Host response to IAV infections in human patients

Using influenza infection as a disease model, we used a systems biology approach to analyse host response and to identify immune pathways that might contribute to disease progression. We recruited influenza patients with varying severity of infection (n=154) and collected peripheral blood samples within 24 hours of their presentation to hospitals. Gene-expression arrays of these samples were analysed using weighted gene co-expression network analysis to detect disease-driving modules. These modules were then ranked based on the weight of their contribution to disease progression and fatality. We recruited patients from 20 hospitals during the period 2009 to 2016. The eligibility criteria included (1) age greater than 18 years and (2) World Health Organization definition of influenza-like illness (fever of 38 C° or higher, cough and illness onset within the last ten days). Eligible patients were assessed by an admitting physician for likelihood of influenza infection. Patients with a high likelihood of infection, based on history and clinical features, were enrolled into the study. Airway samples (nasopharyngeal swab, throat sample or sputum) and a 2.5ml peripheral blood sample (into PAXgene tubes) were obtained in each study participant. Routine investigations were performed, as determined by the admitting physician. Airway samples were tested for bacterial pathogens and common respiratory viruses. Blood samples in PAXgene tubes were later processed for microarray analysis.