Prevalence and risk factors of asymptomatic malaria among underfive children in Huye District, Southern Rwanda

Background: Enhanced malaria control has resulted in its reduction in some areas of Sub Saharan Africa including Rwanda. However, asymptomatic hosts serve as a reservoir for the malaria parasite for communities. The objective of this study was to determine the prevalence of malaria parasites and risk factors associated with malaria infection among children underfive years in Huye district, Rwanda.Methods: This community-based cross sectional study was conducted from May to June 2016 among underfive years children.  Asymptomatic children underfive years of age were randomly selected from 13 villages. Thick and thin blood smears were prepared from each child for malaria parasite diagnosis.  Interviews with parents or guardians were conducted to collect data on malaria associated risk factors. Observations were made of the presence of mosquito breeding sites near and around the homestead.Results: A total of 222 children were included in the study. Nearly a third (28.8%) of the children were within the age of 25-36 months. The majority (54%) of the children were females. Most of the parents/guardians were married (95.9%), nearly all (99.5%) had attended primary school and most (97.3%) were peasants. The overall Plasmodium falciparum prevalence in children was 12.2%. Children aged 1 to 12 months were 3.5 times more likely to have malaria parasites than children aged 13 to 59 months [AOR=3.56; 95%CI=1.18-10.71; p=0.024]. Children who were not sleeping under insecticide treated nets were 15 times more likely to be infected with malaria parasites compared to those who were sleeping under nets [AOR=15.27; 95%CI=4.42-52.82; p<0.001].Conclusion: Malaria parasite prevalence in under-five year children in Huye District, Rwanda is moderate.  The asymptomatic infections in the community forms a reservoir for transmission in the area. Young age of the child and not sleeping under mosquito net were associated with malaria parasite infection. The continuing use of mosquito nets needs to be emphasized

Characterization of malaria vectors in Huye District, Southern Rwanda

Background: Effective control of malaria requires knowledge of vector species, their feeding and resting behaviour as well as breeding habitats. The objective of this study was to determine malaria vector species abundance and identify their larval habitats in Huye district, southern Rwanda.Methods: Adult mosquitoes were collected indoors using light trap and pyrethrum spray catch techniques, and outdoors using light traps. Female Anopheles mosquitoes were identified to species level by morphological characteristics. Enzyme-linked Immunosorbent Assay (ELISA) was used to screen for Plasmodium falciparum circumsporozoite protein and host blood meal sources. Anopheles larvae were sampled using dippers and raised into adult mosquitoes which were identified morphologically.Results: Anopheles gambiae sensu lato comprised of 70% of the 567 Anopheles collected. Other Anopheles species identified were An. funestus 4%, An. squamosus 16.5%, An. maculipalpis 6.5%, An. ziemanni 1.7%, An. pharoensis 1.2 % and An. coustani 0.1%. The majority, 63.5% of the collected mosquitoes were from indoors collections. The overall human blood index was 0.509. The P. falciparum circumsporozoite protein was found in 11 mosquitos including 8 Anopheles gambiae s.l. and 3 secondary vectors out of the 567 tested. The overall sporozoite rate was 1.9%. A total of 661 Anopheline larvae from 22 larval habitats were collected. They comprised of An. gambiae s.l. (89%) and An. ziemanni (11%). The absolute breeding index was 86.4%. The most common larval habitats were in full sunlight with still water like rice paddies and pools of stagnant water.Conclusion: These findings show that Anopheles gambiae s.l. is the dominant malaria vector in the area with other vectors playing a secondary role in malaria transmission. Malaria interventions need to be strengthened to reduce even further the malaria transmission in the area.

Epidemiologies de la mosaïque Africaine de manioc et de la striure brune du manioc dans le système semencier paysan en R.D. Congo: tendances et déterminants

peer reviewedi-CARE : Improved Cassava virus resistance mitigation strategies and development of a disease-free seed syste

Facteurs de risque associés à la dissémination de la striure brune du manioc à travers les voies d'acquisition des boutures à l'Est de la R.D. Congo

peer reviewedVegetatively 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.2. Zero hunge

Analysis of Cassava Brown Streak Disease in Rwanda: Incidence, Dissemination, Genetic Diversity, and Innovative Mitigation Strategies.

Cassava brown streak disease (CBSD), caused by Cassava brown streak ipomoviruses (CBSIs), namely Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), poses a significant threat to global food security. It particularly jeopardizes the food security of tropical Africa, where approximately 450 million people rely heavily on cassava as a staple food and vital income source. In Rwanda, CBSD has rapidly spread since its first report in 2009, with the incidence rising from 18.5% in 2012 to 69% in 2014. This widespread outbreak has resulted in severe consequences, including a shortage of planting materials and a 73% decline in cassava yields. CBSD is primarily transmitted to a longer distance through infected cuttings and, to a shorter distance, by the white fly vector. Infected plants exhibit symptoms on the leaves, stem, and, very importantly, on the storage roots, rendering them unsuitable for consumption. In response to the CBSD outbreak, the government of Rwanda and researchers have joined forces to combat the burden of CBSD. Notably, they started to import and distribute tolerant cassava planting materials to farmers in 2015. Given that infected cuttings are a significant transmission mode for CBSD, it is imperative to break the cycle of disease transmission and minimize the risk of CBSD spread and its consequences by ensuring the availability of healthy planting materials. In this context, in vitro virus cleaning approaches were applied to combat the virus build-up effect over multiple cycles due to cassava's vegetative nature. However, these approaches take time and are often too costly for subsistence crops. Furthermore, studies have been conducted to assess the prevalence and diversity of CBSD causative agents in Rwanda, albeit with a focus limited to partial coat protein, and different breeding research projects have been initiated. These initiatives were reflecting important investments to mitigate the impact of CBSD while acknowledging the need for further extensive research to tackle the disease comprehensively. In this regard, the first goal of this thesis was to conduct a countrywide cassava seed system survey to determine CBSD status following interventions and the risk factors that may contribute to its continued spread in Rwanda. To achieve this, 130 cassava farmers were interviewed across 13 major cassava-growing districts and their fields were visited to evaluate disease incidence. Leaf samples were collected and analyzed using RT-PCR (reverse transcription polymerase chain reaction) to confirm CBSIs infection. The findings revealed that CBSD has spread in all surveyed districts, and the overall incidence was 35.3%, with UCBSV being the most common, accounting for 61% of the infections. Several key risk factors that could contribute to the spread of the disease in Rwanda were also identified, including the source of planting materials, geographical location, knowledge of disease transmission, and disease management practices. These findings highlight the need to develop a robust seed system and train farmers to increase awareness and skills to mitigate the spread and impact of CBSD in cassava farming communities. Recognizing the pivotal role of robust diagnostic tools in fortifying the seed system, the second goal of this thesis was to investigate the genetic diversity of CBSD-causing agents in Rwanda by analyzing whole genomes with innovative methods to provide valuable insights into the evolutionary patterns of CBSIs in Rwanda. High-throughput sequencing (HTS) technologies were applied on 13 pooled samples (corresponding to 13 surveyed districts), enabling us to obtain comprehensive genomic data. Through HTS data analysis, 12 nearly complete consensus genomes of UCBSV were successfully reconstructed. Phylogenetic analysis of these genomes revealed a remarkable reduction in genetic diversity, with a maximum of 0.8% nucleotide divergence between the genomes. Further investigation beyond the consensus sequences utilizing the combination of fixation index (FST) calculation and Principal Component Analysis (PCA) based on SNPs patterns unveiled three distinct UCBSV haplotypes exhibiting geographic clustering. Interestingly, the distribution of haplotype two (H2) was found to be associated with one of the CBSD tolerant cultivars widely distributed to farmers, "NAROCAS1". In addition, HTS allowed the assembly of the partial genome of Manihot esculenta-associated virus 1(MEaV-1) for the first time in Rwanda. Identifying distinct UCBSV haplotypes and their geographic distribution represents the first study in Rwanda, marking a significant advancement into the local patterns of UCBSV evolution, facilitating a better understanding of the disease's spread, and developing targeted control strategies. Considering that the current main CBSD management relies on the distribution of tolerant cultivars susceptible to viral buildup effect, the third objective of this thesis was to transform existing in vitro virus cleaning methods into practical farmer-friendly approaches at the greenhouse and field levels toward CBSD mitigation. The present study assessed the effectiveness of combining greenhouse thermotherapy with chemotherapy and field chemotherapy, employing salicylic acid (SA) and Benzothiadiazole (BTH) on CBSIs-infected cuttings. The results revealed a remarkable reduction in viral loads, especially when combining thermotherapy with SA at 50 mg/L and thermotherapy with BTH at 50 mg/L, which exhibited the most substantial reduction compared to other treatments. Additionally, a significant decrease in the severity of CBSD root symptoms through field chemotherapy was observed among treated plants. These findings highlight the potential effectiveness of these combined approaches in mitigating the impact of CBSD and offer promising avenues for disease management in cassava. Furthermore, RNA sequencing on uninfected cassava plants exogenously treated with SA and BTH was conducted to investigate their impact on the cassava transcriptome. It was revealed that SA and BTH deregulate numerous cassava genes, including genes with potential involvement in plant defense, such as transcription factors (e.g., WRKY), Leucine Rich Repeat (LRR) Protein, Heat shock Protein (HSP), Mitogen-Activated Protein Kinase (MAPK), Cytochrome P450, and ethylene-responsive genes. The gene ontology (GO) enrichment analysis revealed that hormone signaling, defense response, response to stress, and regulation of transcription were among the enriched GO, suggesting their potential role in viral host response. Overall, this thesis contributed significantly to understanding and managing CBSD, providing valuable knowledge for sustainable cassava farming in Rwanda. The countrywide farmers and cassava fields survey provided crucial findings on CBSD status and risk factors, emphasizing the urgency of a robust seed system and farmers' training. The high-resolution investigation into UCBSV genetic diversity through an innovative approach shed light on its evolutionary patterns and geographic distribution, offering insights for targeted control measures. Finally, transforming in vitro virus cleaning methods into greenhouse and field approaches showcased promising results in reducing CBSD severity and viral loads, supported by identifying potential defense-related cassava genes. The present thesis can also serve as the basis for future research. Notably, the innovative approach to characterizing genetic diversity could be applied to study other crucial plant viruses. It is also worth investigating CBSV diversity and the factors driving the evolution of CBSIs in Rwanda. Furthermore, future research is needed to optimize the efficacy of greenhouse and field CBSD mitigation approaches and delve into the specific functions of genes regulated by SA and BTH. Moreover, assessing the impact of chemotherapy on the environment and microbiome and analyzing large-scale cost-benefit viability would provide invaluable insights. These avenues of exploration will undoubtedly contribute to a deeper understanding of virus management strategies and bolster efforts to safeguard plant health and agricultural productivity

Harnessing plant viruses in the metagenomics era: from the development of infectious clones to applications.

peer reviewedRecent metagenomic studies which focused on virus characterization in the entire plant environment have revealed a remarkable viral diversity in plants. The exponential discovery of viruses also requires the concomitant implementation of high-throughput methods to perform their functional characterization. Despite several limitations, the development of viral infectious clones remains a method of choice to understand virus biology, their role in the phytobiome, and plant resilience. Here, we review the latest approaches for efficient characterization of plant viruses and technical advances built on high-throughput sequencing and synthetic biology to streamline assembly of viral infectious clones. We then discuss the applications of plant viral vectors in fundamental and applied plant research as well as their technical and regulatory limitations, and we propose strategies for their safer field applications

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

International audienceCassava 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 13 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 12 districts. The phylogenetic analysis revealed high homology between UCBSV genome sequences, with a maximum of 0.8 % divergence between genomes at the nucleotide level. An in-depth investigation based on Single Nucleotide Polymorphisms (SNP) 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 RT-PCR and Sanger sequencing. Furthermore, the combination of fixation index (FST) calculation and Principal Component Analysis (PCA) based on SNPs 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% 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

Farmer and Field Survey in Cassava-Growing Districts of Rwanda Reveals Key Factors Associated With Cassava Brown Streak Disease Incidence and Cassava Productivity

Cassava ( Manihot esculenta Crantz) is a vital crop in Rwanda where it ranks as the third most consumed staple. However, cassava productivity remains below its yield potential due to several constraints, including important viral diseases, such as cassava brown streak disease (CBSD). Because various factors can be addressed to mitigate the impact of viral diseases, it is essential to identify routes of virus contamination in the cassava agrosystems from the seed system to farmer's practices and knowledge. The present study aimed at (1) assessing the current cassava seed system and farmers' practices and their knowledge of the biotic constraints to cassava production, (2) determining the status of CBSD as well as critical factors associated with its spread through the seed system channels, and (3) determining factors that influence cassava productivity in Rwanda. A cross-sectional study was carried out from May to September 2019 in 13 districts of Rwanda. A total of 130 farmers and cassava fields were visited, and the incidence and severity of CBSD were evaluated. CBSD was detected in all cassava-producing districts. The highest field incidence of CBSD was recorded in the Nyanza district (62%; 95% CI = 56–67%) followed by the Bugesera district (60%; 95% CI = 54–65%), which recorded the highest severity score of 3.0 ± 0.6. RT-PCR revealed the presence of CBSD at the rate of 35.3%. Ugandan cassava brown streak virus was predominant (21.5%) although cassava brown streak virus was 4% and mixed infection was 10%. An informal cassava seed system was dominant among individual farmers, whereas most cooperatives used quality seeds. Cassava production was found to be significantly influenced by the use of fertilizer, size of the land, farming system, cassava viral disease, and type of cassava varieties grown ( p < 0.001). Disease management measures were practiced by a half of participants only. Factors found to be significantly associated with CBSD infection ( p < 0.05) were the source of cuttings, proximity to borders, age of cassava, and knowledge of CBSD transmission and management.info:eu-repo/semantics/publishe