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Open Access Highly Accessed Study protocol

Integrative study of pandemic A/H1N1 influenza infections: design and methods of the CoPanFlu-France cohort

Nathanael Lapidus12*, Xavier de Lamballerie345, Nicolas Salez3, Michel Setbon67, Pascal Ferrari12, Rosemary M Delabre12, Marie-Lise Gougeon8, Frédéric Vely1011129, Marianne Leruez-Ville1314, Laurent Andreoletti1516, Simon Cauchemez17, Pierre-Yves Boëlle1182, Eric Vivier1011129, Laurent Abel131920, Michaël Schwarzinger212223, Michèle Legeas5, Pierre Le Cann5, Antoine Flahault157 and Fabrice Carrat1182

Author Affiliations

1 Institut National de la Santé et de la Recherche Médicale, UMR-S 707, F-75012 Paris, France

2 Université Pierre et Marie Curie-Paris 6, UMR-S 707, F-75012 Paris, France

3 Unité des Virus Emergents, UMR-D 190, Aix-Marseille université and Institut de Recherche pour le Développement, Marseille, France

4 Laboratoire de Virologie, Pôle hospitalier de Microbiologie et Maladies Infectieuses, Assistance Publique, Hôpitaux de Marseille, Marseille, France

5 Ecole des Hautes Etudes en Sante Publique, Rennes, France

6 CNRS – LEST, UMR 6123 Université d’Aix-Marseille, Aix en Provence, France

7 Ecole des Hautes Etudes en Sante Publique, Paris, France

8 Institut Pasteur, Antiviral Immunity, Biotherapy and Vaccine Unit, Paris, France

9 Centre d’Immunologie de Marseille-Luminy (CIML), Université de la Méditerranée UM 631, Campus de Luminy, 13288 Marseille, France

10 Institut National de la Santé et de la Recherche Médicale, UMR-S 631, Marseille, France

11 CNRS, UMR 6102, Marseille, France

12 Assistance Publique, Hôpitaux de Marseille, Hôpital de la Conception, Marseille, France

13 Université Paris Descartes, Sorbonne Paris Cité, EA 36-20 Paris, France

14 Laboratoire de Virologie, Hôpital Necker, AP-HP, Paris, France

15 Unité de Virologie Médicale et Moléculaire, Centre Hospitalier Universitaire, Reims, France

16 IFR 53/EA-4303 (DAT/PPCIDH), Faculté de Médecine, Reims, France

17 Medical Research Council Centre for Outbreak Analysis and Modeling, Department of Infectious Disease Epidemiology, Imperial College, London, UK

18 Assistance Publique-Hôpitaux de Paris, Hôpital Saint Antoine, Unité de Santé Publique, F-75012 Paris, France

19 Laboratoire de Génétique Humaine des Maladies Infectieuses, Institut National de la Santé et de la Recherche Médicale, U 550, Paris, France

20 Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA

21 Institut National de la Santé et de la Recherche Médicale, U 912, Marseille, France

22 Université Aix Marseille, IRD, UMR-S912, Marseille, France

23 Observatoire Régional de la Santé PACA, Marseille, France

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BMC Public Health 2012, 12:417  doi:10.1186/1471-2458-12-417

Published: 7 June 2012



The risk of influenza infection depends on biological characteristics, individual or collective behaviors and the environmental context. The Cohorts for Pandemic Influenza (CoPanFlu) France study was set up in 2009 after the identification of the novel swine-origin A/H1N1 pandemic influenza virus. This cohort of 601 households (1450 subjects) representative for the general population aims at using an integrative approach to study the risk and characteristics of influenza infection as a complex combination of data collected from questionnaires regarding sociodemographic, medical, behavioral characteristics of subjects and indoor environment, using biological samples or environmental databases.


Households were included between December 2009 and July 2010. The design of this study relies on systematic follow-up visits between influenza seasons and additional visits during influenza seasons, when an influenza-like illness is detected in a household via an active surveillance system. During systematic visits, a nurse collects individual and environmental data on questionnaires and obtains blood samples from all members of the household. When an influenza-like-illness is detected, a nurse visits the household three times during the 12 following days, and collects data on questionnaires regarding exposure and symptoms, and biological samples (including nasal swabs) from all subjects in the household. The end of the follow-up period is expected in fall 2012.


The large amount of data collected throughout the follow-up will permit a multidisciplinary study of influenza infections. Additional data is being collected and analyzed in this ongoing cohort. The longitudinal analysis of these households will permit integrative analyses of complex phenomena such as individual, collective and environmental risk factors of infection, routes of transmission, or determinants of the immune response to infection or vaccination.

Influenza a virus H1N1 subtype; Cohort study; Risk factors; France