specimen collection procedure; (ii) no cold-chain requirement to transfer specimens to reference laboratories; (iii) high sensitivity and specificity; (iv) high-throughput, substantially automatized; (v) low cost per specimen, when analysed in large batches; and (vi) applicable also in animals.

La trypanosomiase humaine africaine est une infection parasitaire potentiellement mortelle transmise par la mouche tsé-tsé en Afrique subsaharienne. La forme la plus répandue est causée par Trypanosoma brucei gambiense, les humains constituant son principal réservoir. Établir un diagnostic sur le terrain nécessite un examen microscopique réalisé par du personnel formé à cet effet. Après plus de deux décennies d'efforts soutenus, l'incidence de la maladie diminue fortement et quelques pays historiquement endémiques ne découvrent plus aucun cas. L'objectif de l'Organisation mondiale de la Santé (OMS) est d'éliminer la transmission de la trypanosomiase humaine africaine à T. b. gambiense d'ici 2030, ce qui correspond à zéro cas autochtone pendant au moins cinq années consécutives. Les pays endémiques qui atteignent cet objectif doivent maintenir une surveillance spécifique afin de détecter toute réémergence ou réintroduction. Ce nouveau programme doit s'accompagner de nouveaux outils servant à vérifier l'absence de transmission. L'OMS a donc élaboré un profil de produit cible pour le développement d'un procédé de surveillance transversale de la transmission de T. b. gambiense à l'échelle de la population. Ce procédé doit être effectué dans des laboratoires de référence nationaux ou infranationaux et tester simultanément de nombreux échantillons envoyés depuis des régions rurales isolées. Ce profil de produit comporte notamment les caractéristiques suivantes: (i) une procédure simple de collecte d'échantillons; (ii) aucune exigence concernant le respect de la chaîne du froid lors du transfert des échantillons vers les laboratoires de référence; (iii) un niveau élevé de sensibilité et de spécificité; (iv) un haut débit, en grande partie automatisé; (v) de faibles coûts par échantillon lors d'analyses en masse; et enfin, (vi) applicable aux animaux également.

La tripanosomiasis humana africana es una infección parasitaria potencialmente mortal transmitida por la mosca tsetsé en el África Subsahariana. El principal reservorio es el ser humano, y la forma más común está causada por Trypanosoma brucei gambiense. El diagnóstico práctico requiere un examen microscópico a cargo de personal con formación específica. Tras más de dos décadas de esfuerzos sostenidos, la incidencia de la enfermedad está disminuyendo considerablemente, y en algunos países históricamente endémicos ya no se detectan casos. La Organización Mundial de la Salud (OMS) se ha fijado como objetivo la eliminación de la transmisión de la tripanosomiasis africana humana gambiense para 2030, es decir, cero casos autóctonos durante al menos cinco años consecutivos. Los países endémicos que alcancen este objetivo deben mantener una vigilancia permanente para detectar la reaparición o reintroducción de la enfermedad. Con esta agenda nueva, se necesitan herramientas nuevas para verificar la ausencia de transmisión. Por consiguiente, la OMS ha elaborado un perfil de producto objetivo en el que se pide el desarrollo de un método para la vigilancia transversal a nivel de población sobre la transmisión de T. b. gambiense. El método debe realizarse en laboratorios de referencia nacionales o subnacionales y analizar en paralelo numerosas muestras enviadas desde regiones rurales remotas. Entre otras características, el perfil del producto detalla: (i) un procedimiento sencillo de recogida de muestras; (ii) ningún requisito de cadena de frío para transferir las muestras a los laboratorios de referencia; (iii) alta sensibilidad y especificidad; (iv) alto rendimiento, sustancialmente automatizado; (v) bajo coste por muestra, cuando se analizan en grandes lotes; y (vi) aplicable también en animales.

Target product profile: diagnostic test for Trypanosoma brucei rhodesiense.

Rhodesiense human African trypanosomiasis is a lethal parasitic infection caused by Trypanosoma brucei rhodesiense and transmitted by tsetse flies in eastern and southern Africa. It accounts for around 5% of all cases of human African trypanosomiasis. Currently, there is no simple serological test for rhodesiense human African trypanosomiasis and diagnosis relies on microscopic confirmation of trypanosomes in samples of blood or other tissues. The availability of a simple and accurate diagnostic test would aid the control, surveillance and treatment of the disease. A subcommittee of the World Health Organization's Neglected Tropical Diseases Diagnostics Technical Advisory Group has developed a target product profile for a diagnostic tool to identify T. b. rhodesiense infection. The optimum tool would have a sensitivity and specificity above 99% for detecting T. b. rhodesiense, but be simple enough for use by minimally trained health-care workers in unsophisticated peripheral health facilities or mobile teams in villages. The test should yield a qualitative result that can be easily observed and can be used to determine treatment. An antigen test would be preferable, with blood collected by finger-prick. Ideally, there should be no need for a cold chain, instrumentation or precision liquid handling. The test should be usable between 10 °C and 40 °C and between 10% and 88% relative humidity. Basic training should take under 2 hours and the test should involve fewer than five steps. The unit cost should be less than 1 United States dollar.

La trypanosomiase humaine africaine à T. b. rhodesiense est une infection parasitaire mortelle causée par Trypanosoma brucei rhodesiense et transmise par les mouches tsé-tsé en Afrique orientale et australe. Elle représente environ 5% de l'ensemble des cas de trypanosomiase humaine africaine. À l'heure actuelle, il n'existe aucun test sérologique simple pour l'infection à T. b. rhodesiense et le diagnostic repose sur la confirmation microscopique de la présence de trypanosomes dans des échantillons de sang ou d'autres tissus. Fournir un test de diagnostic simple et précis favoriserait la lutte, la surveillance et la prise en charge de la maladie. Un sous-comité du Groupe consultatif technique sur les produits de diagnostic des maladies tropicales négligées de l'Organisation mondiale de la Santé a donc élaboré un profil de produit cible pour un outil visant à détecter une infection par T. b. rhodesiense. L'outil le plus adapté présenterait un niveau de sensibilité et de spécificité supérieur à 99% pour la détection de T. b. rhodesiense, tout en étant à la portée de professionnels de la santé ayant reçu une formation sommaire, tant dans des structures de santé périphériques basiques qu'au sein d'équipes mobiles dans les villages. Cet outil doit fournir un résultat fiable, facile à interpréter, qui peut servir à établir un traitement. Un test antigénique serait préférable, avec prélèvement de l'échantillon sanguin par le biais d'une piqûre au bout du doigt. Idéalement, l'outil ne doit pas être thermosensible, ni nécessiter un équipement spécifique ou une manipulation de liquides délicate. Le test doit pouvoir être utilisé à une température comprise entre 10 °C et 40 °C, ainsi que dans une humidité relative de 10% à 88%. La formation requise pour son utilisation doit durer moins de deux heures et le test doit être effectué en moins de cinq étapes, Enfin, son coût unitaire doit être inférieur à un dollar américain.

La tripanosomiasis humana africana rhodesiense es una infección letal parasitaria causada por el Trypanosoma brucei rhodesiense, y es transmitida por la mosca tse-tsé en África oriental y meridional. Representa aproximadamente el 5% de todos los casos de tripanosomiasis humana africana. Actualmente, no existe ninguna prueba serológica simple para la tripanosomiasis humana africana rhodesiense, y el diagnóstico se basa en la confirmación microscópica de tripanosomas existentes en muestras de sangre u otros tejidos. Una prueba diagnóstica sencilla y precisa ayudaría a controlar, vigilar y tratar la enfermedad. Un subcomité del Grupo Asesor Técnico de Diagnóstico de Enfermedades Tropicales Desatendidas de la Organización Mundial de la Salud ha creado un perfil de producto objetivo para una herramienta de diagnóstico que permita identificar la infección T. b. rhodesiense. La herramienta óptima tendría una sensibilidad y una especificidad superiores al 99% para detectar la T. b. rhodesiense y, al ser lo suficientemente sencilla, podrían utilizarla trabajadores sanitarios mínimamente formados, en centros sanitarios periféricos no sofisticados, o bien equipos móviles. La prueba debe arrojar un resultado cualitativo de fácil lectura y que pueda utilizarse para determinar el tratamiento. Sería preferible una prueba de antígenos, con sangre extraída mediante punción digital. Idealmente, no debería ser necesaria la cadena de frío, la instrumentación ni la manipulación de líquidos de precisión. La prueba debe poder utilizarse entre 10 °C y 40 °C, con una humedad relativa de entre el 10% y el 88%. La instrucción básica debe llevar menos de 2 horas y la prueba debe incluir menos de cinco pasos. El coste de la unidad debe ser inferior a 1 dólar estadounidense.

Target product profile: Trypanosoma brucei gambiense test for low-prevalence settings.

Having caused devastating epidemics during the 20th century, the incidence of life-threatening human African trypanosomiasis has fallen to historically low levels as a result of sustained and coordinated efforts over the past 20 years. Humans are the main reservoir of one of the two pathogenic trypanosome subspecies, Trypanosoma brucei gambiense, found in western and central Africa. The expected advent of a safe and easy-to-use treatment to be given to seropositive but microscopically unconfirmed individuals would lead to further depletion; in the meantime, the presence of T. b. gambiense infection in the community must be monitored to allow the control strategy to be adapted and the elimination status to be assessed. The World Health Organization has therefore developed a target product profile that describes the optimal and minimal characteristics of an individual laboratory-based test to assess T. b. gambiense infection in low-prevalence settings. Development of the target product profile involved the formation of a Neglected Tropical Diseases Diagnostics Technical Advisory Group and a subgroup on human African trypanosomiasis diagnostic innovation needs, and an analysis of the available products and development pipeline. According to the product profile, the test should ideally: (i) require a minimally invasive or non-invasive specimen, collectable at peripheral facilities by minimally trained health workers; (ii) demonstrate good sensitivity and high specificity; (iii) have a stability of samples allowing transfer to reference laboratories preferably without cold chain; (iv) be stable over a wide range of environmental conditions for more than 2 years; and (v) after marketing, be available at low cost for at least 7 years.

Après avoir causé des épidémies dévastatrices au cours du 20e siècle, la trypanosomiase humaine africaine, potentiellement mortelle, a vu son incidence chuter à un niveau historiquement bas grâce aux efforts conjoints et soutenus déployés ces deux dernières décennies. Les humains constituent le principal réservoir de l'une des deux sous-espèces pathogéniques de trypanosome, Trypanosoma brucei gambiense, que l'on retrouve en Afrique occidentale et centrale. L'arrivée d'un traitement sûr et simple d'utilisation, qui serait administré aux individus séropositifs mais sans confirmation microscopique, devrait entraîner une nouvelle diminution; dans l'intervalle, la présence d'une infection à T. b. gambiense au sein de la communauté doit être surveillée afin de pouvoir adapter la stratégie de lutte et évaluer le statut d'élimination. Par conséquent, l'Organisation mondiale de la Santé a élaboré un profil de produit cible qui détaille les caractéristiques minimales et optimales d'un test individuel en laboratoire visant à confirmer l'infection à T. b. gambiense dans les régions à faible prévalence. La mise au point de ce profil a entraîné la formation d'un Groupe consultatif technique sur le diagnostic des maladies tropicales négligées et d'un sous-groupe consacré aux besoins en matière d'innovation diagnostique pour la trypanosomiase humaine africaine, qui a conduit une analyse des produits existants et des projets de développement. Selon le profil de produit, le test devrait idéalement: (i) nécessiter un prélèvement d'échantillon peu ou non invasif, pouvant être effectué dans des structures périphériques par des professionnels de la santé ayant reçu une formation sommaire; (ii) faire preuve d'un bon niveau de sensibilité et d'un niveau élevé de spécificité; (iii) avoir une stabilité des échantillons permettant le transfert vers des laboratoires de référence, de préférence sans chaîne de froid; (iv) rester stable dans un large éventail de conditions environnementales pendant plus de deux ans; et enfin, (v) après commercialisation, être disponible à bas coût pendant au moins sept ans.

Tras haber causado epidemias devastadoras durante el siglo XX, la incidencia de la tripanosomiasis humana africana potencialmente mortal ha descendido a niveles históricamente bajos gracias a los esfuerzos sostenidos y coordinados de los últimos 20 años. El ser humano es el principal reservorio de una de las dos subespecies patógenas del tripanosoma, Trypanosoma brucei gambiense, presente en África Occidental y Central. La prevista disponibilidad de un tratamiento seguro y fácil de administrar a personas seropositivas, pero no confirmadas al microscopio, permitiría una mayor eliminación; mientras tanto, se debe vigilar la presencia de la infección por T. b. gambiense en la comunidad para poder adaptar la estrategia de control y evaluar el estado de eliminación. Por consiguiente, la Organización Mundial de la Salud ha elaborado un perfil de producto objetivo que describe las características óptimas y mínimas de una prueba de laboratorio individual para evaluar la infección por T. b. gambiense en regiones de baja prevalencia. El desarrollo del perfil de producto objetivo implicó la formación de un Grupo de Asesoramiento Técnico sobre Diagnóstico de Enfermedades Tropicales Desatendidas y un subgrupo sobre las necesidades de innovación en el diagnóstico de la tripanosomiasis humana africana, así como un análisis de los productos disponibles y en desarrollo. Según el perfil objetivo, lo ideal sería que la prueba: (i) requiriera una muestra mínimamente invasiva o no invasiva, que pudiera ser recogida en centros periféricos por personal sanitario con una capacitación mínima; (ii) demostrara una buena sensibilidad y alta especificidad; (iii) tuviera una estabilidad de las muestras que permita su transferencia a laboratorios de referencia, preferiblemente sin cadena de frío; (iv) fuera estable en un amplio rango de condiciones ambientales durante más de 2 años; y (v) tras su comercialización, estuviera disponible a bajo coste durante al menos 7 años.

Target product profile: diagnostic test for Trypanosoma brucei gambiense.

Human African trypanosomiasis is a life-threatening parasitic infection endemic to sub-Saharan Africa. Around 95% of cases are due to Trypanosoma brucei gambiense, found in western and central Africa. Clinical signs and symptoms are nonspecific, current diagnostic tests are not sufficiently accurate, and parasitological confirmation of infection requires microscopic examination of body fluids and specialized techniques for concentrating parasites. Moreover, current treatment is not recommended on the basis of suspicion alone because it is not sufficiently safe. The availability of a simple and accurate diagnostic test to identify individuals harbouring parasites would widen treatment and help decrease disease prevalence. A subcommittee of the World Health Organization's Neglected Tropical Diseases Diagnostics Technical Advisory Group has developed a target product profile for a diagnostic tool to identify T. b. gambiense infection. This tool should have a high sensitivity for detecting T. b. gambiense but be simple enough to use in rural Africa. Ideally, the tool could be applied by any minimally trained individual in an unsophisticated peripheral health facility, or a mobile team in a village with little infrastructure. The test should be able to function under hot and humid conditions. Basic training should take under 2 hours and the test should involve fewer than five steps. There should be no need for instrumentation or precision liquid handling. The test should yield a qualitative result in under 20 minutes that can be easily observed, and one test should be sufficient for determining treatment. A unit cost below 1 United States dollar (US$) would enable mass screening.

La trypanosomiase humaine africaine est une infection parasitaire potentiellement mortelle endémique en Afrique subsaharienne. Dans près de 95% des cas, elle est causée par Trypanosoma brucei gambiense, que l'on trouve en Afrique occidentale et centrale. Les symptômes et signes cliniques sont aspécifiques, les tests de diagnostic existants ne sont pas assez précis et la confirmation parasitologique de l'infection nécessite un examen microscopique des liquides corporels ainsi que des techniques spécialisées pour concentrer les parasites. En outre, il n'est pas recommandé d'entamer le traitement actuel sur la base d'une simple suspicion car celui-ci n'est pas suffisamment sûr. Fournir un test de diagnostic simple et précis permettant d'identifier les individus porteurs de parasites contribuerait à élargir le traitement et à une diminution de la prévalence de la maladie. Un sous-comité du Groupe consultatif technique sur les produits de diagnostic des maladies tropicales négligées de l'Organisation mondiale de la Santé a élaboré un profil de produit cible pour un outil visant à détecter une infection par T. b. gambiense. Cet outil doit être suffisamment sensible pour déceler la présence de T. b. gambiense mais suffisamment simple pour être utilisé dans les régions rurales du continent. Idéalement, il doit pouvoir être employé par toute personne ayant reçu une formation sommaire, tant dans des structures de santé périphériques basiques qu'au sein d'une équipe mobile dans un village doté d'infrastructures restreintes. Par ailleurs, il doit fonctionner dans une atmosphère chaude et humide. La formation requise pour son utilisation doit durer moins de deux heures et le test doit être effectué en moins de cinq étapes, sans exiger d'équipement spécifique ni de manipulation délicate. Cet outil doit fournir un résultat fiable en moins de 20 minutes, facile à interpréter, et un seul test doit suffire à établir un traitement. Enfin, afin d'organiser un dépistage de masse, son coût unitaire ne doit pas dépasser un dollar américain.

La tripanosomiasis humana africana es una infección parasitaria potencialmente mortal endémica del África Subsahariana. Alrededor del 95% de los casos se deben al Trypanosoma brucei gambiense, presente en África Occidental y Central. Los signos y síntomas clínicos no son específicos, las pruebas diagnósticas actuales no son suficientemente precisas y la confirmación parasitológica de la infección requiere el examen microscópico de los fluidos corporales y técnicas especializadas de concentración de parásitos. Además, el tratamiento actual no se recomienda a partir de la sola sospecha porque no es suficientemente seguro. La disponibilidad de una prueba diagnóstica sencilla y precisa para identificar a las personas con parásitos ampliaría el tratamiento y ayudaría a disminuir la prevalencia de la enfermedad. Un subcomité del Grupo de Asesoramiento Técnico sobre Diagnóstico de Enfermedades Tropicales Desatendidas de la Organización Mundial de la Salud ha desarrollado un perfil de producto objetivo para una herramienta de diagnóstico destinada a identificar la infección por T. b. gambiense. Esta herramienta debe tener una alta sensibilidad para detectar T. b. gambiense, pero ser lo suficientemente sencilla para su uso en las regiones rurales de África. Lo ideal sería que la herramienta pudiera ser aplicada por cualquier persona mínimamente capacitada en un centro sanitario periférico poco sofisticado o por un equipo móvil en un pueblo con poca infraestructura. La prueba debería funcionar en condiciones de calor y humedad. La formación básica debe durar menos de 2 horas y la prueba debe constar de menos de cinco pasos. No debe necesitarse instrumentación ni manipulación precisa de líquidos. La prueba debe dar un resultado cualitativo en menos de 20 minutos que pueda observarse fácilmente y debe bastar una prueba para determinar el tratamiento. Su coste unitario, inferior a un dólar estadounidense, permitiría un cribado masivo.

Immunological and biochemical biomarker alterations among SARS-COV-2 patients with varying disease phenotypes in Uganda.

Every novel infection requires an assessment of the host response coupled with identification of unique biomarkers for predicting disease pathogenesis, treatment targets and diagnostic utility. Studies have exposed dysregulated inflammatory response induced by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as significant predictor or cause of disease severity/prognosis and death. This study evaluated inflammatory biomarkers induced by SARS-CoV-2 in plasma of patients with varying disease phenotypes and healthy controls with prognostic or therapeutic potential. We stratified SARS-CoV-2 plasma samples based on disease status (asymptomatic, mild, severe, and healthy controls), as diagnosed by RT-PCR SARS-CoV-2. We used a solid phase sandwich and competitive Enzyme-Linked Immunosorbent Assay (ELISA) to measure levels of panels of immunological (IFN-γ, TNF-α, IL-6, and IL-10) and biochemical markers (Ferritin, Procalcitonin, C-Reactive Protein, Angiotensin II, Homocysteine, and D-dimer). Biomarker levels were compared across SARS-CoV-2 disease stratification. Plasma IFN-γ, TNF-α, IL-6, and IL-10 levels were significantly (P < 0.05) elevated in the severe SARS-CoV-2 patients as compared to mild, asymptomatic, and healthy controls. Ferritin, Homocysteine, and D-dimer plasma levels were significantly elevated in severe cases over asymptomatic and healthy controls. Plasma C-reactive protein and Angiotensin II levels were significantly (P < 0.05) higher in mild than severe cases and healthy controls. Plasma Procalcitonin levels were significantly higher in asymptomatic than in mild, severe cases and healthy controls. Our study demonstrates the role of host inflammatory biomarkers in modulating the pathogenesis of COVID-19. The study proposes a number of potential biomarkers that could be explored as SARS-CoV-2 treatment targets and possible prognostic predictors for a severe outcome. The comprehensive analysis of prognostic biomarkers may contribute to the evidence-based management of COVID-19 patients.

Plant genomics in Africa: present and prospects.

Plants are the world's most consumed goods. They are of high economic value and bring many health benefits. In most countries in Africa, the supply and quality of food will rise to meet the growing population's increasing demand. Genomics and other biotechnology tools offer the opportunity to improve subsistence crops and medicinal herbs in the continent. Significant advances have been made in plant genomics, which have enhanced our knowledge of the molecular processes underlying both plant quality and yield. The sequencing of complex genomes of African plant species, facilitated by the continuously evolving next-generation sequencing technologies and advanced bioinformatics approaches, has provided new opportunities for crop improvement. This review summarizes the achievements of genome sequencing projects of endemic African plants in the last two decades. We also present perspectives and challenges for future plant genomic studies that will accelerate important plant breeding programs for African communities. These challenges include a lack of basic facilities, a lack of sequencing and bioinformatics facilities, and a lack of skills to design genomics studies. However, it is imperative to state that African countries have become key players in the plant genome revolution and genome derived-biotechnology. Therefore, African governments should invest in public plant genomics research and applications, establish bioinformatics platforms and training programs, and stimulate university and industry partnerships to fully deploy plant genomics, particularly in the fields of agriculture and medicine.

Copy number variation in human genomes from three major ethno-linguistic groups in Africa.

BACKGROUND: Copy number variation is an important class of genomic variation that has been reported in 75% of the human genome. However, it is underreported in African populations. Copy number variants (CNVs) could have important impacts on disease susceptibility and environmental adaptation. To describe CNVs and their possible impacts in Africans, we sequenced genomes of 232 individuals from three major African ethno-linguistic groups: (1) Niger Congo A from Guinea and Côte d'Ivoire, (2) Niger Congo B from Uganda and the Democratic Republic of Congo and (3) Nilo-Saharans from Uganda. We used GenomeSTRiP and cn.MOPS to identify copy number variant regions (CNVRs). RESULTS: We detected 7608 CNVRs, of which 2172 were only deletions, 2384 were only insertions and 3052 had both. We detected 224 previously un-described CNVRs. The majority of novel CNVRs were present at low frequency and were not shared between populations. We tested for evidence of selection associated with CNVs and also for population structure. Signatures of selection identified previously, using SNPs from the same populations, were overrepresented in CNVRs. When CNVs were tagged with SNP haplotypes to identify SNPs that could predict the presence of CNVs, we identified haplotypes tagging 3096 CNVRs, 372 CNVRs had SNPs with evidence of selection (iHS > 3) and 222 CNVRs had both. This was more than expected (p < 0.0001) and included loci where CNVs have previously been associated with HIV, Rhesus D and preeclampsia. When integrated with 1000 Genomes CNV data, we replicated their observation of population stratification by continent but no clustering by populations within Africa, despite inclusion of Nilo-Saharans and Niger-Congo populations within our dataset. CONCLUSIONS: Novel CNVRs in the current study increase representation of African diversity in the database of genomic variants. Over-representation of CNVRs in SNP signatures of selection and an excess of SNPs that both tag CNVs and are subject to selection show that CNVs may be the actual targets of selection at some loci. However, unlike SNPs, CNVs alone do not resolve African ethno-linguistic groups. Tag haplotypes for CNVs identified may be useful in predicting African CNVs in future studies where only SNP data is available.

Optimisation of template preparation and laboratory evaluation of the Loopamp™ Trypanosoma brucei kit for detection of parasite DNA in blood.

The Loopamp™ Trypanosoma brucei Detection Kit is the latest addition of molecular techniques for amplification of parasite DNA in biological materials. We have evaluated the kit on a number of preparations of crude templates from the blood of experimentally infected rodents, to provide the best option that can be extrapolated to resource-poor healthcare settings where human African trypanosomiasis (HAT) is endemic. We used rodent blood spiked with T. b. brucei at various serial dilutions to test whole blood, that was concentrated by differential lysis of red blood cells (RBCs) followed by centrifugation, or buffy coat samples recovered from whole blood after centrifugation. We also tested crude templates produced after lysis of blood with sodium dodecyl sulphate (SDS) or Triton X, and storage for up to 28 days at room temperature after spotting on filter paper or glass slides. Concentration by RBC lysis provided the highest analytical sensitivity (0.04 trypanosomes/ml), closely followed by the much cheaper SDS at 0.1 trypanosomes/ml sensitivity. We also monitored the persistence of DNA in lysed blood dried onto filter papers by testing them weekly with the LAMP kit and by PCR for the 177bp repeats characteristic of the T. brucei subspecies. At a concentration of 100 trypanosomes/ml, signals indicating presence of parasite DNA could be detected up to week 10, while at 10 trypanosomes/ml detection of signals was limited to week 4. Thus, an ordinary filter paper provides a convenient medium for preservation of trypanosome DNA at ambient conditions for use with the LAMP kit in the short run. Lysis of samples with SDS enhanced sensitivity by facilitating parasite DNA availability. This opens the avenue to incorporate LAMP in routine algorithms for HAT diagnosis and surveillance, as well as for monitoring elimination programs.

Trypanosoma brucei brucei traverses different biological barriers differently and may modify the host plasma membrane in the process.

Trypanosoma brucei are extracellular hemoflagellate protozoan parasites and one of the causative agents of a devastating zoonotic disease called African Trypanosomiasis. In humans, the disease is caused by Trypanosoma brucei rhodensiense and Trypanosoma brucei gambiense, which cross the blood brain barrier (BBB) causing neurological disorders which culminate in death if untreated. In some domestic animals and laboratory rodents, Trypanosoma brucei brucei causes a disease similar to that in humans. The mechanism by which Trypanosoma brucei brucei invade biological barriers including the BBB has not been fully elucidated. To further address this issue, Mardin Dardy Canine Kidney II (MDCKII) and Human dermal microvascular endothelial cell (HDMEC) monolayers were grown to confluence on transwell inserts to constitute in vitro biological barriers. MDCKII cells were chosen for their ability to form tight junctions similar to those formed by the BBB endothelial cells. Labeled trypanosomes were placed in the upper chamber of transwell inserts layered with confluent MDCKII/HDMEC monolayers and their ability to cross the monolayer over time evaluated. Our results show that only 0.5-1.25% of Trypanosoma brucei brucei were able to migrate across the monolayers after 3 h. By employing immune-staining and confocal microscopic analysis we observed that trypanosomes were located at the tight junctions and inside the cell in the MDCK II monolayers indicating that they crossed the monolayer using both the paracellular and transcellular routes. Our observations also showed that there seemed to be no obvious degradation of junction proteins Zonula Ocludens-1, Occludin and Ecadherin. In the HDMEC cell monolayer, our scanning electron microscopy data showed that Trypanosoma brucei brucei is able to modulate the plasma membrane to form invaginations similar to cuplike structures formed by Tlymphocytes. However these structures seemed to be independent of vascular adhesion molecules suggesting that they could be more like the membrane ruffles formed by certain intracellular bacteria during invasion. Taken together, our data reveal a mechanism by which Trypanosoma brucei brucei is able to cross different biological barriers including the BBB without causing any obvious damage.

Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers.

BACKGROUND: During natural Trypanosoma brucei infections, the parasites differentiate spontaneously into a non-dividing "stumpy" form when a certain level of parasitaemia is attained. This form is metabolically adapted for rapid further differentiation into procyclic forms upon uptake by Tsetse flies. RESULTS: We describe here four central Ugandan isolates of Trypanosoma brucei rhodesiense that have undergone only three rodent passages since isolation from human patients. As expected, SNP analysis shows that these isolates are more closely related to each other than to the commonly used strains Lister 427, Antat1.1, and TREU927. TREU927 generally has smaller copy numbers of repeated genes than the other strains, while Lister 427 trypanosomes with a 30-year history of in vitro culture and cloning have more histone genes than the other isolates. The recently isolated trypanosomes were grown in rats, and their transcriptomes characterised. In comparison with cultured procyclic and bloodstream forms, there were increases in mRNAs encoding the stumpy-form markers ESAG9 and PIP39, with coordinated alterations in the levels of over 600 additional mRNAs. Numerous mRNAs encoding proteins of no known function were either increased or decreased. The products of the mRNAs that were increased in parallel with PIP39 included not only enzymes of procyclic-form metabolism, but also components of the translational and RNA control machineries. Many of the mRNAs that were decreased in cells with elevated PIP39 reflected reduced cell division. CONCLUSIONS: These transcriptomes suggest new avenues for research into the regulation of trypanosome differentiation.

Use of real time polymerase chain reaction for detection of M. tuberculosis, M. avium and M. kansasii from clinical specimens.

BACKGROUND: The incidence of M. tuberculosis (MTB) and non tuberculous Mycobacterium species (NTMs) like M. avium and M. kansasii has increased due to Human Immunodeficiency Virus (HIV) epidemic. Therefore accurate, rapid and cost effective methods for the identification of these NTMs and MTB are greatly needed for appropriate TB management. Thus in this study we evaluated the performance of Lightcycler(®) Mycobacterium detection assay to detect MTB, M. avium and M. kansasii in sputum specimens. METHODS: A total of 241 baseline minimally processed sputum specimens from individual adult TB suspected patients were analyzed by Mycobacterium detection assay (Real-time-PCR) on a LightCycler 480(®) while using liquid culture as a reference standard. RESULTS: Real time PCR had a sensitivity of 100% (95% CI 96-100) and 100% (CI 19-100) for detection of MTB and M. avium respectively. Additionally the assay had a specificity of 99% (95% CI 96-99) and 95% (95% CI 91-97) for identification of MTB and M. avium respectively. The positive predictive value (PPV) for Real time PCR to identify MTB and M. avium among the specimens was 98% (95% CI 94-99) and 15% (95% CI 2-45) respectively. The kappa statistics for Real time PCR to identify MTB and M. avium was 0.9 (95% CI 0.9-1.0) and 0.3 (95% CI-0.03-0.5) respectively. The median time to detection for Real time PCR assay was 2 hours while overall median time to detection for MGIT-positive cultures was 8 days. The sample unit cost for Real time PCR was $ 12 compared to $ 20 for the reference liquid culture. CONCLUSION: The Light cycler(®) Mycobacterium detection assay rapidly and correctly identified MTB and M avium thus has the potential to be adopted in a clinical setting.

Human brucellosis: sero-prevalence and associated risk factors in agro-pastoral communities of Kiboga District, Central Uganda.

BACKGROUND: Brucellosis remains a neglected zoonotic disease among agro-pastoral communities where unprocessed milk and milk products are consumed. A cross-sectional study was carried out in Kiboga district to determine the seroprevalence and risk factors associated with human brucellosis in communities where livestock rearing in a common practice. METHODS: A total of 235 participants were involved in the study. Blood samples from the participants were collected and screened for Brucella using Serum Agglutination Test and Rose Bengal Plate Test. A questionnaire was used to collect data on socio-demographic characteristics and human brucellosis related risk factors. RESULTS: Human Brucella seroprevalence was at 17.0 % (n = 235). The prevalence was highest among males (20.5 %, n = 78) and the elderly - above 60 years (22.2 %, n = 18). Residence in rural areas (OR 3.16, 95 % CI: 1.16-8.56), consuming locally processed milk products (OR 2.54, 95 % CI: 1.12-5.78) and being single (OR 2.44, 95 % CI: 1.05-5.68), were associated with increased risk of brucellosis. DISCUSSION: Human brucellosis seroprevalence was high at 17 %, this was parallel with animal brucellosis prevalence that has been reported to range from 10.2 % to 25.7 % in cattle in the region. The participants were from communities known to habitually consume raw milk and milk products, know to process milk products using bare hands which are major risk factors for brucellosis in humans. This also explains why consumption of unpasteurized milk products was associated with the occurrence of brucellosis in study area. This strengthened the argument that humans get infected through consumption of contaminated animal products as reported in other earlier studies. Males and elderly being more affected because of traditional roles of these groups they play in livestock care and management. The single were also to be more associated to brucellosis, due to the fact that this group consume milk and milk products more as it is readily available in the informal markets as highly nutritious fast foods in this community as also observed in USA. CONCLUSIONS: Brucellosis is highly prevalent in Kiboga district, and therefore, an important public health problem. The transmission risk was aggravated by consumption of unpasteurized milk products, residing in rural settings and being single. There is a need to initiate screening, treat infected humans early, and educate the public about risk factors and appropriate preventive measures of brucellosis.

Pyrethroid resistance and gene expression profile of a new resistant An. gambiae colony from Uganda reveals multiple resistance mechanisms and overexpression of Glutathione-S-Transferases linked to survival of PBO-pyrethroid combination.

Background: The effectiveness of long-lasting insecticidal nets (LLINs) are being threatened by growing resistance to pyrethroids. To restore their efficacy, a synergist, piperonyl butoxide (PBO) which inhibits cytochrome P450s has been incorporated into pyrethroid treated nets. A trial of PBO-LLINs was conducted in Uganda from 2017 and we attempted to characterize mechanisms of resistance that could impact intervention efficacy. Methods: We established an Anopheles gambiae s.s colony in 2018 using female mosquitoes collected from Busia district in eastern Uganda. We first assessed the phenotypic resistance profile of this colony using WHO tube and net assays using a deltamethrin dose-response approach. The Busia colony was screened for known resistance markers and RT-qPCR targeting 15 genes previously associated with insecticide resistance was performed. Results: The Busia colony had very high resistance to deltamethrin, permethrin and DDT. In addition, the colony had moderate resistance to alpha-cypermethrin and lambda-cyhalothrin but were fully susceptible to bendiocarb and fenitrothion. Exposure to PBO in combination with permethrin and deltamethrin resulted in higher mortality rates in both net and tube assays, with a higher mortality observed in net assays than tube assays. The kdr marker, Vgsc-995S was at very high frequency (91.7-98.9%) whilst the metabolic markers Coeae1d and Cyp4j5-L43F were at very low (1.3% - 11.5%) and moderate (39.5% - 44.7%) frequencies respectively. Our analysis showed that gene expression pattern in mosquitoes exposed to deltamethrin, permethrin or DDT only were similar in comparison to the susceptible strain and there was significant overexpression of cytochrome P450s, glutathione-s-transferases (GSTs) and carboxyl esterases (COEs). However, mosquitoes exposed to both PBO and pyrethroid strikingly and significantly only overexpressed closely related GSTs compared to unexposed mosquitoes while major cytochrome P450s were underexpressed. Conclusions: The high levels of pyrethroid resistance observed in Busia appears associated with a wide range of metabolic gene families.

Transcriptome profiles of Trypanosoma brucei rhodesiense in Malawi reveal focus specific gene expression profiles associated with pathology.

BACKGROUND: Sleeping sickness caused by Trypanosoma brucei rhodesiense is a fatal disease and endemic in Southern and Eastern Africa. There is an urgent need to develop novel diagnostic and control tools to achieve elimination of rhodesiense sleeping sickness which might be achieved through a better understanding of trypanosome gene expression and genetics using endemic isolates. Here, we describe transcriptome profiles and population structure of endemic T. b. rhodesiense isolates in human blood in Malawi. METHODOLOGY: Blood samples of r-HAT cases from Nkhotakota and Rumphi foci were collected in PaxGene tubes for RNA extraction before initiation of r-HAT treatment. 100 million reads were obtained per sample, reads were initially mapped to the human genome reference GRCh38 using HiSat2 and then the unmapped reads were mapped against Trypanosoma brucei reference transcriptome (TriTrypDB54_TbruceiTREU927) using HiSat2. Differential gene expression analysis was done using the DeSeq2 package in R. SNP calling from reads that were mapped to the T. brucei genome was done using GATK in order to identify T.b. rhodesiense population structure. RESULTS: 24 samples were collected from r-HAT cases of which 8 were from Rumphi and 16 from Nkhotakota foci. The isolates from Nkhotakota were enriched with transcripts for cell cycle arrest and stumpy form markers, whereas isolates in Rumphi focus were enriched with transcripts for folate biosynthesis and antigenic variation pathways. These parasite focus-specific transcriptome profiles are consistent with the more virulent disease observed in Rumphi and a less symptomatic disease in Nkhotakota associated with the non-dividing stumpy form. Interestingly, the Malawi T.b. rhodesiense isolates expressed genes enriched for reduced cell proliferation compared to the Uganda T.b. rhodesiense isolates. PCA analysis using SNPs called from the RNAseq data showed that T. b. rhodesiense parasites from Nkhotakota are genetically distinct from those collected in Rumphi. CONCLUSION: Our results suggest that the differences in disease presentation in the two foci is mainly driven by genetic differences in the parasites in the two major endemic foci of Rumphi and Nkhotakota rather than differences in the environment or host response.

Impact of environmental factors on Biomphalaria pfeifferi vector capacity leading to human infection by Schistosoma mansoni in two regions of western Côte d'Ivoire.

ABSTRACT: BACKGROUND: Intestinal schistosomiasis remains a worrying health problem, particularly in western Côte d'Ivoire, despite control efforts. It is therefore necessary to understand all the factors involved in the development of the disease, including biotic and abiotic factors. The aim of this study was to examine the factors that could support the maintenance of the intermediate host and its vectorial capacity in western Côte d'Ivoire. METHODS: Data on river physicochemical, microbiological, and climatic parameters, the presence or absence of snails with Schistosoma mansoni, and human infections were collected between January 2020 and February 2021. Spearman rank correlation tests, Mann-Whitney, analysis of variance (ANOVA), and an appropriate model selection procedure were used to analyze the data. RESULTS: The overall prevalence of infected snails was 56.05%, with infection reaching 100% in some collection sites and localities. Of 26 sites examined, 25 contained thermophilic coliforms and 22 contained Escherichia coli. Biomphalaria pfeifferi was observed in environments with lower land surface temperature (LST) and higher relative air humidity (RAH), and B. pfeifferi infection predominated in more acidic environments. Thermal coliforms and E. coli preferred higher pH levels. Lower maximum LST (LST_Max) and higher RAH and minimum LST (LST_Min) were favorable to E. coli, and lower LST_Max favored coliforms. The presence of B. pfeifferi was positively influenced by water temperature (T °C), LST_Min, RAH, and precipitation (Pp) (P < 0.05) and negatively influenced by pH, total dissolved solids (TDS), electrical conductivity (EC), LST_Max, and mean land surface temperature (LST). The parameters pH, TDS, EC, LST_Min, LST, and Pp had a positive impact on snail infection, while LST_Max had a negative impact on infection. Only pH had a positive effect on coliform and E. coli abundance. Of the 701 people examined for human schistosomiasis, 73.13% were positive for the point-of-care circulating cathodic antigen (POC-CCA) test and 12.01% for the Kato-Katz (KK) test. A positive correlation was established between human infections and the abundance of Biomphalaria (r2 = 0.879, P = 0.04959). CONCLUSIONS: The results obtained reflect the environmental conditions that are conducive to the maintenance of S. mansoni infection in this part of the country. To combat this infection as effectively as possible, it will be necessary not only to redouble efforts but also to prioritize control according to the level of endemicity at the village level.

Prevalence of African animal trypanosomiasis among livestock and domestic animals in Uganda: a systematic review and meta-regression analysis from 1980 to 2022.

African animal trypanosomiasis (AAT) is one of the major constraints to animal health and production in sub-Saharan Africa. To inform AAT control in Uganda and help advance along the progressive control pathway (PCP), we characterized AAT prevalence among eight host species in Uganda and explored factors that influence the prevalence variation between studies. We retrieved AAT prevalence publications (n = 2232) for Uganda (1980-2022) from five life sciences databases, focusing on studies specifying AAT detection methods, sample size, and the number of trypanosome-positive animals. Following PRISMA guidelines, we included 56 publications, and evaluated publication bias by the Luis Furuya-Kanamori (LFK) index. National AAT prevalence under DNA diagnostic methods for cattle, sheep and goats was 22.15%, 8.51% and 13.88%, respectively. Under DNA diagnostic methods, T. vivax was the most common Trypanosoma sp. in cattle (6.15%, 95% CI: 2.91-10.45) while T. brucei was most common among small ruminants (goats: 8.78%, 95% CI: 1.90-19.88, and sheep: 8.23%, 95% CI: 4.74-12.50, respectively). Northern and Eastern regions accounted for the highest AAT prevalence. Despite the limitations of this study (i.e., quality of reviewed studies, underrepresentation of districts/regions), we provide insights that could be used for better control of AAT in Uganda and identify knowledge gaps that need to be addressed to support the progressive control of AAT at country level and other regional endemic countries with similar AAT eco-epidemiology.

Assessment of the Impact of Early Diagnosis and Early Treatment in the Integrated Control of East Coast Fever (ECF) Involving Acquired Immunity Induced by Natural Infection in Ankole Cattle.

The integrated control of East Coast fever (ECF) by early diagnosis and treatment involving acquired immunity induced by natural infection in Ankole cattle was assessed. A longitudinal study was carried out in Kiruhura district, southwestern Uganda for six months on 244 Ankole breed of cattle from 18 herds under natural tick challenge and relaxed tick control measures. Calves aged three to six months old were recruited and monitored daily by farmers for detection of ECF clinical symptoms. The reported sick animals were treated using Buparvaquone and treatment outcome determined. Monthly follow-ups and blood collections were done to monitor ECF status. Blood was analyzed for Theileria parva parasites by microscopy, DNA by polymerase chain reaction (PCR) and antibodies by enzyme-linked immunosorbent assay (ELISA). The overall prevalence of ECF clinical disease within six months period was 30.3% (74). The major symptoms of early clinical ECF disease were fever and enlarged parotid or prescapular lymph nodes. Clinical cases were categorized as mild, 24% (18) or moderate, 76% (56). There was an overall recovery rate of 100% (74) of the ECF cases whereby 94.6% (70) recovered promptly and 5.4% (4) recovered slowly. Based on blood analysis, prevalence of ECF at baseline was 3.7% (9) by microscopy, 31.1% (76) by PCR and 38.1% (93) by ELISA. A significant increase (p < 0.05) was shown by the increased number of calves with T. parva specific antibodies in the sera from 38.1% at baseline to 68.8% after six months. High antibody levels (positive percentage ≥ 50%) were detected in all ECF-treated and recovered calves at the end of six months. The acquired immunity to ECF was high in treated and recovered cattle, indicating that natural exposure to infection, accurate early diagnosis and effective treatment enhance development of immune-protection in indigenous cattle in an endemic area. The prominent early clinical symptoms for ECF could be exploited in the development of decision support tools for chemotherapy and other integrated control measures.

Differences in gene expression profiles in early and late stage rhodesiense HAT individuals in Malawi.

T. b. rhodesiense is the causative agent of Rhodesian human African trypanosomiasis (r-HAT) in Malawi. Clinical presentation of r-HAT in Malawi varies between foci and differs from East African HAT clinical phenotypes. The purpose of this study was to gain more insights into the transcriptomic profiles of patients with early stage 1 and late stage 2 HAT disease in Malawi. Whole blood from individuals infected with T. b. rhodesiense was used for RNA-Seq. Control samples were from healthy trypanosome negative individuals matched on sex, age range, and disease foci. Illumina sequence FASTQ reads were aligned to the GRCh38 release 84 human genome sequence using HiSat2 and differential analysis was done in R Studio using the DESeq2 package. XGR, ExpressAnalyst and InnateDB algorithms were used for functional annotation and gene enrichment analysis of significant differentially expressed genes. RNA-seq was done on 23 r-HAT case samples and 28 healthy controls with 7 controls excluded for downstream analysis as outliers. A total of 4519 genes were significant differentially expressed (p adjusted <0.05) in individuals with early stage 1 r-HAT disease (n = 12) and 1824 genes in individuals with late stage 2 r-HAT disease (n = 11) compared to controls. Enrichment of innate immune response genes through neutrophil activation was identified in individuals with both early and late stages of the disease. Additionally, lipid metabolism genes were enriched in late stage 2 disease. We further identified uniquely upregulated genes (log2 Fold Change 1.4-2.0) in stage 1 (ZNF354C) and stage 2 (TCN1 and MAGI3) blood. Our data add to the current understanding of the human transcriptome profiles during T. b. rhodesiense infection. We further identified biological pathways and transcripts enriched than were enriched during stage 1 and stage 2 r-HAT. Lastly, we have identified transcripts which should be explored in future research whether they have potential of being used in combination with other markers for staging or r-HAT.