Biology subjects

Sseruwagi, P.

Publications and source records attributed to Sseruwagi, P..

4 recordsLinked to original sources

bioRxiv2025

Predicting the cross-continental spread of the cassava brown streak disease epidemic in sub-Saharan Africa

Cassava brown streak disease (CBSD) is a major threat to smallholder farmers in sub-Saharan Africa (SSA), where cassava is a staple crop. Caused by cassava brown streak ipomoviruses (CBSIs), CBSD has spread extensively since its detection in Uganda in 2004, raising concerns about ongoing spread through Southern and Central Africa and potential expansion to West Africa, home to the worlds largest cassava producer, Nigeria. Building on a stochastic epidemiological model that predicts CBSD spread at the scale of Uganda, we incorporate extensive field surveillance records to extend the model to all thirty-two major cassava-producing countries in SSA. We then deploy the model to address key strategic questions such as estimating the present day CBSD distribution and predicting rates of ongoing spread towards West Africa. We also evaluate the risk of direct introductions resulting from long range movement of infected planting material, which could trigger outbreaks beyond predicted localised dispersal limits. Our model predicts the likely arrival of CBSD in Nigeria via cross-continental spread within 25 years, and if directly introduced anywhere in West Africa, spreading to most West African nations within 10 years. The risks of ongoing and future CBSD spread highlighted in this study underscore the need for proactive phytosanitation measures, including clean seed programs, vector control, and quarantine policies to curb CBSD spread. Moreover, the model described in this study not only provides estimates for arrival times across SSA, but also lays the foundations for a continental-scale quantitative framework wherein both surveillance and management options can be explored and optimised.

ecology↗

bioRxiv2019

Tree Lab: Portable genomics for early detection of plant viruses and pests in Sub-Saharan Africa

In this case study we successfully teamed the PDQeX DNA purification technology developed by MicroGEM, New Zealand, with the MinION and MinIT mobile sequencing devices developed by Oxford Nanopore Technologies to produce an effective point-of-need field diagnostic system. The PDQeX extracts DNA using a cocktail of thermophilic proteinases and cell wall degrading enzymes, thermo-responsive extractor cartridges and a temperature control unit. This single-step closed system delivers purified DNA with no cross contamination. The MinIT is a newly released data processing unit that converts MinION raw signal output into base called data locally in real time, removing the need for high specification computers and large file transfers from the field. All three devices are battery powered with an exceptionally small footprint that facilitates transport and set up.\n\nTo evaluate and validate capability of the system for unbiased pathogen identification by realtime sequencing in a farmers field setting, we analysed samples collected from cassava plants grown by subsistence farmers in three sub-Sahara African countries (Tanzania, Uganda and Kenya). A range of viral pathogens, all with similar symptoms, greatly reduce yield or completely destroy cassava crops. 800 million people worldwide depend on cassava for food and yearly income, and viral diseases are a significant constraint on its production (https://cassavavirusactionproject.com). Early pathogen detection at a molecular level has great potential to rescue crops within a single growing season by providing results that inform decisions on disease management, use of appropriate virus resistant or replacement planting.\n\nThis case study presented conditions of working in-field with limited or no access to mains power, laboratory infrastructure, internet connectivity and highly variable ambient temperature. An additional challenge is that, generally, plant material contains inhibitors of downstream molecular processes making effective DNA purification critical. We successfully undertook real-time on-farm genome sequencing of samples collected from cassava plants on three farms, one in each country. Cassava mosaic begomoviruses were detected by sequencing leaf, stem, tuber and insect samples. The entire process, from arrival on farm to diagnosis including sample collection, processing and provisional sequencing results was complete in under 4 hours. The need for accurate, rapid and on-site diagnosis grows as globalized human activity accelerates. This technical breakthrough has applications that are relevant to human and animal health, environmental management and conservation.

genomics↗

bioRxiv2018

Real time portable genome sequencing for global food security

The United Nations has listed Zero Hunger as one of the 17 global sustainable development goals to end extreme poverty by 2030. Plant viruses are a major constraint to crop production globally causing an estimated $30 billion in damage 1 leaving millions of people food insecure 2. In Africa, agriculture employs up to 50% of the workforce, yet only contributes 15% to the GDP on average 3, suggesting that there is low productivity and limited value addition. This can be addressed through continued innovation in the fields of science and technology as suggested in the Science Agenda for Agriculture in Africa (S3A) 4. Sustainable management of plant viruses and their associated vectors must include efficient diagnostics for surveillance, detection and identification to inform disease management, including the development and strategic deployment of virus resistant varieties. To date, researchers have been utilizing conventional methods such as; PCR, qPCR, high throughput sequencing (RNA-Seq, DNA-Seq) and Sanger sequencing for pathogen identification. However, these methods are both costly and time consuming, delaying timely control actions. The emergence of new tools for real-time diagnostics, such as the Oxford Nanopore MinION, have recently proven useful for early detection of Ebola 6 and Zika 7,8, even in low resourced laboratories. For the first time globally, the MinION portable pocket DNA sequencer was used to sequence whole plant virus genomes. We used this technology to identify the begomoviruses causing the devastating CMD which is ravaging smallholder farmers crops in sub-Saharan Africa. Cassava, a carbohydrate crop from which tapioca originates, is a major source of calories for over eight hundred (800) million people worldwide. With this technology, farmers struggling with diseased crops can take immediate, restorative action to improve their livelihoods based on information about the health of their plants, generated using a portable, real-time DNA sequencing device.

plant biology↗

bioRxiv2017

A novel method for single whitefly (Bemisia tabaci) transcriptomes reveals an eleven amino acid deletion in the NusG protein in the bacterial endosymbiont Portiera aleyrodidarum

BackgroundBemisia tabaci species (whiteflies) are the worlds most devastating insect pests within crops in the tropics. They cause billions of dollars (US) of damage each year and are leaving farmers in the developing world food insecure. Understanding the genetic and transcriptomic composition of these insect pests, the viruses they transmit and the microbiota is crucial to sustainable insect and virus management solutions for farmers. Currently, publically available transcriptome data for B. tabaci has been generated from pooled samples (mainly inbred lab colonies) consisting of several individuals because whiteflies are small (approximately 0.2 mm wide and 0.1 mm in height). Pooling individuals can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technology limitations. Therefore, the understanding of whitefly-microbiotad-viral species composition of an individual field-collected whitefly has also remained unknown. In this study, we developed a single whitefly RNA extraction procedure and subsequently successfully sequenced the transcriptome of four individual adult SubdSaharan Africa (SSA1) B. tabaci.\n\nResultsTranscriptome sequencing on individual whiteflies resulted in between 39-42 million raw reads. De novo assembly of trimmed reads yielded between 65,000-162,000 transcripts across all four B. tabaci transcriptomes. In addition, Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase (mtCOI) grouped the four whiteflies within the SSA1 clade. BLAST searches on assembled transcripts within the four individual transcriptomes identified five endosymbionts; the primary endosymbiont Portiera,aleyrodidarum and four secondary endosymbionts: Arsenophonus, Wolbachia, Rickettsia, and Cardinium spp. These five endosymbionts were predominant across all four SSA1 B. tabaci study samples with prevalence levels of between 54.1d75%. Nucleotide and amino acid sequence alignments of the NusG gene of P. aleyrodidarum for the SSA1 B. tabaci transcriptomes of samples WF2 and WF2b revealed an eleven amino acid residue deletion that was absent in samples WF1 and WF2a. Comparison of the protein structure of the NusG protein from P. aleyrodidarum in SSA1 with known NusG structures showed the deletion resulted in a shorter D loop. Although NusG is key in regulating of transcription elongation, it is believed that the shortening of the loop region in the N-terminal domain is unlikely to affect transcription termination. Therefore, the effect of variability in this region across species is unknown.\n\nConclusionIn this study, we optimised a single whitefly high quality RNA extraction procedure and successfully carried out individual whitefly transcriptome sequencing on adult B. tabaci whiteflies. This enabled the detection of unique genetic differences in the NusG genes of the primary endosymbiont P. aleyrodidarum in four field-collected SSA1 whiteflies that may not have been detected using lab-pooled B. tabaci isolines. The use of field-collected specimens means that both time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. In addition, the methods we have developed here are applicable to any small organism where RNA quantity has limited transcriptome studies.

genetics↗