Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly
International audience 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 usuall...
Published in: | Microbial Genomics |
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Online Access: | https://hal.archives-ouvertes.fr/hal-03863848 https://hal.archives-ouvertes.fr/hal-03863848/document https://hal.archives-ouvertes.fr/hal-03863848/file/Dotto-Maurel-2022-MicrobGenom-Evaluation.pdf https://doi.org/10.1099/mgen.0.000895 |
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ftunivnantes:oai:HAL:hal-03863848v1 2023-05-15T15:58:21+02:00 Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly Dotto-Maurel, Aurélie Pelletier, Camille Morga, Benjamin Jacquot, Maude Faury, Nicole Dégremont, Lionel Bereszczynki, Maëlis Delmotte, Jean Escoubas, Jean-Michel Chevignon, Germain Adaptation et Santé des Invertébrés Marins (ASIM) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Interactions Hôtes-Pathogènes-Environnements (IHPE) Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM) 2022-11-10 https://hal.archives-ouvertes.fr/hal-03863848 https://hal.archives-ouvertes.fr/hal-03863848/document https://hal.archives-ouvertes.fr/hal-03863848/file/Dotto-Maurel-2022-MicrobGenom-Evaluation.pdf https://doi.org/10.1099/mgen.0.000895 en eng HAL CCSD Society for General Microbiology info:eu-repo/semantics/altIdentifier/doi/10.1099/mgen.0.000895 hal-03863848 https://hal.archives-ouvertes.fr/hal-03863848 https://hal.archives-ouvertes.fr/hal-03863848/document https://hal.archives-ouvertes.fr/hal-03863848/file/Dotto-Maurel-2022-MicrobGenom-Evaluation.pdf doi:10.1099/mgen.0.000895 info:eu-repo/semantics/OpenAccess ISSN: 2057-5858 EISSN: 2057-5858 Microbial Genomics https://hal.archives-ouvertes.fr/hal-03863848 Microbial Genomics, 2022, 8 (11), ⟨10.1099/mgen.0.000895⟩ https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000895 Crassostrea gigas Illumina ostreid herpesvirus type 1 oxford nanopore technologies tangential flow filtration virus [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] info:eu-repo/semantics/article Journal articles 2022 ftunivnantes https://doi.org/10.1099/mgen.0.000895 2022-12-07T00:23:34Z International audience 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. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Université de Nantes: HAL-UNIV-NANTES Pacific Microbial Genomics 8 11 |
institution |
Open Polar |
collection |
Université de Nantes: HAL-UNIV-NANTES |
op_collection_id |
ftunivnantes |
language |
English |
topic |
Crassostrea gigas Illumina ostreid herpesvirus type 1 oxford nanopore technologies tangential flow filtration virus [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] |
spellingShingle |
Crassostrea gigas Illumina ostreid herpesvirus type 1 oxford nanopore technologies tangential flow filtration virus [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] Dotto-Maurel, Aurélie Pelletier, Camille Morga, Benjamin Jacquot, Maude Faury, Nicole Dégremont, Lionel Bereszczynki, Maëlis Delmotte, Jean Escoubas, Jean-Michel Chevignon, Germain Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly |
topic_facet |
Crassostrea gigas Illumina ostreid herpesvirus type 1 oxford nanopore technologies tangential flow filtration virus [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] |
description |
International audience 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. |
author2 |
Adaptation et Santé des Invertébrés Marins (ASIM) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Interactions Hôtes-Pathogènes-Environnements (IHPE) Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM) |
format |
Article in Journal/Newspaper |
author |
Dotto-Maurel, Aurélie Pelletier, Camille Morga, Benjamin Jacquot, Maude Faury, Nicole Dégremont, Lionel Bereszczynki, Maëlis Delmotte, Jean Escoubas, Jean-Michel Chevignon, Germain |
author_facet |
Dotto-Maurel, Aurélie Pelletier, Camille Morga, Benjamin Jacquot, Maude Faury, Nicole Dégremont, Lionel Bereszczynki, Maëlis Delmotte, Jean Escoubas, Jean-Michel Chevignon, Germain |
author_sort |
Dotto-Maurel, Aurélie |
title |
Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly |
title_short |
Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly |
title_full |
Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly |
title_fullStr |
Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly |
title_full_unstemmed |
Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly |
title_sort |
evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly |
publisher |
HAL CCSD |
publishDate |
2022 |
url |
https://hal.archives-ouvertes.fr/hal-03863848 https://hal.archives-ouvertes.fr/hal-03863848/document https://hal.archives-ouvertes.fr/hal-03863848/file/Dotto-Maurel-2022-MicrobGenom-Evaluation.pdf https://doi.org/10.1099/mgen.0.000895 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
ISSN: 2057-5858 EISSN: 2057-5858 Microbial Genomics https://hal.archives-ouvertes.fr/hal-03863848 Microbial Genomics, 2022, 8 (11), ⟨10.1099/mgen.0.000895⟩ https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000895 |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1099/mgen.0.000895 hal-03863848 https://hal.archives-ouvertes.fr/hal-03863848 https://hal.archives-ouvertes.fr/hal-03863848/document https://hal.archives-ouvertes.fr/hal-03863848/file/Dotto-Maurel-2022-MicrobGenom-Evaluation.pdf doi:10.1099/mgen.0.000895 |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1099/mgen.0.000895 |
container_title |
Microbial Genomics |
container_volume |
8 |
container_issue |
11 |
_version_ |
1766394088640217088 |