Table 2

Planned aetiological investigations

PathogenPlatformSpecimen type
Dengue virusPCRVenous blood
Chikungunya virusPCRVenous blood
Pan-FlavivirusPCRVenous blood
Pan-AlphavirusPCRVenous blood
Orientia tsutsugamushiPCRVenous blood
Rickettsia sppPCRVenous blood
Leptospira sppPCRVenous blood
Eubacteria (16 s rDNA)PCRVenous blood
Influenza A virusPCR*Nasopharyngeal swab
Influenza B virusPCR*Nasopharyngeal swab
Respiratory syncytial virusPCR*Nasopharyngeal swab
Bacterial bloodstream infectionBlood cultureVenous 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.