Horizon / Plein textes La base de ressources documentaires de l'IRD

IRD

 

Publications des scientifiques de l'IRD

Marston D. A., McElhinney L. M., Ellis R. J., Horton D. L., Wise E. L., Leech S. L., David D., de Lamballerie Xavier, Fooks A. R. (2013). Next generation sequencing of viral RNA genomes. Bmc Genomics, 14, 444. ISSN 1471-2164

Lien direct chez l'éditeur doi:10.1186/1471-2164-14-444

Titre
Next generation sequencing of viral RNA genomes
Année de publication2013
Type de documentArticle référencé dans le Web of Science WOS:000321663800001
AuteursMarston D. A., McElhinney L. M., Ellis R. J., Horton D. L., Wise E. L., Leech S. L., David D., de Lamballerie Xavier, Fooks A. R.
SourceBmc Genomics, 2013, 14, p. 444. p. 444 ISSN 1471-2164
RésuméBackground: With the advent of Next Generation Sequencing (NGS) technologies, the ability to generate large amounts of sequence data has revolutionized the genomics field. Most RNA viruses have relatively small genomes in comparison to other organisms and as such, would appear to be an obvious success story for the use of NGS technologies. However, due to the relatively low abundance of viral RNA in relation to host RNA, RNA viruses have proved relatively difficult to sequence using NGS technologies. Here we detail a simple, robust methodology, without the use of ultra-centrifugation, filtration or viral enrichment protocols, to prepare RNA from diagnostic clinical tissue samples, cell monolayers and tissue culture supernatant, for subsequent sequencing on the Roche 454 platform. Results: As representative RNA viruses, full genome sequence was successfully obtained from known lyssaviruses belonging to recognized species and a novel lyssavirus species using these protocols and assembling the reads using de novo algorithms. Furthermore, genome sequences were generated from considerably less than 200 ng RNA, indicating that manufacturers' minimum template guidance is conservative. In addition to obtaining genome consensus sequence, a high proportion of SNPs (Single Nucleotide Polymorphisms) were identified in the majority of samples analyzed. Conclusions: The approaches reported clearly facilitate successful full genome lyssavirus sequencing and can be universally applied to discovering and obtaining consensus genome sequences of RNA viruses from a variety of sources.
Plan de classementEntomologie médicale / Parasitologie / Virologie [052] ; Biotechnologies [084]
LocalisationFonds IRD
Identifiant IRDPAR00010730
Lien permanenthttp://www.documentation.ird.fr/hor/PAR00010730

Export des données

Disponibilité des documents

Télechargment fichier PDF téléchargeable

Lien sur le Web lien chez l'éditeur

Accès réservé en accès réservé

HAL en libre accès sur HAL


Accès aux documents originaux :

Le FDI est labellisé CollEx

Accès direct

Bureau du chercheur

Site de la documentation

Espace intranet IST (accès réservé)

Suivi des publications IRD (accès réservé)

Mentions légales

Services Horizon

Poser une question

Consulter l'aide en ligne

Déposer une publication (accès réservé)

S'abonner au flux RSS

Voir les tableaux chronologiques et thématiques

Centres de documentation

Bondy

Montpellier (centre IRD)

Montpellier (MSE)

Cayenne

Nouméa

Papeete

Abidjan

Dakar

Niamey

Ouagadougou

Tunis

La Paz

Quito