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

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

Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani

Research output: Contribution to journal › Article › peer-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 language	English
Pages (from-to)	391-397
Number of pages	7
Journal	New Microbiologica
Volume	34
Issue number	4
Publication status	Published - 2011

Keywords

High-throughput pyrosequencing
Influenza
Nasopharyngeal swabs

ASJC Scopus subject areas

Microbiology (medical)

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Assembly and characterization of pandemic influenza A H1N1 genome in nasopharyngeal swabs using high-throughput pyrosequencing. / Bartolini, Barbara; Chillemi, Giovanni; Abbate, Isabella; Bruselles, Alessandro; Rozera, Gabriella; Castrignanò, Tiziana; Paoletti, Daniele; Picardi, Ernesto; Desideri, Alessandro; Pesole, Graziano; Capobianchi, Maria R.

In: New Microbiologica, Vol. 34, No. 4, 2011, p. 391-397.

Research output: Contribution to journal › Article › peer-review

Bartolini, Barbara ; Chillemi, Giovanni ; Abbate, Isabella ; Bruselles, Alessandro ; Rozera, Gabriella ; Castrignanò, Tiziana ; Paoletti, Daniele ; Picardi, Ernesto ; Desideri, Alessandro ; Pesole, Graziano ; Capobianchi, Maria R. / Assembly and characterization of pandemic influenza A H1N1 genome in nasopharyngeal swabs using high-throughput pyrosequencing. In: New Microbiologica. 2011 ; Vol. 34, No. 4. pp. 391-397.

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AU - Bartolini, Barbara

AU - Chillemi, Giovanni

AU - Abbate, Isabella

AU - Bruselles, Alessandro

AU - Rozera, Gabriella

AU - Castrignanò, Tiziana

AU - Paoletti, Daniele

AU - Picardi, Ernesto

AU - Desideri, Alessandro

AU - Pesole, Graziano

AU - Capobianchi, Maria R.

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AB - 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.

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

Abstract

Keywords

ASJC Scopus subject areas

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