Assembly and characterization of pandemic influenza A H1N1 genome in nasopharyngeal swabs using high-throughput pyrosequencing

Barbara Bartolini, Giovanni Chillemi, Isabella Abbate, Alessandro Bruselles, Gabriella Rozera, Tiziana Castrignanò, Daniele Paoletti, Ernesto Picardi, Alessandro Desideri, Graziano Pesole, Maria R. Capobianchi

Research output: Contribution to journalArticlepeer-review

Abstract

De novo high-throughput pyrosequencing was used to detect and characterize 2009 pandemic influenza A (H1N1) virus directly in nasopharyngeal swabs in the context of the microbial community. Data were generated with a prior sequenceindependent amplification by 454 pyrosequencing on GS-FLX platform (Roche). Influenza A assembled reads allowed near full-length genome reconstruction with the simultaneous analysis of site-specific heterogeneity. The molecular approach applied proved to be a powerful tool to characterize the new pandemic H1N1 influenza virus in clinical samples. This approach could be of great value in identifying possibly new reassortants that may occur in the near future.

Original languageEnglish
Pages (from-to)391-397
Number of pages7
JournalNew Microbiologica
Volume34
Issue number4
Publication statusPublished - 2011

Keywords

  • High-throughput pyrosequencing
  • Influenza
  • Nasopharyngeal swabs

ASJC Scopus subject areas

  • Microbiology (medical)

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