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Abstract Cassava is infected by numerous geminiviruses in Africa and India that cause devastating losses to poor farmers. We here describe the molecular diversity of seven representative cassava mosaic geminiviruses (CMGs) infecting cassava from multiple locations in Tanzania. We report for the first time the presence of two isolates in East Africa: (EACMCV-[TZ1] and EACMCV-[TZ7]) of the species East African cassava mosaic Cameroon virus, originally described in West Africa. The complete nucleotide sequence of EACMCV-[TZ1] DNA-A and DNA-B components shared a high overall sequence identity to EACMCV-[CM] components (92% and 84%). The EACMCV-[TZ1] and -[TZ7] genomic components have recombinations in the same genome regions reported in EACMCV-[CM], but they also have additional recombinations in both components. Evidence from sequence analysis suggests that the two strains have the same ancient origin and are not recent introductions. EACMCV-[TZ1] occurred widely in the southern part of the country. Four other CMG isolates were identified: two were close to the EACMV-Kenya strain (named EACMV-[KE/TZT] and EACMV-[KE/TZM] with 96% sequence identity); one isolate, TZ10, had 98% homology to EACMV-UG2Svr and was named EACMV-UG2 [TZ10]; and finally one isolate was 95% identical to EACMV-[TZ] and named EACMV-[TZ/YV]. One isolate of African cassava mosaic virus with 97% sequence identity with other isolates of ACMV was named ACMV-[TZ]. It represents the first ACMV isolate from Tanzania to be sequenced. The molecular variability of CMGs was also evaluated using partial B component nucleotide sequences of 13 EACMV isolates from Tanzania. Using the sequences of all CMGs currently available, we have shown the presence of a number of putative recombination fragments that are more prominent in all components of EACMV than in ACMV. This new knowledge about the molecular CMG diversity in East Africa, and in Tanzania in particular, has led us to hypothesize about the probable importance of this part of Africa as a source of diversity and evolutionary change both during the early stages of the relationship between CMGs and cassava and in more recent times. The existence of multiple CMG isolates with high DNA genome diversity in Tanzania and the molecular forces behind this diversity pose a threat to cassava production throughout the African continent.

Formal systems supporting the delivery of high-quality cassava seed are being established in several key cassava producing countries in Africa. Questions remain, however, about the value of certified cassava seed when compared to seed which is recycled multiple times, which is standard farmer practice. A study was therefore conducted to compare fresh cassava root yields of high-quality seed (HQS) versus farmer-saved (recycled) seed (FSS) for three widely grown improved cassava varieties in Tanzania namely: Mkuranga1 , Kiroba and Mkombozi . Field experiments were established in two sites in different agricultural zones: Mkuranga (Coast Zone) and Maruku (Lake Victoria Zone). Four HQS sources (pre-basic, basic, certified, quality-declared), collectively referred to as HQS, were compared with FSS with respect to cassava brown streak disease (CBSD) foliar and root incidences, fresh root yield, marketable fresh root yield, and usable fresh root yield for each variety in the two locations. Results showed that foliar CBSD incidence in FSS was significantly greater than it was for HQS in Mkuranga1 and Kiroba varieties but not for Mkombozi . CBSD root incidence was on average six times more in FSS than in HQS. When comparing FSS with the specific certified seed treatment (CS), 25.8% of the roots were unusable due to CBSD root necrosis for FSS, compared to only 3.7% for CS. CS gave an overall fresh root yield which was 7.5 t/ha more than FSS, representing an 80.6% increase. Yield benefits derived from planting HQS were similar for Kiroba (+80.7%), Mkombozi (+81.3%) and Mkuranga1 (+79.5%), as well as across each of the four HQS classes. When also considering losses arising from severe CBSD root necrosis, the overall yield benefit arising from using CS when compared to FSS was 135%. The average estimated income gain for this increase was US$ 2279/ha, which is many times the estimated cost of obtaining certified seed. These results highlight the value of high quality seed systems and the potential gains that farmers can realize from planting high quality certified seed rather than recycling existing crops., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Cassava is an important food crop in western Kenya, yet its production is challenged by pests and diseases that require routine monitoring to guide development and deployment of control strategies. Field surveys were conducted in 2022 and 2023 to determine the prevalence, incidence and severity of cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), whitefly numbers and incidence of cassava green mite (CGM) in six counties of western Kenya. Details of the encountered cassava varieties were carefully recorded to determine the adoption of improved varieties. A total of 29 varieties were recorded, out of which 13 were improved, although the improved varieties were predominant in 60% of fields and the most widely grown variety was MM96/4271. The CMD incidence was higher in 2022 (26.4%) compared to 2023 (10.1%), although the proportion of CMD attributable to whitefly infection was greater (50.6%) in 2023 than in 2022 (18.0%). The CBSD incidence in 2022 was 6.4%, while in 2023 it was 4.1%. The CMD incidence was significantly lower (5.9%) for the improved varieties than it was for the local varieties (35.9%), although the CBSD incidence did not differ significantly between the improved (2.3%) and local varieties (9.7%). Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) were both detected. Most infections were single CBSV infections (82.9%), followed by single UCBSV (34.3%) and coinfection with both viruses (16.7%). Whiteflies were more abundant in 2023, in which 28% of the fields had super-abundant populations of >100/plant, compared to 5% in 2022. KASP SNP genotyping designated 92.8% of the specimens as SSA-ECA for 2022, while it was 94.4% for 2023. The cassava green mite incidence was 65.4% in 2022 compared to 79.9% in 2023. This study demonstrates that cassava viruses, whiteflies and cassava green mites continue to be important constraints to cassava production in western Kenya, although the widespread cultivation of improved varieties is reducing the impact of cassava viruses. The more widespread application of high-quality seed delivery mechanisms could further enhance the management of these pests/diseases, coupled with wider application of IPM measures for whiteflies and mites.

Bemisia tabaci (Gennadius) is as a major pest of vegetable crops in Cameroon. These sap-sucking insects are the main vector of many viruses infecting plants, and several cryptic species have developed resistance against insecticides. Nevertheless, there is very little information about whitefly species on vegetable crops and the endosymbionts that infect them in Cameroon. Here, we investigated the genetic diversity of whiteflies and their frequency of infection by endosymbionts in Cameroon. Ninety-two whitefly samples were collected and characterized using mitochondrial cytochrome oxidase I (mtCOI) markers and Kompetitive Allele Specific PCR (KASP). The analysis of mtCOI sequences of whiteflies indicated the presence of six cryptic species (mitotypes) of Bemisia tabaci , and two distinct clades of Bemisia afer and Trialeurodes vaporariorum . Bemisia tabaci mitotypes identified included: MED on tomato, pepper, okra, and melon; and SSA1-SG1, SSA1-SG2, SSA1-SG5, SSA3, and SSA4 on cassava. The MED mitotype predominated in all regions on the solanaceous crops, suggesting that MED is probably the main phytovirus vector in Cameroonian vegetable cropping systems. The more diverse cassava-colonizing B. tabaci were split into three haplogroups (SNP-based grouping) including SSA-WA, SSA4, and SSA-ECA using KASP genotyping. This is the first time that SSA-ECA has been reported in Cameroon. This haplogroup is predominant in regions currently affected by the severe cassava mosaic virus disease (CMD) and cassava brown streak virus disease (CBSD) pandemics. Three endosymbionts including Arsenophonus, Rickettsia , and Wolbachia were present in female whiteflies tested in this study with varying frequency. Arsenophonus , which has been shown to influence the adaptability of whiteflies, was more frequent in the MED mitotype (75%). Cardinium and Hamiltonella were absent in all whitefly samples. These findings add to the knowledge on the diversity of whiteflies and their associated endosymbionts, which, when combined, influence virus epidemics and responses to whitefly control measures, especially insecticides.

The Global Plant Health Assessment (GPHA) is a collective, volunteer-based effort to assemble expert opinions on plant health and disease impacts on ecosystem services based on published scientific evidence. The GPHA considers a range of forest, agricultural, and urban systems worldwide. These are referred to as (Ecoregion × Plant System), i.e., selected case examples involving keystone plants in given parts of the world. The GPHA focuses on infectious plant diseases and plant pathogens, but encompasses the abiotic (e.g., temperature, drought, and floods) and other biotic (e.g., animal pests and humans) factors associated with plant health. Among the 33 (Ecoregion × Plant System) considered, 18 are assessed as in fair or poor health, and 20 as in declining health. Much of the observed state of plant health and its trends are driven by a combination of forces, including climate change, species invasions, and human management. Healthy plants ensure (i) provisioning (food, fiber, and material), (ii) regulation (climate, atmosphere, water, and soils), and (iii) cultural (recreation, inspiration, and spiritual) ecosystem services. All these roles that plants play are threatened by plant diseases. Nearly none of these three ecosystem services are assessed as improving. Results indicate that the poor state of plant health in sub-Saharan Africa gravely contributes to food insecurity and environmental degradation. Results further call for the need to improve crop health to ensure food security in the most populated parts of the world, such as in South Asia, where the poorest of the poor, the landless farmers, are at the greatest risk. The overview of results generated from this work identifies directions for future research to be championed by a new generation of scientists and revived public extension services. Breakthroughs from science are needed to (i) gather more data on plant health and its consequences, (ii) identify collective actions to manage plant systems, (iii) exploit the phytobiome diversity in breeding programs, (iv) breed for plant genotypes with resilience to biotic and abiotic stresses, and (v) design and implement plant systems involving the diversity required to ensure their adaptation to current and growing challenges, including climate change and pathogen invasions., Competing Interests: The author(s) declare no conflict of interest.

The cassava whitefly Bemisia tabaci causes damage in cassava through the feeding and vectoring of plant viruses that cause cassava mosaic and cassava brown streak diseases. This study sought to explore the efficacy of cutting dipping in flupyradifurone for whitefly control and the impact of the mode of application on whitefly parasitism under farmer field conditions. The insecticide treatment significantly reduced adult whiteflies by 41%, nymphs by 64%, and cassava mosaic disease (CMD) incidence by 16% and increased root yield by 49%. The whitefly parasitism rate by Encarsia spp. parasitoids was 27.3 and 21.1%, while Eretmocerus spp. had 26.7 and 18.0% in control and flupyradifurone, respectively, and these differences were not significant. Electropenetrography recordings of whitefly feeding behaviour on flupyradifurone-treated plants showed significantly reduced probing activity and a delay in reaching the phloem as compared to the control. The findings from this study demonstrated that cassava cutting dipping in flupyradifurone significantly reduces whitefly numbers and cassava mosaic disease incidence, thus contributing to a significant root yield increase in cassava. Flupyradifurone applied through cutting dips does not significantly impact parasitism rates in cassava fields. Routine monitoring of parasitoids and predators in insecticide-treated versus control fields should be emphasized to determine the impact of pesticides on these beneficial non-target organisms.

Pests and diseases are key biotic constraints limiting banana production among smallholder farmers in Eastern and Central Africa. Climate changemay favour pest and disease development and further exacerbate the vulnerability of smallholder farming systems to biotic constraints. Information on effects of climate change on pests and pathogens of banana is required byby policy makers and researchers in designing control strategies and adaptation plans. Since altitude is inversely related to temperature, this study used the occurrence of key banana pests and diseases along an altitude gradient as a proxy for the potential impact of changes in temperature associated with global warming on pests and diseases. We assessed the occurrence of banana pests and diseases in 93 banana fields across three altitude ranges in Burundi and 99 fields distributed in two altitude ranges in Rwanda watersheds. Incidence and prevalence of Banana Bunchy Top Disease (BBTD) and Fusarium wilt (FW) was significantly associated with temperature and altitude in Burundi, revealing that increasing temperatures may lead to upward movement of banana diseases. No significant associations with temperature and altitude were observed for weevils, nematodes and Xanthomonas wilt of banana (BXW). Data collected in this study provides a baseline to verify and guide modelling work to predict future pest and disease distribution according to climate change scenarios. Such information is useful in informing policy makers and designing appropriate management strategies., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors.)

A novel butenolide insecticide-flupyradifurone (Sivanto SL 200)-was evaluated for efficacy against cassava-colonizing Bemisia tabaci whitefly under laboratory, screenhouse and field conditions. LC50 values from leaf disc spray assays were comparable for both flupyradifurone (12.7 g a.i/100 L) and imidacloprid (12.6 g a.i/100 L). Both insecticides caused high levels of adult whitefly mortality in leaf disc and leaf dip assays when compared to untreated controls. In screenhouse-based trials, longer soaking (60 min) with flupyradifurone or imidacloprid was more effective than shorter soaking durations (15 or 30 min). In field spraying experiments, flupyradifurone significantly reduced whiteflies, and both insecticides demonstrated powerful knockdown effects on whitefly adult abundances over a period up to 24 h. Single cutting dip application of flupyradifurone reduced whitefly adult abundance by 2 to 6 times, and nymphs by 2 to 13 times. Lower whitefly abundances resulting from insecticide application reduced the incidence of CMD or CBSD. In addition, in field experiments, whiteflies were fewer during the long rainy season (Masika) and on cassava variety Mkuranga1. The findings from this study demonstrate that cutting dips with flupyradifurone could be incorporated as a management tactic against cassava whiteflies. This would ideally be combined in an IPM strategy with other cassava virus and virus vector management tactics including host-plant resistance, phytosanitation and the use of clean seed.

A comprehensive assessment of cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) was carried out in Comoros where cassava yield (5.7 t/ha) is significantly below the African average (8.6 t/ha) largely due to virus diseases. Observations from 66 sites across the Comoros Islands of Mwali, Ngazidja, and Ndzwani revealed that 83.3% of cassava fields had foliar symptoms of CBSD compared with 95.5% for CMD. Molecular diagnostics confirmed the presence of both cassava brown streak ipomoviruses (CBSIs) and cassava mosaic begomoviruses (CMBs). Although real-time RT-PCR only detected the presence of one CBSI species ( Cassava brown streak virus , CBSV) the second species ( Ugandan cassava brown streak virus , UCBSV) was identified using next-generation high-throughput sequencing. Both PCR and HTS detected the presence of East African cassava mosaic virus (EACMV). African cassava mosaic virus was not detected in any of the samples. Four whitefly species were identified from a sample of 131 specimens: Bemisia tabaci , B. afer , Aleurodicus dispersus , and Paraleyrodes bondari . Cassava B. tabaci comprised two mitotypes: SSA1-SG2 (89%) and SSA1-SG3 (11%). KASP SNP genotyping categorized 82% of cassava B. tabaci as haplogroup SSA-ESA. This knowledge will provide an important base for developing and deploying effective management strategies for cassava viruses and their vectors.

The present study characterizes Bemisia tabaci and Bemisia afer from cassava in eastern Democratic Republic of Congo (DRC). The Mitochondrial COI sequencing revealed the occurrence of six cassava B. tabaci mitotypes, which were designated into four haplogroups (SSA-ECA, SSA-CA, SSA2, and SSA-ESA) using KASP SNP genotyping. SSA-ECA (72%) was the most prevalent and occurred in the northern part of the surveyed area, in the Ituri and Nord/Sud-Kivu provinces, whilst SSA-CA (21%) was present in the south, primarily in Haut-Katanga. SSA-ECA was predominant in the areas of north-eastern DRC most severely affected by cassava brown streak disease and was also reported in the new outbreak area in Pweto territory, Haut-Katanga, in the south. Bemisia afer comprised two major clusters with 85.5% of samples in cluster one, while the rest were in cluster two, which has no reference sequence in GenBank. This study provides important information on the genetic diversity of B. tabaci and B. afer in eastern DRC. This knowledge will be used as a basis for further studies to understand and to identify the role of whitefly haplogroups, their population densities and consequences for virus epidemics and spread as well as leading to improved vector and virus management strategies.

Cassava plays a key role in ensuring food security and generating income for smallholder farmers throughout Central Africa, particularly in the Democratic Republic of Congo (DRC). This status is threatened, however, by cassava brown streak disease (CBSD), which has expanded its incidence and range in eastern DRC. The study described here comprises the first extensive assessment of temporal change in the occurrence of CBSD and its causal viruses in DRC, based on surveys conducted during 2016 and 2018. Cassava fields were inspected in Ituri, Nord-Kivu, Sud-Kivu, Tanganyika, and Haut-Katanga provinces within eastern DRC to record foliar incidence and severity of CBSD. Leaf samples were collected for virus detection and species-level identification. New occurrences of CBSD, confirmed by virus diagnostic tests, were recorded in two provinces (Haut-Katanga and Sud-Kivu) and nine previously unaffected territories, covering an area of >62,000 km 2 , and at up to 900 km from locations of previously published reports of CBSD in DRC. Overall, average CBSD incidence within fields was 13.2% in 2016 and 16.1% in 2018. In the new spread zone of Haut-Katanga, incidence increased from 1.7 to 15.9%. CBSD is now present in provinces covering 321,000 km 2 , which is approximately 14% of the total area of DRC. This represents a major expansion of the CBSD epidemic, which was only recorded from one province (Nord-Kivu) in 2012. Both Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus were detected in Ituri, Nord-Kivu, and Sud-Kivu, but only CBSV was detected in Haut-Katanga. Overall, these results confirm the increasing threat that CBSD poses to cassava production in DRC and describe an important expansion in the African pandemic of CBSD.

Nuru is a deep learning object detection model for diagnosing plant diseases and pests developed as a public good by PlantVillage (Penn State University), FAO, IITA, CIMMYT, and others. It provides a simple, inexpensive and robust means of conducting in-field diagnosis without requiring an internet connection. Diagnostic tools that do not require the internet are critical for rural settings, especially in Africa where internet penetration is very low. An investigation was conducted in East Africa to evaluate the effectiveness of Nuru as a diagnostic tool by comparing the ability of Nuru, cassava experts (researchers trained on cassava pests and diseases), agricultural extension officers and farmers to correctly identify symptoms of cassava mosaic disease (CMD), cassava brown streak disease (CBSD) and the damage caused by cassava green mites (CGM). The diagnosis capability of Nuru and that of the assessed individuals was determined by inspecting cassava plants and by using the cassava symptom recognition assessment tool (CaSRAT) to score images of cassava leaves, based on the symptoms present. Nuru could diagnose symptoms of cassava diseases at a higher accuracy (65% in 2020) than the agricultural extension agents (40-58%) and farmers (18-31%). Nuru's accuracy in diagnosing cassava disease and pest symptoms, in the field, was enhanced significantly by increasing the number of leaves assessed to six leaves per plant (74-88%). Two weeks of Nuru practical use provided a slight increase in the diagnostic skill of extension workers, suggesting that a longer duration of field experience with Nuru might result in significant improvements. Overall, these findings suggest that Nuru can be an effective tool for in-field diagnosis of cassava diseases and has the potential to be a quick and cost-effective means of disseminating knowledge from researchers to agricultural extension agents and farmers, particularly on the identification of disease symptoms and their management practices., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2020 Mrisho, Mbilinyi, Ndalahwa, Ramcharan, Kehs, McCloskey, Murithi, Hughes and Legg.)

Cassava brown steak disease (CBSD), caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), is the most important biotic constraint to cassava production in East and Central Africa. Concerted efforts are required to prevent further spread into West Africa as well as to reduce losses in areas already affected. The study reported here was part of a five-country (Kenya, Malawi, Mozambique, Tanzania and Uganda) programme that aimed to identify superior cassava cultivars resistant to CBSD and to disseminate them widely in the region. Seventeen tissue-cultured and virus-tested cultivars were evaluated in Tanzania across nine sites with diverse CBSD inoculum conditions. Experiments were planted using an alpha-lattice design and assessments were made of surrounding inoculum pressure, CBSD foliar and root incidence and root yield at harvest. There were large differences in CBSD infection between sites, with greatest spread recorded from the north-western Lake (Victoria) zone. Differences were driven by Bemisia tabaci whitefly vector abundance and CBSD inoculum pressure. Both CBSV and UCBSV were almost equally represented in cassava fields surrounding experimental plots, although CBSV predominated in the north-west whilst UCBSV was more frequent in coastal and southern sites. However, the incidence of CBSV was much greater than that of UCBSV in initially virus-free experimental plots, suggesting that CBSV is more virulent. Cultivars could be categorised into three groups based on the degree of CBSD symptom expression in shoots and roots. The seven cultivars (F10_30R2, Eyope, Mkumba, Mkuranga1, Narocass1, Nase3 and Orera) in the most resistant category each had shoot and root incidences of less than 20%. Fresh root yield differed between sites and cultivars, but there was no genotype by environment interaction for this trait, probably attributable to the large fertility and soil moisture differences between sites. Susceptible cultivars and the local check performed well in the absence of CBSD pressure, highlighting the importance of exploiting quality and yield traits of local landraces in breeding programmes. Overall, our results emphasized the importance of applying a balanced strategy for CBSD management. This should use both improved and local germplasm resources to generate high yielding cultivars for specific end-user traits, and combine the deployment of improved cultivars with phytosanitary control measures including the use of healthy planting material and planting during periods of reduced CBSD infection., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

The geographic pattern of cropland is an important risk factor for invasion and saturation by crop-specific pathogens and arthropods. Understanding cropland networks supports smart pest sampling and mitigation strategies. We evaluate global networks of cropland connectivity for key vegetatively propagated crops (banana and plantain, cassava, potato, sweet potato, and yam) important for food security in the tropics. For each crop, potential movement between geographic location pairs was evaluated using a gravity model, with associated uncertainty quantification. The highly linked hub and bridge locations in cropland connectivity risk maps are likely priorities for surveillance and management, and for tracing intraregion movement of pathogens and pests. Important locations are identified beyond those locations that simply have high crop density. Cropland connectivity risk maps provide a new risk component for integration with other factors-such as climatic suitability, genetic resistance, and global trade routes-to inform pest risk assessment and mitigation., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Institute of Biological Sciences.)

Bemisia tabaci is a cryptic species complex that requires the use of molecular tools for identification. The most widely used approach for achieving this is the partial sequencing of the mitochondrial DNA cytochrome oxidase I gene ( COI ). A more reliable single nucleotide polymorphism (SNP)-based genotyping approach, using Nextera restriction-site-associated DNA (NextRAD) sequencing, has demonstrated the existence of six major haplogroups of B. tabaci on cassava in Africa. However, NextRAD sequencing is costly and time-consuming. We, therefore, developed a cheaper and more rapid diagnostic using the Kompetitive Allele-Specific PCR (KASP) approach. Seven sets of primers were designed to distinguish the six B. tabaci haplogroups based on the NextRAD data. Out of the 152 whitefly samples that were tested using these primer sets, 151 (99.3%) produced genotyping results consistent with NextRAD. The KASP assay was designed using NextRAD data on whiteflies from cassava in 18 countries across sub-Saharan Africa. This assay can, therefore, be routinely used to rapidly diagnose cassava B. tabaci by laboratories that are researching or monitoring this pest in Africa. This is the first study to develop an SNP-based assay to distinguish B. tabaci whiteflies on cassava in Africa, and the first application of the KASP technique for insect identification.

Bemisia tabaci (Gennadius) is a polyphagous, highly destructive pest that is capable of vectoring viruses in most agricultural crops. Currently, information regarding the distribution and genetic diversity of B. tabaci in South Sudan is not available. The objectives of this study were to investigate the genetic variability of B. tabaci infesting sweet potato and cassava in South Sudan. Field surveys were conducted between August 2017 and July and August 2018 in 10 locations in Juba County, Central Equatoria State, South Sudan. The sequences of mitochondrial DNA cytochrome oxidase I (mtCOI) were used to determine the phylogenetic relationships between sampled B. tabaci . Six distinct genetic groups of B. tabaci were identified, including three non-cassava haplotypes (Mediterranean (MED), Indian Ocean (IO), and Uganda) and three cassava haplotypes (Sub-Saharan Africa 1 sub-group 1 (SSA1-SG1), SSA1-SG3, and SSA2). MED predominated on sweet potato and SSA2 on cassava in all of the sampled locations. The Uganda haplotype was also widespread, occurring in five of the sampled locations. This study provides important information on the diversity of B. tabaci species in South Sudan. A comprehensive assessment of the genetic diversity, geographical distribution, population dynamics, and host range of B. tabaci species in South Sudan is vital for its effective management.

Cassava brown streak disease (CBSD) is currently the most devastating cassava disease in eastern, central and southern Africa affecting a staple crop for over 700 million people on the continent. A major outbreak of CBSD in 2004 near Kampala rapidly spread across Uganda. In the following years, similar CBSD outbreaks were noted in countries across eastern and central Africa, and now the disease poses a threat to West Africa including Nigeria - the biggest cassava producer in the world. A comprehensive dataset with 7,627 locations, annually and consistently sampled between 2004 and 2017 was collated from historic paper and electronic records stored in Uganda. The survey comprises multiple variables including data for incidence and symptom severity of CBSD and abundance of the whitefly vector (Bemisia tabaci). This dataset provides a unique basis to characterize the epidemiology and dynamics of CBSD spread in order to inform disease surveillance and management. We also describe methods used to integrate and verify extensive field records for surveys typical of emerging epidemics in subsistence crops.

Cassava brown streak disease (CBSD), caused by cassava brown streak ipomoviruses (CBSIs), has become the most debilitating biotic stress to cassava production in East and Central Africa. Lack of CBSD-resistant varieties has necessitated the search for alternative control measures. Most smallholder farmers reuse stems from previous crops for planting in the new season. Recycling planting material in this way can lead to "degeneration" owing to the compounding effects of disease. In this study, degeneration was defined as the increase in CBSD incidence and reduction in marketable root yield over time. An experiment was established to study the rates of degeneration in selected cassava varieties Chereko, KBH2002&#95;135, Kipusa, Kizimbani, and Mkuranga1 and cultivars Kiroba and Kikombe under high-CBSD inoculum conditions in Bagamoyo, Tanzania from 2013 to 2017. The experiment was replicated across two seasons: the first planted during the long rains (Masika) between March and June and the second planted during the short rains (Vuli) between October and December. Mean abundance of the whitefly vector ( Bemisia tabaci ) was much greater during the Vuli season (>19 insects per plant) than the Masika season (<2 insects per plant). CBSD shoot symptoms occurred naturally and were observed only on Kikombe, Kiroba, and Kipusa. New materials had overall lower CBSD shoot incidences (1.5%) compared with recycled materials (6.9%) in Masika, although no significant differences were obvious in Vuli. However, Masika (8.7%) had an overall lower CBSD shoot incidence than Vuli (16.5%) in the varieties that had shoot symptoms. CBSD root incidences were higher in Vuli (10.3%) than Masika (4.4%), and root yields in Masika (29.4 t/ha) were significantly greater than those in Vuli (22.5 t/ha). The highest percentage of roots rendered unusable owing to CBSD was observed in Vuli. There was significantly higher unusable root incidence in recycled materials (3.7%) than in new materials (1.4%) in Masika but not in Vuli. Overall root yield was similar between recycled and new materials in either season. Significant reductions in root yield over the course of the experiment were observed both in Masika and Vuli, whereas changes in marketable yield were significant only in Masika. Differences in the response of varieties to degeneration led to the identification of four degeneration patterns, namely "strong," "moderate," "mild," and "delayed" degeneration. The strongest effects of degeneration were most obvious in the susceptible cultivar (Kikombe), which also had the lowest marketable yield in either season. Seasonal differences were a key driver of degeneration, because its effects were much greater in Vuli than Masika. To the best of our knowledge, this work reports the first study of degeneration caused by cassava viruses.[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

The whitefy Bemisia tabaci, a species complex consisting of many morphologically indistinguishable species divided into distinct clades, is one of the most globally important agricultural pests and plant virus vectors. Cassava-colonizing B. tabaci transmits viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). Half of all cassava plants in Africa are affected by these viral diseases, resulting in annual production losses of more than US$ 1 billion. Here we report the draft genome of the cassava whitefly B. tabaci Sub-Saharan Africa - East and Central Africa (SSA-ECA), the super-abundant population that has been associated with the rapid spread of viruses causing the pandemics of CMD and CBSD. The SSA-ECA genome assembled from Illumina short reads has a total size of 513.7 Mb and a scaffold N50 length of 497 kb, and contains 15,084 predicted protein-coding genes. Phylogenetic analysis suggests that SSA-ECA diverged from MEAM1 around 5.26 million years ago. A comprehensive genetic analysis of cassava-colonizing B. tabaci in Africa was also conducted, in which a total of 243 whitefly specimens were collected from 18 countries representing all major cassava-growing regions in the continent and genotyped using NextRAD sequencing. Population genomic analyses confirmed the existence of six major populations linked by gene flow and inferred the distribution patterns of these populations across the African continent. The genome of SSA-ECA and the genetic findings provide valuable resources and guidance to facilitate whitefly research and the development of strategies to control cassava viral diseases spread by whiteflies., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Misuse and poor handling of chemical pesticides in agriculture is hazardous to the health of farmers, consumers, and to the environment. We studied the pest and disease management practices and the type of pesticides used in four root, tuber, and banana (RTB) crops in Rwanda and Burundi through in-depth interviews with a total of 811 smallholder farmers. No chemical pesticides were used in banana in either Rwanda and Burundi, whereas the use of insecticides and fungicides in potato was quite frequent. Nearly all insecticides and about one third of the fungicides used are moderately hazardous. Personal protective equipment was used by less than a half of the interviewed farmers in both countries. Reported cases of death due to self- or accidental-poisoning among humans and domestic animals in the previous 12 months were substantial in both countries. Training of farmers and agrochemical retailers in safe use of pesticide and handling and, use of integrated pest management approaches to reduce pest and disease damage is recommended.

Whiteflies of the Bemisia tabaci species complex are economically important pests of cassava. In Africa, they cause greatest damage through vectoring viruses responsible for cassava mosaic disease and cassava brown streak disease. Several cryptic species from the B. tabaci complex colonize cassava and neighboring crops, but the feeding interactions between the different crops and B. tabaci species are unknown. The electrical penetration graph (EPG) technique makes it possible to conduct detailed feeding studies of sap-sucking insects by creating an electric circuit through the insect and the plant. The apparatus measures the voltage fluctuations while the wired-up insect feeds and produces graphs that describe feeding behavior. We utilized EPG to explore the feeding behavior of cassava-colonizing whiteflies (SSA1-SG3) on cassava, sweet potato, tomato, and cotton; and sweet potato-colonizing whiteflies (MED and IO) on cassava and sweet potato. Results show that: (1) feeding of SSA1-SG3 is not restricted to cassava. The least preferred host for SSA1-SG3 was tomato, where probing was delayed by 99 min compared to 10 min on other hosts, furthermore mean duration of phloem ingestion events was 36 min compared to 260 min on cassava. (2) Feeding of MED on cassava appeared to be non-functional, as it was characterized by short total phloem ingestion periods (<1 h) and few, short ingestion events, in contrast to feeding on sweet potato which was characterized by long phloem ingestion periods (>5 h). (3) Wire diameter affects the feeding in a statistically and practically significant manner. Implications for whitefly control and studies of host whitefly resistance are discussed.

Here, we report a method to clean cassava plants from viral infections that cause cassava mosaic and brown streak diseases in Africa. Infected plants of resistant or tolerant varieties from Malawi, Mozambique, Kenya, Tanzania and Uganda were cleaned in the UK using a combination of tissue culture, chemotherapy and thermotherapy. In the first cycle of our virus-indexing procedure, we successfully cleaned 27 of the 31 varieties (87%), and after an additional three cleaning cycles, all plants were virus-free. Virus-free tissue-cultured plants were shipped back to Africa for distribution to farmers. This first cross-boundary effort provides important lessons for mitigating the two-major cassava viral diseases.

Management of geminiviruses is a worldwide challenge because of the widespread distribution of economically important diseases caused by these viruses. Regardless of the type of agriculture, management is most effective with an integrated pest management (IPM) approach that involves measures before, during, and after the growing season. This includes starting with resistant cultivars and virus- and vector-free transplants and propagative plants. For high value vegetables, protected culture (e.g., greenhouses and screenhouses) allows for effective management but is limited owing to high cost. Protection of young plants in open fields is provided by row covers, but other measures are typically required. Measures that are used for crops in open fields include roguing infected plants and insect vector management. Application of insecticide to manage vectors (whiteflies and leafhoppers) is the most widely used measure but can cause undesirable environmental and human health issues. For annual crops, these measures can be more effective when combined with host-free periods of two to three months. Finally, given the great diversity of the viruses, their insect vectors, and the crops affected, IPM approaches need to be based on the biology and ecology of the virus and vector and the crop production system. Here, we present the general measures that can be used in an IPM program for geminivirus diseases, specific case studies, and future challenges.

Cassava brown streak disease (CBSD) is arguably the most dangerous current threat to cassava, which is Africa's most important food security crop. CBSD is caused by two RNA viruses: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). The roles of the whitefly Bemisia tabaci (Gennadius) and farmer practices in the spread of CBSD were investigated in a set of field and laboratory experiments. The virus was acquired and transmitted by B. tabaci within a short time (5-10 min each for virus acquisition and inoculation), and was retained for up to 48 hr. Highest virus transmission (60%) was achieved using 20-25 suspected viruliferous whiteflies per plant that were given acquisition and inoculation periods of 24 and 48 hr, respectively. Experiments mimicking the agronomic practices of cassava leaf picking or the use of contaminated tools for making cassava stem cuttings did not show the transmission of CBSV or UCBSV. Screenhouse and field experiments in Tanzania showed that the spread of CBSD next to spreader rows was high, and that the rate of spread decreased with increasing distance from the source of inoculum. The disease spread in the field up to a maximum of 17 m in a cropping season. These results collectively confirm that CBSV and UCBSV are transmitted by B. tabaci semipersistently, but for only short distances in the field. This implies that spread over longer distances is due to movements of infected stem cuttings used for planting material. These findings have important implications for developing appropriate management strategies for CBSD.

Bemisia tabaci threatens production of cassava in Africa through vectoring viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). B. tabaci sampled from cassava in eight countries in Africa were genotyped using NextRAD sequencing, and their phylogeny and population genetics were investigated using the resultant single nucleotide polymorphism (SNP) markers. SNP marker data and short sequences of mitochondrial DNA cytochrome oxidase I (mtCOI) obtained from the same insect were compared. Eight genetically distinct groups were identified based on mtCOI, whereas phylogenetic analysis using SNPs identified six major groups, which were further confirmed by PCA and multidimensional analyses. STRUCTURE analysis identified four ancestral B. tabaci populations that have contributed alleles to the six SNP-based groups. Significant gene flows were detected between several of the six SNP-based groups. Evidence of gene flow was strongest for SNP-based groups occurring in central Africa. Comparison of the mtCOI and SNP identities of sampled insects provided a strong indication that hybrid populations are emerging in parts of Africa recently affected by the severe CMD pandemic. This study reveals that mtCOI is not an effective marker at distinguishing cassava-colonizing B. tabaci haplogroups, and that more robust SNP-based multilocus markers should be developed. Significant gene flows between populations could lead to the emergence of haplogroups that might alter the dynamics of cassava virus spread and disease severity in Africa. Continuous monitoring of genetic compositions of whitefly populations should be an essential component in efforts to combat cassava viruses in Africa., (© The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

To improve understanding of the dynamics of the cassava mosaic disease (CMD) pandemic front, geospatial approaches were applied to the analysis of 3 years' data obtained from a 2-by-2° (approximately 222-by-222 km) area of northwestern Tanzania. In total, 80 farmers' fields were assessed in each of 2009, 2010, and 2011, with 20 evenly distributed fields per 1-by-1° quadrant. CMD-associated variables (CMD incidence, CMD severity, vector-borne CMD infection, and vector abundance) increased in magnitude from 2009 to 2010 but showed little change from 2010 to 2011. Increases occurred primarily in the two westernmost quadrants of the study area. A pandemic "front" was defined by determining the values of CMD incidence and whitefly abundance where predicted disease gradients were greatest. The pandemic-associated virus (East African cassava mosaic virus-Uganda) and vector genotype (Bemisia tabaci sub-Saharan Africa 1-subgroup 1) were both present within the area bounded by the CMD incidence front but both also occurred ahead of the front. The average speed and direction of movement of the CMD incidence front (22.9 km/year; southeast) and whitefly abundance front (46.6 km/year; southeast) were calculated, and production losses due to CMD were estimated to range from US$4.3 million to 12.2 million.

Pathogen buildup in vegetative planting material, termed seed degeneration, is a major problem in many low-income countries. When smallholder farmers use seed produced on-farm or acquired outside certified programs, it is often infected. We introduce a risk assessment framework for seed degeneration, evaluating the relative performance of individual and combined components of an integrated seed health strategy. The frequency distribution of management performance outcomes was evaluated for models incorporating biological and environmental heterogeneity, with the following results. (1) On-farm seed selection can perform as well as certified seed, if the rate of success in selecting healthy plants for seed production is high; (2) when choosing among within-season management strategies, external inoculum can determine the relative usefulness of 'incidence-altering management' (affecting the proportion of diseased plants/seeds) and 'rate-altering management' (affecting the rate of disease transmission in the field); (3) under severe disease scenarios, where it is difficult to implement management components at high levels of effectiveness, combining management components can be synergistic and keep seed degeneration below a threshold; (4) combining management components can also close the yield gap between average and worst-case scenarios. We also illustrate the potential for expert elicitation to provide parameter estimates when empirical data are unavailable. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Bacterial diversity underpins many ecosystem functions; however, the impact of within-species variation on the relationship between diversity and function remains unclear. Processes involving strain differentiation, such as niche radiation, are often overlooked in studies that focus on phylogenetic variation. This study used bacterial isolates assembled in two comparable microcosm experiments to test how species variation affected ecosystem function. We compared the relationship between diversity and activity (CO 2 production) in increasingly diverse multispecies microcosms and with multiple ecotypes of a single species. The bacteria used were isolated from a low-diversity environment and are species of potential clinical significance such as Pseudomonas aeruginosa. All isolates were profiled for single carbon source utilisation. These data showed an increased breadth of resource use in the multiple ecotypes when compared to the mixed-species. The study observed significantly increasing respiration in more complex mixed-species assemblages, which was not observed when ecotypes of a single species were combined. We further demonstrate that the variation observed in the bacterial activity was due to the roles of each of the constituent isolates; between different species, the interactions between the isolates drove the variation in activity, whilst in single species, assemblage variation was due to which isolates were present. We conclude that both between- and within-species variations play different roles in community function, although through different mechanisms, and should be included in models of changing diversity and ecosystem functioning.

Cassava brown streak disease (CBSD) is the most important virus disease of cassava and a major food security threat in Africa. Yearly economic losses of up to $100 million USD have been attributed to CBSD. The lack of information on plant-virus interactions has restricted progress in breeding for CBSD resistance. Virus quantification is becoming a major tool for the quick and reliable assessment of plant host resistance. Therefore, a protocol for specific absolute quantification of Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) was developed. CBSV and UCBSV coat protein (CP) specific standard templates: CBSV (pFer2, 826bp) and UCBSV (pUF1-R1-1, 732) respectively were generated and maintained in a TA cloning vector. These were used to construct standard curves using a TaqMan qPCR assay. Standard curves with acceptable amplification efficiencies (90-105%) and coefficients of determination (R 2 ) greater than 0.99 were obtained. Infected cassava plants were sampled from a screenhouse and the field and used to validate this assay. Results obtained by testing several screenhouse and field samples revealed consistent absolute quantification assays for different CBSV and UCBSV isolates. This study presents the first protocol for absolute quantification of CBSVs and is expected to accelerate screening for CBSD resistance and hence breeding for CBSD resistance. The use of the method presented here should improve the clarity of virus quantification data as the results obtained are not influenced by varietal, host, seasonal or environmental conditions. Screening efficiency will also be greatly improved as there is no need for the use of reference genes consequently allowing for a larger number of samples to be analyzed. This will increase experimental precision in a timely and cost effective manner., (Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.)

The sweetpotato whitefly, Bemisia tabaci (Gennadius) is the vector of the cassava mosaic geminiviruses (CMGs) that cause cassava mosaic disease (CMD). Synergistic interactions between B. tabaci and CMGs have been hypothesized as a cause of whitefly "super-abundance," which has been a key factor behind the spread of the severe CMD pandemic through East and Central Africa. The current study investigated this hypothesis by conducting experiments with CMD-susceptible cassava varieties infected with different CMGs in both the north-western Lake Zone region (pandemic affected) and the eastern Coast Zone where CMD is less severe. Male and female pairs of B. tabaci were placed in clip cages for 48 h on plants of three cassava varieties at each of the two locations. There were significantly more eggs laid on CMG-infected than on CMG-free plants in the Lake Zone, whereas in Coast Zone, there were no significant differences. There were no significant differences in proportions, mortality, and development duration of immature stages of B. tabaci among virus states and cassava variety in the two locations. The overall number of eggs was significantly higher with longer development duration of the immature stages in the Lake than in the Coast Zone, whereas mortality was significantly higher in the Coast than in the Lake Zone. Based on these results, it is concluded that there was no net positive synergistic interaction between CMGs and B. tabaci for either lowland coastal or mid-altitude inland populations. Consequently, other factors seem more likely to be the cause of the "super-abundance," and require further investigation., (© The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Cassava brown streak disease (CBSD), caused by cassava brown streak viruses, is recognized as one of the most important plant disease threats to African food security. This study describes the incidence and severity of the different symptom types caused by CBSD, derived from extensive surveys in the country most severely affected by the disease: Tanzania. Total plant incidence and mean root severity of CBSD, recorded from 341 farmers' fields, were both greater in the Coast Zone (49.5% and 3.05), than in the Lake Zone (32.7% and 2.57). Overall, the differing incidences recorded declined in the following order: total plant incidence (39.1%), plant shoot incidence (33.4%), plant root incidence (19.3%), root incidence (10.5%), and unusable root incidence (5.4%). The much lower-than-anticipated loss due to the root necrosis that is characteristic of CBSD was offset by large reductions of root number in plants expressing foliar symptoms of CBSD (15.7% in the Coast Zone and 5.5% in the Lake Zone). These data suggest that the effects of CBSD on the growth of affected plants are greater than those due to root spoilage. Based on these two factors, annual losses due to CBSD in the parts of Tanzania surveyed were estimated at >860,000 t, equivalent to more than U.S.$51 million. A novel approach to using farm-derived data on the responses of the most frequently cultivated varieties to CBSD infection allowed the grouping of the varieties into four categories, based on their relative resistance or tolerance to infection. This tool should be of value to breeders in identifying and selecting for sources of resistance or tolerance in both local and exotic germplasm, and should ultimately contribute to enhancing the management of one of Africa's most damaging crop diseases.

A survey was conducted from April to May 2014 in 214 farmers' fields located across six major cassava-producing provinces (Western, Northwestern, Northern, Luapula, Lusaka, and Eastern) of Zambia to determine the status of cassava mosaic disease (CMD) and the species diversity of associated cassava mosaic geminiviruses (CMG). Mean CMD incidence varied across all six provinces but was greatest in Lusaka Province (81%) and least in Northern Province (44%). Mean CMD severity varied slightly between provinces, ranging from 2.78 in Eastern Province to 3.00 in Northwestern Province. Polymerase chain reaction discrimination of 226 survey samples, coupled with complete DNA-A genome sequence analysis, revealed the presence of African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), and East African cassava mosaic Malawi virus (EACMMV) as single or mixed infections of different proportions. Single-virus infections were predominant, occurring in 62.8% (ACMV), 5.8% (EACMMV), and 2.2% (EACMV) of samples relative to mixed-virus infections, which occurred in 19.5% (ACMV + EACMMV), 0.4% (ACMV + EACMV), and 0.9% (ACMV + EACMV + EACMMV) of samples. Phylogenetic analysis revealed the segregation of virus isolates from Zambia into clades specific to ACMV, EACMV, and EACMMV, further confirming the presence of all three viruses in Zambia. The results point to a greater diversity of CMG across major cassava-growing provinces of Zambia and implicate contaminated cassava cuttings in disease spread.

Unlabelled: Cassava mosaic begomoviruses (CMBs) cause cassava mosaic disease (CMD) across Africa and the Indian subcontinent. Like all members of the geminivirus family, CMBs have small, circular single-stranded DNA genomes. We report here the discovery of two novel DNA sequences, designated SEGS-1 and SEGS-2 (forsequencesenhancinggeminivirussymptoms), that enhance symptoms and break resistance to CMD. The SEGS are characterized by GC-rich regions and the absence of long open reading frames. Both SEGS enhanced CMD symptoms in cassava (Manihot esculentaCrantz) when coinoculated withAfrican cassava mosaic virus(ACMV),East African cassava mosaic Cameroon virus(EACMCV), orEast African cassava mosaic virus-Uganda(EACMV-UG). SEGS-1 also overcame resistance of a cassava landrace carrying the CMD2 resistance locus when coinoculated with EACMV-UG. Episomal forms of both SEGS were detected in CMB-infected cassava but not in healthy cassava. SEGS-2 episomes were also found in virions and whiteflies. SEGS-1 has no homology to geminiviruses or their associated satellites, but the cassava genome contains a sequence that is 99% identical to full-length SEGS-1. The cassava genome also includes three sequences with 84 to 89% identity to SEGS-2 that together encompass all of SEGS-2 except for a 52-bp region, which includes the episomal junction and a 26-bp sequence related to alphasatellite replication origins. These results suggest that SEGS-1 is derived from the cassava genome and facilitates CMB infection as an integrated copy and/or an episome, while SEGS-2 was originally from the cassava genome but now is encapsidated into virions and transmitted as an episome by whiteflies., Importance: Cassava is a major crop in the developing world, with its production in Africa being second only to maize. CMD is one of the most important diseases of cassava and a serious constraint to production across Africa. CMD2 is a major CMD resistance locus that has been deployed in many cassava cultivars through large-scale breeding programs. In recent years, severe, atypical CMD symptoms have been observed occasionally on resistant cultivars, some of which carry the CMD2 locus, in African fields. In this report, we identified and characterized two DNA sequences, SEGS-1 and SEGS-2, which produce similar symptoms when coinoculated with cassava mosaic begomoviruses onto a susceptible cultivar or a CMD2-resistant landrace. The ability of SEGS-1 to overcome CMD2 resistance and the transmission of SEGS-2 by whiteflies has major implications for the long-term durability of CMD2 resistance and underscore the need for alternative sources of resistance in cassava., (Copyright © 2016 Ndunguru et al.)

Objectives: Acute viral respiratory illnesses are associated with acquisition of Pseudomonas aeruginosa infection in cystic fibrosis (CF) patients. This study aimed to pilot a protocol for a randomized controlled trial to determine whether oral antipseudomonal antibiotics used at the onset of such episodes might delay onset of infection with this organism., Methods: A total of 41 children with CF aged 2-14 years, without chronic Pseudomonas infection, were randomized to receive ciprofloxacin (n = 28) or placebo (n = 13) at the onset of acute viral respiratory infections on an intention to treat basis, during a study period of up to 32 months., Results: There were no unexpected adverse events believed related to the use of the study medication. The rate of withdrawal from the study was low (approximately 7%) and did not differ between groups. Randomization was effective and acceptable to participants. Primary and secondary outcome measures all favoured active treatment, but there were no significant between group differences. The median rate of Pseudomonas isolates was 0/patient/year (interquartile range 0-0.38) in both the active and placebo groups. Kaplan-Meier survival curves showed no significant difference in time to first Pseudomonas isolate between groups., Conclusions: This study demonstrated the clinical feasibility of using oral ciprofloxacin in CF patients at times of viral infection. Within this sample size, no significant association was found between active treatment and decreased growth of Pseudomonas in follow-up microbiological samples. A definitive study would require at least 320 children to demonstrate significant differences in the rate of pseudomonal isolates., (© The Author(s), 2015.)