The COVID-19 pandemic strongly affected mobility around the world. Public transport was particularly hindered, since people may perceive it as unsafe and decide to avoid it. Moreover, in Switzerland, several restrictions were applied at the beginning of the first pandemic wave (16/03/2020), to reduce the contagion. This study observes how the pandemic affected travel behaviour of public transport users, focusing on route choice and recurrent trips. We conducted a travel survey based on GPS tracking during the first pandemic wave, following 48 users for more than 4 months. The very same users were also tracked in spring 2019, allowing a precise comparison of travel behaviour before and during the pandemic. We analyse how the pandemic affected users, in terms of travel distance, mode share and location during the day. We specifically focus on recurrent trips, commuting and non-commuting, observing how mode and route changed between the two different periods. Finally, we estimate a route choice model for public transport (Mixed Path Size Logit), based on trips during the two different years, to identify how the route choice criteria changed during the pandemic. The main differences identified in travel behaviour during the pandemic are a different perception of costs of transfers and of travel time in train, and that users no longer have a clear preferred route for a recurrent trip, but often choose different routes.