This first comprehensive study addresses important issues of the identification of markers for severity of p-H1N1-09 infection and dynamics of immune responses in severe disease by evaluating several parameters. The investigations were initiated during the early phase of the pandemic when isolation of all the Figure 3 . Gene expression analysis. Gene expression profiles of total PBMCs from blood samples of mild and critically ill cases and lung aspirate cells from critically ill cases were determined using TaqMan Low Density immune panel arrays. PBMCs from six healthy individuals were taken as controls, which were treated as replicate arrays to calculate the mean baseline expression level for each gene. The fold changes in the gene expression levels were calculated in relation with the controls. Values for eighty-seven genes were hierarchically clustered on log2 transformation. The corresponding gene of each cluster is listed by a gene symbol on the right-hand side of the images. a) Cluster image of gene expression analysis of PBMCs from mild and critically ill cases and lung aspirate cells from critically ill cases: PBMC samples from mild cases are denoted as M (M1, M2, M13). First sample taken after admission from each critically ill case was taken for the comparison and are denoted as S1-1, S2-1, S21-1. Single samples from critically ill patients are denoted as S8, S12 etc. Lung aspirate samples are denoted as L. b) Cluster image of gene expression analysis of sequential blood samples from critically ill cases: Total PBMCs from the sequential blood samples of severe cases obtained on different post admission days are denoted as S1-1, S1-2, …S21-8). doi:10.1371/journal.pone.0013099.g003 p-H1N1-09 mild infections in designated wards was obligatory. Therefore, we could collect samples before the initiation of the antiviral therapy and the data truly represents acute phase of mild disease. On the other hand, critically ill patients were given Oseltamivir immediately after the confirmation of the infection and the samples were collected subsequently. As underlying medical conditions were present in one of the 2 survivors and 7/ 13 critically ill patients, association of co-morbidities alone does not seem to be responsible for complications or aberrant immune response.