Phylogenesis and Clinical Aspects of Pandemic 2009 Influenza A (H1N1) Virus Infection

Massimo Ciccozzi 1, Muhammed Babakir-Mina 2, 3, Alessandra Lo Presti 1, Fabbio Marcuccilli 2, Carlo Federico Perno 2, 3, Marco Ciotti*, 2
1 Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanita’, Rome, Italy
2 Laboratory of Molecular Virology, Foundation Polyclinic Tor Vergata, Viale Oxford, 81- 00133, Rome, Italy
3 Virology, Department of Experimental Medicine and Biochemistry, Tor Vergata University, Rome, Italy

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* Address correspondence to this author at the Laboratory of Molecular Virology, Foundation Polyclinic Tor Vergata, Viale Oxford, 81-00133, Rome, Italy; Tel.: +39 06 20902087; Fax: +39 06 20902078; E-mail:


During the spring of 2009, a new influenza A (H1N1) virus of swine origin emerged and spread worldwide causing a pandemic influenza. Here, 329 naso-pharyngeal swabs collected from patients with flu-like symptoms were analyzed by real-time PCR for the presence of H1N1 2009 pandemic virus. Twenty-five samples collected from immunocompetent and immunodepressed patients contained the H1N1 pandemic virus. Phylogenetic analysis of the hemagglutinin and neuraminidase genes showed no obvious differences in terms of similarity and/or homology between the sequences identified in immunocompetent individuals and those obtained from immunocompromised patients. Pre-existing clinical conditions may influence the outcome of H1N1 disease.

Keywords: H1N1 pandemic virus, swine flu, respiratory infections, phylogenetic analysis, influenza surface antigens..