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We wish to express our sincere thanks and appreciation to Mr Paul Loubser and colleagues from Buffelsfontein Game & Nature Reserve and to Mrs. Hestelle Melville and Miss Laurenda Van Breda from the University of the Western Cape Nature Reserve Unit. We also thank Michel Peterschmitt for helpful discussions and Stephane Blanc for effective manuscript review. DPM, AV and GWH are supported by the National Research Foundation of South Africa (Grant No TTK1207122745). PH is supported by the Polyomyelitis Research Foundation (Grant No 15/102). This work was supported by Direction Generale de l'Armement (Grant No 201160060) (Ministere de la Defense, France), The Metaprogramme INRA Meta-omics of microbial ecosystems (Grant No 24000466) and CIRAD.

Analysis of institutional authors

Escriu, FernandoAuthor

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September 17, 2019
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Article

Molecular characterization and prevalence of two capulaviruses: Alfalfa leaf curl virus from France and Euphorbia caput-medusae latent virus from South Africa

Publicated to:Virology. 493 142-153 - 2016-06-01 493(), DOI: 10.1016/j.virol.2016.03.016

Authors: Bernardo, Pauline; Muhire, Brejnev; Francois, Sarah; Deshoux, Maelle; Hartnady, Penelope; Farkas, Kata; Kraberger, Simona; Filloux, Denis; Fernandez, Emmanuel; Galzi, Serge; Ferdinand, Romain; Granier, Martine; Marais, Armelle; Blasco, Pablo Monge; Candresse, Thierry; Escriu, Fernando; Varsani, Arvind; Harkins, Gordon W.; Martin, Darren P.; Roumagnac, Philippe;

Affiliations

CIRAD INRA SupAgro, UMR BGPI, Campus Int Montferrier Baillarguet, Montpellier 5, France - Author
CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France - Author
CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France. - Author
CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France. Electronic address: philippe.roumagnac@cirad.fr. - Author
CNRS IRD UM1 UM2, UMR 5290, MIVEGEC, Ave Agropolis, Montpellier, France - Author
CNRS-IRD-UM1-UM2, UMR 5290, MIVEGEC, Avenue Agropolis, Montpellier, France. - Author
Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa. - Author
Ctr Invest & Tecnol Agroalimentaria Aragon CITA, Unidad Sanidad Vegetal, Av Montanana 930, Zaragoza 50059, Spain - Author
Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, USA - Author
INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France - Author
INRA, UMR 1333, DGIMI, F-34060 Montpellier, France - Author
INRA, UMR 1333, DGIMI, Montpellier, France - Author
INRA, UMR Biol Fruit & Pathol 1332, Villenave Dornon, France - Author
School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand - Author
School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand. - Author
South African National Bioinformatics Institute, MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Cape Town, South Africa. - Author
Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, South Africa. - Author
Unidad de Sanidad Vegetal, Centro de Investigacion y Tecnologıa Agroalimentaria de Aragon (CITA), Av. Montañana 930, 50059 Zaragoza, Spain - Author
Unidad de Sanidad Vegetal, Centro de Investigacion y Tecnologıa Agroalimentaria de Aragon (CITA), Av. Montañana 930, 50059 Zaragoza, Spain. - Author
Unidad de Sanidad Vegetal, Instituto Agroalimentario de Aragón IA2 (CITA - Universidad de Zaragoza), Av. Montañana 930, 50059 Zaragoza, Spain. - Author
Univ Bordeaux, UMR Biol Fruit & Pathol 1332, Villenave Dornon, France - Author
Univ Canterbury, Biomol Interact Ctr, Private Bag 4800, Christchurch 1, New Zealand - Author
Univ Canterbury, Sch Biol Sci, Private Bag 4800, Christchurch 1, New Zealand - Author
Univ Cape Town, Dept Clin Lab Sci, Struct Biol Res Unit, Observatory, South Africa - Author
Univ Cape Town, Fac Hlth Sci, Computat Biol Grp, Inst Infect Dis & Mol Med, Observatory, South Africa - Author
Univ Florida, Dept Plant Pathol, Gainesville, FL 32611 USA - Author
Univ Florida, Emerging Pathogens Inst, Gainesville, FL USA - Author
Univ Western Cape, South African Natl Bioinformat Inst, MRC Unit Bioinformat Capac Dev, Cape Town, South Africa - Author
Univ Zaragoza, CITA, Inst Agroalimentario Aragon IA2, Unidad Sanidad Vegetal, Av Montanana 930, Zaragoza 50059, Spain - Author
Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France. - Author
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Abstract

Little is known about the prevalence, diversity, evolutionary processes, genomic structures and population dynamics of viruses in the divergent geminivirus lineage known as the capulaviruses. We determined and analyzed full genome sequences of 13 Euphorbia caput-medusae latent virus (EcmLV) and 26 Alfalfa leaf curl virus (ALCV) isolates, and partial genome sequences of 23 EcmLV and 37 ALCV isolates. While EcmLV was asymptomatic in uncultivated southern African Euphorbia caput-medusae, severe alfalfa disease symptoms were associated with ALCV in southern France. The prevalence of both viruses exceeded 10% in their respective hosts. Besides using patterns of detectable negative selection to identify ORFs that are probably functionally expressed, we show that ALCV and EcmLV both display evidence of inter-species recombination and biologically functional genomic secondary structures. Finally, we show that whereas the EcmLV populations likely experience restricted geographical dispersion, ALCV is probably freely moving across the French Mediterranean region. (C) 2016 Elsevier Inc. All rights reserved.

Keywords

alfalfa leaf curl viruseuphorbia caput-medusae latent virusfrancegeminiviridaegenome organizationprevalencerecombinationsecondary structuresouth africaAlfalfa leaf curl virusDiseaseDiversityEuphorbia caput-medusae latent virusEvolutionaryFranceGeminiviridaeGeminivirusGenome organizationGenome sequenceIdentificationNucleotide-sequenceOrganizationPrevalenceRecombinationSecondary structureSecondary structuresSouth africaSpainStranded-dna virus

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Virology due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2016, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Virology.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations from Scopus Elsevier, it yields a value for the Field-Weighted Citation Impact from the Scopus agency: 1.08, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 14, 2024)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Field Citation Ratio (FCR) from Dimensions: 4.7 (source consulted: Dimensions Sep 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-09-28, the following number of citations:

  • WoS: 27
  • Scopus: 36
  • Europe PMC: 16

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-09-28:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 59.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 59 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 13.75.
  • The number of mentions on the social network X (formerly Twitter): 2 (Altmetric).
  • The number of mentions in news outlets: 2 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: France; New Zealand; South African Republic; United States of America.