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Open AccessArticle

A New Prevalent Densovirus Discovered in Acari. Insight from Metagenomics in Viral Communities Associated with Two-Spotted Mite (Tetranychus urticae) Populations

1
DGIMI, Univ Montpellier, INRA, F-34095 Montpellier, France
2
ISEM, Univ Montpellier, CNRS, IRD, EPHE, F-34095 Montpellier, France
3
Centre for Ecology, Evolution and Environmental Changes (cE3c), Univ Lisbon, Faculty of Science, P-1749016 Lisbon, Portugal
4
CIRAD, UMR BGPI, F-34398 Montpellier, France
5
BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, F-34398 Montpellier, France
6
MIVEGEC, Univ Montpellier, CNRS, IRD, F-34394 Montpellier, France
*
Author to whom correspondence should be addressed.
Viruses 2019, 11(3), 233; https://doi.org/10.3390/v11030233
Received: 29 December 2018 / Revised: 19 February 2019 / Accepted: 28 February 2019 / Published: 7 March 2019
(This article belongs to the Special Issue New Insights into Parvovirus Research)
Viral metagenomics and high throughput sequence mining have revealed unexpected diversity, and the potential presence, of parvoviruses in animals from all phyla. Among arthropods, this diversity highlights the poor knowledge that we have regarding the evolutionary history of densoviruses. The aim of this study was to explore densovirus diversity in a small arthropod pest belonging to Acari, the two-spotted spider mite Tetranychus urticae, while using viral metagenomics based on virus-enrichment. Here, we present the viromes obtained from T. urticae laboratory populations made of contigs that are attributed to nine new potential viral species, including the complete sequence of a novel densovirus. The genome of this densovirus has an ambisens genomic organization and an unusually compact size with particularly small non-structural proteins and a predicted major capsid protein that lacks the typical PLA2 motif that is common to all ambidensoviruses described so far. In addition, we showed that this new densovirus had a wide prevalence across populations of mite species tested and a genomic diversity that likely correlates with the host phylogeny. In particular, we observed a low densovirus genomic diversity between the laboratory and natural populations, which suggests that virus within-species evolution is probably slower than initially thought. Lastly, we showed that this novel densovirus can be inoculated to the host plant following feeding by infected mites, and circulate through the plant vascular system. These findings offer new insights into densovirus prevalence, evolution, and ecology. View Full-Text
Keywords: parvovirus; viral metagenomics; virus diversity; virus phylogeny; agricultural pests; arthropod; mite; viral communities; viral ecology parvovirus; viral metagenomics; virus diversity; virus phylogeny; agricultural pests; arthropod; mite; viral communities; viral ecology
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François, S.; Mutuel, D.; Duncan, A.B.; Rodrigues, L.R.; Danzelle, C.; Lefevre, S.; Santos, I.; Frayssinet, M.; Fernandez, E.; Filloux, D.; Roumagnac, P.; Froissart, R.; Ogliastro, M. A New Prevalent Densovirus Discovered in Acari. Insight from Metagenomics in Viral Communities Associated with Two-Spotted Mite (Tetranychus urticae) Populations. Viruses 2019, 11, 233.

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