Detection of viable viruses such as SARS-CoV-2 in air remains difficult, due to their usually low concentration and the negative impacts on viability that air sampling forces have on fragile enveloped viruses. This work establishes a new method of detecting and fractionating such particles; and demonstrates that SARS-CoV-2 generated by nebulisers have the potential to transmit to the deep lung; highly relevant to in vivo models. These data will also inform further in vitro aerosol studies and set the foundation for in vivo studies designed to understand transmission and disease caused by the aerosol route of infection with SARS-CoV-2, and may aid in informing infection prevention and control policies for indoor air.