title: Intra-host viral variability in children clinically infected with H1N1 (2009) pandemic influenza.
abstract: Recent in-depth genetic analyses of influenza A virus samples have revealed patterns of intra-host viral genetic variability in a variety of relevant systems. These have included laboratory infected poultry, horses, pigs, chicken eggs and swine respiratory cells, as well as naturally infected poultry and horses. In humans, next generation sequencing techniques have enabled the study of genetic variability at specific positions of the viral genome. The present study investigated how 454 pyrosequencing could help unravel intra-host genetic diversity patterns on the full-length viral hæmagglutinin and neuraminidase genes from human H1N1 (2009) pandemic influenza clinical cases. This approach revealed unexpected patterns of co-infection in a 3-week old toddler, arising from rapid and complex reassortment phenomena on a local epidemiological scale. It also suggested the possible existence of very low frequency mutants resistant to neuraminidase inhibitors in two untreated patients. As well as revealing patterns of intra-host viral variability, this report highlights technical challenges in the appraisal of scientifically and medically relevant topics such as the natural occurrence of homologous recombination or very low frequency drug-resistant variants in influenza virus populations.
authors.affiliation: Université de Toulouse, INP, ENVT, Toulouse F-31076, France; INRA, UMR 1225, IHAP, Toulouse F-31076, France. Electronic address: v.bourret@envt.fr.
authors.forename: Vincent
authors.initials: V
authors.lastname: Bourret
authors.affiliation: Université de Toulouse, INP, ENVT, Toulouse F-31076, France; INRA, UMR 1225, IHAP, Toulouse F-31076, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Croville
authors.affiliation: INSERM, UMR 1043, Toulouse F-31300, France; Laboratoire de Virologie, CHU Purpan, 330 Avenue de Grande Bretagne, F-31300 Toulouse, France.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Mansuy
authors.affiliation: INSERM, UMR 1043, Toulouse F-31300, France; Laboratoire de Virologie, CHU Purpan, 330 Avenue de Grande Bretagne, F-31300 Toulouse, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Mengelle
authors.affiliation: Plateforme Bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, 31326 Auzeville Castanet-Tolosan, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Mariette
authors.affiliation: Plateforme Bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, 31326 Auzeville Castanet-Tolosan, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: GeT-PlaGe, Genotoul, INRA Auzeville, F-31326 Castanet-Tolosan, France.
authors.forename: Clémence
authors.initials: C
authors.lastname: Genthon
authors.affiliation: INSERM, UMR 1043, Toulouse F-31300, France; Laboratoire de Virologie, CHU Purpan, 330 Avenue de Grande Bretagne, F-31300 Toulouse, France.
authors.forename: Jacques
authors.initials: J
authors.lastname: Izopet
authors.affiliation: Université de Toulouse, INP, ENVT, Toulouse F-31076, France; INRA, UMR 1225, IHAP, Toulouse F-31076, France.
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Guérin
mesh_terms: D000483:Alleles; D024882:Drug Resistance, Viral / Q000235:genetics; D005814:Genes, Viral; D014644:Genetic Variation; D016679:Genome, Viral; D054884:Host-Pathogen Interactions; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification* / Q000187:drug effects / Q000235:genetics*; D007251:Influenza, Human / Q000453:epidemiology* / Q000821:virology*; D009154:Mutation; D010802:Phylogeny
keywords: 2009 H1N1 pandemic; Deep sequencing; Influenza A; Intra-host viral diversity; Next generation sequencing; Pyrosequencing