SARS-CoV-2 superinfection can masquerade as COVID-19 flare or non-infectious ARDS. No method of diagnosis of bacterial pneumonia exists for non-intubated patients. Lower respiratory culture results in ~1 week and not all pathogens can be cultured. Differential diagnoses have contradictory treatments. We aimed to compare host transcriptomics of Delta variant versus other variants. We aimed to characterize microbiome of upper and lower airway in patients with COVID-19
