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High-density resequencing DNA microarrays in public health emergencies

Nature Biotechnology volume 28, pages 25–27 (2010)Cite this article

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To the Editor:

Despite epidemiological intelligence and microbiological surveillance systems or programs, virus emergence mostly occurs by surprise. Influenza A virus offers a paradigm of such a situation: the world was focusing on a threat due to highly pathogenic (H5N1) avian influenza A virus in Asia1. Instead, it faced a novel reassortant swine-origin H1N1 influenza A virus (H1N1pdm) with pandemic potential on the American continent2. Seasonal influenza surveillance and pandemic preparedness are potent incentives to develop rapid, specific, sensitive and robust diagnostic tools for laboratories, particularly the World Health Organization's (WHO; Geneva) National Influenza Centers and other laboratories in different countries specialized in epidemic responses. Here, we describe the use of random non-PCR–based nucleic acid amplification and high-density resequencing DNA microarrays to rapidly identify reassorted influenza A virus strains of swine origin. Such an approach could prove useful for public health authorities attempting to detect and identify reassortment events in future outbreaks.

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Figure 1: Phylogenetic trees of PB2 and H1 genes belonging to influenza A viruses isolated over a long period of time across a wide geographical area and from a variety of host species.

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Acknowledgements

This study was supported by Programme Transversal de Recherche (PTR DEVA n°246) from Institut Pasteur (France). We thank the sponsorship of Total-Institut Pasteur for their financial support of this research program. We thank the EU-funded RIVERS program (Sixth Framework Program SSP-5-B-INFLUENZA 04 405: Resistance of Influenza Viruses in Environmental Reservoirs and Systems). We thank all members of Laboratory for Urgent Response to Biological Threats (CIBU) and Système d'Astreinte Microbiologique for their contribution and G.K. Kennedy, P. Dickinson and Affymetrix's staff, who were involved in the design and manufacture of this second generation of microarrays (UC1 AI062613 (Kennedy) from the US National Institute of Allergy and Infectious Diseases, National Institutes of Health).

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Authors and Affiliations

  1. Institut Pasteur, Unit of Epidemiology and Pathophysiology Oncogenic Virus and CNRS URA3015, Paris, France

    Nicolas Berthet, Claudia Filippone & Antoine Gessain

  2. Institut Pasteur, Laboratory for Urgent Response to Biological Threats (CIBU), Paris, France

    India Leclercq, Amélie Dublineau, Sayuri Shigematsu, Ana Maria Burguière & Jean-Claude Manuguerra

  3. Université Paris Diderot, Paris, France

    India Leclercq

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  1. Nicolas Berthet
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  2. India Leclercq
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  7. Antoine Gessain
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  8. Jean-Claude Manuguerra
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Correspondence to Jean-Claude Manuguerra.

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Supplementary Fig. 1, Supplementary Tables 1–3, Data, Methods (PDF 106 kb)

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Berthet, N., Leclercq, I., Dublineau, A. et al. High-density resequencing DNA microarrays in public health emergencies. Nat Biotechnol 28, 25–27 (2010). https://doi.org/10.1038/nbt0110-25

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