FN Archimer Export Format PT J TI Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly BT AF Dotto-Maurel, Aurelie Pelletier, Camille Morga, Benjamin Jacquot, Maude Faury, Nicole Dégremont, Lionel Bereszczynki, Maëlis Delmotte, Jean Escoubas, Jean-Michel Chevignon, Germain AS 1:1;2:1;3:1;4:1;5:1;6:1;7:2;8:2;9:2;10:1; FF 1:PDG-RBE-ASIM;2:PDG-RBE-ASIM;3:PDG-RBE-ASIM;4:PDG-RBE-ASIM;5:PDG-RBE-ASIM;6:PDG-RBE-ASIM;7:;8:;9:;10:PDG-RBE-ASIM; C1 Ifremer, ASIM, F-17390 La Tremblade, France IHPE, Univ. Montpellier, CNRS, Ifremer, UPVD, F-34095 Montpellier, France C2 IFREMER, FRANCE CNRS, FRANCE SI LA TREMBLADE SE PDG-RBE-ASIM UM IHPE IN WOS Ifremer UPR WOS Cotutelle UMR DOAJ copubli-france IF 3.9 TC 1 UR https://archimer.ifremer.fr/doc/00804/91607/97585.pdf LA English DT Article DE ;Crassostrea gigas;Illumina;ostreid herpesvirus type 1;oxford nanopore technologies;tangential flow filtration;virus AB Whole-genome sequencing is widely used to better understand the transmission dynamics, the evolution and the emergence of new variants of viral pathogens. This can bring crucial information to stakeholders for disease management. Unfortunately, aquatic virus genomes are usually difficult to characterize because most of these viruses cannot be easily propagated in vitro. Developing methodologies for routine genome sequencing of aquatic viruses is timely given the ongoing threat of disease emergence. This is particularly true for pathogenic viruses infecting species of commercial interest that are widely exchanged between production basins or countries. For example, the ostreid herpesvirus type 1 (OsHV-1) is a Herpesvirus widely associated with mass mortality events of juvenile Pacific oyster Crassostrea gigas. Genomes of Herpesviruses are large and complex with long direct and inverted terminal repeats. In addition, OsHV-1 is unculturable. It therefore accumulates several features that make its genome sequencing and assembly challenging. To overcome these difficulties, we developed a tangential flow filtration (TFF) method to enrich OsHV-1 infective particles from infected host tissues. This virus purification allowed us to extract high molecular weight and high-quality viral DNA that was subjected to Illumina short-read and Nanopore long-read sequencing. Dedicated bioinformatic pipelines were developed to assemble complete OsHV-1 genomes with reads from both sequencing technologies. Nanopore sequencing allowed characterization of new structural variations and major viral isomers while having 99,98 % of nucleotide identity with the Illumina assembled genome. Our study shows that TFF-based purification method, coupled with Nanopore sequencing, is a promising approach to enable in field sequencing of unculturable aquatic DNA virus. PY 2022 PD NOV SO Microbial Genomics SN 2057-5858 PU Microbiology Society VL 8 IS 11 UT 000993252000007 DI 10.1099/mgen.0.000895 ID 91607 ER EF