@article{fdi:010065449,
  title = {{R}apid next-generation sequencing of dengue, {EV}-{A}71 and {RSV}-{A} viruses},
  author = {{B}aronti, {C}{\'e}cile and {P}iorkowski, {G}. and {L}eparc-{G}offart, {I}. and de {L}amballerie, {X}avier and {D}ubot {P}{\'e}r{\`e}s, {A}udrey},
  editor = {},
  language = {{ENG}},
  abstract = {{A}ccurate characterisation of viral strains constitutes a crucial objective for the management of modern virus collections. {N}ext-generation sequencing ({NGS}) provides technical solution for fast and cost-effective full genome sequencing. {H}ere, we report protocols for rapid full-genome characterisation of {RNA} viruses of medical importance: dengue virus, enterovirus {A}71 and respiratory syncytial virus {A}, based on a specific amplification step followed by {NGS}-sequencing. {A} subset of full-length genome sequences representing the genetic diversity of each virus type was selected in {G}en{B}ank and used to design primer sets allowing the amplification of the complete genome in 3-8 overlapping {PCR} fragments. {T}he technique was used for characterising 53 strains (33 {DENV}, 8 {EV}-{A}71,12 {RSV}-{A}) from various genotypes and origins. {I}n a single assay, and in just 4 days, it provided for all strains an excellent genomic coverage (similar to 99% including complete {ORF} for all strains) and accurate sequences with high number of reads per position (250-3500 on average). {T}he elaboration of specific {PCR}-based full-genome sequencing protocols for diverse virus groups is likely to revolutionise the characterisation of viral isolates in modern collection, but also to contribute in the next future to the study of {RNA} viruses directly from biological samples.},
  keywords = {{N}ext-generation sequencing ; {I}on torrent ; {S}pecific amplification ; {D}engue virus ; {E}nterovirus {A}71 ; {H}uman respiratory syncytial virus {A}},
  booktitle = {},
  journal = {{J}ournal of {V}irological {M}ethods},
  volume = {226},
  numero = {},
  pages = {7--14},
  ISSN = {0166-0934},
  year = {2015},
  DOI = {10.1016/j.jviromet.2015.09.004},
  URL = {https://www.documentation.ird.fr/hor/fdi:010065449},
}