Respiratory syncytial virus (RSV) bronchiolitis causes severe respiratory tract infection in infants, frequently necessitating mechanical ventilatory support. However, life-saving, mechanical ventilation aggravates lung inflammation. We set up a model to dissect the host molecular response to mechanical ventilation in RSV infection. Furthermore, the response to induced hypercapnic acidosis, reported to dampen the inflammatory response to mechanical ventilation in non-infectious models, was assessed.BALB/c mice were inoculated with RSV or mock-suspension and ventilated for 5 h on day 5 post inoculation.Mechanical ventilation of infected mice resulted in enhanced cellular influx and increased concentrations of pro-inflammatory cytokines in the bronchoalveolar space. Microarray analysis showed that enhanced inflammation was associated with a molecular signature of a stress response to mechanical ventilation with little effect on the virus-induced innate immune response. Hypercapnic acidosis during mechanical ventilation of infected mice did not change host transcript profiles.We conclude that mechanical ventilation during RSV infection adds a robust but distinct molecular stress response to virus-induced innate immunity activation, emphasising the importance of lung-protective mechanical ventilation strategies. Induced hypercapnic acidosis has no major effect on host transcription profiles during mechanical ventilation for RSV infection, suggesting that this is a safe approach to minimise ventilator-induced lung injury.KEYWORDS: Gene expression profiles, hypercapnic acidosis, mice, respiratory syncytial virus, ventilator-induced lung injury R espiratory syncytial virus (RSV) is the most common cause of seasonal acute respiratory tract illness of all ages [1,2]. More than 50% of all infants are infected with RSV during the first yr of life and by the age of 2 yrs almost all children have been infected [3]. Of these children ,1-2% will need hospitalisation and ,10% of these hospitalised children (,0.1% of all children) will require mechanical ventilation for a severe RSV infection during their first yr of life [4]. Hence, RSV infection is the most frequent cause of non-elective paediatric intensive care unit (PICU) admission for mechanical ventilatory support in infants during the winter season [5]. RSV pathogenesis is not completely understood. In humans, severe RSV infection results in a predominantly neutrophil infiltrate in bronchoalveolar lavage fluid (BALF) [6] and a strong innate pro-inflammatory response, reflected by exhaustion of the peripheral blood neutrophil pool after peak values of viral load and disease severity [7]. In mice, the innate immune response is characterised by induction of type I interferon (IFN)-regulated genes and chemokine genes, and genes involved in inflammation and antigen processing [8].Although life-saving, mechanical ventilation may induce or aggravate pulmonary inflammation and lung injury. Ventilator-induced lung injury (VILI) results from relatively high tidal volumes...