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      eDNA Increases the Detectability of Ranavirus Infection in an Alpine Amphibian Population

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          Abstract

          The early detection and identification of pathogenic microorganisms is essential in order to deploy appropriate mitigation measures. Viruses in the Iridoviridae family, such as those in the Ranavirus genus, can infect amphibian species without resulting in mortality or clinical signs, and they can also infect other hosts than amphibian species. Diagnostic techniques allowing the detection of the pathogen outside the period of host die-off would thus be of particular use. In this study, we tested a method using environmental DNA (eDNA) on a population of common frogs ( Rana temporaria) known to be affected by a Ranavirus in the southern Alps in France. In six sampling sessions between June and September (the species’ activity period), we collected tissue samples from dead and live frogs (adults and tadpoles), as well as insects (aquatic and terrestrial), sediment, and water. At the beginning of the breeding season in June, one adult was found dead; at the end of July, a mass mortality of tadpoles was observed. The viral DNA was detected in both adults and tadpoles (dead or alive) and in water samples, but it was not detected in insects or sediment. In live frog specimens, the virus was detected from June to September and in water samples from August to September. Dead tadpoles that tested positive for Ranavirus were observed only on one date (at the end of July). Our results indicate that eDNA can be an effective alternative to tissue/specimen sampling and can detect Ranavirus presence outside die-offs. Another advantage is that the collection of water samples can be performed by most field technicians. This study confirms that the use of eDNA can increase the performance and accuracy of wildlife health status monitoring and thus contribute to more effective surveillance programs.

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          Most cited references 67

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          ESTIMATING SITE OCCUPANCY RATES WHEN DETECTION PROBABILITIES ARE LESS THAN ONE

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            Emerging infectious disease and the loss of biodiversity in a Neotropical amphibian community.

             K R Lips,  F Brem,  R Brenes (2006)
            Pathogens rarely cause extinctions of host species, and there are few examples of a pathogen changing species richness and diversity of an ecological community by causing local extinctions across a wide range of species. We report the link between the rapid appearance of a pathogenic chytrid fungus Batrachochytrium dendrobatidis in an amphibian community at El Copé, Panama, and subsequent mass mortality and loss of amphibian biodiversity across eight families of frogs and salamanders. We describe an outbreak of chytridiomycosis in Panama and argue that this infectious disease has played an important role in amphibian population declines. The high virulence and large number of potential hosts of this emerging infectious disease threaten global amphibian diversity.
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              Metagenomics and future perspectives in virus discovery

              Highlights ► Viruses are the most abundant and most diverse biological entity of the biosphere. ► Rate of virus discoveries by metagenomics: higher than all other methods combined. ► Sequences with no homolog in public database are not all ‘junk’ — but treasure trove and blueprint of virus discovery. ► Metagenomics finds fields of application in clinical virology, public health and beyond. ► We propose the metagenomic Koch's postulates to identify unculturable etiological agents.
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                Author and article information

                Journal
                Viruses
                Viruses
                viruses
                Viruses
                MDPI
                1999-4915
                06 June 2019
                June 2019
                : 11
                : 6
                Affiliations
                [1 ]CEFE, EPHE-PSL, CNRS, Univ. Montpellier, Univ Paul Valéry Montpellier 3, IRD, Biogeography and Vertebrate Ecology, 1919 route de Mende, 34293 Montpellier, France; veronique.arnal@ 123456cefe.cnrs.fr (V.A.); marie.poulain@ 123456cefe.cnrs.fr (M.P.)
                [2 ]SPYGEN, 17 Rue du Lac Saint-André, 73370 Le Bourget-du-Lac, France; alice.valentini@ 123456spygen.com (A.V.); tony.dejean@ 123456spygen.com (T.D.)
                Author notes
                [* ]Correspondence: claude.miaud@ 123456cefe.cnrs.fr ; Tel.: +33-(0)4-67-61-33-43
                Article
                viruses-11-00526
                10.3390/v11060526
                6631829
                31174349
                © 2019 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                Categories
                Technical Note

                Microbiology & Virology

                virus surveillance, edna, ranavirus, common frog, rana temporaria, early detection

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