TABLE 88-2.

Diagnostic Tests and the Specimens Used for Various Viral Agents

viral Agent	Diagnostic lests	Specimens Used
Adenovirus	FA, PCR, culture, shell vial	NR BAL fluid, tissue
Arboviruses (California encephalitis, Colorado tick fever, EEE, SLE, WEE, West Nile)	Serology, PCR, and immunohistochemistry for some	Serum (acute and convalescent), CSF
Enteroviruses (echoviruses, Coxsackie viruses, enteroviruses)	PCR, culture, serology available for some	CSF, pharynx, stool,* serum (acute and convalescent)
Hantavirus	Culture, PCR, serology	BAL fluid, serum
Hepatitis viruses	Serology for all	Serum
•HAV	Anti-HAV IgM	Serum
•HBV	HBsAg, anti-HBcAb IgM, PCR	Serum, liver
•HCV	Anti-HCV, PCR	Serum, liver
•HDV	Anti-HDV, PCR	Serum, liver
•HEV	Anti-HEV IgM, PCR	Serum, liver
•HGV	PCR (not widely available)	Serum
Herpes viruses
•CMV	FA, PCR, culture, shell vial, serology, buffy coat antigen	NR BAL, blood, tissue, urine, plasma
•EBV	PCR, serology, in situ hybridization	Serum, tissue, CSF
•HHV-6	PCR	Plasma or serum, CSF
•HSV 1 and 2	PCR, FA, culture	CSF, base of lesion, tissue, NP, conjunctiva, stool (neonates)
•VZV	Culture, FA	Base of lesion, tissue
Influenza A and B	FA, culture, IA (rapid)	NR BAL fluid, tissue
JC Virus	Brain biopsy†, PCR	Brain, CSF
LCMV	Serology	Serum
Measles (rubeola)	Serology, culture (rarely grows)	Serum
•SSPE	Oligoclonal bands, IgG, measles titer	CSF
Mumps	Serology, culture (rarely grows)	Serum, pharynx, urine, CSF
Parainfluenza	FA, cultures	NR tissue, BAL fluid
Parvovirus	PCR, serology	Blood, serum
Rabies virus	CSF antibody, virus isolation/culture (rarely helpful), fluorescent microscopy (consult ID)	Punch biopsy (nape of neck), brain, saliva, CSF, urine
Retrovi ruses
•HIV	PCR, serology	Serum, plasma, blood, CSF,
•HTLV	PCR, serology	Serum, tissue
Rotavirus	EIA	Stool
RSV	FA, culture, shell vial, IA (rapid)	NR BAL, tissue
Rubella	Serology, culture	Serum, NR pharynx, CSF, blood, urine

BAL, bronchoalveolar lavage; CSF, cerebrospinal fluid; CMV, cytomegalovirus; EEE, eastern equine encephalitis; EBV, Epstein-Barr virus; EIA, enzyme immunoassay; FA, fluorescence assay; HAV, hepatitis A virus; HBcAb, hepatitis B core antibody; HBsAg, hepatitis B surface antigen; HBV, hepatitis B virus; HCV, hepatitis C virus; HDV, hepatitis D virus; HEV, hepatitis E virus; HGV, hepatitis G virus; HHV-6, human herpesvirus 6; HIV, human immunodeficiency virus; HSV, herpes simplex virus; HTLV, human T-lymphotropic virus; IA, immunoassay; ID, infectious disease; IgM, immunoglobulin M; JCV, JC virus; LCMV, lymphocytic choriomeningitis virus; NP, nasopharyngeal; PCR, polymerase chain reaction; RSV, respiratory syncytial virus; SLE, St. Louis encephalitis; SSPE, subacute sclerosing panencephalitis; VZV, varicella-zoster virus; WEE, western equine encephalitis.

^*Enteroviruses are shed in the stool for weeks and may not be diagnostic.

^†Gold standard.