Table 2.

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.