A library preparation optimized for RNA virus metagenomics allows sensitive detection of an arbovirus in wild-caught vectors. P14

Gil Patricia, Dupuy Virginie, Koual Rachid, Gueye Fall Assane, Biteye Biram, Gimonneau Geoffrey, Marie Albane, Francés Benoit, Lambert Grégory, Rakotoarivony Ignace, Gardes Laëtitia, Balenghien Thomas, Garros Claire, Gutierrez Serafin. 2018. A library preparation optimized for RNA virus metagenomics allows sensitive detection of an arbovirus in wild-caught vectors. P14. In : Book of abstract Pathobiome 2018. INRA. Ajaccio : INRA, Résumé, 40-41. Pathobiome, Ajaccio, France, 18 Mars 2018/20 Mars 2018.

Résumé : The study of viral communities has recently been boosted by the use of the so-called high-throughput sequencing (HTS) technologies. Coupled with random amplification of nucleic acids, HTS allows the identification of viral species present in a given sample without a-priori knowledge on their identity but their resemblance to known viruses. The huge interest of this approach for virus ecology and diagnostics has triggered several technical improvements in most steps required in virus metagenomics, from nucleic-acid extraction to bioinformatics analysis of sequencing results. Surprisingly, there is yet a key step that has received little attention, that of library preparation. Here, we describe a library preparation for exploring viral diversity in a large number of samples with the use of high-throughput sequencing. This method uses custom adaptors that are PCR ligated, allowing low cost, high multiplexing and fully exploitable read lengths. After validation of our method with artificial viral communities, we have tested it with two samples set from wild-caught arthropod vectors showing that our approach allows to identify an arbovirus in highly-degraded samples with a relatively high sensitivity.

Mots-clés libres : Metagenomics, Arboviruses

Auteurs et affiliations

• Gil Patricia, CIRAD-BIOS-UMR ASTRE (FRA)
• Dupuy Virginie, CIRAD-BIOS-UMR ASTRE (FRA)
• Koual Rachid, CIRAD-BIOS-UMR ASTRE (FRA)
• Gueye Fall Assane, ISRA (SEN)
• Biteye Biram, ISRA (SEN)
• Gimonneau Geoffrey, UM1 (FRA) ORCID: 0000-0002-0613-841X
• Marie Albane, EID (FRA)
• Francés Benoit, EID (FRA)
• Lambert Grégory, EID (FRA)
• Rakotoarivony Ignace, CIRAD-BIOS-UMR ASTRE (FRA)
• Gardes Laëtitia, CIRAD-BIOS-UMR ASTRE (FRA)
• Balenghien Thomas, CIRAD-BIOS-UMR ASTRE (MAR)
• Garros Claire, CIRAD-BIOS-UMR ASTRE (REU) ORCID: 0000-0003-4378-5031
• Gutierrez Serafin, CIRAD-BIOS-UMR ASTRE (FRA) ORCID: 0000-0002-5277-7239

Source : Cirad-Agritrop (https://agritrop.cirad.fr/587518/)

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