Title Systems-level comparison of host responses induced by pandemic and seasonal influenza A H 1 N 1 viruses in primary human type Ilike alveolar epithelial cells in vitro

Background: Pandemic influenza H1N1 (pdmH1N1) virus causes mild disease in humans but occasionally leads to severe complications and even death, especially in those who are pregnant or have underlying disease. Cytokine responses induced by pdmH1N1 viruses in vitro are comparable to other seasonal influenza viruses suggesting the cytokine dysregulation as seen in H5N1 infection is not a feature of the pdmH1N1 virus. However a comprehensive gene expression profile of pdmH1N1 in relevant primary human cells in vitro has not been reported. Type I alveolar epithelial cells are a key target cell in pdmH1N1 pneumonia. Methods: We carried out a comprehensive gene expression profiling using the Affymetrix microarray platform to compare the transcriptomes of primary human alveolar type I-like alveolar epithelial cells infected with pdmH1N1 or seasonal H1N1 virus. Results: Overall, we found that most of the genes that induced by the pdmH1N1 were similarly regulated in response to seasonal H1N1 infection with respect to both trend and extent of gene expression. These commonly responsive genes were largely related to the interferon (IFN) response. Expression of the type III IFN IL29 was more prominent than the type I IFN IFNb and a similar pattern of expression of both IFN genes was seen in pdmH1N1 and seasonal H1N1 infection. Genes that were significantly down-regulated in response to seasonal H1N1 but not in response to pdmH1N1 included the zinc finger proteins and small nucleolar RNAs. Gene Ontology (GO) and pathway over-representation analysis suggested that these genes were associated with DNA binding and transcription/translation related functions. Conclusions: Both seasonal H1N1 and pdmH1N1 trigger similar host responses including IFN-based antiviral responses and cytokine responses. Unlike the avian H5N1 virus, pdmH1N1 virus does not have an intrinsic capacity for cytokine dysregulation. The differences between pdmH1N1 and seasonal H1N1 viruses lay in the ability of seasonal H1N1 virus to down regulate zinc finger proteins and small nucleolar RNAs, which are possible viral transcriptional suppressors and eukaryotic translation initiation factors respectively. These differences may be biologically relevant and may represent better adaptation of seasonal H1N1 influenza virus to the host. * Correspondence: malik@hkucc.hku. hk † Contributed equally Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China Full list of author information is available at the end of the article Lee et al. Respiratory Research 2010, 11:147 http://respiratory-research.com/content/11/1/147 © 2010 Lee et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background Pandemic H1N1 remains a mild disease although occasionally severe complications and death may ensue, especially in those who are pregnant or have underlying respiratory, cardiac or endocrine diseases or morbid obesity [1]. We and others have demonstrated that pdmH1N1 virus does not differ from seasonal influenza viruses in its induction of cytokine responses in human macrophages and epithelial cells [2-4]. This suggests that the cytokine dysregulation seen in H5N1 infection is not an intrinsic feature of the pdmH1N1 virus. The pdmH1N1 virus arose from genetic reassortment between influenza viruses endemic in swine, a North American triple-reassortant swine influenza virus acquiring a neuraminidase and matrix (M) gene segment from viruses of the Eurasian-avian-like swine virus lineage [5,6]. Since these swine viruses have in turn originated via complex genetic reassortments between swine, avian and human influenza viruses, the pdmH1N1 virus has a novel gene constellation with virus gene segments that are derived from human (PB1), classical swine H1N1 (HA, NP, NS), Eurasian avian-like swine (M, NA) and avian (PB2, PA) sources. While the precursor swine viruses were clearly well adapted to circulate in pigs for periods ranging from 11 (North American triple reassortant) to 90 (classical swine) years, evolutionary dating analysis suggests that the pdmH1N1 virus transmitted in humans only a few months prior to its detection in March 2009 [6]. Using the Affymetrix microarray platform, we had previously demonstrated that avian H5N1 viruses elicit host responses that were qualitatively similar but quantitatively markedly different to seasonal influenza H1N1 virus in human macrophages [7]. As the tracheo-bronchial epithelium, type I and II alveolar epithelial cells and macrophages are key target cells for pdmH1N1 infection [8] and the most serious complication of pdmH1N1 disease is primary viral pneumonia, we employed type I-like alveolar epithelial cells as a model to examine the host transcriptomes induced by pdmH1N1 viruses compared with that of seasonal H1N1 viruses using the same Affymetrix microarray platform. We aimed to identify the mechanistic differences in host responses induced by these two H1N1 viruses, in order to provide insights into virus pathogenesis, which may in turn be relevant to therapeutic strategies for the treatment of influenza.