Sequence analysis of in vivo defective interfering-like RNA of influenza a H1N1 pandemic virus

Kazima Saira, Xudong Lin, Jay V. DePasse, Rebecca Halpin, Alan Twaddle, Timothy Stockwell, Brian Angus, Alessandro Cozzi-Lepri, Marina Delfino, Vivien Dugan, Dominic E. Dwyer, Matthew Freiberg, Andrzej Horban, Marcelo Losso, Ruth Lynfield, Deborah N. Wentworth, Edward C. Holmes, Richard Davey, David E. Wentworth, Elodie Ghedin

Research output: Contribution to journalArticle

Abstract

Influenza virus defective interfering (DI) particles are naturally occurring noninfectious virions typically generated during in vitro serial passages in cell culture of the virus at a high multiplicity of infection. DI particles are recognized for the role they play in inhibiting viral replication and for the impact they have on the production of infectious virions. To date, influenza virus DI particles have been reported primarily as a phenomenon of cell culture and in experimentally infected embryonated chicken eggs. They have also been isolated from a respiratory infection of chickens. Using a sequencing approach, we characterize several subgenomic viral RNAs from human nasopharyngeal specimens infected with the influenza A(H1N1)pdm09 virus. The distribution of these in vivo-derived DI-like RNAs was similar to that of in vitro DIs, with the majority of the defective RNAs generated from the PB2 (segment 1) of the polymerase complex, followed by PB1 and PA. The lengths of the in vivo-derived DI-like segments also are similar to those of known in vitro DIs, and the in vivo-derived DI-like segments share internal deletions of the same segments. The presence of identical DI-like RNAs in patients linked by direct contact is compatible with transmission between them. The functional role of DI-like RNAs in natural infections remains to be established.

Original languageEnglish (US)
Pages (from-to)8064-8074
Number of pages11
JournalJournal of Virology
Volume87
Issue number14
DOIs
StatePublished - Jul 2013

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H1N1 Subtype Influenza A Virus
Pandemics
pandemic
Defective Viruses
influenza
Human Influenza
Sequence Analysis
sequence analysis
RNA
viruses
Orthomyxoviridae
Virion
Chickens
virion
Cell Culture Techniques
Serial Passage
cell culture
infection
Viral RNA
Infection

ASJC Scopus subject areas

  • Immunology
  • Virology

Cite this

Sequence analysis of in vivo defective interfering-like RNA of influenza a H1N1 pandemic virus. / Saira, Kazima; Lin, Xudong; DePasse, Jay V.; Halpin, Rebecca; Twaddle, Alan; Stockwell, Timothy; Angus, Brian; Cozzi-Lepri, Alessandro; Delfino, Marina; Dugan, Vivien; Dwyer, Dominic E.; Freiberg, Matthew; Horban, Andrzej; Losso, Marcelo; Lynfield, Ruth; Wentworth, Deborah N.; Holmes, Edward C.; Davey, Richard; Wentworth, David E.; Ghedin, Elodie.

In: Journal of Virology, Vol. 87, No. 14, 07.2013, p. 8064-8074.

Research output: Contribution to journalArticle

Saira, K, Lin, X, DePasse, JV, Halpin, R, Twaddle, A, Stockwell, T, Angus, B, Cozzi-Lepri, A, Delfino, M, Dugan, V, Dwyer, DE, Freiberg, M, Horban, A, Losso, M, Lynfield, R, Wentworth, DN, Holmes, EC, Davey, R, Wentworth, DE & Ghedin, E 2013, 'Sequence analysis of in vivo defective interfering-like RNA of influenza a H1N1 pandemic virus', Journal of Virology, vol. 87, no. 14, pp. 8064-8074. https://doi.org/10.1128/JVI.00240-13
Saira, Kazima ; Lin, Xudong ; DePasse, Jay V. ; Halpin, Rebecca ; Twaddle, Alan ; Stockwell, Timothy ; Angus, Brian ; Cozzi-Lepri, Alessandro ; Delfino, Marina ; Dugan, Vivien ; Dwyer, Dominic E. ; Freiberg, Matthew ; Horban, Andrzej ; Losso, Marcelo ; Lynfield, Ruth ; Wentworth, Deborah N. ; Holmes, Edward C. ; Davey, Richard ; Wentworth, David E. ; Ghedin, Elodie. / Sequence analysis of in vivo defective interfering-like RNA of influenza a H1N1 pandemic virus. In: Journal of Virology. 2013 ; Vol. 87, No. 14. pp. 8064-8074.
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