We sequenced and genotyped SARS-CoV-2, influenza, adenovirus, and respiratory syncytial virus (RSV), among other pathogens, from residual anterior nasal swabs self-collected for rapid SARS-CoV-2 antigen testing at the US Naval Academy. This is a key proof-of-concept for an acute respiratory infection surveillance approach, which could leverage prevalent SARS-CoV-2 antigen self-testing.