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Human Adenovirus Diversity in Water Samples Using a Next-Generation Amplicon Sequencing Approach

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Abstract

This study aims to establish a straightforward and original workflow for high-throughput typing of human adenoviruses (HAdVs) in environmental samples. Occurrence of HAdVs in water is well documented worldwide, but data on diversity of HAdV types circulating in water are scarcely available. Here, the characterisation of viral particles was performed by determination of amplicon sequences using a next-generation sequencing (NGS) approach. Adenoviral DNA was either directly isolated from wastewater or river water concentrates or after a cell culture passage. Genome amplification targeted a hyper variable region of the hexon gene, allowing the discrimination of the 54 human adenoviral types described until now. After read generation on the benchtop MiSeq platform (Illumina), data were analysed using the Mothur software for identification of all HAdV species and types simultaneously present in a unique sample. NGS results showed a relatively wide HAdV diversity of up to six types in one sample, whereas Sanger sequencing always only retrieved the dominant one. Detected types included HAdV-1, HAdV-2, HAdV-3, HAdV-6, HAdV-12, HAdV-31, HAdV-40 and HAdV-41, HAdV-41 being the most abundant in tested samples. In addition, the influence of the cell line (A549 vs 293A cells) on the infectious HAdV typing results was clearly determined. The 293A appeared to be the most suitable cell line allowing the detection of a larger diversity of infectious HAdVs and reflecting a more realistic initial species distribution than using the A549 cells. These findings demonstrated the feasibility of amplicon sequencing NGS approach to identify viruses in complex environmental water samples.

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Acknowledgments

The present work was carried out in the framework of the LorLux network (French name, RésEAU LorLux) supported by the National Research Fund, Luxembourg, and the Lorraine region, France. The authors would like to thank D. Collard and A. Tavares Furtado for their excellent technical assistance and Dr. M. Calusinska for her precious help in bioinformatics data treatment. Dr. C. Penny and Dr. L. Hoffmann are also acknowledged for final reading of the manuscript.

Conflict of interest

The authors declare that they have no conflict of interest.

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The manuscript does not contain clinical studies or patient data.

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Authors and Affiliations

  1. Department of Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, 4422, Belvaux, Luxembourg

    Leslie Ogorzaly, Cécile Walczak, Mélissa Galloux & Henry-Michel Cauchie

  2. French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54000, Nancy, France

    Stéphanie Etienne & Benoît Gassilloud

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  1. Leslie Ogorzaly
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  2. Cécile Walczak
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  6. Henry-Michel Cauchie
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Correspondence to Leslie Ogorzaly.

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Ogorzaly, L., Walczak, C., Galloux, M. et al. Human Adenovirus Diversity in Water Samples Using a Next-Generation Amplicon Sequencing Approach. Food Environ Virol 7, 112–121 (2015). https://doi.org/10.1007/s12560-015-9194-4

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  • DOI: https://doi.org/10.1007/s12560-015-9194-4

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