Two distinct diagnostic tests, a host/pathogen RNA sequencing platform, and spatially-resolved tissue mapping tools were created by a multidisciplinary team of Weill Cornell Medicine and NewYork-Presbyterian Hospital-led researchers and used to map SARS-CoV-2 infections at the height of the initial COVID-19 outbreak in New York City. These alternatives to the gold standard RT-PCR test expand the repertoire of tools available to the public health community and together offer the benefits of speed, simplicity, and in-depth knowledge about the virus.