Table 6.
Categories of testing performed in diagnostic and research virology.
| Category of testing | Specific viruses | Methodology |
|---|---|---|
| Respiratory viruses | Influenza A and B, RSV, PIV 1–4, hMPV, rhinoviruses, enteroviruses, coronaviruses, adenoviruses | Rapid antigen tests (influenza A and B, RSV), fluorescent antibody staining (influenza A and B, RSV, PIV 1–3, adenoviruses, hMPV), culture, multiplex NAAT, RS [14], SERS [18] |
| Gastrointestinal viruses | Rotavirus, norovirus, adenovirus, astrovirus | Rapid antigen tests (rotavirus, norovirus, adenovirus), NAAT |
| Mucocutaneous viruses | HSV, VZV, HPV | Fluorescent antibody staining (HSV and ZVZ), culture (HSV and VZV), NAAT |
| Central nervous system viruses | HSV, VZV, CMV, EBV, HHV-6, JCV, enteroviruses, parechoviruses, West Nile virus, other arboviruses | NAAT, serology (West Nile and other arboviruses) |
| Opportunistic agents | CMV, EBV, BKV, HHV-6, adenoviruses | NAAT, antigen detection (CMV pp65 assay), cytology (BKV) |
| Mononucleosis syndrome in non-immunocompromised individuals | EBV, CMV, HIV | Serology, NAAT, IR [8] |
| HIV, HCV, HBV viral loads | HIV, HCV, HBV | NAAT, RS [7] |
| Viral Genotyping | HCV, HBV, HPV | Nucleotide sequencing, reverse hybridization, NAAT (Cleavase reaction for HPV) |
| HIV, HCV, HBV diagnosis | HIV, HCV, HBV | Serology, NAAT |
| Systemic infections of childhood | Parvovirus B19, measles virus, rubella virus, mumps virus | Serology, NAAT |
| Tropical and emerging infections | Dengue virus, Zika virus, Yellow Fever virus and other flaviviruses; Chikungunya and other alphaviruses; hemorrhagic fever viruses including arenaviruses, bunyaviruses, and filoviruses; Hendra and Nipah viruses | Serology, culture, NAAT (hemorrhagic fever testing is done in BSL-4 laboratories), NMR spectroscopy [16] |
| Unknown virus | Any | Culture, microarray, nucleotide sequencing, NGS, MSF [17] |
BKV, BK virus; CMV, cytomegalovirus; EBV, Epstein-Barr virus; HBV, hepatitis B virus; HCV, hepatitis C virus; HHV-6, human herpes virus 6; HIV, human immunodeficiency virus; hMPV, human metapneumovirus; HPV, human papillomavirus; HSV, herpes simplex virus; IR, Infrared spectroscopy; JCV, JC virus; MFS, molecular fluorescence spectroscopy; NAAT, nucleic acid amplification testing; NGS, next-generation sequencing; NMR, nuclear magnetic resonance spectroscopy; PIV, parainfluenza virus; RS, Raman spectroscopy; RSV, respiratory syncytial virus; SERS, surface-enhanced Raman spectroscopy; VZV, varicella-zoster virus.
Updated from Storch and Wang [68].