Emerging and re-emerging zoonoses constitute major threats to human health and cause considerable socioeconomic problems globally. This has been the case in four influenza A virus pandemics during the last century, several outbreaks of Ebola and Zikavirus and lastly by the third coronavirus outbreak within 18 years, the COVID-19 pandemic caused by the SARS-CoV-2 virus. The aim of this proposal is to develop a platform for single cell transcriptomics of infected cells in a BSL-3 environment. Specifically we will study infection with different lineages of the SARS-CoV-2 and influenza virus in a number of different cell types predominantly from the human respiratory tract.