Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso

Cowpea, ( Vigna unguiculata L. (Walp)) is an annual tropical grain legume. Often referred to as "poor man's meat", cowpea is one of the most important subsistence legumes cultivated in West Africa due to the high protein content of its seeds. However, African cowpea production can be seriously constrained by viral diseases that reduce yields. While twelve cowpea-infecting viruses have been reported from Africa, only three of these have so-far been reported from Burkina Faso. Here we use a virion-associated nucleic acids (VANA)-based metagenomics method to screen for the presence of cowpea viruses from plants collected from the three agro-climatic zones of Burkina Faso. Besides the three cowpea-infecting virus species which have previously been reported from Burkina Faso (Cowpea aphid borne mosaic virus [Family Potyviridae ], the Blackeye cowpea mosaic virus--a strain of Bean common mosaic virus--[Family Potyviridae ] and Cowpea mottle virus [Family Tombusviridae ]) five additional viruses were identified: Southern cowpea mosaic virus (Sobemovirus genus), two previously uncharacterised polerovirus-like species (Family Luteoviridae ), a previously uncharacterised tombusvirus-like species (Family Tombusviridae ) and a previously uncharacterised mycotymovirus-like species (Family Tymoviridae ). Overall, potyviruses were the most prevalent cowpea viruses (detected in 65.5% of samples) and the Southern Sudan zone of Burkina Faso was found to harbour the greatest degrees of viral diversity and viral prevalence. Partial genome sequences of the two novel polerovirus-like and tombusvirus-like species were determined and RT-PCR primers were designed for use in Burkina Faso to routinely detect all of these cowpea-associated viruses

Strict adherence to malaria rapid test results might lead to a neglect of other dangerous diseases: a cost benefit analysis from Burkina Faso

<p>Abstract</p> <p>Background</p> <p>Malaria rapid diagnostic tests (RDTs) have generally been found reliable and cost-effective. In Burkina Faso, the adherence of prescribers to the negative test result was found to be poor. Moreover, the test accuracy for malaria-attributable fever (MAF) is not the same as for malaria infection. This paper aims at determining the costs and benefits of two competing strategies for the management of MAF: presumptive treatment for all or use of RDTs.</p> <p>Methods</p> <p>A cost benefit analysis was carried out using a decision tree, based on data previously obtained, including a randomized controlled trial (RCT) recruiting 852 febrile patients during the dry season and 1,317 in the rainy season. Cost and benefit were calculated using both the real adherence found by the RCT and assuming an ideal adherence of 90% with the negative result. The main parameters were submitted to sensitivity analysis.</p> <p>Results and discussion</p> <p>At real adherence, the test-based strategy was dominated. Assuming ideal adherence, at the value of 525 € for a death averted, the total cost of managing 1,000 febrile children was 1,747 vs. 1,862 € in the dry season and 1,372 vs. 2,138 in the rainy season for the presumptive vs. the test-based strategy. For adults it was 2,728 vs. 1,983 and 2,604 vs. 2,225, respectively. At the subsidized policy adopted locally, assuming ideal adherence, the RDT would be the winning strategy for adults in both seasons and for children in the dry season.</p> <p>At sensitivity analysis, the factors most influencing the choice of the better strategy were the value assigned to a death averted and the proportion of potentially severe NMFI treated with antibiotics in patients with false positive RDT results. The test-based strategy appears advantageous for adults if a satisfactory adherence could be achieved. For children the presumptive strategy remains the best choice for a wide range of scenarios.</p> <p>Conclusions</p> <p>For RDTs to be preferred, a positive result should not influence the decision to treat a potentially severe NMFI with antibiotics. In the rainy season the presumptive strategy always remains the better choice for children.</p

Assessing the adaptability and resilience of cowpea and maize varieties to various climatic zones of Côte d’Ivoire

Abstract The cultivation of cowpea and maize is common, but it is carried out without a prior selection of varieties that can effectively adapt to the specific climatic conditions of the zones. This study aimed at assessing cowpea and maize varieties in different ecological zones in order to identify the resilient varieties with respect to zone. The experiments were conducted in three different climatic and vegetation zones of Côte d’Ivoire: tropical rainforest zone, forest-savannah mosaic, and sub-Sudanian savannah in South, Centre-West, and North Côte d’Ivoire, respectively. In each zone, a randomized complete block design was used. Four varieties of both cowpea and maize were used. The analysis of variance was realized using grain yield data to compare varieties and climatic zones. The best varieties obtained differed according to the zones. Thus, in the tropical rain forest zone, the cowpea variety KVX780-6 and maize variety Violet de Katiola were the most yielding, with 593.30 kg ha−1 and 1270.84 kg ha−1, respectively. In forest-savannah mosaic, the cowpea variety KVX745-11P and maize variety SR21 obtained the highest yields, with 761.82 kg ha−1 and 2212.99 kg ha−1, respectively. The cowpea variety Tiligre and maize variety SR21 were the most productive in the sub-Sudanian savannah zone, with yields of 327.31 kg ha−1 and 1797.3 kg ha−1, respectively. Overall, the highest yield of cowpea (513.20 kg ha−1) and maize (1757.13 kg ha−1) were observed in forest-savannah mosaic. The best cowpea and maize varieties identified in each zone can be recommended to farmers

Molecular Variability and Genetic Structure of IYMV in Burkina Faso

International audienceImperata yellow mottle virus (IYMV, Sobemovirus) was first described in 2008 in the southwestern region of Burkina Faso (West Africa). The genetic diversity of IYMV was not documented up to day. In this study, the variability of CP of IYMV was evaluated through the molecular characterization of 38 isolates collected in the western part of Burkina Faso. Comparison of sequences of these new isolates and one IYMV sequence available in GenBank revealed that the average nucleotide diversity was low. The ratio of non-synonymous over synonymous nucleotide substitutions per site was low, indicating a CP diversification under strong purifying selection. Despite of the low nucleotide diversity, phylogenetic analyses revealed segregation of IYMV isolates into six major clades. There was no correlation of phylogenetic grouping of isolates based on geographical location. This is the first study of the genetic diversity of IYMV

Pathogenicity of rice yellow mottle virus and screening of rice accessions from the Central African Republic

Abstract Background Rice yellow mottle virus (RYMV) of the genus Sobemovirus is the most important viral pathogen of rice causing more damage to rice crop in Sub Saharan Africa. The aim of this study was to conduct pathogenic characterization of RYMV isolates from the Central African Republic (CAR) and to screen commonly cultivated rice accessions in the country for resistance/tolerance to the virus. Methods The pathogenicity of RYMV isolates was studied by mechanical inoculation with comparison to differential rice lines highly resistant to RYMV available at the Institute of Environment and Agricultural Research (INERA) in Burkina Faso. To screen commonly cultivated rice accessions in CAR, characterized RYMV isolates from the country were used as inoculum sources. Resistant breaking (RB) isolates were used to prepare RB-inoculum, whereas non-resistant breaking isolates (nRB) were used for nRB-inoculum. Results Overall 102 isolates used in this study, 29.4% were able to overcome the high resistance genes in the rice cultivars Gigante and Tog7291. All isolates were distributed within three distinct pathogenic profiles. The first profile constituted of 6.9% of the isolates was able to break down the resistance in rice cultivar Gigante only. The second pathogenic profile made of 19.6% of isolates was able to infect Tog7291 only. The third profile, 2.9% of isolates overcame simultaneously resistance genes in both rice cultivars Gigante and Tog7291. Out of isolates able to break down the resistance gene in cultivar Gigante, a single isolate was found to be non-infectious to the susceptible control IR64. Data from screening showed that all accessions were susceptible to RYMV, although IRAT213 was found to be partially resistant to both nRB-inoculum and RB-inoculum. Conclusion The present study can be considered as the first in the Central African Republic, it gives a caution on the high risk of RYMV damage to rice production in the country. Beside, skills of pathogenic profiles of RYMV isolates will contribute to better disease management

Complete genome sequences of cowpea polerovirus 1 and cowpea polerovirus 2 infecting cowpea plants in Burkina Faso

The full-length genome sequences of two novel poleroviruses found infecting cowpea plants, cowpea polerovirus 1 (CPPV1) and cowpea polerovirus 2 (CPPV2), were determined using overlapping RT-PCR and RACE-PCR. Whereas the 5845-nt CPPV1 genome was most similar to chickpea chlorotic stunt virus (73% identity), the 5945-nt CPPV2 genome was most similar to phasey bean mild yellow virus (86% identity). The CPPV1 and CPPV2 genomes both have a typical polerovirus genome organization. Phylogenetic analysis of the inferred P1-P2 and P3 amino acid sequences confirmed that CPPV1 and CPPV2 are indeed poleroviruses. Four apparently unique recombination events were detected within a dataset of 12 full polerovirus genome sequences, including two events in the CPPV2 genome. Based on the current species demarcation criteria for the family Luteoviridae, we tentatively propose that CPPV1 and CPPV2 should be considered members of novel polerovirus species

Maximum-likelihood phylogenetic trees depicting the relatedness of cowpea viruses from Burkina Faso.

<p>A) Maximum-likelihood phylogenetic trees of partial <i>cp</i> genes from nine isolates of Cowpea polerovirus 1 and representative species from the family <i>Luteoviridae</i>. SCYLV, Sugarcane yellow leaf virus; PLRV, Potato leafroll virus; PeVYV, Pepper vein yellows virus; CpCSV, Chickpea chlorotic stunt virus; BrYV, Brassica yellows virus; BWYV, Beet western yellows virus; BYDV, Barley yellow dwarf virus; BLRV, Bean leafroll virus; SbDV, Soybean dwarf virus; PEMV-1, Pea enation mosaic virus-1; GRAV, Groundnut rosette assistor virus; PBMYV, Phasey bean mild yellows virus. B) Maximum-likelihood phylogenetic trees of partial <i>RdRp</i> genes from four isolates of Cowpea tombusvirid-1 and representative species from the family <i>Tombusviridae</i>. TurCV, Turnip crinkle virus; MNSV, Melon necrotic spot virus; MCMV, Maize chlorotic mottle virus; JCSMV, Johnsongrass chlorotic stripe mosaic virus; OCSV, Oat chlorotic stunt virus; TNV A, Tobacco necrosis virus A; OLV1, Olive latent virus 1; PMV, Panicum mosaic virus; CMMV, Cocksfoot mild mosaic virus; CarMV, Carnation mottle virus; MWLMV, Maize white line mosaic virus; PNSV, Pelargonium necrotic spot virus; CIRV, Carnation Italian ringspot virus; GaMV, Galinsoga mosaic virus; FNSV, Furcraea necrotic streak virus; LWSV, Leek white stripe virus; BBSV, Beet black scorch virus; SCNMV, Sweet clover necrotic mosaic virus; CRSV, Carnation ringspot virus; CkMV, Cocksfoot mottle virus. C) Maximum-likelihood phylogenetic trees of partial <i>RdRp</i> gene from 5 isolates of CPMoV from Burkina Faso and representative species from Carmovirus genus and from the family <i>Tombusviridae</i>. CCFV, Cardamine chlorotic fleck virus; SYMMV, Soybean yellow mottle mosaic virus; HCRV, Hibiscus chlorotic ringspot virus; PSNV, Pea stem necrosis virus; MNSCG, Melon necrotic spot virus; CymRSV, Cymbidium ringspot tombusvirus; MPV-PM75, Moroccan pepper virus. D: Maximum-likelihood phylogenetic trees of partial <i>RdRp</i> genes from five isolates of SCPMV from Burkina Faso and representative species of the Sobemovirus genus. SCPMV, Southern cowpea mosaic virus; RYMV, Rice yellow Mottle virus; CfMV, Cocksfoot mottle virus_sobemovirus; SCMoV, Subterranean clover mottle virus; SYCMV, Soybean yellow common mosaic virus; SBMV, Southern bean mosaic virus; SeMV, Sesbania mosaic virus; CarMV, Carnation mottle virus. For all four trees, branches associated with a filled dot have bootstrap support above 90 per cent whereas those with an unfilled dot have bootstrap support above 70 per cent. All branches with less than 50 percent bootstrap support were collapsed.</p