Molecular diversity, geographic distribution and host range of monocot-infecting mastreviruses in Africa and surrounding islands

Kraberger, Simona; Saumtally, S.; Pande, Daniel; Khoodoo, M. H. R.; Dhayan, S.; Dookun-Saumtally, A.; Shepherd, Dionne N.; Hartnady, Penelope; Atkinson, Richard L.; Lakay, Francisco; Hanson, Britt; Redhi, Devasha; Monjane, Adérito Luis; Windram, Oliver P.; Walters, Matthew; Oluwafemi, Sunday; Michel-Lett, Jean; Lefeuvre, Pierre; Martin, Darren P.; Varsani, Arvind

doi:10.1016/j.virusres.2017.07.001

Cited by 14 publications

(19 citation statements)

References 41 publications

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“…NGS applications in plant virology began in 2009 (Blawid, Silva & Nagata, 2017) and have been increasingly applied in the de novo discovery of RNA and DNA viruses as well as viroids due to their rise as a rapid and relatively inexpensive mode of viral detection (Wamonje et al, 2017; Ndunguru et al, 2015). Previous reports of using NGS for novel viral discovery and subsequent evolutionary analysis are well-documented (Ndunguru et al, 2015; Kraberger et al, 2017). In this study, we used this approach to obtain near-complete genomes of BCMNV and CABMV and gain further insights into the evolutionary relationships of BCMNV and CABMV.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary insights ofBean common mosaic necrosis virusandCowpea aphid-borne mosaic virus

Wainaina

Kubatko

Harvey

et al. 2019

PeerJ

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Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well–supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.

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Section: Introductionmentioning

confidence: 99%

Evolutionary insights ofBean common mosaic necrosis virusandCowpea aphid-borne mosaic virus

Wainaina

Kubatko

Harvey

et al. 2019

PeerJ

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“…As a proof of concept, this new metagenomic methodology was applied to a set of non-cultivated plants sampled from a single farm on Reunion Island. In addition to finding viruses that belong to two of the six mastreviruses species that have previously been detected on Reunion Island, MSV and maize streak Reunion virus (MSRV) 6,17 , this article further highlights the gaps that likely remain in our appreciation of mastrevirus diversity on this island by discovering mastreviruses that could represent three new mastrevirus species.…”

Section: Introductionmentioning

confidence: 89%

“…These mastreviruses have collectively been called the “African streak viruses” (AfSV). There are presently thirteen recognised AfSV species, nine of which have been found infecting both cultivated and non-cultivated host species, four of which have only been found infecting non-cultivated grasses 6 .…”

Section: Introductionmentioning

confidence: 99%

“…The development and widespread use of rolling circle amplification (RCA) based protocols for the recovery of complete mastrevirus genome sequences has vastly increased the feasibility of identifying viruses in large numbers of non-cultivated plant samples 6 . RCA has facilitated both the discovery of many new mastreviruses, and the characterization of diverse strain groups within already known species.…”

Section: Introductionmentioning

confidence: 99%

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Exploring the diversity of Poaceae-infecting mastreviruses on Reunion Island using a viral metagenomics-based approach

Claverie

Ouattara

Hoareau

et al. 2019

Sci Rep

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Mostly found in Africa and its surrounding islands, African streak viruses (AfSV) represent the largest group of known mastreviruses. Of the thirteen AfSV species that are known to infect either cultivated or wild Poaceae plant species, six have been identified on Reunion Island. To better characterize AfSV diversity on this island, we undertook a survey of a small agroecosystem using a new metagenomics-based approach involving rolling circle amplification with random PCR amplification tagging (RCA-RA-PCR), high-throughput sequencing (Illumina HiSeq) and the mastrevirus reads classification using phylogenetic placement. Mastreviruses that likely belong to three new species were discovered and full genome sequences of these were determined by Sanger sequencing. The geminivirus-focused metagenomics approach we applied in this study was useful in both the detection of known and novel mastreviruses. The results confirm that Reunion Island is indeed a hotspot of AfSV diversity and that many of the mastrevirus species have likely been introduced multiple times. Applying a similar approach in other natural and agricultural environments should yield sufficient detail on the composition and diversity of geminivirus communities to precipitate major advances in our understanding of the ecology and the evolutionary history of this important group of viruses.

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“…While MSV-A strain has recurrently been reported in maize from Burkina Faso (Kraberger et al 2017), it was only identified once in rice fields in this country (Konaté and Traoré 1992).…”

Section: Introductionmentioning

confidence: 95%

Old foe, new host: epidemiology, genetic diversity and pathogenic characterization of maize streak virus in rice fields from Burkina Faso

Fouad,

Barro,

Bangratz

et al. 2023

Preprint

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Rice is of critical significance regarding food security worldwide including in Africa. Only two viruses impacting rice production in Africa have been deeply investigated for decades: the rice yellow mottle virus (Solemoviridae) and the rice stripe necrosis virus (Benyviridae). Using viral metagenomics, we aimed at exploring the diversity of viruses circulating in Burkina Faso rice fields. We performed an epidemiological survey in this country between 2016 and 2019 involving 57 small farmer’s rice fields under two production systems (rainfed lowlands and irrigated areas). More than 2700 rice samples were collected withouta priori(not based on symptom observation) following a regular scheme. In addition, wild and cultivated (maize and sugarcane)Poaceaegrowing nearby rice fields were also collected. Unexpectedly, metagenomics detected maize streak virus (MSV,Geminiviridae) in analyzed rice samples. Further molecular analyses using RCA-PCR showed that MSV is widely distributed and highly prevalent in both rainfed lowlands and irrigated rice areas. MSV-A and MSV-G strains were identified. MSV-G, exclusively identified so far in wild grasses, was the most prevalent strain while MSV-A, known to cause severe symptoms in maize, was sporadically identified. No genetic differentiation was detected between MSV isolates either infecting wild or cultivated plant species. Using infectious clones in experimental conditions, we confirmed the pathogenicity of both MSV strains on rice. Thus, in addition to contribute to the epidemiological surveillance of rice production in Africa, our results illuminate new epidemiological and pathogenic aspects of one of the most studied plant viruses with significant economic consequences in Africa.FundingFrench National Research Agency «Investissements d’avenir» program (ANR-10-LABX-001-01), Agropolis Fondation (ANR-16-IDEX-006), French National Research Agency “young researchers” program (ANR-20-CE35-0008-01), CGIAR Research Program on Rice Agri-food Systems (RICE), Cooperation and cultural action department of the French Embassy (SCAC) in Burkina Faso.

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Molecular diversity, geographic distribution and host range of monocot-infecting mastreviruses in Africa and surrounding islands

Cited by 14 publications

References 41 publications

Evolutionary insights ofBean common mosaic necrosis virusandCowpea aphid-borne mosaic virus

Evolutionary insights ofBean common mosaic necrosis virusandCowpea aphid-borne mosaic virus

Exploring the diversity of Poaceae-infecting mastreviruses on Reunion Island using a viral metagenomics-based approach

Old foe, new host: epidemiology, genetic diversity and pathogenic characterization of maize streak virus in rice fields from Burkina Faso

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