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Open AccessArticle

Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations

1
Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université François Rabelais de Tours, Faculté des Sciences et Techniques, Avenue Monge-Parc Grandmont, 37200 Tours, France
2
Institut de Génomique, CEA, Génoscope, 2 rue Gaston Crémieux, 91057 Evry, France
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Author to whom correspondence should be addressed.
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Academic Editor: Johnson Mak
Viruses 2015, 7(7), 3625-3646; https://doi.org/10.3390/v7072788
Received: 21 May 2015 / Revised: 30 June 2015 / Accepted: 1 July 2015 / Published: 7 July 2015
Viruses rely on widespread genetic variation and large population size for adaptation. Large DNA virus populations are thought to harbor little variation though natural populations may be polymorphic. To measure the genetic variation present in a dsDNA virus population, we deep sequenced a natural strain of the baculovirus Autographa californica multiple nucleopolyhedrovirus. With 124,221X average genome coverage of our 133,926 bp long consensus, we could detect low frequency mutations (0.025%). K-means clustering was used to classify the mutations in four categories according to their frequency in the population. We found 60 high frequency non-synonymous mutations under balancing selection distributed in all functional classes. These mutants could alter viral adaptation dynamics, either through competitive or synergistic processes. Lastly, we developed a technique for the delimitation of large deletions in next generation sequencing data. We found that large deletions occur along the entire viral genome, with hotspots located in homologous repeat regions (hrs). Present in 25.4% of the genomes, these deletion mutants presumably require functional complementation to complete their infection cycle. They might thus have a large impact on the fitness of the baculovirus population. Altogether, we found a wide breadth of genomic variation in the baculovirus population, suggesting it has high adaptive potential. View Full-Text
Keywords: genome population variation; quasispecies theory; AcMNPV; high-throughput sequencing genome population variation; quasispecies theory; AcMNPV; high-throughput sequencing
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Chateigner, A.; Bézier, A.; Labrousse, C.; Jiolle, D.; Barbe, V.; Herniou, E.A. Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations. Viruses 2015, 7, 3625-3646.

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