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Maize lethal necrosis (MLN) is a maize disease caused by the maize chlorotic mottle virus (MCMV), a potyvirus which causes yield losses of 30–100%. The present study aimed to isolate nanobodies against the MCMV coat protein (CP) for the diagnosis of MLN. MCMV CP expressed in Escherichia coli was used for llama immunization. VHH (i.e. variable heavy domain of heavy chain) gene fragments were prepared from blood drawn from the immunized llama and used to generate a library in E. coli TG1 cells. MCMV specific nanobodies were selected by three rounds of phage display and panning against MCMV CP. The selected nanobodies were finally expressed in E. coli WK6 cells and purified. Eleven MCMV‐specific nanobodies were identified and shown to detect MCMV in infected maize plants. Thus, our results show that nanobodies isolated from llama immunized with MCMV CP can distinguish infected and healthy maize plants, potentially enabling development of affordable MCMV detection protocols.

OverviewThe roadmap adopted by the World Health Organization (WHO) for eliminating neglected tropical diseases aims to eliminate schistosomiasis, as a public health concern, by 2030. While progress has been made towards reducing schistosomiasis morbidity control in several sub-Saharan African countries, there is still more that needs to be done. Proper surveillance using accurate diagnostics with acceptable sensitivity and specificity is essential for evaluating the success of all efforts against schistosomiasis. Microscopy, despite its low sensitivity, remains the gold standard approach for diagnosing the disease. Although many efforts have been made to develop new diagnostics based on circulating parasite proteins, genetic markers, schistosome egg morphology, and their paramagnetic properties, none has been robust enough to replace microscopy. This review highlights common diagnostic approaches for detecting schistosomiasis in field and clinical settings, major challenges, and provides new and novel opportunities and diagnosis pathways that will be critical in supporting elimination of schistosomiasis.MethodsWe searched for relevant and reliable published literature from PubMed, Scopus, google scholar, and Web of science. The search strategies were primarily determined by subtopic, and hence the following words were used (schistosom*, diagnosis, Kato-Katz, antibody test, circulating antigen, POC-CCA, UCP-LF-CAA, molecular diagnostics, nucleic acid amplification test, microfluidics, lab-on a disk, lab-on chip, recombinase polymerase amplification (RPA), LAMP, portable sequencer, nanobody test, identical multi-repeat sequences, diagnostic TPPs, REASSURED, extraction free), and Boolean operators AND and/OR were used to refine the searching capacity. Due to the global public health nature of schistosomiasis, we also searched for reliable documents, reports, and research papers published by international health organizations, World Health Organization (WHO), and Center for Disease control and Elimination.

Objectives: Tanzania observed a gradual increase in the number of measles cases since 2019 with a large outbreak recorded during 2022. This study describes the trend of measles in Tanzania over a 5-year period from 2018-2022. Methods: This was a descriptive study conducted using routine measles case-based surveillance system including 195 councils of the United Republic of Tanzania. Results: Between 2018 and 2022 there were 12,253 measles cases reported. Out of 10,691 (87.25%) samples tested by enzyme-linked immunosorbent assay, 903 (8.4%) were measles immunoglobulin M positive. The highest number of laboratory-confirmed measles cases was in 2022 (64.8%), followed by 2020 (13.8%), and 2019 (13.5%). Out of 1279 unvaccinated cases, 213 (16.7%) were laboratory-confirmed measles cases compared to 77/723 (10.6%) who were partially vaccinated and 71/1121 (6.3%) who were fully vaccinated (P 90% since 2013 while MCV2 increased gradually reaching 88% in 2022. Conclusions: Accumulation of susceptible children to measles due to suboptimal measles vaccination coverage over the years has resulted in an increase in the number of laboratory-confirmed measles cases in Tanzania with more cases recorded during the COVID-19 pandemic. Strengthening surveillance, routine immunization, and targeted strategies are key to achieving the immunity levels required to interrupt measles outbreaks.

Reports of Rift Valley fever (RVF), a highly climate-sensitive zoonotic disease, have been rather frequent in Kenya. Although multiple empirical analyses have shown that machine learning methods outperform time series models in forecasting time series data, there is limited evidence of their application in predicting disease outbreaks in Africa. In recent times, the literature has reported several applications of machine learning in facilitating intelligent decision-making within the healthcare sector and public health. However, there is a scarcity of information regarding the utilization of the XGBoost model for predicting disease outbreaks. Within the provinces of Kenya, the incidence of Rift Valley fever was more prominent in the Rift Valley (26.80%) and Eastern (20.60%) regions. This study investigated the correlation between the occurrence of RVF (rapid vegetation failure) and several climatic variables, including humidity, clay content, elevation, slope, and rainfall. The correlation matrix revealed a modest linear dependence between different climatic variables and RVF cases, with the highest correlation, a mere 0.02903, observed for rainfall. The XGBoost model was trained using these climate variables and achieved outstanding performance measures including an AUC of 0.8908, accuracy of 99.74%, precision of 99.75%, and recall of 99.99%. The analysis of feature importance revealed that rainfall was the most significant predictor. These findings align with previous studies demonstrating the significance of weather conditions in RVF outbreaks. The study’s results indicate that incorporating advanced machine learning models that consider several climatic variables can significantly enhance the prediction and management of RVF incidence.

IntroductionSchistosomiasis (Bilharzia), a neglected tropical disease caused by Schistosoma parasites, afflicts over 240 million people globally, disproportionately impacting Sub-Saharan Africa. Current diagnostic tests, despite their utility, suffer from limitations like low sensitivity. Polymerase chain reaction (PCR) and quantitative real-time PCR (qPCR) remain the most common and sensitive nucleic acid amplification tests. Still, the sensitivity of nucleic acid amplification tests is significantly affected by the copy number of amplification targets, resulting in underestimation of true Schistosoma infections, especially in low transmission settings. Additionally, lengthy qPCR run times pose challenges when dealing with large sample volumes and limited resources. In this study, the identical multi-repeat sequences (IMRS) were used as a novel approach to enhance the sensitivity of nucleic acid-based Bilharzia diagnosis.MethodsTo identify novel genomic repeat regions, we utilized the IMRS algorithm, with modifications to enable larger target region (100-200bp) identification instead of smaller sequences (18-30bp). These regions enabled customised primer-probe design to suit requirements for qPCR assay. To lower the qPCR amplification times, the assay was conducted using fast cycling condition. Regression analysis, and qPCR data visualization was conducted using Python programming.ResultsUsing Schistosoma mansoni and S. haematobium, we found that IMRS-based qPCR, employing genus-specific primers and TaqMan probes, offers exceptional analytical sensitivity, detecting as little as a single genome copy per microliter within 36 minutes.DiscussionThe lowest concentration of DNA detected using IMRS-based PCR and qPCR represented tenfold improvement over conventional PCR. As part of further development, there is a need to compare IMRS-based qPCR against other qPCR methods for Schistosoma spp. Nonetheless, IMRS-based diagnostics promise a significant advancement in bilharzia diagnosis, particularly in low-transmission settings, potentially facilitating more effective control and treatment strategies.

Abstract Peste des petits ruminants (PPR) is an infectious viral disease, primarily of small ruminants such as sheep and goats, but is also known to infect a wide range of wild and domestic Artiodactyls including African buffalo, gazelle, saiga and camels. The livestock-wildlife interface, where free-ranging animals can interact with captive flocks, is the subject of scrutiny as its role in the maintenance and spread of PPR virus (PPRV) is poorly understood. As seroconversion to PPRV indicates previous infection and/or vaccination, the availability of validated serological tools for use in both typical (sheep and goat) and atypical species is essential to support future disease surveillance and control strategies. The virus neutralisation test (VNT) and enzyme-linked immunosorbent assay (ELISA) have been validated using sera from typical host species. Still, the performance of these assays in detecting antibodies from atypical species remains unclear. We examined a large panel of sera (n = 793) from a range of species from multiple countries (sourced 2015–2022) using three tests: VNT, ID VET N-ELISA and AU-PANVAC H-ELISA. A sub-panel (n = 30) was also distributed to two laboratories and tested using the luciferase immunoprecipitation system (LIPS) and a pseudotyped virus neutralisation assay (PVNA). We demonstrate a 75.0–88.0% agreement of positive results for detecting PPRV antibodies in sera from typical species between the VNT and commercial ELISAs, however this decreased to 44.4–62.3% in sera from atypical species, with an inter-species variation. The LIPS and PVNA strongly correlate with the VNT and ELISAs for typical species but vary when testing sera from atypical species.

Tilapia, a significant aquaculture species globally, relies heavily on feed for its production. While numerous studies have investigated the impact of soybean and seaweed-based diets on tilapia, a comprehensive understanding remains elusive. This review aimed at evaluating and synthesizing the existing literature on these diets' effects, focusing on growth performance, feed utilization, and gut microbiota. A systematic search of databases was conducted using Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and a total of 57 studies were included in the qualitative analysis and 24 in the meta-analysis. The results indicated that soybean-based diets, at a 59.4% inclusion level improved the Specific Growth Rate (SGR) of tilapia with an effect size of -2.14 (95% CI: -2.92, -1.37; p < 0.00001; I2 = 99%) and did not improve the feed conversion rate (FCR), as the effect size was 1.80 (95% CI: 0.72, 2.89; p = 0.001; I2 = 100%). For seaweed-based diets, at a 15,9% inclusion level did not improve SGR, with an effect size of -0.74 (95% CI: -1.70, 0.22; p = 0.13; I2 = 99%), and the FCR with an effect size of -0.70 (95% CI: -1.94, 0.54; p = 0.27; I2 = 100%). Regarding the gut microbiota, was noted a lack of studies meeting the inclusion criteria for tilapia. However, findings from studies on other farmed fishes suggested that soybean and seaweed-based diets could have diverse effects on gut microbiota composition and promote the growth of beneficial microbiota. This study suggests that incorporating soybean-based diets at 59.4% inclusion can improve the SGR of tilapia. Seaweed-based diets, while not demonstrating improvement in the analyzed parameters with an inclusion level of 15.9%, have the potential to contribute to the sustainability of the aquaculture industry when incorporated at lower levels.

ABSTRACTIntroduction: Despite global evidence of chikungunya fever (CHIKF) in humans that is caused by chikungunya virus (CHIKV), little is known about the occurrence of CHIKF in Malawi. This study was conducted to determine the seroprevalence of CHIKF and to molecularly confirm the presence of CHIKV ribonucleic acid (RNA) among febrile outpatients seeking health care at Mzuzu Central Hospital in the Northern Region of Malawi.Methods: Enzyme-immunosorbent assay (ELISA) was used to detect the presence or absence of specific antibodies against CHIKV. Reverse transcription-polymerase chain reaction (RT-PCR) was conducted on randomly selected anti-CHIKV IgM-positive samples to detect CHIKV RNA.Results: Out of 119 CHIKF suspected samples analyzed, 73 tested positive for anti-CHIKV IgM antibodies, with an overall seroprevalence of 61.3%. Most of the CHIKV infected individuals presented with joint pain, abdominal pain, vomiting and nose bleeding with seroprevalence of 45.2%, 41.1%, 16.4% and 12.3%, respectively. All the randomly selected samples that were positive for CHIKV anti-IgM by ELISA had detectable CHIKV RNA by RT-PCR.Conclusion: The presence of anti-CHIKV IgM antibodies suggests the presence of recent CHIKV infection. We therefore recommend for the inclusion of CHIKF as the differential diagnosis in febrile ill patients in Mzuzu city, Malawi.

Abstract Background Viral haemorrhagic fevers (VHF) cause significant economic and public health impact in Sub-Saharan Africa. Community knowledge, awareness and practices regarding such outbreaks play a pivotal role in their management and prevention. This study was carried out to assess community knowledge, attitude and practices regarding VHF in five geo-ecological zones in Tanzania. Methods A cross-sectional study was conducted in Buhigwe, Kalambo, Kyela, Kinondoni, Kilindi, Mvomero, Kondoa and Ukerewe districts representing five geo-ecological zones in Tanzania. Study participants were selected by multistage cluster sampling design. A semi-structured questionnaire was used to collect socio-demographic and information related to knowledge, attitude and practices regarding VHFs. Descriptive statistics and logistic regression were used for the analysis. Results A total of 2,965 individuals were involved in the study. Their mean age was 35 (SD ± 18.9) years. Females accounted for 58.2% while males 41.8%. Most of the respondents (70.6%; n = 2093) had never heard of VHF, and those who heard, over three quarters (79%) mentioned the radio as their primary source of information. Slightly over a quarter (29.4%) of the respondents were knowledgeable, 25% had a positive attitude, and 17.9% had unfavourable practice habits. The level of knowledge varied between occupation and education levels (P

Abstract African swine fever (ASF) caused by ASF virus (ASFV) is an infectious transboundary animal disease notifiable to the World Organization for Animal Health causing high mortality in domestic pigs and wild boars threatening the global domestic pig industry. To date, twenty-four ASFV genotypes have been described and currently genotypes II, IX, X, XV and XVI are known to be circulating in Tanzania. Despite the endemic status of ASF in Tanzania, only one complete genome of ASFV from the country has been described. This study describes the first complete genome sequence of ASFV genotype XV. In addition, the first Tanzanian complete genome of ASFV genotype IX and three ASFV strains belonging to genotype II collected during ASF outbreaks in domestic pigs in Tanzania were determined in this study using Illumina sequencing and comparative genomics analysis. The generated ASFV complete genome sequences ranged from 171,004 to 184,521 base pairs in length with an average GC content of 38.53% and encoded 152 to 187 open reading frames. The results of this study provide insights into the genomic structure of ASFV and can be used to monitor changes within the ASFV genome and improve our understanding of ASF transmission dynamics.

The emergence of new virulent genotypes and the continued genetic drift of Newcastle disease virus (NDV) implies that distinct genotypes of NDV are simultaneously evolving in different geographic locations across the globe, including throughout Africa, where NDV is an important veterinary pathogen. Expanding the genomic diversity of NDV increases the possibility of diagnostic and vaccine failures. In this review, we systematically analyzed the genetic diversity of NDV genotypes in Africa using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Information published between 1999 and 2022 were used to obtain the genetic background of different genotypes of NDV and their geographic distributions in Africa. The following genotypes were reported in Africa: I, II, III, IV, V, VI, VII, VIII, XI, XIII, XIV, XVII, XVIII, XX, and XXI. A new putative genotype has been detected in the Democratic Republic of the Congo. However, of 54 African countries, only 26 countries regularly report information on NDV outbreaks, suggesting that this number may be vastly underestimated. With eight different genotypes, Nigeria is the country with the greatest genotypic diversity of NDV among African countries. Genotype VII is the most prevalent group of NDV in Africa, which was reported in 15 countries. A phylogeographic analysis of NDV sequences revealed transboundary transmission of the virus in Eastern Africa, Western and Central Africa, and in Southern Africa. A regional and continental collaboration is recommended for improved NDV risk management in Africa.

Soil-transmitted helminth (STH) infections are caused by roundworms, hookworms, whipworms, and thread worms. Accurate diagnosis is essential for effective treatment, prevention, and control of these infections. This study evaluates a new diagnostic method called Single-image Parasite Quantification (SIMPAQ), which uses a lab-on-a-disc (LoD) technique to isolate STH eggs into a single imaging zone for digital analysis. The study evaluates the purification performance of the SIMPAQ technique for detecting STH eggs in animal samples. This was a cross-sectional study conducted among 237 pigs and 281 dogs in the Morogoro region in Tanzania. Faecal samples were collected and processed with the LoD technique, as well as flotation and McMaster (McM) methods for comparison purposes. The overall prevalence of STH infections was high as per the LoD technique (74%), followed by McM (65.44%) and flotation (65.04%). Moreover, the overall performance of the LoD technique, using McM as the gold standard, was 93.51% (sensitivity), 60.89% (specificity), 81.91% (PPV), and 83.21% (NPV). The LoD technique exhibited high prevalence, sensitivity, and NPV, which demonstrates its value for STH egg detection and its crucial role in the era of accurate STH diagnosis, promoting proper management of the infection.

The global spread of African swine fever (ASF) in recent decades has led to the need for technological advances in sampling and diagnostic techniques. The impetus for these has been the need to enable sampling by lay persons and to obtain at least a preliminary diagnosis in the field for early control measures to be put in place before final laboratory confirmation. In rural Africa, rapid diagnosis is hampered by challenges that include lack of infrastructure as well as human and financial resources. Lack of animal health personnel, access to affordable means to transport field samples to a laboratory, and lack of laboratories with the capacity to make the diagnosis result in severe under-reporting of ASF, especially in endemic areas. This review summarizes the challenges identified in gap analyses relevant to low- and middle-income countries, with a focus on Africa, and explore the opportunities provided by recent research to improve field diagnosis and quality of diagnostic samples used. Sampling techniques include invasive sampling techniques requiring trained personnel and non-invasive sampling requiring minimal training, sampling of decomposed carcass material, and preservation of samples in situations where cold chain maintenance cannot be guaranteed. Availability and efficacy of point-of-care (POC) tests for ASF has improved considerably in recent years and their application, as well as advantages and limitations, are discussed. The adequacy of existing laboratory diagnostic capacity is evaluated and opportunities for networking amongst reference and other laboratories offering diagnostic services are discussed. Maintaining laboratory diagnostic efficiency in the absence of samples during periods of quiescence is another issue that requires attention, and the role of improved laboratory networking is emphasized. Early diagnosis of ASF is key to managing the disease spread. Therefore, the establishment of the Africa Chapter of the Global African Swine Fever Research Alliance (GARA) increases opportunities for collaboration and networking among the veterinary diagnostic laboratories in the region.

Maize (Zea mays L.) is a staple food for many households in sub-Saharan Africa (SSA) and also contributes to the gross domestic product (GDP). However, the maize yields reported in most SSA countries are very low and this is mainly attributed to biotic and abiotic stresses. These stresses have been exacerbated by climate change which has led to long periods of drought or heavy flooding and the emergence of new biotic stresses. Few reports exist which compile the biotic stresses affecting maize production in SSA. Here, five major biotic stresses of maize in Kenya are presented which are attributed to high yield losses. They include Maize lethal necrosis, fall armyworm, gray leaf spot, turcicum leaf blight and desert locusts. Maize lethal necrosis and fall armyworm are new biotic stresses to the Kenyan maize farmer while gray leaf spot, and turcicum leaf blight are endemic to the region. The invasion by the desert locusts is speculated to be caused by climate change. The biotic stresses cause a reduction in maize yield of 30–100% threatening food security. Therefore, this review focuses on the cause, control measures employed to control these diseases and future prospective. There should be deliberate efforts from the government and researchers to control biotic stresses affecting maize yields as the effect of these stresses is being exacerbated by the changing climate.

Background and Objectives: Mosquito-borne viral diseases (MBVDs) create a dramatic health situation worldwide. There is a need to improve the understanding of factors to be addressed in intervention programmes. This study explored community knowledge, attitudes, and practices (KAP) regarding MBVD in Kinshasa. Materials and Methods: A cross-sectional survey was carried out between January and April 2019. The socio-demographic and KAP data collected through a questionnaire were analysed using Epi Info 7. Results: The study included 1464 male and female respondents aged from 18 to 70 years old. Open garbage cans and outdoor water storage units were found in 61.2% and 33.4% of respondent residences, respectively. Polluted water bodies (80.3%) were the most mentioned as mosquito breeding places. Among 86.6% of the respondents that had heard about yellow fever, 12% knew that it is an MBVD. The majority of respondents (72.5%) were perceived to be at risk of contracting MBVD. Environment sanitation (58%) and insecticide use (25%) were among the measures implemented to control mosquitoes. The greater overall knowledge score and attitude were not associated with good practice. Conclusion: The residents of Kinshasa had limited knowledge of MBVD. Raising awareness and educational sessions are essential in empowering the community regarding the correct attitudes and practices to effectively manage the risk posed by MBVD.

Maize Lethal Necrosis (MLN) is a disease of maize reported in Kenya in 2012 that results in yield losses of up to 100%. The epidemiology of MLN is complex as the disease is caused by the synergistic interaction of 2 viruses (Maize chlorotic mottle virus (MCMV) and a potyvirus). In addition, multiple reservoirs and transmission pathways exist for the spread of MLN. The current study was conducted to understand farmers’ maize production practices, their understanding of MLN, and the status of MLN in Kenya. Therefore, a survey of 406 randomly selected farmers was conducted in Bomet, Narok, Kirinyaga, Embu, and Nakuru. To confirm the presence of MLN, maize leaf samples were collected from 18 fields and tested for MCMV and SCMV by molecular techniques. MLN Symptoms observed included chlorotic mottle on leaves, necrosis, and premature plant death. MCMV and SCMV were detected in all the maize growing regions at varying levels of incidence, and severity. Sequence analysis of the partial coat protein genes of randomly selected positive samples of the two viruses showed little variability within the studied isolates and those retrieved from the GenBank. The results indicated that MLN is still prevalent in Kenya with farmers’ planting susceptible varieties.

Objectives: Data on Rift Valley fever virus (RVFV) prevalence in urban settings and pastoral areas of Tanzania are scarce. We performed a cross-sectional study of RVFV seroprevalence and determinants in humans and animals from Ilala, Rufiji, and Sengerema districts of Tanzania. Methods: Blood samples from the study participants were tested for anti-RVFV immunoglobulin G (IgG) antibodies using an enzyme-linked immunosorbent assay. Logistic regression was used to determine association between exposure risk practices and RVFV seropositivity. Results: The study involved 664 humans, 361 cattle, 394 goats, and 242 sheep. The overall anti-RVFV IgG seroprevalence in humans and animals was 2.1% (95% confidence interval [CI] 0.01-0.04) and 9.5% (n = 95, 95% CI 0.08-0.12), respectively. Seroprevalence in humans in Rufiji, Ilala, and Sengerema was 3.0% (n = 225, 95% CI 0.01-0.06), 1.8% (n = 230, 95% CI-0.005- 0.04), and 1.4% (n = 209, 95% CI 0.01-0.04), respectively (P >0.05). Seroprevalence in animals in Sengerema, Rufiji, and Ilala was 12.1% (n = 40, 95% CI 0.09-0.16), 11.1% (n = 37, 95% CI 0.08-0.15), and 5.4% (n = 18, 95% CI 0.03-0.08), respectively (P = 0.006). Handling of carcasses increased the odds of RVFV seropositivity 12-fold (odds ratio 11.84, 95% CI 1.97-71.16). Conclusion: The study confirms previous occurrence of RVFV in multiple species in the study districts. Animal handling practices appear to be essential determinants of seropositivity.

Abstract Background In recent years there have been reports of viral haemorrhagic fever (VHF) epidemics in sub-Saharan Africa where malaria is endemic. VHF and malaria have overlapping clinical presentations making differential diagnosis a challenge. The objective of this study was to determine the prevalence of selected zoonotic VHFs and malaria co-infections among febrile patients seeking health care in Tanzania. Methods This facility-based cross-sectional study was carried out between June and November 2018 in Buhigwe, Kalambo, Kyela, Kilindi, Kinondoni, Kondoa, Mvomero, and Ukerewe districts in Tanzania. The study involved febrile patients seeking health care from primary healthcare facilities. Blood samples were collected and tested for infections due to malaria, Crimean-Congo haemorrhagic fever (CCHF), Ebola virus disease (EVD), Marburg virus disease (MVD), Rift Valley fever (RVF) and yellow fever (YF). Malaria infections were tested using rapid diagnostics tests while exposure to VHFs was determined by screening for immunoglobulin M antibodies using commercial enzyme-linked immunosorbent assays. The Chi-square test was used to compare the proportions. Results A total of 308 participants (mean age = 35 ± 19 years) were involved in the study. Of these, 54 (17.5%) had malaria infection and 15 (4.8%) were positive for IgM antibodies against VHFs (RVF = 8; CCHF = 2; EBV = 3; MBV = 1; YF = 1). Six (1.9%) individuals had both VHF (RVF = 2; CCHF = 1; EVD = 2; MVD = 1) and malaria infections. The highest co-infection prevalence (0.6%) was observed among individuals aged 46‒60 years (P

Between April 2018 and November 2020, the Democratic Republic of Congo (DRC) experienced its 11th Ebola virus disease (EVD) outbreak. Tanzania’s cross-border interactions with DRC through regular visitors, traders, and refugees are of concern, given the potential for further spread to neighboring countries. This study aimed to estimate the risk of introducing EVD to Tanzania from DRC. National data for flights, boats, and car transport schedules from DRC to Tanzania covering the period of May 2018 to June 2019 were analyzed to describe population movement via land, port, and air travel and coupled with available surveillance data to model the risk of EVD entry. The land border crossing was considered the most frequently used means of travel and the most likely pathway of introducing EVD from DRC to Tanzania. High probabilities of introducing EVD from DRC to Tanzania through the assessed pathways were associated with the viability of the pathogen and low detection capacity at the ports of entry. This study provides important information regarding the elements contributing to the risk associated with the introduction of EBV in Tanzania. It also indicates that infected humans arriving via land are the most likely pathway of EBV entry, and therefore, mitigation strategies including land border surveillance should be strengthened.

Abstract Background Tanzania has experienced periodic dengue outbreaks with increased incidence since 2010. However, there is limited information on vector dynamics and transmission risk in most parts of the country. This study was conducted to determine Aedes mosquito abundance, larval indices and dengue virus infection rate as risk indicators for DENV transmission in Kinondoni district, Dar es Salaam, Tanzania. Methods A cross-sectional study was conducted in three wards of Kinondoni district in Tanzania between December 2019 and January 2020. In each ward, three streets were randomly selected for adult and immature mosquito sampling. The adult mosquitoes were collected using Mosquito Magnet traps, while mosquito larvae and pupae were inspected in water-holding containers in the selected household compounds. The detection of dengue virus (DENV) in female Aedes mosquitoes was done using a one-step reverse transcription–polymerase chain reaction (RT–PCR) method. Results Of the 1416 adult female mosquitoes collected, Ae. aegypti accounted for 16.8% (n = 238). A total of 333 water-holding containers were inspected and 201 (60.4%) had at least an Aedes larvae or pupae. Water-holding containers supporting the breeding of Aedes larvae and pupae included discarded car tires, flowerpots and small and large plastic containers. The overall House Index, Container Index and Breteau Index were 55.1%, 60.4% and 114.2, respectively. None of the 763 female Aedes mosquitoes tested by RT–PCR was found to be infected with DENV. Conclusion The presence and abundance Ae. aegypti mosquitoes and the large proportion of water-holding containers infested with the mosquito larvae and pupae put residents of Kinondoni district at high risk of DENV transmission. Our findings emphasize the need for continuous mosquito vector surveillance and control to prevent the possibility of future DENV outbreaks in Tanzania.

Plastics are of great significance in today’s world due to their extensive use such as packaging food and carrying other goods, which have improved the quality of human life. However, plastics have low biodegradability and are persistent in the environment, becoming a major source of pollution. With regard to the current methods used in the management of plastic wastes, the degradation of plastics using beneficial soil microorganisms has recently gained attention due to their ability to degrade different types of plastics including polyethylene (PE) polymers. The study herein was conducted to isolate and identify microorganisms from agricultural soils capable of degrading plastics. Soil samples were inoculated into nutrient, potato dextrose, and starch-casein agar for the isolation of bacteria, fungi, and actinomycetes, respectively. During isolation, fungi and bacterial plates were incubated for 5 days and for 14 days, respectively. The population of bacteria ranged from 1 × 105 to 1.215 × 105 and that of fungi from 1.604 × 104 to 8.6 × 104 whereby actinomycetes ranged from 1.045 × 105 to 2.995 × 105 CFU/g of soil. However, the tested microorganisms showed significant (p ≤ 0.05) differences in the ability to degrade PE bags and bottles as depicted by the diameters of clear zones around the colonies. The diameters of clear zones ranged from 19.3 to 47.5 mm and 25.9 to 32.2 mm after 17 days for bacteria and actinomycetes, respectively, and those of fungi ranged from 30.0 to 66.3 mm after 13 days. Among the bacteria, actinomycetes, and fungi, unsequenced bacterial and actinomycete isolates B1 and A3 as well as Aspergillus sp. (F7) were the most efficient degraders of PE plastic bags. This retrospective study sheds light on our understanding and the need for the bioprospecting of agricultural soils, water bodies, and landfills containing plastic wastes that could lead to the identification of more efficient microbial species with the ability to degrade plastics.

Background: This study was conducted to determine the seroprevalence and risk factors of chikungunya (CHIKV), dengue (DENV), and Zika (ZIKV) viruses in Tanzania.Methods: The study covered the districts of Buhigwe, Kalambo, Kilindi, Kinondoni, Kondoa, Kyela, Mvomero, and Ukerewe in Tanzania. Blood samples were collected from individuals recruited from households and healthcare facilities. An ELISA was used to screen for immunoglobulin G antibodies against CHIKV, DENV, and ZIKV.Results: A total of 1818 participants (median age 34 years) were recruited. The overall CHIKV, DENV, and ZIKV seroprevalence rates were 28.0%, 16.1%, and 6.8%, respectively. CHIKV prevalence was highest in Buhigwe (46.8%), DENV in Kinondoni (43.8%), and ZIKV in Ukerewe (10.6%) and Mvomero (10.6%). Increasing age and frequent mosquito bites were significantly associated with CHIKV and DENV seropositivity (P < 0.05). Having piped water or the presence of stagnant water around the home (P < 0.01) were associated with higher odds of DENV seropositivity. Fever was significantly associated with increased odds of CHIKV seropositivity (P < 0.001). Visiting mines had higher odds of ZIKV seropositivity (P < 0.05).Conclusions: These findings indicate that DENV, CHIKV, and ZIKV are circulating in diverse ecological zones of Tanzania. There is a need to strengthen the control of mosquito-borne viral diseases in Tanzania.

Abstract Background Asymptomatic malaria infections largely remain undetected and act as a reservoir for continuous transmission. The study assessed the prevalence of submicroscopic asymptomatic malaria infections and anaemia in two rural low (300 m above sea level) and highland (700 m asl) settings of Korogwe District north-eastern Tanzania. Methods A cross-sectional malariometric survey involving individuals aged 0–19 years was conducted in June 2018 in the two rural villages. Venous blood was collected from eligible study participants for estimation of haemoglobin level, detection of malaria by rapid diagnostic test (RDT), quantification of malaria parasitaemia by microscopy, as well as dried blood spot (DBS) for determining submicroscopic infections by PCR targeting the small subunit of the ribosomal ribonucleic acid (ssrRNA) of human Plasmodium. Results Out of 565 individuals tested, 211 (37.3%) were malaria positive based on RDT, whereas only 81 (14.3%) were positive by microscopy. There was no significant difference in the prevalence between the highland and the lowland village, p = 0.19 and p = 0.78 microscopy and RDT, respectively. Three out of 206 (1.5%) RDT/microscopy negative samples were P. falciparum positive by PCR. Of the 211 RDT and 81 microscopy positive, 130 (61.6%) and 33 (40.7%), respectively, were defined as being asymptomatic. Of the 565 individuals, 135 (23.9%) were anaemic (haemoglobin

Animals have been identified as the potential reservoirs of rotavirus group A (RVA) for human infection. However, very little is known regarding the genotype and genomic profiles of circulating RVA in Tanzanian piglets. The rotavirus genetic diversity and genome analysis was assessed among piglets from Southern highlands and Eastern Tanzania. A total of 241 faecal samples were collected from piglets in the regions of Mbeya, Iringa, and Morogoro. RVA was detected and genotyped using reverse transcription polymerase chain reaction (RT-PCR). Sanger dideoxynucleotide cycle sequencing of the viral protein (VP) 4 and VP7 genes was afterwards performed to confirm the RT-PCR results. Selected genotypes were subjected to whole genome sequencing. The overall prevalence of RVA was 35.26% (85/241) in piglets (30.58% in Mbeya, 43.75% in Iringa and 31.16% in Morogoro). Upon genotyping, the G genotypes were G4 (26), G9 (10), G3 (6), G5 (3) and the remaining 40 were untypeable, while the P genotype, were P[6] (35), P[13] (3) and the remaining 47 were untypeable. The G4P[6] were the predominant genotype followed by G3P[6], G3P[13], G4P[13] and G5P[13] were most common genotypes combinations. On phylogenetic analysis, G4 was grouped to lineage V, sublineages VIIa and VIIc, G9 to lineage I, G5 to lineage II, G3 to lineage IV, P[6] to lineage V and sublineage Ic and the P[13] to lineage IV. We revealed amino acid differences between the circulating G4 and the G4 in the ProSystems RCE vaccine used in pigs. The whole genome reveals genomic constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1, G5-P[x]-I5-R1-C1-M1-A8-N1-Tx-E1-H1, G3/G4-P[13]/P[6]-Ix-R1-C1-M1-A8-N1-T1-E1-H1, G3-P[6]-Ix-R1-C1-M1-A8-N1-Tx-E1-H1 and G9-P[x]-Ix-R1-C1-M1-Ax-N1-Tx-E1-H1. The VP7 gene of G9, the VP4 gene of P[6] and NSP4 (E1) gene of some genotypes clustered together and closely related to humans origin or porcine-human reassortant strains with nucleotide similarities ranging from 97.90% to 99.74% from neighboring countries, implying possibility intragenogroup reassortment and interspecies transmission. The higher strain diversity observed within the gene segments highlight the importance of genomic analysis and continuous monitoring of RVA genotypes. Further research is needed to determine the risk factors associated with RVA infection in Tanzanian pigs in order to properly design a control program.

Newcastle disease virus is a significant avian pathogen with the potential to decimate poultry populations all over the world and cause enormous economic losses. Distinct NDV genotypes are currently causing outbreaks worldwide. Due to the high genetic diversity of NDV, virulent strains that may result in a lack of vaccine protection are more likely to emerge and ultimately cause larger epidemics with massive economic losses. Thus, a more comprehensive understanding of the circulating NDV genotypes is critical to reduce Newcastle disease (ND) burden. In this study, NDV strains were isolated and characterized from backyard poultry farms from Tanzania, East Africa in 2021. Reverse-transcription polymerase chain reaction (RT-PCR) based on fusion (F) gene amplification was conducted on 79 cloacal or tracheal swabs collected from chickens during a suspected ND outbreak. Our results revealed that 50 samples out 79 (50/79; 63.3%) were NDV-positive. Sequencing and phylogenetic analyses of the selected NDV isolates showed that 39 isolates belonged to subgenotype VII.2 and only one isolate belonged to subgenotype XIII.1.1. Nucleotide sequences of the NDV F genes from Tanzania were closely related to recent NDV isolates circulating in southern Africa, suggesting that subgenotype VII.2 is the predominant subgenotype throughout Tanzania and southern Africa. Our data confirm the circulation of two NDV subgenotypes in Tanzania, providing important information to design genotype-matched vaccines and to aid ND surveillance. Furthermore, these results highlight the possibility of the spread and emergence of new NDV subgenotypes with the potential of causing future ND epizootics.

Objective: To determine the seroprevalence of selected zoonotic viral hemorrhagic fevers (VHFs) and their associated risk factors in Tanzania. Methods: Blood samples were collected from consenting outpatients and community members in eight districts selected from five ecological zones of Tanzania. Serum was harvested and tested for the presence of immunoglobulin G (IgG) and M (IgM) antibodies against Crimean-Congo hemorrhagic fever (CCHF), Ebola virus disease (EVD), Marburg virus disease (MVD), Rift Valley fever (RVF), and yellow fever (YF). Results: The presence of IgM and IgG antibodies against CCHF, EVD, MVD, RVF, and YF was detected in 64 of 500 samples (12.8%). The prevalences of IgM and IgG antibodies to CCHF, EVD, MVD, RFV, and YF were 2.0%, 3.4%, 1.2%, 4.8%, and 1.4%, respectively. Contact with wild animals (OR = 1.2, CI = 1.3–1.6) and keeping goats (OR = 1.3, CI = 1.5–1.9) were significantly associated with RVF, while contact with bats (OR = 1.2, CI = 1.1–1.5) was associated with MVD. Conclusion: The findings of this study provide evidence of exposure to CCHF, EVD, MVD, RVF, and YF in Tanzania. Since most of these VHFs occurred without apparent clinical forms of the disease, these findings call for the need to strengthen the surveillance system and management of febrile illnesses in Tanzania.

Transboundary pathogens pose a threat to livelihood security in countries such as Zambia and Tanzania. This study aimed to investigate the seroprevalence of peste des petits ruminants virus (PPRV), foot and mouth disease virus (FMDV), sheep and goat pox virus (SGPV), Rift Valley fever virus (RVFV) and Brucella spp. in sheep and goats along the Tanzania-Zambia border. Another aim was to assess the association between certain predictor variables and seroprevalence, focusing on trade and proximity to an international border, to a town and to the Tanzania-Zambia highway. During September-October 2018, 486 serum samples from small ruminants in Zambia and 491 in Tanzania were collected and analyzed using enzyme-linked immunosorbent assays (ELISA). A questionnaire focused on management strategies was administered to each household. The animal-level seroprevalence in Zambia was 0.21% [95% confidence interval (CI) (0.01–1.14) for PPRV, 1.03% (95% CI 0.33–2.39) for FMDV, 0% (95% CI 0–0.76) for SGPV, 2.26% (95% CI 1.14–4.01) for RVFV and 1.65% (95% CI 0.71–3.22) for Brucella spp.]. In Tanzania, animal-level seroprevalence was 2.85% (95% CI 1.57–4.74) for PPRV, 16.9% (95% CI 13.7–20.5) for FMDV, 0.20% (95% CI 0.01–1.13) for SGPV, 3.26% (95% CI 1.87–5.24) for RVFV and 20.0% (95% CI 14.5–26.5) for Brucella spp. For PPRV (OR 6.83, 95% CI 1.37–34.0, p = 0.019) and FMDV (OR 5.68, 95% CI 1.58–20.3, p = 0.008), herds situated more than 30 km from an international border were more likely to be seropositive, while being located 10–30 km (OR 4.43, 95% CI 1.22–16.1 p = 0.024) from a border was identified as a risk factor for Brucella spp. For FMDV (OR 79.2, 95% CI 4.52–1388.9, p = 0.003), being situated within 30 km from a town was associated with seropositivity. Furthermore, contact with wild ruminants (OR 18.2, 95% CI 1.36–244), and the presence of sheep in the household (OR 5.20, 95% CI 1.00–26.9, p = 0.049), was associated with seropositivity for PPRV, and FMDV. No significant associations between trade or distance to the Tan-Zam highway and seroprevalence were found. We recommend that the impact of trade and proximity to borders, towns and roads should be further evaluated in larger studies, ideally incorporating aspects such as temporal trade fluctuations.

Abstract Background African swine fever (ASF) is a highly fatal viral hemorrhagic disease of domestic pigs that threatens livelihoods and food security. In Africa, ASF virus (ASFV) circulates in sylvatic (transmission between warthogs and soft argasid ticks) and domestic (transmission between domestic pigs) cycles, with outbreaks resulting from ASFV spill-over from sylvatic cycle. A number of outbreaks were reported in different parts of Tanzania between 2015 and 2017. The present study investigated ASFV transmission patterns through viral DNA sequencing and phylogenetic analysis. A total of 3120 tissue samples were collected from 2396 domestic pigs during outbreaks at different locations in Tanzania between 2015 and 2017. Partial sequencing of the B646L (p72) gene was conducted for diagnostic confirmation and molecular characterization of ASFV. Phylogenetic analysis to study the relatedness of current ASFV with those that caused previous outbreaks in Tanzania and representatives of all known 24 ASFV was performed using the Maximum Composite Likelihood model with 1000 bootstrap replications in MEGA 6.0. Results ASFV was confirmed to cause disease in sampled domestic pigs. ASFV genotypes II, IX, and X were detected from reported outbreaks in 2015–2017. The current ASFV isolates were similar to those recently documented in the previous studies in Tanzania. The similarities of these isolates suggests for continuous circulation of ASFV with virus maintenance within the domestic pigs. Conclusions Genetic analysis confirmed the circulation of ASFV genotypes II, IX, and X by partial B646L (p72) gene sequencing. The similarities of current isolates to previously isolated Tanzanian isolates and pattern of disease spread suggest for continuous circulation of ASF with virus’ maintenance in the domestic pigs. Although certain viral genotypes seem to be geographically restricted into certain zones within Tanzania, genotype II seems to expand its geographical range northwards with the likelihood of spreading to other states of the East African Community. The spread of ASFV is due to breach of quarantine and transportation of infected pigs via major highways. Appropriate control measures including zoosanitary measures and quarantine enforcement are recommended to prevent ASF domestic circulation in Tanzania.

Abstract Background The emergence and spread of antimicrobial resistance (AMR) present a challenge to disease control in East Africa. Resistance to beta-lactams, which are by far the most used antibiotics worldwide and include the penicillins, cephalosporins, monobactams and carbapenems, is reducing options for effective control of both Gram-positive and Gram-negative bacteria. The World Health Organization, Food and Agricultural Organization and the World Organization for Animal Health have all advocated surveillance of AMR using an integrated One Health approach. Regional consortia also have strengthened collaboration to address the AMR problem through surveillance, training and research in a holistic and multisectoral approach. This review paper contains collective information on risk factors for transmission, clinical relevance and diversity of resistance genes relating to extended-spectrum beta-lactamase-producing (ESBL) and carbapenemase-producing Enterobacteriaceae, and Methicillin-resistant Staphylococcus aureus (MRSA) across the human, animal and environmental compartments in East Africa. Main body The review of the AMR literature (years 2001 to 2019) was performed using search engines such as PubMed, Scopus, Science Direct, Google and Web of Science. The search terms included ‘antimicrobial resistance and human-animal-environment’, ‘antimicrobial resistance, risk factors, genetic diversity, and human-animal-environment’ combined with respective countries of East Africa. In general, the risk factors identified were associated with the transmission of AMR. The marked genetic diversity due to multiple sequence types among drug-resistant bacteria and their replicon plasmid types sourced from the animal, human and environment were reported. The main ESBL, MRSA and carbapenem related genes/plasmids were the bla CTX-Ms (45.7%), SCCmec type III (27.3%) and IMP types (23.8%), respectively. Conclusion The high diversity of the AMR genes suggests there may be multiple sources of resistance bacteria, or the possible exchange of strains or a flow of genes amongst different strains due to transfer by mobile genetic elements. Therefore, there should be harmonized One Health guidelines for the use of antibiotics, as well as regulations governing their importation and sale. Moreover, the trend of ESBLs, MRSA and carbapenem resistant (CAR) carriage rates is dynamic and are on rise over time period, posing a public health concern in East Africa. Collaborative surveillance of AMR in partnership with regional and external institutions using an integrated One Health approach is required for expert knowledge and technology transfer to facilitate information sharing for informed decision-making.

Abstract Background Mosquito-borne viral infections have in recent years, become a public health threat globally. This review aimed to provide an overview of the ecological and epidemiological profiles of mosquito-borne viral infections in the Democratic Republic of the Congo (DRC). Methods A search of literature was conducted using Google Scholar, PubMed and the WHO website using the following keywords: “Democratic Republic of the Congo”, “Zaire”, “Belgian Congo” and either of the following: “mosquito-borne virus”, “arbovirus”, “yellow fever”, “dengue”, “chikungunya”, “West Nile”, “Rift Valley fever”, “O’nyong’nyong”, “Zika”, “epidemiology”, “ecology”, “morbidity”, “mortality”. Published articles in English or French covering a period between 1912 and October 2018 were reviewed. Results A total of 37 articles were included in the review. The findings indicate that the burden of mosquito-borne viral infections in DRC is increasing over time and space. The north-western, north-eastern, western and central regions have the highest burden of mosquito-borne viral infections compared to south and eastern highland regions. Yellow fever, chikungunya, dengue, Zika, Rift Valley fever, West Nile and O’nyong’nyong have been reported in the country. These mosquito-borne viruses were found circulating in human, wildlife and domestic animals. Yellow fever and chikungunya outbreaks have been frequently reported. Aedes aegypti and Ae. simpsoni were documented as the main vectors of most of the mosquito-borne viral infections. Heavy rains, human movements, forest encroachment and deforestation were identified as drivers of mosquito-borne viruses occurrence in DRC. Conclusions Mosquito-borne viral infections are becoming common and a serious public health problem in DRC. In the current context of climate change, there is urgent need to improve understanding on ecological and epidemiology of the diseases and strengthen surveillance systems for prompt response to epidemics in DRC.

Abstract Peste des petits ruminants virus causes a highly contagious disease, which poses enormous economic losses in domestic animals and threatens the conservation of wild herbivores. Diagnosis remains a cornerstone to the Peste des petits ruminants Global Control and Eradication Strategy, an initiative of the World Organisation for Animal Health and the Food and Agriculture Organisation. The present review presents the peste des petits ruminants diagnostic landscape, including the practicality of commercially available diagnostic tools, prototype tests and opportunities for new technologies. The most common peste des petits ruminants diagnostic tools include; agar gel immunodiffusion, counter-immunoelectrophoresis, enzyme-linked immunosorbent assays, reverse transcription polymerase chain reaction either gel-based or real-time, reverse transcription loop-mediated isothermal amplification, reverse transcription recombinase polymerase amplification assays, immunochromatographic lateral flow devices, luciferase immunoprecipitation system and pseudotype-based assays. These tests vary in their technical demands, but all require a laboratory with exception of immunochromatographic lateral flow and possibly reverse transcription loop-mediated isothermal amplification and reverse transcription recombinase polymerase amplification assays. Thus, we are proposing an efficient integration of diagnostic tests for rapid and correct identification of peste des petits ruminants in endemic zones and to rapidly confirm outbreaks. Deployment of pen-side tests will improve diagnostic capacity in extremely remote settings and susceptible wildlife ecosystems, where transportation of clinical samples in the optimum cold chain is unreliable.

Since its discovery, polymerase chain reaction (PCR) has emerged as an important technology for the diagnosis and identification of infectious diseases. It is a highly sensitive and reliable nucleic acids (NA) detection tool for various sample types. However, stool, which carries the most abundant micro-organisms and physiological byproducts, remains to be the trickiest clinical specimen for molecular detection of pathogens. Herein, we demonstrate the novel application of hydrogel microparticles as carriers of viral RNA from stool samples without prior RNA purification for real-time polymerase chain reaction (qPCR). In each microparticle of primer-incorporated network (PIN) as a self-sufficient reaction compartment, immobilized reverse transcription (RT) primers capture the viral RNA by hybridization and directly initiate RT of RNA to generate a pool of complementary DNA (PIN-cDNA pool). Through a simple operation with a portable thermostat device, a PIN-cDNA pool for influenza A virus (IAV) was obtained in 20 min. The PIN-cDNA pools can be stored at room temperature, or directly used to deliver cDNA templates for qPCR. The viral cDNA templates were freely released in the subsequent qPCR to allow amplification efficiency of over 91%. The assay displayed good linearity, repeatability, and comparable limit of detection (LoD) with a commercialized viral RNA purification kit. As a proof of concept, this technology carries a huge potential for onsite application to improve human and animal infectious disease surveillance activities using stool samples without the need for a laboratory or centrifuge for sample preparation.

Dengue is a worldwide public health concern. The current study assessed the extent of human exposure to the dengue virus in relation to the distribution pattern of Aedes aegypti and Ae. albopictus in Kinshasa. Cross-sectional surveys were carried out in 2021 and 2022. The baseline entomological survey involved 19 municipalities using a grid cell sampling approach. All containers holding water were inspected for the presence of larvae in each grid. The collected larvae were kept in an insectary until the adult emergence for morphological identification. Four hundred febrile patients attending the hospital were screened for the presence of dengue antibodies (IgG, IgM) and NS1 antigen using a rapid diagnostic test (RDT) Biosynex®. Residences of positive cases were geo-referenced. We evaluated 1850 grid cells, of which 19.5% were positive for Aedes larvae. The positive grid cells were identified in the Ndjili (44.0%), Mont Ngafula (32.0%) and Ngaliema (26.0%), and Limete (32.0%) municipalities. The Ae. aegypti (11.2%) predominated in the northwestern, and Ae. albopictus (9.1%) appeared in the high vegetation coverage areas. Of 61 (15.3%) participants exposed to dengue, 8.3% presented acute dengue. Young, (6–17 years), male, and Mont Amba district participants were most exposed to dengue. In conclusion, dengue occurrence in Kinshasa overlaps somewhat the geographical and ecological distributions of Ae. aegypti and Ae. albopictus. Both species are not homogenously distributed, likely due to environmental factors. These findings can assist the targeted control activities.

African swine fever (ASF) is a contagious viral disease that causes high mortality, approaching 100%, in domestic pigs and wild boars. The disease has neither a cure nor a vaccine, and it is caused by an ASF virus (ASFV), the only member of the family Asfarviridae, genus Asfivirus, and the only known DNA arbovirus. Twenty-four genotypes of ASFV have been described to date, and all of them have been described in Africa. ASF is endemic in Burundi, and several outbreaks have been reported in the country; the disease continues to economically impact on small-scale farmers. This study aimed at genetic characterization of ASFV that caused an ASF outbreak in the Rutana region, Burundi, in the year 2018. Tissue samples from domestic pigs that died as a result of a severe hemorrhagic disease were collected in order to confirm the disease using polymerase chain reaction (PCR) and to conduct partial genome sequencing. Nucleotide sequences were obtained for the B646L (p72) gene, the intergenic fragment between the I73R and I329L genes, and the central variable region (CVR) of the B602L gene. Phylogenetic analysis of the Burundian 2018 ASFV grouped the virus within B646L (p72) genotype X and clustered together with those reported during the 1984 and 1990 outbreaks in Burundi with high nucleotide identity to some ASFV strains previously reported in neighboring East African countries, indicating a regional distribution of this ASFV genotype. Analysis of the intergenic fragment between I73R and I329L genes showed that the Burundian 2018 ASFV described in this study lacked a 32–base pair (bp) fragment present in the reference genotype X strain, Kenya 1950. In addition, the strain described in this study had the signature AAABNAABA at the CVR (B602L) gene and showed 100% amino acid sequence identity to viruses responsible for recent ASF outbreaks in the region. The virus described in this study showed high genetic similarities with ASFV strains previously described in domestic pigs, wild suids, and soft ticks in East African countries, indicating a possible common wild source and continuous circulation in domestic pigs in the region.

Peste-des-petits-ruminants virus (PPRV) is currently the focus of a control and eradication program. Full genome sequencing has the opportunity to become a powerful tool in the eradication program by improving molecular epidemiology and the study of viral evolution. PPRV is prevalent in many resource-constrained areas, with long distances to laboratory facilities, which can lack the correct equipment for high-throughput sequencing. Here we present a protocol for near full or full genome sequencing of PPRV. The use of a portable miniPCR and MinION brings the laboratory to the field and in addition makes the production of a full genome possible within 24 h of sampling. The protocol has been successfully used on virus isolates from cell cultures and field isolates from tissue samples of naturally infected goats.

IntroductionEbola virus disease (EVD) is one of the deadliest haemorrhagic fevers affecting humans and non-human primates. Thirty-four outbreaks have been reported in Africa since it was first recognised in 1976. This review analysed 42 years of EVD outbreaks and identified various challenges and opportunities for its control and prevention in Sub-Saharan Africa.MethodsA literature search of relevant articles on EVD was done in PubMed, Web of Science and Google Scholar electronic databases. Articles published from 1976 to 2019 were reviewed to document reports of EVD outbreaks in Sub-Saharan Africa. Data extraction focused on the year of outbreak, geographical spread, virus strain involved, number of cases and deaths, case fatality, and outbreak management. Analyses of trends in case fatality were performed by calculating ORs between times.ResultsIn the past four decades, a total of 34 EVD outbreaks affecting 34 356 cases and causing 14 823 deaths were reported in 11 countries in Sub-Saharan Africa. The overall case fatality rate (95% CI) was 66% (62 to 71) and did not change substantially over time (OR in 2019 vs 1976=1.6 (95% CI 1.5 to 1.8), p

Porcine cysticercosis is a neglected and underestimated disease caused by metacestode stage of the tapeworm, Taenia solium (T. solium). Pigs are the intermediate hosts of T. solium while human are the only known definitive host. The disease has an economic consequence because the affected farmers lose 50−100 percent of the value of pigs if they are infected. Lack of affordable, easy to use, sensitive, and specific molecular diagnostic tools for detection of infections at the farm level hinders the control of porcine cysticercosis in endemic areas. A number of DNA based diagnostic assays for the detection of T. solium infections in pigs have been developed and evaluated but none is applicable at low-resource areas where this disease is an endemic. This review focuses mainly on DNA based diagnostic methods, their sensitivity, specificity, and utilization at low-resource areas. We summarized data from 65 studies on the current DNA-detection based diagnostic techniques for T. solium cysticercosis in porcine, published in English between the years 2000–2018, identified through PubMed search engine. Of the different polymerase chain reaction (PCR) assays developed for identification of T. solium, the most sensitive (97−100%) and specific (100%) one is nested PCR. One study utilized loop-mediated isothermal amplification (LAMP) as a diagnostic tool for the detection of T. solium infections though its field use was never determined. Recombinase polymerase amplification (RPA) has been evaluated as a diagnostic tool for a variety of diseases, but has never been exploited for the diagnosis of cysticercosis/taeniasis. In conclusion, several molecular methods have been developed and evaluated in lab settings. However, there is need to validate these methods as a diagnostic tool to diagnose porcine cysticercosis in low-resource areas.

Abstract Background Plague is a flea-borne zoonotic and invasive disease caused by a gram negative coccobacillus bacterium called Yersinia pestis. Plague has caused three devastating pandemics globally namely: the Justinian, Black Death and Oriental plague. The disease in the Eastern Province of Zambia has been reported in Nyimba and Sinda Districts in the past 15 years. The aim of this study was to investigate the molecular epidemiology of plague in the two affected districts. Polymerase Chain Reaction (PCR), targeting Plasminogen activator gene (pla gene) of Y. pestis, was performed on suspected human bubo aspirates (n = 7), rodents (n = 216), shrews (n = 27) and fleas (n = 1494). Of these, one positive sample from each source or host was subjected to sequencing followed by phylogenetic analysis. Results The plasminogen activator gene (pla gene) of Y. pestis was detected in 42.8% bubo aspirates, 6.9% rodents, 3.7% shrew and 0.8% fleas. The fleas were from pigs (n = 4), goats (n = 5) and rodents (n = 3). The sequencing and phylogenetic analysis suggested that the pla gene of Y. pestis in Nyimba and Sinda was similar and the isolates demonstrated a high degree of evolutionary relationship with Antiqua strains from the Republic of Congo and Kenya. Conclusion It can be concluded that pla gene of Y. pestis was present in various hosts in the two districts and the strains circulating in each district were similar and resembles those in the Republic of Congo and Kenya.

The presence of nutritional and health-benefiting compounds has increased awareness of orphan leafy vegetables such as Cleome gynandra (CG), whose phytochemicals vary among accessions and organs during growth. This study investigated the polyphenol accumulation and antioxidant activities (AOA) of eight CG accessions from the vegetative stage to the seed set stage. Plants were separated into leaves and stem (LS), flowers, and silique organs, and extracts were analyzed for total phenolic content (TPC), total flavonoid content (TFC), rutin and astragalin content, and AOA using 2,2-diphenyl-1-picrylhydrazyl-hydrate (DPPH) and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS). There were significant interaction effects of growth stages and accessions that contributed to changes in compounds content and AOA. TPC accumulated in plant generative parts, whereas flavonoids accumulated in young plant organs. HPLC profiling revealed that rutin was the most abundant compound in all organs, with flowers having the highest levels, while astragalin was only found in flowers. Silique extracts, particularly accession KF-14, recorded the highest TPC, which corresponded to the strongest radical scavenging activity in ABTS and DPPH assays and a strong linear correlation. The germplasm contained accessions with significantly different and varying levels of bioactive compounds and AOA. These findings potentiate the exploitation of CG organs such as siliques for AOA, flowers for rutin and astragalin, and young shoots for flavonoids. Moreover, the significant accumulation of the compounds in particular accessions of the germplasms suggest that such superior accessions may be useful candidates in genetic breeding programs to improve CG vegetable.

Peste des petits ruminants virus (PPRV) causes a highly devastating disease of sheep and goats that threatens food security, small ruminant production and susceptible endangered wild ruminants. With policy directed towards achieving global PPR eradication, the establishment of cost-effective genomic surveillance tools is critical where PPR is endemic. Genomic data can provide sufficient in-depth information to identify the pockets of endemicity responsible for PPRV persistence and viral evolution, and direct an appropriate vaccination response. Yet, access to the required sequencing technology is low in resource-limited settings and is compounded by the difficulty of transporting clinical samples from wildlife across international borders due to the Convention on International Trade in Endangered Species (CITES) of Wild Fauna and Flora, and Nagoya Protocol regulations. Oxford nanopore MinION sequencing technology has recently demonstrated an extraordinary performance in the sequencing of PPRV due to its rapidity, utility in endemic countries and comparatively low cost per sample when compared to other whole-genome (WGS) sequencing platforms. In the present study, Oxford nanopore MinION sequencing was utilised to generate complete genomes of PPRV isolates collected from infected goats in Ngorongoro and Momba districts in the northern and southern highlands of Tanzania during 2016 and 2018, respectively. The tiling multiplex polymerase chain reaction (PCR) was carried out with twenty-five pairs of long-read primers. The resulting PCR amplicons were used for nanopore library preparation and sequencing. The analysis of output data was complete genomes of PPRV, produced within four hours of sequencing (accession numbers: MW960272 and MZ322753). Phylogenetic analysis of the complete genomes revealed a high nucleotide identity, between 96.19 and 99.24% with lineage III PPRV currently circulating in East Africa, indicating a common origin. The Oxford nanopore MinION sequencer can be deployed to overcome diagnostic and surveillance challenges in the PPR Global Control and Eradication program. However, the coverage depth was uneven across the genome and amplicon dropout was observed mainly in the GC-rich region between the matrix (M) and fusion (F) genes of PPRV. Thus, larger field studies are needed to allow the collection of sufficient data to assess the robustness of nanopore sequencing technology.

We investigated antibiotic resistance profiles of Escherichia coli among 960 samples obtained from chickens (236), humans (243), rodents (101) and soil (290). E. coli was isolated from 650 (67.7%) samples. Isolation frequency varied significantly between chickens, humans, rodents and soil samples, being 81.6%, 86.5%, 79.2% and 31.0%, respectively (p < 0.001). Resistance rates were particularly higher against imipenem (79.8%), cefotaxime (79.7%) and tetracycline (73.7%) and moderate against amoxicillin-clavulanate (49.4%). Overall, 78.8% of the isolates were multidrug-resistant (MDR) among which, 38.8%, 25.1%, 12.9% and 2.5% exhibited resistance to three, four, five and six different classes of antibiotics, respectively. Multidrug-resistant E. coli were observed in 27.7%, 30.3%, 10.8% and 10.0% of the isolates from chickens, humans, rodents and soil samples, respectively. Our results show high levels of antimicrobial resistance including MDR in E. coli isolated from chickens, humans, rodents and soil samples in Karatu, Northern Tanzania. Comprehensive interventions using a one-health approach are needed and should include improving (i) awareness of the community on judicious use of antimicrobial agents in humans and animals, (ii) house conditions and waste management and (iii) rodent control measures.

Peste des petits ruminants virus (PPRV) causes a highly devastating disease, peste des petits ruminants (PPR) of sheep and goats, that threatens food security, small ruminant production, and the conservation of wild small ruminants in many developing countries, especially in Africa. Robust serological and molecular diagnostic tools are available to detect PPRV infection, but they were mainly developed for domestic sheep and goats. The presence of a wide host range for PPRV does present serological diagnostic challenges. New innovative diagnostic tools are needed to detect PPRV in atypical hosts (e.g., Camelidae, Suidae, and Bovinae), in wildlife ecosystems and in complex field situations. Interestingly, single-domain antigen binding fragments (nanobodies) derived from heavy-chain-only camelid antibodies have emerged as a new hope in the development of accurate, rapid, and cost-effective diagnostic tools in veterinary and biomedical fields that are suitable for low-income countries. The main objective of this study was to construct an immune nanobody library to retrieve PPRV-reactive nanobodies that enable the development of diagnostic and therapeutic nanobodies in the future. Here, a strategy was developed whereby an alpaca (Vicugna pacos) was immunized with a live attenuated vaccine strain (PPRV/N/75/1) to raise an affinity-matured immune response in the heavy-chain-only antibody classes. The nanobody gene repertoire was engineered in pMECS-GG phagemid, whereby a ccdB gene (encoding a lethal protein) was substituted by the nanobody gene. An immune nanobody library with approximately sixty-four million independent transformants was constructed, of which 100% contained an insert with the proper size of nanobody gene. Following phage display and biopanning, nine nanobodies that specifically recognise completely inactivated PPRV were identified on enzyme-linked immunosorbent assay. They showed superb potency in rapidly identifying PPRV, which is likely to open a new perspective in the diagnosis and possible treatment of PPR infection.

The effect of salt treatment on Brassica carinata (BC) microgreens grown under different light wavelengths on glucosinolates (GLs) and phenolic compounds were evaluated. Quantifiable GLs were identified using ultra-high performance-quadrupole time of flight mass spectrometry. Extracts’ ability to activate antioxidant enzymes (superoxide dismutase (SOD) and catalase (CAT)) was evaluated on human colorectal carcinoma cells (HCT116). Furthermore, BC compounds’ ability to activate expression of nuclear transcription factor-erythroid 2 related factor (Nrf2) and heme-oxygenase-1 (HO-1) proteins was examined using specific antibodies on HCT116 cells. Sinigrin (SIN) was the abundant GLs of the six compounds identified and its content together with total aliphatic GLs increased in saline conditions. Fluorescent (FL) and blue plus red (B1R1) lights were identified as stable cultivation conditions for microgreens, promoting biomass and glucobrassicin contents, whereas other identified individual and total indole GLs behaved differently in saline and non-saline environments. Blue light-emitting diodes and FL light in saline treatments mostly enhanced SIN, phenolics and antioxidant activities. The increased SOD and CAT activities render the BC microgreens suitable for lowering oxidative stress. Additionally, activation of Nrf2, and HO-1 protein expression by the GLs rich extracts, demonstrate their potential to treat and prevent oxidative stress and inflammatory disorders. Therefore, effective salt treatments and light exposure to BC microgreens present an opportunity for targeted regulation of growth and accumulation of bioactive metabolites.

Peste des petits ruminants (PPR) is an important transboundary animal disease of domestic small ruminants, camels, and wild artiodactyls. The disease has significant socio-economic impact on communities that depend on livestock for their livelihood and is a threat to endangered susceptible wild species. The aim of this review was to describe the introduction of PPR to Tanzania and its subsequent spread to different parts of the country. On-line databases were searched for peer-reviewed and grey literature, formal and informal reports were obtained from Tanzanian Zonal Veterinary Investigation Centres and Laboratories, and Veterinary Officers involved with PPR surveillance were contacted. PPR virus (PPRV) was confirmed in northern Tanzania in 2008, although serological data from samples collected in the region in 1998 and 2004, and evidence that the virus was already circulating in Uganda in 2003, suggests that PPRV might have been present earlier than this. It is likely that the virus which became established in Tanzania was introduced from Kenya between 2006–7 through the cross-border movement of small ruminants for trade or grazing resources, and then spread to eastern, central, and southern Tanzania from 2008 to 2010 through movement of small ruminants by pastoralists and traders. There was no evidence of PPRV sero-conversion in wildlife based on sera collected up to 2012, suggesting that they did not play a vectoring or bridging role in the establishment of PPRV in Tanzania. PPRV lineages II, III and IV have been detected, indicating that there have been several virus introductions. PPRV is now considered to be endemic in sheep and goats in Tanzania, but there has been no evidence of PPR clinical disease in wildlife species in Tanzania, although serum samples collected in 2014 from several wild ruminant species were PPRV sero-positive. Similarly, no PPR disease has been observed in cattle and camels. In these atypical hosts, serological evidence indicates exposure to PPRV infection, most likely through spillover from infected sheep and goats. Some of the challenges for PPRV eradication in Tanzania include movements of small ruminants, including transboundary movements, and the capacity of veterinary services for disease surveillance and vaccination. Using wildlife and atypical domestic hosts for PPR surveillance is a useful indicator of endemism and the ongoing circulation of PPRV in livestock, especially during the implementation of vaccination to control or eliminate the disease in sheep and goats. PPR disease has a major socio-economic impact in Tanzania, which justifies the investment in a comprehensive PPRV eradication programme.

Background: Diseases caused by mosquito-borne viruses are among the most important emerging diseases that threaten human and animal health, particularly in Africa. However, little attention has been paid to these diseases in the Democratic Republic of the Congo (DRC). The present cross-sectional study was undertaken between March and May 2014 to investigate the presence of mosquito-borne viruses in mosquitoes collected from five municipalities of Kinshasa, DRC. Methods: Mosquitoes were collected using BG-Sentinel traps and battery-powered aspirators. Female mosquitoes were pooled according to their genera and sampling locations, preserved in RNAlater, and later screened for viruses using reverse transcription PCR (RT-PCR) assays. Results: A total of 2922 mosquitoes were collected and 29 pools of female mosquitoes, containing approximately 30 mosquitoes each, were tested. Twelve of the 29 (41.4%) mosquito pools were found to be infected with at least one arbovirus, with eight (27.5%) pools positive for Alphavirus, nine (31%) for Flavivirus, and five (17.2%) for Bunyaviridae. Chikungunya, o’nyong’nyong, and Rift valley fever viruses were detected. Conclusions: The present study shows that mosquitoes in Kinshasa carry mosquito-borne viruses that may have serious public health implications. Further investigations on the presence of mosquito-borne viruses in the human and livestock populations of Kinshasa and DRC are recommended.

Rift Valley fever (RVF) is a zoonotic viral disease caused by the RVF phlebovirus (RVFV) that infects a variety of animal species including sheep and goats. Sera (n = 893) collected between 2013 and 2015 from randomly selected indigenous sheep and goats in seven provinces of the Democratic Republic of the Congo (DRC) were tested for the presence of specific immunoglobulin G (IgG) and M (IgM) against RVFV, using two commercially available enzyme-linked immunosorbent assays. The reverse transcription polymerase chain reaction (RT-PCR) was also used to detect RVFV nucleic acid. There was significant variation in true seroprevalence of RVFV for both sheep and goats between the seven provinces investigated. Values ranged from 0.0 (95% confidence interval [CI] 0.0–6.55) to 23.81 (95% CI 12.03–41.76) for goat and 0.0 (95% CI 0.0–7.56) to 37.11 (95% CI 15.48–65.94) for sheep, respectively. One serum (1.85%) out of 54 that tested positive for IgG was found to be IgM-positive. This same sample was also positive by RT-PCR indicating an active or recent infection. These findings report the presence of RVFV in small ruminants in the DRC for the first time and indicate variations in exposure to the virus in different parts of the country.

Peste des petits ruminants (PPR) is a viral disease of goats and sheep that occurs in Africa, the Middle East and Asia with a severe impact on livelihoods and livestock trade. Many wild artiodactyls are susceptible to PPR virus (PPRV) infection, and some outbreaks have threatened endangered wild populations. The role of wild species in PPRV epidemiology is unclear, which is a knowledge gap for the Global Strategy for the Control and Eradication of PPR. These studies aimed to investigate PPRV infection in wild artiodactyls in the Greater Serengeti and Amboseli ecosystems of Kenya and Tanzania. Out of 132 animals purposively sampled in 2015–2016, 19.7% were PPRV seropositive by ID Screen PPR competition enzyme-linked immunosorbent assay (cELISA; IDvet, France) from the following species: African buffalo, wildebeest, topi, kongoni, Grant’s gazelle, impala, Thomson’s gazelle, warthog and gerenuk, while waterbuck and lesser kudu were seronegative. In 2018–2019, a cross-sectional survey of randomly selected African buffalo and Grant’s gazelle herds was conducted. The weighted estimate of PPRV seroprevalence was 12.0% out of 191 African buffalo and 1.1% out of 139 Grant’s gazelles. All ocular and nasal swabs and faeces were negative by PPRV real-time reverse transcription-polymerase chain reaction (RT-qPCR). Investigations of a PPR-like disease in sheep and goats confirmed PPRV circulation in the area by rapid detection test and/or RT-qPCR. These results demonstrated serological evidence of PPRV infection in wild artiodactyl species at the wildlife–livestock interface in this ecosystem where PPRV is endemic in domestic small ruminants. Exposure to PPRV could be via spillover from infected small ruminants or from transmission between wild animals, while the relatively low seroprevalence suggests that sustained transmission is unlikely. Further studies of other major wild artiodactyls in this ecosystem are required, such as impala, Thomson’s gazelle and wildebeest.

We determined the phenotypic profile of multidrug-resistant (MDR) Escherichia coli isolated from 698 samples (390 and 308 from poultry and domestic pigs, respectively). In total, 562 Enterobacteria were isolated. About 80.5% of the isolates were E. coli. Occurrence of E. coli was significantly higher among domestic pigs (73.1%) than in poultry (60.5%) (p = 0.000). In both poultry and domestic pigs, E. coli isolates were highly resistant to tetracycline (63.5%), nalidixic acid (53.7%), ampicillin (52.3%), and trimethoprim/sulfamethoxazole (50.9%). About 51.6%, 65.3%, and 53.7% of E. coli were MDR, extended-spectrum beta lactamase-producing enterobacteriaceae (ESBL-PE), and quinolone-resistant, respectively. A total of 68% of the extended-spectrum beta lactamase (ESBL) producers were also resistant to quinolones. For all tested antibiotics, resistance was significantly higher in ESBL-producing and quinolone-resistant isolates than the non-ESBL producers and non-quinolone-resistant E. coli. Eight isolates were resistant to eight classes of antimicrobials. We compared phenotypic with genotypic results of 20 MDR E. coli isolates, ESBL producers, and quinolone-resistant strains and found 80% harbored blaCTX-M, 15% aac(6)-lb-cr, 10% qnrB, and 5% qepA. None harbored TEM, SHV, qnrA, qnrS, qnrC, or qnrD. The observed pattern and level of resistance render this portfolio of antibiotics ineffective for their intended use.

Dengue contributes a significant burden on global public health and economies. In Africa, the burden of dengue virus (DENV) infection is not well described. This review was undertaken to determine the prevalence of dengue and associated risk factors. A literature search was done on PubMed/MEDLINE, Scopus, Embase, and Google Scholar databases to identify articles published between 1960 and 2020. Meta-analysis was performed using a random-effect model at a 95% confidence interval, followed by subgroup meta-analysis to determine the overall prevalence. Between 1960 and 2020, 45 outbreaks were identified, of which 17 and 16 occurred in East and West Africa, respectively. Dengue virus serotype 1 (DENV-1) and DENV-2 were the dominant serotypes contributing to 60% of the epidemics. Of 2211 cases reported between 2009 and 2020; 1954 (88.4%) were reported during outbreaks. Overall, the prevalence of dengue was 29% (95% CI: 20–39%) and 3% (95% CI: 1–5%) during the outbreak and non-outbreak periods, respectively. Old age (6/21 studies), lack of mosquito control (6/21), urban residence (4/21), climate change (3/21), and recent history of travel (3/21) were the leading risk factors. This review reports a high burden of dengue and increased risk of severe disease in Africa. Our findings provide useful information for clinical practice and health policy decisions to implement effective interventions.