Planned aetiological investigations
| Pathogen | Platform | Specimen type |
| Dengue virus | PCR | Venous blood |
| Chikungunya virus | PCR | Venous blood |
| Pan-Flavivirus | PCR | Venous blood |
| Pan-Alphavirus | PCR | Venous blood |
| Orientia tsutsugamushi | PCR | Venous blood |
| Rickettsia spp | PCR | Venous blood |
| Leptospira spp | PCR | Venous blood |
| Eubacteria (16 s rDNA) | PCR | Venous blood |
| Influenza A virus | PCR* | Nasopharyngeal swab |
| Influenza B virus | PCR* | Nasopharyngeal swab |
| Respiratory syncytial virus | PCR* | Nasopharyngeal swab |
| Bacterial bloodstream infection | Blood culture | Venous blood |
Blood cultures are collected at the discretion of the treating clinician and results provided to the treating clinical team. All other aetiological investigations are performed retrospectively using standardised protocols at reference laboratories.
*Nasopharyngeal swab specimens will be tested using the BioFire FilmArray Respiratory Pathogen 2 panel which includes a broader range of aetiological targets (www.biofiredx.com/products/the-filmarray-panels/filmarrayrp).65 However, as causality can be difficult to determine for some of these agents, they have not all been named here.