A subset of individuals has prolonged disease after COVID-19, which is known as long COVID or post-acute sequelae of COVID-19 (PASC). The underlying mechanisms are poorly understood, in part owing to a lack of experimental models. Frere et al. followed hamsters for up to a month after SARS-CoV-2 infection, looking at changes in different tissues, and compared the data with influenza A virus (IAV) infection. Both viruses triggered a similar host response dominated by type I interferon and pathology mostly of the lung with limited involvement of other organs. However, at 31 days post infection, SARS-CoV-2 showed stronger peribronchiolar metaplasia in the lung and tubular atrophy in the kidney. Furthermore, SARS-CoV-2 caused persistent inflammation in the olfactory bulb and epithelium, which was not seen in IAV-infected hamsters. Similar transcriptomic changes were seen in olfactory tissues from human autopsy samples of people recovered from COVID-19. The authors conclude that hamsters could potentially be used for further mechanistic and interventional studies of long COVID.