Pathogens for which all Seattle Flu Study respiratory specimens are tested using a TaqMan RT-PCR
| Viruses | Bacteria |
| Influenza A—H3N2 | Streptococcus pneumoniae |
| Influenza A—H1N1 | Mycoplasma pneumoniae |
| Influenza A—Pan | Chlamydia pneumoniae |
| Influenza B | |
| Influenza C | |
| Respiratory syncytial viruses A and B | |
| Parainfluenza viruses 1–4 | |
| Coronavirus 229E, NL63, OC43 and HKU1 | |
| Adenovirus | |
| Rhinovirus | |
| Human metapneumovirus | |
| Human parechovirus | |
| Enterovirus* | |
| Enterovirus D68 | |
| Human bocavirus |
*All enterovirus species A, B, C, D and G, including: all Coxsackie serotypes under species A, B, C; all Echovirus serotypes; all Poliovirus serotypes.1–3