Influenza A viruses (IAVs) are contagious pathogens responsible for respiratory infection in humans. The respiratory tract is the initial site of viral infection and to establish an infection and propagate successfully, the influenza virus must evade the innate immune system, whose main role is to prevent or restrict viral replication. In addition, the innate immune system plays an important role in activating the adaptive immune response, which is crucial in resolving the infection. Here, using single-cell RNA sequencing, we aim to study the heterogeneity of the immune responses during in the upper respiratory tract during acute human influenza infection compared with convalescence. For this we have collected nasopharyngeal aspirates (NPA) from patients during influenza season. Keeping in mind the fragile nature of these samples and to streamline the processing steps for single cell workflow, we have fixed the samples at the point of collection. Currently we are in discussion with the National Genomics Infrastructure (NGI) facility for processing the fixed samples for library preparation followed by RNA sequencing. This will generate large amounts of raw single cell sequencing data, which will be processed and analyzed at the National Bioinformatics Infrastructure Sweden (NBIS).