High-throughput sequencing of complete genomes of ipomoviruses associated with an epidemic of cassava brown streak disease in the Comoros Archipelago

Scussel, Sarah; Candresse, Thierry; Marais, Armelle; Claverie, Sohini; Hoareau, Murielle; Azali, Hamza A; Verdin, Eric; Tepfer, Mark; Filloux, Denis; Fernandez, Emmanuel; Roumagnac, Philippe; Robène, Isabelle; Lefeuvre, Pierre; Jourda, Cyril; Roux-Cuvelier, Michel; Lett, Jean‐Michel

doi:10.1007/s00705-019-04228-7

Cited by 7 publications

(8 citation statements)

References 16 publications

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“…This isolate was highly similar to an isolate from Tanzania (93.4% pairwise nucleotide identity) than to those previously reported from Malawi (86.9 to 87.0%) [ 91 ]. Similar studies have also been performed in Mozambique [ 65 ] and Comoros [ 66 ] and they strongly support the existence of new isolate lineages. The rampant spread of CBSD has triggered intense scientific mobilization to better understand the epidemiology, sequence diversity, host interactions and integrated control management of the disease.…”

Section: Host Plants Subjected To Htssupporting

confidence: 83%

“…Viral diseases are an impending disaster to cassava production unless proper integrative control strategies are strictly observed. HTS has been used to unravel the etiology of some of the most damaging viral diseases of cassava in Cameroon [ 101 ], Comoros [ 66 ], Malawi [ 91 ], Mozambique [ 65 ], Tanzania [ 107 , 114 ], Togo [ 101 ] and Uganda [ 114 ].…”

Section: Host Plants Subjected To Htsmentioning

confidence: 99%

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High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

Ibaba

Gubba

2020

Plants

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High-throughput sequencing (HTS) application in the field of plant virology started in 2009 and has proven very successful for virus discovery and detection of viruses already known. Plant virology is still a developing science in most of Africa; the number of HTS-related studies published in the scientific literature has been increasing over the years as a result of successful collaborations. Studies using HTS to identify plant-infecting viruses have been conducted in 20 African countries, of which Kenya, South Africa and Tanzania share the most published papers. At least 29 host plants, including various agricultural economically important crops, ornamentals and medicinal plants, have been used in viromics analyses and have resulted in the detection of previously known viruses and novel ones from almost any host. Knowing that the effectiveness of any management program requires knowledge on the types, distribution, incidence, and genetic of the virus-causing disease, integrating HTS and efficient bioinformatics tools in plant virology research projects conducted in Africa is a matter of the utmost importance towards achieving and maintaining sustainable food security.

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Section: Host Plants Subjected To Htssupporting

confidence: 83%

Section: Host Plants Subjected To Htsmentioning

confidence: 99%

High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

Ibaba

Gubba

2020

Plants

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“…The presence of mismatches in probe binding sites has been implicated for false negative real-time RT-PCR studies elsewhere [ 50 ]. The Adams et al [ 36 ] assay was designed at a time when there were no sequences available from Comoros, but which were later identified to contain isolates that were phylogenetically distant from other East African isolates [ 51 ]. Next-generation sequencing offers a suitable approach in addressing challenges of false negative results such as the results obtained in this study where isolates of both CBSIs (CBSV and UCBSV) were detected, supporting earlier findings of the presence of CBSV and UCBSV in Comoros [ 30 , 51 ].…”

Section: Discussionmentioning

confidence: 99%

Epidemiological Analysis of Cassava Mosaic and Brown Streak Diseases, and Bemisia tabaci in the Comoros Islands

Shirima

Wosula

Hamza³

et al. 2022

Viruses

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A comprehensive assessment of cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) was carried out in Comoros where cassava yield (5.7 t/ha) is significantly below the African average (8.6 t/ha) largely due to virus diseases. Observations from 66 sites across the Comoros Islands of Mwali, Ngazidja, and Ndzwani revealed that 83.3% of cassava fields had foliar symptoms of CBSD compared with 95.5% for CMD. Molecular diagnostics confirmed the presence of both cassava brown streak ipomoviruses (CBSIs) and cassava mosaic begomoviruses (CMBs). Although real-time RT-PCR only detected the presence of one CBSI species (Cassava brown streak virus, CBSV) the second species (Ugandan cassava brown streak virus, UCBSV) was identified using next-generation high-throughput sequencing. Both PCR and HTS detected the presence of East African cassava mosaic virus (EACMV). African cassava mosaic virus was not detected in any of the samples. Four whitefly species were identified from a sample of 131 specimens: Bemisia tabaci, B. afer, Aleurodicus dispersus, and Paraleyrodes bondari. Cassava B. tabaci comprised two mitotypes: SSA1-SG2 (89%) and SSA1-SG3 (11%). KASP SNP genotyping categorized 82% of cassava B. tabaci as haplogroup SSA-ESA. This knowledge will provide an important base for developing and deploying effective management strategies for cassava viruses and their vectors.

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“…In addition to these previously unknown viruses, the results further indicated the presence of CBSVs and/or CMGs in three cassava samples (Table 1). Cassava brown streak virus (CBSV, isolate KOR6, GU563327) was detected in one of the plants from the DR Congo, while Uganda cassava brown streak virus (UCBSV, isolate KM) [20] and/or EACMV were detected in samples from Mayotte. 1 Isolates were named considering two letters of the code of the country where the landraces were collected-three letters of the landrace short acronym-and a number (when multiple contigs from the same landrace were obtained)…”

Section: Identification Of Closteroviridae Members In Cassavamentioning

confidence: 99%

Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands

Kwibuka

Bisimwa

Blouin

et al. 2021

Viruses

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Cassava is one of the most important staple crops in Africa and its production is seriously damaged by viral diseases. In this study, we identify for the first time and characterize the genome organization of novel ampeloviruses infecting cassava plants in diverse geographical locations using three high-throughput sequencing protocols [Virion-Associated Nucleotide Acid (VANA), dsRNA and total RNA], and we provide a first analysis of the diversity of these agents and of the evolutionary forces acting on them. Thirteen new Closteroviridae isolates were characterized in field-grown cassava plants from the Democratic Republic of Congo (DR Congo), Madagascar, Mayotte, and Reunion islands. The analysis of the sequences of the corresponding contigs (ranging between 10,417 and 13,752 nucleotides in length) revealed seven open reading frames. The replication-associated polyproteins have three expected functional domains: methyltransferase , helicase, and RNA-dependent RNA polymerase (RdRp). Additional open reading frames code for a small transmembrane protein, a heat-shock protein 70 homolog (HSP70h), a heat shock protein 90 homolog (HSP90h), and a major and a minor coat protein (CP and CPd respectively). Defective genomic variants were also identified in some cassava accessions originating from Madagascar and Reunion. The isolates were found to belong to two species tentatively named Manihot esculenta-associated virus 1 and 2 (MEaV-1 and MEaV-2). Phylogenetic analyses showed that MEaV-1 and MEaV-2 belong to the genus Ampelovirus, in particular to its subgroup II. MEaV-1 was found in all of the countries of study, while MEaV-2 was only detected in Madagascar and Mayotte. Recombination analysis provided evidence of intraspecies recombination occurring between the isolates from Madagascar and Mayotte. No clear association with visual symptoms in the cassava host could be identified.

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High-throughput sequencing of complete genomes of ipomoviruses associated with an epidemic of cassava brown streak disease in the Comoros Archipelago

Cited by 7 publications

References 16 publications

High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

Epidemiological Analysis of Cassava Mosaic and Brown Streak Diseases, and Bemisia tabaci in the Comoros Islands

Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands

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