Field Monitoring of Avian Influenza Viruses: Whole-Genome Sequencing and Tracking of Neuraminidase Evolution Using 454 Pyrosequencing
| Autor: | Olivier Bouchez, Jérôme Mariette, Jean-Luc Guérin, Guillaume Croville, Johanna Barbieri, Christelle Camus-Bouclainville, Christophe Klopp, Sébastien M. Soubies |
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| Přispěvatelé: | Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), This project was partly supported by French Region Midi-Pyrénées. |
| Rok vydání: | 2012 |
| Předmět: |
Microbiology (medical)
Turkeys animal diseases Molecular Sequence Data Mutation Missense Hemagglutinins Viral Neuraminidase Hemagglutinin (influenza) Genome Viral medicine.disease_cause Genome Disease Outbreaks Evolution Molecular Viral Proteins 03 medical and health sciences symbols.namesake Virology medicine Animals Sequence Deletion 030304 developmental biology Whole genome sequencing Genetics Sanger sequencing 0303 health sciences [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health biology 030306 microbiology virus diseases Sequence Analysis DNA United States Influenza A virus subtype H5N1 Ducks Amino Acid Substitution Influenza in Birds Viral evolution [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology biology.protein symbols RNA Viral Pyrosequencing [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie |
| Zdroj: | Journal of Clinical Microbiology Journal of Clinical Microbiology, American Society for Microbiology, 2012, 50 (9), pp.2881-2887. ⟨10.1128/JCM.01142-12⟩ |
| ISSN: | 1098-660X 0095-1137 |
| Popis: | Adaptation of avian influenza viruses (AIVs) from waterfowl to domestic poultry with a deletion in the neuraminidase (NA) stalk has already been reported. The way the virus undergoes this evolution, however, is thus far unclear. We address this question using pyrosequencing of duck and turkey low-pathogenicity AIVs. Ducks and turkeys were sampled at the very beginning of an H6N1 outbreak, and turkeys were swabbed again 8 days later. NA stalk deletions were evidenced in turkeys by Sanger sequencing. To further investigate viral evolution, 454 pyrosequencing was performed: for each set of samples, up to 41,500 reads of ca. 400 bp were generated and aligned. Genetic polymorphisms between duck and turkey viruses were tracked on the whole genome. NA deletion was detected in less than 2% of reads in duck feces but in 100% of reads in turkey tracheal specimens collected at the same time. Further variations in length were observed in NA from turkeys 8 days later. Similarly, minority mutants emerged on the hemagglutinin (HA) gene, with substitutions mostly in the receptor binding site on the globular head. These critical changes suggest a strong evolutionary pressure in turkeys. The increasing performances of next-generation sequencing technologies should enable us to monitor the genomic diversity of avian influenza viruses and early emergence of potentially pathogenic variants within bird flocks. The present study, based on 454 pyrosequencing, suggests that NA deletion, an example of AIV adaptation from waterfowl to domestic poultry, occurs by selection rather than de novo emergence of viral mutants. |
| Databáze: | OpenAIRE |
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