Unsuccessful Cassava Brown Streak Disease (CBSD) evaluation attempts in western Democratic Republic of Congo and implications with cassava root necrosis disease (CRND) etiology

Open Access ArticleCassava brown streak disease (CBSD) is the second most important virus disease after Cassava mosaic disease (CMD), infecting cassava (ManihotesculetaCrantz) in Africa. The disease is caused by two distinct viruses, Cassava brown streak virus [2, 3] and Ugandan Cassava brown streak virus (family, Potyviridae: genus, Ipomovirus). Transmission of CBSV from one plant to another is reported to occur through grafting CBSV-free with infected cuttings and subsequent dissemination by infected cuttings. The basic approach to control of CBSD is selecting planting material from symptomless mother plants. Graft inoculation is the most efficient and effective of the techniques for CBSD virus transmission and consequently cuttings are the most effective way of the disease spreading. In early 2000s, cassava root necrosis similar to those of CBSD were reported in western provinces of Democratic Republic of Congo (RDC) (Kinshasa and Kongo Central) and up to date PCR diagnoses did not detect any causal agent related to the observed symptoms and the disease which was still referred as ‘CBSD-like disease’. Due to lack of molecular data and the similarity of root symptoms with CBSD, the existence of a virus has always been suspected to be the cause of CBSD-like propagation. Thus, 2 field experiments were proposed in order to verify the existence of a systematic transmission of a possible CBSD related virus, knowing that CBSD viruses are transmitted efficiently by cuttings. The first trial focused on the field evaluation of CBSD – like infected and apparently uninfected planting materials, while the second trial involved the importation of tanzanian CBSD resistant genotypes for evaluation in INERA Mvuazi research center under CBSD-like infection conditions. Results of the first trial did not show a systemic transmission of any CBSD-like pathogen while CBSD-resistant parents involved in the second trial all succumbed to CBSD-like disease

First report and preliminary evaluation of cassava root necrosis in Angola

Open Access ArticleCassava is a main staple food for 800 million people world-wide. Production is limited by pest and pathogens. The most devastating cassava viruses are Cassava Brown Streak Virus and Uganda Cassava Brown Streak Virusboth causing severe root necrosis called Cassava Brown Streak Disease. In the last 10 years, the Cassava Brown Streak Disease (CBSD)has spread across Africa from the east coast of Africa to central Africa. Similar root necrosis to cassava brown streak disease has also been identified in the Democratic Republic of Congo where the first symptoms were identified in 2002 in Kinshasa and Kongo central province. In 2012, the presence of CBSD was confirmed in eastern Democratic Republic of Congo. All attempts since 2002 in western Democratic Republic of Congo to identify the cause of these root necrosis have failed. In 2017, a team of scientists surveying the Songololo Territory in the Kongo central province at the northern Angola, identified the same root necrosis similar to CBSD in several localities bordering Angola. These unexpected results will foreshadow the presence of cassava root necrosis in Angola. This preliminary investigation in northern Angola was conducted specifically in the Zaire province and the territory of Mbanza Kongo at approximatively 62 kms from the Democratic Republic of Congo border in order to verify, whether or not, these root necrosis are present in Angola. Results obtained from this exploratory survey in several fields of the Zaire province and territory of Mbanza Kongo confirmed, for the first time, the presence of cassava root necrosis in Angola, similar to CBSD, as identified in western DRC

Assessing the severity and the incidence of Cassava Root Necrosis Disease (CRND) in western Democratic Republic of Congo

Open Access ArticleCassava is the staple food in the Democratic Republic of Congo (DRC) where both the roots and leaves are consumed. This crop is susceptible to several viral diseases, including Cassava Mosaic Disease(CMD) and Cassava Brown Streak Disease(CBSD) in eastern DRC. Following earlier studies that show root necrosis occurring in western DR Care not due to CBSD but to Cassava Root Necrosis Disease (CRND), an exploratory survey was conducted in western DRC from 2016 to 2017 in order to determine the distribution, the severity and the incidence of this disease (previously known as CBSD-like disease). NGS ( Next Generation Sequencing) results confirmed all the previous negative results obtained using PCR and CBSV primers. This suggests that microorganisms such as bacteria or fungi could be responsible for cassava root necrosis in western DRC and is not CBSD as predicted. Five provinces (Bas-Congo, Kinshasa, Bandundu, Equateur and Kasai-Oriental) were surveyed and data were collected according to the harmonized protocols adopted by countries within the West African Virus Epidemiology (WAVE) project. Statistical tests (ANOVA) performed on our data showed that CRND severity did not vary significantly among the provinces of Kinshasa, Bandundu and Bas-Congo which are the areas most affected by the disease. Bas-Congo and Kinshasa provinces presented the highest maximum disease severity (score 3 and 5 respectively), while Equateur province had the lowest disease severity score. Equateur province also had the highest percentage of healthy plants and few plants presented mild symptoms. The overall average of cassava root necrosis severity in western DRC ranged around 1.88 ± 0.08, an approximate score of 2. The overall mean incidence of CRND in western DRC was 22.24 ± 2.4% but reached 100% in localities considered as hotspots (Lukuakua in Bas-Congo and Nguma in Plateau des Batékés). The behaviour of cassava varieties against CRND is similar with CBSD in East Africa, most of improved varieties and landraces are susceptible to both diseases. Correlation analyses showed a positive correlation (r = 0.6940) between severity and incidence of CRND. Therefore, Bas-Congo province is the most affected province, while the province of Equateur is the least affected province in western DRC. Further investigations, including genomic surveillance, should also be conducted in the eastern DRC where CBSD is confirmed to know if CRND is found in conjunction with CBSD and to report possible instances of mixed infections. For medium-term disease control, our study suggests that the development and deployment of control measures including cultivars with resistance to CRND and CBSD should be a priority

Effet des champignons mycorhiziens Arbusculaires sur le phosphore des sols tropicaux et implication dans la biosynthèse du caroténoïde du manioc

Open Access Journal; Published online: 31 March 2019Objectifs : Evaluer du point de vue agronomique les avantages attribués aux champignons mycorhiziens arbusculaires (CMA) par rapport aux sols des zones des forêts humides et vérifier le rôle que le phosphore mobilisé par ces champignons jouerait dans la biosynthèse du caroténoïde. Méthodologie et résultats : Deux variétés de manioc étaient soumises aux inoculations apportées seules ou combinées aux autres fertilisants. Les analyses de sol effectuées en amont et en aval du manioc ont permis de constater des changements significatifs en ce qui concerne l'acidité mesurée à 4,6 de pH avant le manioc et 6,3 après inoculation des CMA. Des changements sont également observés sur la structure du sol où on a observé des modifications partant de la structure particulaire au départ à une structure grumeleuse après application de fumier combiné aux inoculations des CMA. Ces inoculations ont fait augmenter la teneur du phosphore dans le sol à 7,5 %, l’azote à 4 % et le carbone à 13%. Le rendement du manioc a donné des moyennes de 55 t ha-1 de racines sous inoculation contre 21 t ha-1 de racines lorsque le sol n’était pas traité. On a noté des modifications significatives du caroténoïde total dans la racine de manioc lorsque le sol était inoculé et était plus pourvu en phosphore. Conclusions et champs d’application des résultats : les champignons mycorhiziens sont présents dans les sols tropicaux des forêts humides et peuvent être multipliés sous le sorgho. Lorsqu’ils sont inoculés en champ de manioc, ils permettent à la fois des accroissements de rendement du manioc, la disponibilisation du phosphore autrefois complexé par les cations acides du sol et l’accélération de la biosynthèse du caroténoïde total du manioc jaune. La possibilité de réaliser des multiplications en cascade de ces champignons et leur conditionnement sur des substrats stériles permettra de fabriquer des inocula locaux qui pourront être utilisés comme fertilisant biologique en lieu et place des fertilisants minéraux conventionnels. Objectives: To evaluate agronomically the advantages attributed to Arbuscular Mycorrhizal Fungi (AMF) compared to soils in humid forest zones and verify the role that phosphorus mobilized by these fungi would play in the biosynthesis of carotenoid of yellow cassava. Methodology and results: Two varieties of cassava were inoculated alone or in combination with other fertilizers. Soil tests carried out before cassava cultivation and after harvest showed significant changes in acidity measured at 4.6 pH before cassava and 6.3 after inoculation with AMF. Changes were also observed in soil grain size with 71% sand initially and 65.5% after application of manure combined with inoculations (LSD.05 = 2.7%). These inoculations increased the soil phosphorus content to 7.5%, nitrogen to 4% and carbon to 13%. Cassava yield averaged 55 t ha-1 under inoculation versus 21 t ha-1 when the soil was untreated. Significant changes in total carotenoid in the cassava root were noted when the soil was inoculated and had a higher phosphorus content. Conclusions and application findings: Mycorrhizal fungi are present in tropical soils of moist forests and can be propagated under sorghum. When inoculated in the cassava field, they allow both increases in cassava yield, the availability of phosphorus once complexed by acidic soil cations and the acceleration of the total carotenoid biosynthesis of yellow cassava. The possibility of performing cascade multiplications of these fungi and their conditioning on sterile substrates will make local inocula that can be used as biological fertilizer instead of conventional mineral fertilizers

Attempts to identify Cassava Brown Streak Virus in western Democratic Republic of Congo

Open Access ArticleRoot necrosis similar to those of the cassava brown streak disease (CBSD) were observed on cassava in western provinces of the Democratic Republic of Congo (DR.Congo) in the early 2000’s. However molecular laboratory diagnosis were not able to detect any causative agent responsible for the attacks, hence, the disease related to these symptoms was named CBSD-like disease. In order to assess the distribution and the incidence of the CBSD-like disease, surveys were carried out in four western provinces, comprising, Kwango and Kwilu, Sud Ubangi, Kinshasa and Kongo Central. CBSD-like disease was observed in all surveyed provinces on the basis of root symptoms because foliar symptoms were different to those of the documented cases of CBSD in other parts of east Africa. CBSD-like disease incidence was high in Kongo Central and Sud Ubangi, exceeding an average of 50 %, but low in Kwango and Kwilu (32.8%) and in Kinshasa (19.1%). During the surveys, cassava leaf samples were collected for lab identification of the causal agent. PCR diagnosis was done on these samples using primers specific for the two known CBSVs. All samples tested negative with no amplification of DNA fragments of the correct size. Thus, further analysis on the causative organism is needed using Next Generation Sequencing (NGS) approaches. NGS approaches will help also to identify the causative organism in other Central Africa countries (Angola, Congo-Brazzaville and Gabon) where such cassava root necrosis have been reported or are suspected

Post-vaccination COVID-19: A case-control study and genomic analysis of 119 breakthrough infections in partially vaccinated individuals

BACKGROUND: Post-vaccination infections challenge the control of the COVID-19 pandemic. METHODS: We matched 119 cases of post-vaccination SARS-CoV-2 infection with BNT162b2 mRNA, or ChAdOx1 nCOV-19, to 476 unvaccinated patients with COVID-19 (Sept 2020-March 2021), according to age and sex. Differences in 60-day all-cause mortality, hospital admission, and hospital length of stay were evaluated. Phylogenetic, single nucleotide polymorphism (SNP) and minority variant allele (MVA) full genome sequencing analysis was performed. RESULTS: 116/119 cases developed COVID-19 post first vaccination dose (median 14 days, IQR 9 - 24 days). Overall, 13/119 (10∙9%) cases and 158/476 (33∙2%) controls died (p<0.001), corresponding to 4∙5 number needed to treat (NNT). Multivariably, vaccination was associated with 69∙3% (95%CI 45∙8 - 82∙6) relative risk (RR) reduction in mortality. Similar results were seen in subgroup analysis for patients with infection onset ≥14 days after first vaccination (RR reduction 65∙1%, 95%CI 27∙2 - 83∙2, NNT 4∙5), and across vaccine subgroups (BNT162b2: RR reduction 66%, 95%CI 34∙9 - 82∙2, NNT 4∙7, ChAdOx1: RR reduction 78∙4%, 95%CI 30∙4 - 93∙3, NNT 4∙1). Hospital admissions (OR 0∙80, 95%CI 0∙51 - 1∙28), and length of stay (-1∙89 days, 95%CI -4∙57 - 0∙78) were lower for cases, while Ct values were higher (30∙8 versus 28∙8, p = 0.053). B.1.1.7 was the predominant lineage in cases (100/108, 92.6%) and controls (341/446, 76.5%). Genomic analysis identified one post-vaccination case harboring the E484K vaccine escape mutation (B.1.525 lineage). CONCLUSIONS: Previous vaccination reduces mortality when B.1.1.7 is the predominant lineage. No significant lineage-specific genomic changes during phylogenetic, SNP and MVA analysis were detected

A global framework for action to improve the primary care response to chronic non-communicable diseases: a solution to a neglected problem.

BACKGROUND: Although in developing countries the burden of morbidity and mortality due to infectious diseases has often overshadowed that due to chronic non-communicable diseases (NCDs), there is evidence now of a shift of attention to NCDs. DISCUSSION: Decreasing the chronic NCD burden requires a two-pronged approach: implementation of the multisectoral policies aimed at decreasing population-level risks for NCDs, and effective and affordable delivery of primary care interventions for patients with chronic NCDs. The primary care response to common NCDs is often unstructured and inadequate. We therefore propose a programmatic, standardized approach to the delivery of primary care interventions for patients with NCDs, with a focus on hypertension, diabetes mellitus, chronic airflow obstruction, and obesity. The benefits of this approach will extend to patients with related conditions, e.g. those with chronic kidney disease caused by hypertension or diabetes. This framework for a "public health approach" is informed by experience of scaling up interventions for chronic infectious diseases (tuberculosis and HIV). The lessons learned from progress in rolling out these interventions include the importance of gaining political commitment, developing a robust strategy, delivering standardised interventions, and ensuring rigorous monitoring and evaluation of progress towards defined targets. The goal of the framework is to reduce the burden of morbidity, disability and premature mortality related to NCDs through a primary care strategy which has three elements: 1) identify and address modifiable risk factors, 2) screen for common NCDs and 3) and diagnose, treat and follow-up patients with common NCDs using standard protocols. The proposed framework for NCDs borrows the same elements as those developed for tuberculosis control, comprising a goal, strategy and targets for NCD control, a package of interventions for quality care, key operations for national implementation of these interventions (political commitment, case-finding among people attending primary care services, standardised diagnostic and treatment protocols, regular drug supply, and systematic monitoring and evaluation), and indicators to measure progress towards increasing the impact of primary care interventions on chronic NCDs. The framework needs evaluation, then adaptation in different settings. SUMMARY: A framework for a programmatic "public health approach" has the potential to improve on the current unstructured approach to primary care of people with chronic NCDs. Research to establish the cost, value and feasibility of implementing the framework will pave the way for international support to extend the benefit of this approach to the millions of people worldwide with chronic NCDs

Cassava yield loss in farmer fields was mainly caused by low soil fertility and suboptimal management practices in two provinces of the Democratic Republic of Congo

Article purchasedA better understanding of the factors that contribute to low cassava yields in farmers’ fields is required to guide the formulation of cassava intensification programs. Using a boundary line approach, we analysed the contribution of soil fertility, pest and disease infestation and farmers’ cultivation practices to the cassava yield gap in Kongo Central (KC) and Tshopo (TSH) provinces of the Democratic Republic of Congo. Data were obtained by monitoring 42 and 37 farmer-managed cassava fields during two cropping cycles in KC and one cropping cycle in TSH, respectively. Each field was visited three times over the cassava growing period for the observations. Logistic model was fitted against the observed maximum cassava root yields and used to calculate the achievable yield per field and for individual factor. At field level, the factor that led to the lowest achievable yield (Yup(i)1) was considered as the dominant yield constraint. Cassava yield loss per field was expressed as the increase in the maximal root yield observed per province (Yatt- attainable yield) compared to Yup(i)1. Yatt was 21 and 24 t ha−1 in TSH and KC, respectively. With the cassava varieties that farmers are growing in the study areas, pests and diseases played a sparse role in the yield losses. Cassava mosaic was the only visible disease we observed and it was the dominant yield constraint in 3% and 12% of the fields in KC and TSH, respectively. The frequent yield constraints were suboptimal field management and low soil fertility. Cultivation practices and soil parameters led to Yup(i)1 in 47% and 50% of the fields in KC, and in 47% and 41% of those in TSH, respectively. Individual soil parameters were the yield constraint in few fields, suggesting that large-scale programs in terms of lime application or recommendation of the blanket fertilisers would result in sparse efficacy. In KC, yield losses caused by low soil fertility averaged 6.2 t ha−1 and were higher than those caused by suboptimal field management (5.5 t ha−1); almost nil for cassava mosaic disease (CMD). In TSH, yield losses caused by low soil fertility (4.5 t ha−1) were lower than those caused by suboptimal field management (6.5 t ha−1) and CMD (6.1 t ha−1). Irrespective of the constraint type, yield loss per field was up to 48% and 64% of the Yatt in KC and TSH, respectively. Scenario analysis indicated that the yield losses would remain at about two third of these levels while the dominant constraint was only overcome. We concluded that integrated and site-specific management practices are needed to close the cassava yield gap and maximize the efficacy of cassava intensification programs

Late Ebola virus relapse causing meningoencephalitis: a case report

Background: There are thousands of survivors of the 2014 Ebola outbreak in west Africa. Ebola virus can persist in survivors for months in immune-privileged sites; however, viral relapse causing life-threatening and potentially transmissible disease has not been described. We report a case of late relapse in a patient who had been treated for severe Ebola virus disease with high viral load (peak cycle threshold value 13·2). Methods: A 39-year-old female nurse from Scotland, who had assisted the humanitarian effort in Sierra Leone, had received intensive supportive treatment and experimental antiviral therapies, and had been discharged with undetectable Ebola virus RNA in peripheral blood. The patient was readmitted to hospital 9 months after discharge with symptoms of acute meningitis, and was found to have Ebola virus in cerebrospinal fluid (CSF). She was treated with supportive therapy and experimental antiviral drug GS-5734 (Gilead Sciences, San Francisco, Foster City, CA, USA). We monitored Ebola virus RNA in CSF and plasma, and sequenced the viral genome using an unbiased metagenomic approach. Findings: On admission, reverse transcriptase PCR identified Ebola virus RNA at a higher level in CSF (cycle threshold value 23·7) than plasma (31·3); infectious virus was only recovered from CSF. The patient developed progressive meningoencephalitis with cranial neuropathies and radiculopathy. Clinical recovery was associated with addition of high-dose corticosteroids during GS-5734 treatment. CSF Ebola virus RNA slowly declined and was undetectable following 14 days of treatment with GS-5734. Sequencing of plasma and CSF viral genome revealed only two non-coding changes compared with the original infecting virus. Interpretation: Our report shows that previously unanticipated, late, severe relapses of Ebola virus can occur, in this case in the CNS. This finding fundamentally redefines what is known about the natural history of Ebola virus infection. Vigilance should be maintained in the thousands of Ebola survivors for cases of relapsed infection. The potential for these cases to initiate new transmission chains is a serious public health concern

Recurrent SARS-CoV-2 mutations in immunodeficient patients

Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COVID-19 Genomics UK (COG-UK) dataset. The spike gene receptor-binding domain and N-terminal domain (NTD) were identified as mutation hotspots. Numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally a mutation in the envelope gene, T30I was determined to be the second most frequent recurrently occurring mutation arising in persistent infections. A high proportion of recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimisation.There is an apparent selective pressure for mutations that aid cell–cell transmission within the host or persistence which are often different from mutations that aid inter-host transmission, although the fact that multiple recurrent de novo mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted