Table 2.

Summary of samples and analyses in Uganda and Sweden.^a

Specimens (type and tests)		Inclusion (Day 0)	Day 3	Clinical analyses (when/where)	Type of research analyses (when/where)
Cases
	Blood: Hematology, biochemistry, HIV serology (and confirmation), malaria RDTb, culture, plasma biobank	6 mL	1-2 mL	Routine clinical analyses (same day at the Epicentre Laboratory).	Proteomics analyses for profiling of biomarkers including MxAe (later at the SciLifeLabf).
	CSFc: Biochemistry, microscopy and cytology, culture, MEd-PCR panel, PCR, biobank	2 mL	—	Routine clinical analyses including ME-PCR panel (same day at the Epicentre Laboratory).	Proteomics analyses for profiling of biomarkers including MxA (later at the SciLifeLab).
	Nasopharyngeal swabs: Biobank	1 swab	—	—	Typing of bacteria and bacterial whole-genome sequencing (later at the Karolinska Institutet and SciLifeLab).
Controls
	Blood: Hematology, HIV serology (and confirmation), malaria RDT, biobank	1-2 mL	—	Routine clinical analyses (same day at the Epicentre Laboratory).	Proteomics analyses for profiling of biomarkers including MxA (later at the SciLifeLab).
	Nasopharyngeal swabs: Biobank	1 swab	—	—	Typing of bacteria and bacterial whole-genome sequencing (later at the Karolinska Institutet and SciLifeLab).

^aAdditional testing for clinical care, such as TB GeneXpert or TB ZN, was performed according to clinical needs and at the discretion of the medical officer.

^bRDT: rapid diagnostic test

^cCSF: cerebrospinal fluid.

^dME: meningitis/encephalitis.

^eMxA: Myxovirus resistance protein A

^fSciLifeLab: Science for Life Laboratory.