A library preparation optimized for metagenomics of RNA viruses

Gil Patricia, Dupuy Virginie, Koual Rachid, Loire Etienne, Exbrayat Antoni, Rakotoarivony Ignace, Fall Assane Gueye, Gimonneau Geoffrey, Marie Albane, Francés Benoit, Lambert Grégory, Reveillaud Julie, Gardes Laëtitia, Balenghien Thomas, Garros Claire, Albina Emmanuel, Gutierrez Serafin. 2019. A library preparation optimized for metagenomics of RNA viruses. In : 13th EPIZONE Annual Meeting "Breaking Walls" - Abstract Book. Mettenleiter Thomas C. (ed.), Beer Martin (ed.), Conraths Franz J. (ed.), Blome Sandra (ed.), Bussmann Bianca M. (ed.). FLI, German Federal Research Institute for Animal Health. Berlin : Friedrich-Loeffler-Institut, Résumé, p. 154. EPIZONE Annual Meeting. 13, Berlin, Allemagne, 26 August 2019/28 August 2019.

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Abstract : Our understanding on the structure and role of viral communities in animal hosts has not yet reached the knowledge level attained on the bacteriome. This situation is, among others, probably due to technical constraints in adapting metagenomics, a main tool in bacteriome studies, to the characterisation of viral communities. Technical developments have been achieved for most steps of viral metagenomics. However, there is yet a key step that has received little attention, that of library preparation. This situation is surprising because developments in library preparation have largely facilitated bacteriome studies. Here, we present a library preparation optimized for metagenomics of RNA viruses from animals. The library has been designed to provide advantages found in metabarcoding libraries used in bacteriome studies, while allowing shotgun sequencing as required in viral metagenomics. We have validated a full metagenomics approach incorporating our library preparation and using mock viral communities. We have further tested our approach in two pilot studies with field-caught insects, all vectors of viral diseases. Our approach provided a fold increase in virus-like sequences compared to other studies, and nearly-full genomes from new virus species. Moreover, our results suggested conserved trends in virome composition in a mosquito species, and thus the existence of deterministic forces shaping its virome. Finally, the sensitivity of our approach was relatively good when compared to a commercial diagnostic PCR for the detection of an arbovirus in field-caught vectors. Our approach could facilitate studies on viral communities from animals and the democratisation of metagenomics in virus ecology.

Auteurs et affiliations

  • Gil Patricia, CIRAD-BIOS-UMR ASTRE (FRA)
  • Dupuy Virginie, CIRAD-BIOS-UMR ASTRE (FRA)
  • Koual Rachid, CIRAD-BIOS-UMR ASTRE (FRA)
  • Loire Etienne, CIRAD-BIOS-UMR ASTRE (FRA)
  • Exbrayat Antoni, CIRAD-BIOS-UMR ASTRE (FRA)
  • Rakotoarivony Ignace, CIRAD-BIOS-UMR ASTRE (FRA)
  • Fall Assane Gueye, ISRA (SEN)
  • Gimonneau Geoffrey, CIRAD-BIOS-UMR INTERTRYP (BFA) ORCID: 0000-0002-0613-841X
  • Marie Albane, EID (FRA)
  • Francés Benoit, EID (FRA)
  • Lambert Grégory, EID (FRA)
  • Reveillaud Julie, INRA (FRA)
  • Gardes Laëtitia, CIRAD-BIOS-UMR ASTRE (GLP)
  • Balenghien Thomas, CIRAD-BIOS-UMR ASTRE (MAR)
  • Garros Claire, CIRAD-BIOS-UMR ASTRE (FRA) ORCID: 0000-0003-4378-5031
  • Albina Emmanuel, CIRAD-BIOS-UMR ASTRE (GLP)
  • Gutierrez Serafin, CIRAD-BIOS-UMR ASTRE (FRA) ORCID: 0000-0002-5277-7239

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