Genetic characterization of fungal biodiversity in storage grains : towards enhancing food safety in northern Uganda

Worldwide fungal contamination leads to both quantitative and qualitative grain losses during crop growth and/or storage. A greater proportion of grains contamination with toxins often occurs in sub-Saharan Africa, where control measures are limited. We determined fungal diversity and their toxin production ability in household grains meant for human consumption to highlight the risk of mycotoxin exposure among people from northern Uganda. The study underlines the high diversity of fungi that group into 15 genera; many of which are plant pathogens with toxigenic potential. Fusarium verticillioides was the most common fungal species isolated from household grains. The study also indicates that northern Uganda is favored by a high proportion of toxigenic isolates of F. verticillioides, F. andiyazi, and F. proliferatum, which are characterized by a high fumonisins production capability. The fumonisins production ability was not dependent on the species, grain types, and haplotype group to which the isolates belong. The contamination of most household grains with fungi capable of producing a high amount of toxin shows that most people are exposed to an elevated amount of mycotoxins, which shows the frequent problems with mycotoxins that have been reported in most parts of sub-Saharan Africa

Mycotoxin profile of staple grains in northern Uganda : understanding the level of human exposure and potential risks

Mycotoxins are toxic metabolites of fungi that contaminate food and feed. These toxins can cause acute and chronic health threats to both humans and animals. In sub-Saharan Africa, exposure to mycotoxins is chronic and under-reported. The study explores contamination of grains (sorghum, maize, groundnut, millet) with four mycotoxins (aflatoxins, fumonisins, ochratoxins, and deoxynivalenol) and dietary exposure to quantify associated health risks in northern Uganda. The results underscored the high prevalence of mycotoxins, only 7% of the samples were free from toxins. Sorghum grains seemed to be the most susceptible to toxin contamination, whereas in millet the toxin levels were, in general, the lowest. Besides, the results showed that the majority of grains were contaminated with more than one mycotoxin and that the toxin pattern was dependent on the grain type. Co-contamination with all four mycotoxins mainly occurred in sorghum grains. Besides the differences between grain types, there were also significant differences in toxins levels depending on the district where the grains came from. The estimated daily intakes for the mycotoxins were far above the recommended tolerable daily intake (TDI), especially for sorghum. So, it can be concluded that the majority of the people whose diet is mainly based on sorghum are exposed to multiple mycotoxins in a single diet and at a dose above the TDI. Such exposure to multiple mycotoxins elevates the associated health risks. Millet grains, which were the least contaminated, can provide an alternative to sorghum. However, to tackle the mycotoxin problem, other control and prevention mechanisms, e.g. good agricultural practices and optimized storage must be further explored and implemented in sub-Saharan Africa

Wolbachia association with the tsetse fly, Glossina fuscipes fuscipes, reveals high levels of genetic diversity and complex evolutionary dynamics

BACKGROUND: Wolbachia pipientis, a diverse group of α-proteobacteria, can alter arthropod host reproduction and confer a reproductive advantage to Wolbachia-infected females (cytoplasmic incompatibility (CI)). This advantage can alter host population genetics because Wolbachia-infected females produce more offspring with their own mitochondrial DNA (mtDNA) haplotypes than uninfected females. Thus, these host haplotypes become common or fixed (selective sweep). Although simulations suggest that for a CI-mediated sweep to occur, there must be a transient phase with repeated initial infections of multiple individual hosts by different Wolbachia strains, this has not been observed empirically. Wolbachia has been found in the tsetse fly, Glossina fuscipes fuscipes, but it is not limited to a single host haplotype, suggesting that CI did not impact its population structure. However, host population genetic differentiation could have been generated if multiple Wolbachia strains interacted in some populations. Here, we investigated Wolbachia genetic variation in G. f. fuscipes populations of known host genetic composition in Uganda. We tested for the presence of multiple Wolbachia strains using Multi-Locus Sequence Typing (MLST) and for an association between geographic region and host mtDNA haplotype using Wolbachia DNA sequence from a variable locus, groEL (heat shock protein 60). RESULTS: MLST demonstrated that some G. f. fuscipes carry Wolbachia strains from two lineages. GroEL revealed high levels of sequence diversity within and between individuals (Haplotype diversity = 0.945). We found Wolbachia associated with 26 host mtDNA haplotypes, an unprecedented result. We observed a geographical association of one Wolbachia lineage with southern host mtDNA haplotypes, but it was non-significant (p = 0.16). Though most Wolbachia-infected host haplotypes were those found in the contact region between host mtDNA groups, this association was non-significant (p = 0.17). CONCLUSIONS: High Wolbachia sequence diversity and the association of Wolbachia with multiple host haplotypes suggest that different Wolbachia strains infected G. f. fuscipes multiple times independently. We suggest that these observations reflect a transient phase in Wolbachia evolution that is influenced by the long gestation and low reproductive output of tsetse. Although G. f. fuscipes is superinfected with Wolbachia, our data does not support that bidirectional CI has influenced host genetic diversity in Uganda

Esperanza Window Traps for the collection of anthropophilic blackflies (Diptera: Simuliidae) in Uganda and Tanzania.

There is an increasing need to evaluate the impact of chemotherapeutic and vector-based interventions as onchocerciasis affected countries work towards eliminating the disease. The Esperanza Window Trap (EWT) provides a possible alternative to human landing collections (HLCs) for the collection of anthropophilic blackflies, yet it is not known whether current designs will prove effective for onchocerciasis vectors throughout sub-Saharan Africa. EWTs were deployed for 41 days in northern Uganda and south eastern Tanzania where different Simulium damnosum sibling species are responsible for disease transmission. The relative efficacy of EWTs and HLCs was compared, and responses of host-seeking blackflies to odour baits, colours, and yeast-produced CO2 were investigated. Blue EWTs baited with CO2 and worn socks collected 42.3% (2,393) of the total S. damnosum s.l. catch in northern Uganda. Numbers were comparable with those collected by HLCs (32.1%, 1,817), and higher than those collected on traps baited with CO2 and BG-Lure (25.6%, 1,446), a synthetic human attractant. Traps performed less well for the collection of S. damnosum s.l. in Tanzania where HLCs (72.5%, 2,432) consistently outperformed both blue (16.8%, 563) and black (10.7%, 360) traps baited with CO2 and worn socks. HLCs (72.3%, 361) also outperformed sock-baited (6.4%, 32) and BG-Lure-baited (21.2%, 106) traps for the collection of anthropophilic Simulium bovis in northern Uganda. Contrasting blackfly distributions were observed on traps in Uganda and Tanzania, indicating differences in behaviour in each area. The success of EWT collections of S. damnosum s.l. in northern Uganda was not replicated in Tanzania, or for the collection of anthropophilic S. bovis. Further research to improve the understanding of behavioural responses of vector sibling species to traps and their attractants should be encouraged

Spatio-temporal distribution of Spiroplasma infections in the tsetse fly (Glossina fuscipes fuscipes) in northern Uganda

Copyright: © 2019 Schneider et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Tsetse flies (Glossina spp.) are vectors of parasitic trypanosomes, which cause human (HAT) and animal African trypanosomiasis (AAT) in sub-Saharan Africa. In Uganda, Glossina fuscipes fuscipes (Gff) is the main vector of HAT, where it transmits Gambiense disease in the northwest and Rhodesiense disease in central, southeast and western regions. Endosymbionts can influence transmission efficiency of parasites through their insect vectors via conferring a protective effect against the parasite. It is known that the bacterium Spiroplasma is capable of protecting its Drosophila host from infection with a parasitic nematode. This endosymbiont can also impact its host\u27s population structure via altering host reproductive traits. Here, we used field collections across 26 different Gff sampling sites in northern and western Uganda to investigate the association of Spiroplasma with geographic origin, seasonal conditions, Gff genetic background and sex, and trypanosome infection status. We also investigated the influence of Spiroplasma on Gff vector competence to trypanosome infections under laboratory conditions. Generalized linear models (GLM) showed that Spiroplasma probability was correlated with the geographic origin of Gff host and with the season of collection, with higher prevalence found in flies within the Albert Nile (0.42 vs 0.16) and Achwa River (0.36 vs 0.08) watersheds and with higher prevalence detected in flies collected in the intermediate than wet season. In contrast, there was no significant correlation of Spiroplasma prevalence with Gff host genetic background or sex once geographic origin was accounted for in generalized linear models. Additionally, we found a potential negative correlation of Spiroplasma with trypanosome infection, with only 2% of Spiroplasma infected flies harboring trypanosome co-infections. We also found that in a laboratory line of Gff, parasitic trypanosomes are less likely to colonize the midgut in individuals that harbor Spiroplasma infection. These results indicate that Spiroplasma infections in tsetse may be maintained by not only maternal but also via horizontal transmission routes, and Spiroplasma infections may also have important effects on trypanosome transmission efficiency of the host tsetse. Potential functional effects of Spiroplasma infection in Gff could have impacts on vector control approaches to reduce trypanosome infections

Retraction.

This is a retraction of 'Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa' 10.1126/science.add873

Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa.

The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection

Prevalence of sweetpotato viruses in Acholi sub-region, northern Uganda

The purpose of the study was to identify different viruses infecting sweetpotato and the level of co-infection and spatial distribution of the viruses within the Acholi sub-region of northern Uganda. Multiplex PCR was used to screen and determine level of co-infection in 380 sweetpotato plants. The PCR scores were computed to give overall frequency of occurrence of different viruses. The spatial distribution of viruses was represented on an ArcGIS map. Of all screened samples, 24% (92/380) were infected with at least one virus. Sweetpotato feathery mottle virus (65/92), sweetpotato chlorotic fleck virus (17/92) and sweetpotato mild mottle virus (8/92) were the most frequent viruses detected. Of sampled fields, 74% (28/38) had at least one virus-infected sweetpotato plant. The four viruses detected are the major viruses causing significant yield losses in major sweetpotato growing regions of Uganda and East Africa. The findings of limited distribution and low prevalence of the viruses in the region indicate it causes less burden to sweetpotato production in the sub-region compared with other parts of Uganda. Keywords: Sweetpotato mild mottle virus, Sweetpotato chlorotic fleck virus, Chlorotic fleck virus, Northern Ugand

Synergy and Timing: A Concurrent Mass Medical Campaign Predicted to Augment Indoor Residual Spraying for Malaria

Background: Control programmes for high burden countries are tasked with charting effective multi-year strategies for malaria control within significant resource constraints. Synergies between different control tools, in which more than additive benefit accrues from interventions used together, are of interest because they may be used to obtain savings or to maximize health impact per expenditure. One commonly used intervention in sub-Saharan Africa is indoor residual spraying (IRS), typically deployed through a mass campaign. While possible synergies between IRS and long-lasting insecticide-treated nets (LLINs) have been investigated in multiple transmission settings, coordinated synergy between IRS and other mass medical distribution campaigns have not attracted much attention. Recently, a strong timing-dependent synergy between an IRS campaign and a mass drug administration (MDA) was theoretically quantified. These synergistic benefits likely differ across settings depending on transmission intensity and its overall seasonal pattern. Methods: High coverage interventions are modelled in different transmission environments using two methods: a Ross–Macdonald model variant and openmalaria simulations. The impact of each intervention strategy was measured through its ability to prevent host infections over time, and the effects were compared to the baseline case of deploying interventions in isolation. Results: By modelling IRS and MDA together and varying their deployment times, a strong synergy was found when the administered interventions overlapped. The added benefit of co-timed interventions was robust to differences in the models. In the Ross–Macdonald model, the impact compared was roughly double the sequential interventions in most transmission settings. Openmalaria simulations of this medical control augmentation of an IRS campaign show an even stronger response with the same timing relationship. Conclusions: The strong synergies found for these control tools between the complementary interventions demonstrate a general feature of effective concurrent campaign-style vector and medical interventions. A mass treatment campaign is normally short-lived, especially in higher transmission settings. When co-timed, the rapid clearing of the host parasite reservoir via chemotherapy is protected from resurgence by the longer duration of the vector control. An effective synchronous treatment campaign has the potential to greatly augment the impact of indoor residual spraying. Mass screening and treatment (MSAT) with highly sensitive rapid diagnostic tests may demonstrate a comparable trend while mass LLIN campaigns may similarly coordinate with MDA/MSAT