Table 3.

Summarized of storage and analysis of clinical samples

Type of sample	Procedure	Minimum process volume required	Container	At time	Place of analysis	Storage	Shipment	Destructionh
Venous or finger/heel prick whole blood or plasma	HIV 1–2 RT-PCR POC automated nucleic acid testing platform (ALERE®)	0.3 ml	Cartridge/	Yes	Locally	No	No	According to manufacturer
			Capillary/
			EDTA
Venous whole blood	Total blood count Automatic coulter	0.5 ml	EDTA	Yes	Locally	No	No
Venous whole blood	ALT, Creatinine, Glucose	0.5 ml	Dry tube	Yes	Locally	No	No
	Automatic analyzer
Venous whole blood	CD4 (absolute number and %)	0.2 ml	EDTA	Yes	Locallye	No	No
Venous whole blood	HIV viral load	1 ml	EDTA	Yes	Locallye	No	No
NPAa	Xpert MTB/RIF Ultra (TB PCR)	2–5 ml	Mucus extractor	Yes	Locally	No	No	According to manufacturer
Stools	Xpert MTB/RIF Ultra (TB PCR)	5 g	Stools container	Yes	Locally	No	No	According to manufacturer
Urine	Fujifilm TB LAM	5 ml	Urine container	Yes	Locally	No	No	According to manufacturer
Venous whole bloodf	CMV viral load	1 ml	EDTA	No	Zambia	− 80 °C+/−  10 °C,	Only DNA ambient
Salivaf	CMV viral load	Swab	Universal Transport Medium	No	Zambia	−80 °C+/− 10 °C	Only DNA ambient
Sub-study and ancillary tests
Venous whole bloodb	PK1:t = 0, 2, 4, 6, 8, and 12 h after intake	1 ml each	Heparin	No	NTL	−80 °C+/− 10 °C	Dry ice
Venous whole bloodb	PK2: t = 0, 2, 4, 6, 8, 12/24 h after intake	0.5 ml each	EDTA	No	NTL	−80 °C+/− 10 °C	Dry ice
Venous whole bloodb	PK3: t = 2 and 5 after intake	1 ml each	Lithium heparin	No	NTL	−80 °C+/− 10 °C	Dry ice
Venous whole bloodb	PK4: t = 2	0.5 ml	Lithium heparin	No	NTL	−80 °C+/− 10 °C	Dry ice
Blood, NPA, CSF and post-mortem tru-cutc	Advanced histopathological and microbiologicalg	10 ml, 2–5 ml, 10 ml, cylinders	EDTA	No	Spain	−80 °C+/−  10 °C	Dry ice
			Dry tube
			Dry tube
NPAd,f	Cytokine levels	~ 2.5 ml (mucus + SPS)	Mucus extractor	No	Malawi	−80 °C+/− 10 °C	Dry ice	Following local guidelines
NPAd,f	CMV viral load, genotyping	~ 2.5 ml	Dry tube	No	Zambia	−80 °C+/− 10 °C	Dry ice	Following local guidelines

Abbreviations: RT-PCR real-time polymerase chain reaction, ALT alanine transaminase, SPS saline physiological solution, PCR polymerase chain reaction, CMV cytomegalovirus, POC point of care, NPA nasopharyngeal aspirate, CSF cerebrospinal fluid, TB tuberculosis, EDTA Ethylene-diamine tetra-acetic acid, MTB/RIF Mycobacterium tuberculosis DNA and resistance to rifampicin, LAM lipoarabinomannan, PK pharmacokinetics, NTL The Netherlands

^aIn the recruitment visit the NPAs will be performed in one action. In case the infant participates in the ancillary immune study the sample will be shared in 3 aliquots

^bSub-study performed only in Uganda, Zambia, and Zimbabwe

^cSub-study performed only in Mozambique and Zambia

^dAncillary study performed only in Blantyre and Lusaka Hospital in Zambia

^eSome sites will send to the national referral laboratories

^fLeftovers, in Zambia and Malawi, will be stored and later analyzed by molecular methods to identify potential differential causal pathogens and markers of bacterial and mycobacterial antibiotic resistance

^gBassat Q, Castillo P, Martínez MJ et al. Validity of a minimally invasive autopsy tool for the cause of death determination in pediatric deaths in Mozambique: An observational study. PLoS Med. 2017 Jun 20;14(6): e1002317

^hAccording to trial SOPs for the sample, local guidelines and according protocol