Iridoviridae are known to cause disease in sturgeons in North America. Here, histological and molecular methods were used to screen for this family of virus in sturgeons from various European farms with low-to-high morbidity. Some histological samples revealed basophilic cells in the gill and labial epithelia, strongly suggesting the accumulation of iridovirus particles. Newly developed generic PCR tests targeting the major capsid protein (MCP) gene of sturgeon iridoviruses identified in North America, namely the white sturgeon iridovirus and the Namao virus (NV), produced positive signals in most samples from four sturgeon species: Russian (Acipenser gueldenstaedtii), Siberian (A. baerii), Adriatic (A. naccarii) and beluga (Huso huso). The sequences of the PCR products were generally highly similar one another, with nucleotide identities greater than 98%. They were also related to (74-88%), although distinct from, American sturgeon iridoviruses. These European viruses were thus considered variants of a single new virus, provisionally named Acipenser iridovirus-European (AcIV-E). Moreover, three samples infected with AcIV-E showed genetic heterogeneity, with the co-existence of two sequences differing by five nucleotides. One of our European samples carried a virus distinct from AcIV-E, but closely related to NV identified in Canada (95%). This study demonstrates the presence of two distinct sturgeon iridoviruses in Europe: a new genotype AcIV-E and an NV-related virus.
New genomic sequence data were acquired for the Acipenser iridovirus-European (AcIV-E), a virus whose complete genome and classification still remain to be elucidated. Here, we obtained the first full-length Major capsid protein (MCP) gene sequence for AcIV-E, as well as two additional open reading frames (ORFs) adjacent to the MCP gene. BLAST searches of the first ORF (α) resulted in no match to any gene or protein in the public databases. The other ORF (β) was identified as a subunit of a replication factor C (RFC), known to function as a clamp loader in eukaryotes, archae and some viruses. The presence of similar RFC genes was confirmed in two distinct, yet related, viruses, the white sturgeon iridovirus and a European variant of Namao virus. The existence of an RFC gene in AcIV-E suggests a genome size larger than that of other classifiable members of the family Iridoviridae along with a mode of replication involving an interaction between a clamp loader and a proliferating nuclear cell antigen. Sequencing and comparison of the full-length RFC gene from various sturgeon samples infected with AcIV-E revealed two distinct clusters of sequences within one particular sample in which the coexistence of two lineages had previously been predicted based on analysis of the partial MCP gene sequence. These genetic data provide further evidence of the circulation of at least two concurrent AcIV-E lineages, sometimes co-infecting cultured European sturgeon.
-Sphaerothecum destruens has emerged as a serious parasite of fish. Its life cycle, as well as its association with Asian cyprinids, allows it to infect a wide range of hosts. The topmouth gudgeon (Pseudorasbora parva), an invasive species that has rapidly colonized Europe, has been shown to be a healthy carrier of the parasite. However, in France, the presence of S. destruens and its possible association with P. parva have not yet been demonstrated. Here, we screened topmouth gudgeon DNA for S. destruens using PCR amplification of an 18S rRNA gene fragment of the parasite. Sequencing and phylogenetic analysis confirmed the presence of S. destruens in the invasive fish species. Our results suggest that P. parva can be a potent vector of the parasite, and has the potential to become a major ecological and economic threat to the French fish population.Keywords: Sphaerothecum destruens / Pseudorasbora parva / invasive species / topmouth gudgeon / France Résumé -Première mise en évidence de l'association de Sphaerothecum destruens avec Pseudorasbora parva en France. Sphaerothecum destruens est apparu dans la littérature scientifique comme un redoutable parasite émergent de poissons. Son cycle de vie, ainsi que son association à un cyprinidé d'origine asiatique, lui permettent d'infecter un large spectre d'hôtes. En effet, le goujon asiatique (Pseudorasbora parva) s'est révélé être porteur sain de ce parasite dans plusieurs études et représente une des espèces invasives ayant colonisé le plus rapidement l'Europe et notamment la France. Bien que le statut de porteur sain ait été donné au goujon asiatique, à notre connaissance, aucune étude n'a été menée en France afin de démontrer cette association. Par conséquent, l'objectif de cette étude a été d'évaluer la présence de S. destruens dans ce pays et la possibilité de considérer Pseudorasbora parva comme un vecteur de la maladie. Ceci a été confirmé par amplification PCR d'un fragment du gène ARNr 18S du parasite, réalisée sur un extrait d'ADN obtenu à partir de plusieurs goujons. Un séquençage et une analyse phylogénétique ont par la suite confirmé qu'il s'agissait bien de S. destruens. Ces résultats permettent donc d'affirmer que l'espèce invasive P. parva pourrait présenter une grande menace aussi bien écologique qu'économique sur le territoire français.
To develop a library-dependent method of fecal sources tracking, a reference library of 6,368 Escherichia coli isolates was constructed based on fecal samples collected around the Arcachon Bay, in 2010, and in French Basque Country, Landes and Béarn, between 2017 and 2018. Different schemes of source identification were tested: use of the complete or filtered library; characterization of the isolates based on ERIC – PCR or MALDI-TOF mass spectrometry; assignment using either similarity-based classifiers or SVM. With the exception of one scheme which was discarded since it turned out to use self-assignment, all tested schemes resulted in low rates of correct classifications (<35%), and significant rates of incorrect classifications (> 15%). The E. coli genotypic diversity of the library likely explained it. Shannon diversity index ranged from 0 to 3.03 for several wildlife species and for sewage treatment plant effluents, respectively, showing discrepancies among sources. The uneven genotypic composition of the library was attested by the Pielou index value (0.54), the high proportion of non-discriminatory genotypes (> 91% of isolates) and the very low proportion of discriminatory genotypes (< 3%). The results question the relevance of developing such a method for identifying sources of fecal contamination on such a coastline.
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