Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

Background: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA. Methods: We used next-generation sequencing to identify viruses associated to maize lethal necrosis in Kenya through a metagenomics analysis. Symptomatic and asymptomatic leaf samples were collected from maize and sorghum representing sixteen counties. Results: Complete and partial genomes were assembled for MCMV, SCMV, Maize streak virus (MSV) and Maize yellow dwarf virus-RMV (MYDV-RMV). These four viruses (MCMV, SCMV, MSV and MYDV-RMV) were found together in 30 of 68 samples. A geographic analysis showed that these viruses are widely distributed in Kenya. Phylogenetic analyses of nucleotide sequences showed that MCMV, MYDV-RMV and MSV are similar to isolates from East Africa and other parts of the world. Single nucleotide polymorphism, nucleotide and polyprotein sequence alignments identified three genetically distinct groups of SCMV in Kenya. Variation mapped to sequences at the border of NIb and the coat protein. Partial genome sequences were obtained for other four potyviruses and one polerovirus. Conclusion: Our results uncover the complexity of the maize lethal necrosis epidemic in Kenya. MCMV, SCMV, MSV and MYDV-RMV are widely distributed and infect both maize and sorghum. SCMV population in Kenya is diverse and consists of numerous strains that are genetically different to isolates from other parts of the world. Several potyviruses, and possibly poleroviruses, are also involved

Wavelet Analysis on the Variability and the Teleconnectivity of the Rainfall of the Congo Basin for 1940 – 1999.

International audienceIt is known that the spatial and temporal variability’s of rainfall in the Congo Basin are complex because of its size, diversity of climates, topography, seasonal migration of the intertropical convergence zone (ITCZ), and the influence of oceans SST variations.This basin is characterized by low density of meteorological stations associated with a high percentage of missing data which is a high source of uncertainty for the results.However gridded database of rainfall (CRU, IRD,…) are available and can be used for various needs such as regional studies and modeling.We propose to quantify this variability using a wavelet analysis.Wavelet analysis of the Congo basin rainfall shows some energy bands:Annual fluctuations are the most representative and the most structured signal, explaining more than 30 % of the total rainfall variability;Multi-year fluctuations have a lower contribution (less than 10 %) during this period. It is clear that rainfall is highly structured by the annual cycle so that a transformation of rainfall data is requiredand allows to evidence the eventual connection of 2 to 8 and 8 to 16 years bands.We can observe three major shifts (around 1960, 1970 and 1983) in the signal (instationarities) of the rainfall in the Congo, Kasai and Oubangui basin’s, which affected the 2-4 years, 4-8 and the 8-16 bands.The wavelets coherence confirms a weak relationship between the rainfalls of the Congo basin and the Pacific and tropical Atlantic long term SST forcing

First Report of Maize chlorotic mottle virus Infecting Maize in the Democratic Republic of the Congo

Maize (Zea mays L.) is a major food and fodder crop cultivated on 1.54 million ha in the Democratic Republic of the Congo (DRC). In December 2013, unusually severe chlorotic mottle symptoms and pale green streaks were observed in local varieties (Mudishi 1 and 2, Bambou, Kasayi, H614, H613, and Mugamba) and exotic varieties (H520, H624, H403, HDK8031, and ZM607) in Beni, Lubero, and Rutshuru territories at 1,015 to 1,748 m elevation in North Kivu Province. Symptoms were prominent on newly emerging leaves that later developed marginal necrosis resembling the symptoms of maize lethal necrosis (MLN), caused by a dual infection of Maize chlorotic mottle virus (MCMV, genus Machlomovirus) and Sugarcane mosaic virus (SCMV, genus Potyvirus). Each of these viruses, but particularly MCMV, is also known to cause severe mosaic and mottling symptoms in maize (4). In January 2014, symptomatic and asymptomatic samples (n = 20) from disease-affected fields in Beni and Lubero provinces were collected for virus testing using Whatman FTA Classic Cards (1) and analyzed for MCMV (2681F: 5?-ATGAGAGCAGTTGGGGAATGCG and 3226R: 5?-CGAATCTACACACACACACTCCAGC) and SCMV (8679F: 5?-GCAATGTCGAAGAAAATGCG and 9595R: 5?-GTCTCTCACCAAGAGACTCGCAGC) by reverse transcription (RT)-PCR (4). Samples were also analyzed for Maize streak virus (MSV, genus Mastrevirus), an endemic virus in DRC, by PCR using MSV specific primers (MSV215-234: CCAAAKDTCAGCTCCTCCG and MSV1770-1792: TTGGVCCGMVGATGTASAG) (3). A DNA product of expected size (~520 bp) resulted only for MCMV in all the symptomatic plant samples. None of the samples tested positive for SCMV or MSV. RT-PCR analyses were performed to ascertain the absence of potyviruses using the degenerate potyvirus primers (CIFor: 5?GGIVVIGTIGGIWSIGGIAARTCIAC and CIRev: 5?ACICCRTTYTCDATDATRTTIGTIGC3?) (2) were also negative. Occurrence of MCMV in symptomatic samples was further confirmed by antigen-coated plate (ACP)-ELISA using anti-MCMV rabbit polyclonal antibodies produced at the Virology Unit, IITA, Ibadan, Nigeria. The RT-PCR product of MCMV was purified and sequenced in both directions (GenBank Accession No. KJ699379). Pairwise comparison of 518 bp nucleotide sequence corresponding to p32 and p37 open reading frames of MCMV by BLASTn search revealed 99.8% nucleotide sequence identity with an MCMV isolate from Kenya (JX286709), 98 to 99% identity with the isolates from China (JQ982468 and KF010583), and 96% identity with the isolates from the United States (X14736 and EU358605). MCMV is a newly emerging virus in Africa, first detected during a severe MLND outbreak in 2011 in Kenya (4). This disease has since become a serious threat to maize production in East Africa. MCMV has been reported in maize from Kenya, Rwanda, Tanzania, and Uganda. To our knowledge, this is the first report of MCMV occurrence in DRC. This finding confirms the further geographic expansion of MCMV and illustrates the need for further studies to identify vectors and also create awareness about the disease and to strengthen surveillance to prevent its further spread in the continent

Field Assessment of the Potential Role of Fusarium Species in the Pathogenesis of Coffee Wilt Disease in Democratic Republic of Congo

Aim: To determine the probable role of 3 species of Fusarium (F. falciforme, F. solani and                       F. stilboides) in the pathogenesis of Coffee Wilt Disease (CWD). Study Design: The field trial was performed using a Randomized Completed Block Design (RCBD) replicates three times. Place and Duration of the Study: The study was conduct in the Experimental Garden of Department of Biology, Faculty of Sciences, University of Kinshasa in Democratic Republic of Congo, between November 2005 and February 2006. Methodology: Four Fusarium species (F. falciforme, F. solani, F. stilboides and F. xylarioides) were inoculated alone, or the first three strains were inoculated in combination with F. xylarioides in coffee seedlings 10 months old. Observations were focused on the time of expression of main CWD symptoms, the rate of each symptom observed, and the presence of each pathogen in dead woods of inoculated seedlings.   Results: Results obtained showed that all Fusarium species induced main symptoms of CWD at varying moment and degrees. Chronologically, leaf yellowing appeared an average 25 dai, followed by leaf browning (46 dai), leaf drying (61 dai), mortality (75 dai) and defoliation (77 dai). Significant differences (P = .05) were observed between treatments considered. All Fusarium induced seedlings mortality and were isolated in dead woods at 1 – 4 cm from the point of inoculation. In general, the search of synergistic interaction between Fusarium spp. inoculated in combination with F. xylarioides showed enhanced ability to induce various symptoms of CWD when species are used together.  Conclusion: The present study demonstrates that CWD could be reconsidered as a parasitic complex, and in natural conditions all Fusarium species used present a danger for coffee growing