TABLE 2.
Specimen collection and suggested investigative diagnostics (adapted from https://www.who.int/publications/i/item/who-unkhep-laboratory-2022.1). SARS-CoV-2: Severe acute respiratory syndrome coronavirus-2; CMV = cytomegalovirus; EBV = Epstein-Barr virus; HSV-1 and 2 = herpes simplex virus type 1 and 2; VZV = varicella-zoster virus; HHV-6 and 7 = human herpesvirus 6 and 7; RSV = respiratory syncytial virus; NAAT = nucleic acid amplification test.
| Specimen type | Test | Pathogens |
|---|---|---|
| Whole blood | NAAT | SARS-CoV-2, adenovirus, enterovirus, parechovirus, CMV, EBV, HSV-1, HSV-2, VZV, HHV-6, HHV-7, parvovirus B19, Leptospira spp. and metagenomics |
| Serology | HIV, rubella virus, anti streptolysin O titre, Leptospira spp. and Coxiella burnetti | |
| Culture | Standard culture for bacteria/fungi | |
| Toxicology | Local investigations according to medical history and geography | |
| Throat swab (oro/naso-pharyngeal) | NAAT | Respiratory virus panel (including adenovirus, human bocavirus, influenza, parainfluenza, rhinovirus/enterovirus, RSV, metapneumovirus, SARS-CoV-2), Mycoplasma spp. |
| Culture | Standard bacterial panel, including Streptococcus group A | |
| Stool | NAAT | Adenovirus, astrovirus, enterovirus, rotavirus, norovirus, sapovirus, enterovirus |
| Culture | Standard bacterial stool pathogen panel, including Salmonella spp. | |
| Urine | NAAT | Adenovirus, Leptospira spp. |
| Culture | Standard bacterial urine culture | |
| Toxicology | Local investigations according to medical history and geography | |
| Liver tissue | Metagenomics | All pathogens |