Blood Bank/Pheresis Chemistry Frisbee Laboratory Hematology		Immunology Microbiology Molecular Diagnostics Virology

Guide to Viral Diagnosis

I. GUIDELINES FOR SPECIMEN COLLECTION

A. Test ordering

B. Viral antibody studies

C. Specimen collection for viral culture: labeling, timing, collection devices, and holding temperature

D. Specimen collection instructions for selected specimens

II. VIROLOGY TEST SELECTION ORGANIZED BY VIRUS (alphabetical listing):

Virus suspected, Clinical Syndromes, Test Selection and Special Instructions and Time to Result

III. CLINICAL SYNDROMES:

Viruses Associated, Specimens to Collect and Test Method of Choice

IV. INTERPRETATION OF TEST RESULTS

V. SERVICES OFFERED AT THE VIROLOGY REFERENCE LABORATORY, VA-CT

I. GUIDELINES FOR SPECIMEN COLLECTION
(Back to Table of Contents)

A. Test ordering

CCSS: to avoid mistakes in test ordering, please use appropriate order screens.Type in by free text only those tests not available in the standard virology menu.

Virology requisitions: Use Virology I for virus isolation and antigen requests; use Virology II for viral antibody requests and HIV requisition for HIV antibody and HIV-1 viral load requests.

Provide clinical information and/or virus suspected so that the laboratory can select the proper culture systems.

B. Viral antibody studies

For immune status testing, a single serum sample is sufficient.

To detect acute infection, both acute and convalescent sera are generally required to detect an antibody rise. Virus infections whose clinical symptoms are immune-mediated are exceptions (e.g. EBV, HBV, parvovirus B19).

C. Specimen collection for viral culture

Please note: Specimen containers that are not labeled will be rejected.

Collect specimens for culture early in illness when viral shedding is maximal.

Sample	Collection device*	Holding Temperature	Comments
Virus isolation or antigen test:
Swabs	Use viral transport medium Large swab for throat, lesion, etc. Small wire shaft swab for nasopharynx in young children or urethral samples	Refrigerate	Viral transport medium with swabs can be obtained from the hospital storeroom.*
Body fluids, BAL, stool	Use sterile leakproof containers	Refrigerate	Do not dilute body fluids or BAL in transport medium
Tissues	Place in tubes containing liquid viral transport media to keep tissue moist	Refrigerate	Viral transport medium can be obtained from hospital storeroom.*
Blood (Leukocytes or plasma)	Collect 2 lavender top tubes.Collection time required	Room temperature	Sample must be processed within 4-6 hours of collection. Lab closed from Saturday 4:30 pm to Monday 8:00 am
Viral antibody test:
Blood (serum)	Collect 1 red top tube	Room Temperature

*transport medium and swabs can also be obtained from the Tube Room (by Hematology) when Virology is closed.

D. Specimen collection instructions for selcted specimens
(Back to Table of Contents)

Nasopharynx swab	Insert swab into nasopharynx, just past point of resistance. Leave in place for 1 min or rotate to dislodge respiratory epithelial cells; remove and place in transport medium. For small children, thin, flexible wire shaft can be used.
Nasopharynx aspirate	Use suction pump connected to a catheter through a mucus trap; catheter should be French gauge 8 for infants, French gauge 12 for adults. Insert catheter as far into nose as possible. Specimen should be taken from posterior part of nasal mucosa which is lined with respiratory epithelium, and not from anterior part which is lined with squamous epithelium. Collect as much of NP secretions as possible; do not dilute sample with saline unless necessary.
Throat swab	Swab posteror pharyngeal wall, not buccal mucosa, tonsils, tongue or palate. Swab firmly and thoroughly. Throat swabs are suboptimal for DFA testing due to predominance of squamous instead of respiratory epithelial cells obtained.
Lesion swab	Clean lesion with sterile saline soaked gauze pad. Unroof vesicles or remove crusts. Firmly swab base and margins of the lesion, obtaining fluid and cells. After sample collection, clean lesion thoroughly with betadine. Do not use disinfectant prior to sample collection or virus may be inactivated.
Rectal swab	Stool specimen required for enteric pathogens; rectal swab to swab rectal mucosa can be done for proctitis.

II. VIROLOGY TEST SELECTION ORGANIZED BY VIRUS
(Back to Table of Contents)

Virus suspected	Clinical symptoms	Specimens	Tests	Special instructions and comments	Time to result
Adenovirus types 1-47	URI, pharyngitis, pneumonia, conjunctivitis, keratoconjunctivitis, hepatitis, hemorrhagic cystitis, gastroenteritis, intussusception, genital infections	Throat swab, eye swab, urine, BAL, tissue, stool	Virus isolation	Rapid centrifugation culture can be performed if requested	1-14 days
		NP aspirate or swab; eye swab	Immunostain (DFA)	DFA detects only 60% of culture positives.	2-4 hours
Enteric adenovirus types 40,41	Gastroenteritis	Stool	Electron microscopy (EM) or antigen detection by ELISA	Special request (sent out)	7-14 days
Arboviruses (Eastern equine, Western equine, St. Louis encephalitis, LaCrosse, Jamestown Canyon, West Nile, POW)	Encephalitis, aseptic meningitis in summertime	Blood (red top), acute and convalescent, CSF	Arbovirus IgM and IgG antibody in CSF and serum	Sent to State Lab Encephalitis/ meningitis form to be filled out.	2-7 days
		CSF, Brain biopsy	PCR, Virus isolation	No longer available at Yale. Special arrangements may be possible; call laboratory.
BK virus (Polyomavirus)	Hemorrhagic cystitis especially in bone marrow transplants, ureteral stenosis post kidney transplant; tubulointerstitial nephritis, URI, tonsilitis	Urine	Virus detection by shell vial centrifugation culture	Requires special test; please request "BK virus"	2-4 days
Cytomegalovirus (CMV)	Fever, leukopenia, mononucleosis, hepatitis, pneumonia, oral, esophageal and gastrointestinal ulcerations neurologic syndromes	BAL, tissue biopsies; urine, saliva	Virus isolation	Both conventional culture and rapid centrifugation culture (1-3 day turnaround) are performed	1-21 days
		Blood leukocytes (2 lavender tubes); Use to rapidly quantify viral load and monitor therapy	CMV antigenemia preferred for blood; order culture if drug resistance suspected or if negative antigenemia and still suspect CMV	Blood samples must be processed within 6 hrs of collection; therefore collection times must be provided.	2-24 hours
		Blood (red top) actue and convalescent	Antibody (IgM and/or IgG)	Antibody mainly useful to confirm primary infection or to determine immune status; do NOT use to follow seropositive patients.	1-3 days
	Encephalitis	CSF (1-2 ml)	PCR or antigen test	PCR special request (sent out)	3-7 days
	Cytomegalic inclusion disease (congenital infection)	Urine (collected within 3 weeks of birth)	Virus isolation	To diagnose infection as congenital, and not perinatal, must obtain urine within 3 wks of birth	1-21 days
Dengue	Fever, myalgias, rash; hemorrhagic fever	Serum	Antibody Virus isolation	Serum sent to State Laboratory; virus isolation done at CDC	7-14 days
Enterovirus	Summer rashes, aseptic meningitis, encephalitis, herpangina, hand-foot-mouth disease, myocarditis, pleurodynia, paralytic disease	Throat swab, stool, CSF, skin lesion swab, biopsy tissue	Virus isolation (coxsackie A virus may not grow in routine cell cultures)	Collect stool, not rectal swab, for best results. Note: Diagnosis by antibody titer is not practical or reliable	1-14 days
		CSF	Nasba or RT-PCR	Preferred test for CSF; sensitivity varies with virus type	1-3 days
Epstein-Barr virus (EBV)	Infectious mononucleosis (I.M.)	Blood (red top)	Heterophile antibody (monospot)	Positive in 90% of adults and less than 50% of children with I.M.	1 day
	Also hepatitis, pneumonitis, neurologic syndromes, hemolytic anemia, thrombocytopenia, hemophagocytic syndrome	Blood (red top)	EBV antibody panel: VCA IgG, VCA IgM, and EBNA antibodies	Request if heterophile antibody is negative or if unusual clinical presentation	3-7 days
	Lymphoproliferative disease	Biopsy tissue, whole blood	Nucleic acid hybridization or quantitative PCR	By special arrangement with Dr. Greg Howe (ext. 74237)	7 days
	Nasopharyngeal carcinoma (NPC)	Blood (red top)	EBV antibody panel and VCA IgA antibody	EBV VCA IgA available by special request (sent out); Elevated VCA IgA antibody useful in early NPC detection and monitoring for recurrence	3-7 days
Hantavirus Pulmonary Syndrome (HPS)	Pneumonia, ARDS in previously healthy individual	Blood (red top)	Antibody	Sent to State Health Dept; a form, available in the virology laboratory, must be filled out.	3-7 days
		Biopsy tissues	Virus isolation and PCR	Sent to CDC via State Health Dept.	Weeks to months
Hepatitis A	Acute hepatitis, relapsing hepatitis	Blood (red top)	Antibody (anti-HAV IgM)	Can be ordered as single tests or as part of acute hapatitis panel	1-3 days
	Immune status, for travelers to HAV endemic ares		Antibody (anti-HAV total)	Specify "immune status"	2-7 days
Hepatitis B See test interpretation guide	Acute hepatitis, chronic hepatitis, hepatocellular carcinoma, cirrhosis, polyarteritis nodosa	Blood (red top)	HBsAg, anti-HBc total and IgM, anti-HBs, HBeAg and anti-HBe	Can be ordered as single tests, as part of acute hepatitis, chronic hepatitis or hepatitis B virus panels	2-4 days
		Blood (red top)	HBV DNA	Quantitation of HBV DNA should be done prior to therapy and to monitor response (HBV DNA test sent out)	7-10 days
Hepatitis C See test interpretation guide	Acute hepatitis, chronic hepatitis, hepatocellular carcinoma, cirrhosis, essential mixed cryoglobulinemia, porphyria	Blood (red top)	Antibody (anti-HCV EIA)	Can be ordered as a single test, as part of acute hepatitis or chronic hepatitis panels	1-3 days
			Antibody (anti-HCV RIBA)	HCV RIBA is reflexively performed only for samples with low-positive EIA O.D. values. If EIA value is high, RIBA is done only if requested	2-7 days
			HCV RNA (RT-PCR)	Quantitation of HCV RNA should be done prior to therapy and a quantitative or qualitative test to monitor response	3-7 days
			HCV genotype	Determine to guide therapy	1-2 weeks
Hepatitis D (Delta)	Acute hepatitis, chronic hepatitis, fulminant hepatitis, deterioration of chronic HBsAg carrier	Blood (red top)	Antibody (anti-HDV or anti-Delta) Delta antigen	Patient must be HBsAG positive to be infected with HDV. Rarely detectable in serum. Test sent out.	7 days
Hepatitis E	Acute hepatitis, with prurius, joint pain, cholestasis; 20% mortality in pregnant women	Blood (red top)	Antibody (anti-HEV IgM, IgG)	Test sent out.	1-2 weeks
Herpes simplex virus (HSV) types 1 and 2	Cold sore, gingivostomatitis, skin lesions, genital lesions, meningitis, esophagitis, proctitis, hepatitis, pneumonia	Lesion swab, biopsy tissue, mucosal swab, CSF	Virus isolation	Virus isolation is most sensitive test for HSV, especially for asymptomatic shedding	1-7 days
		Lesion swab	Immunostain (DFA)	Must have adequate cells for valid result; routine for all lesion swabs; if positive DFA, culture not done	2-4 hrs
	Encephalitis, recurrent lymphocytic meningitis	CSF	PCR	Detects < 0.5 copies/µL	1-3 days
Human immunodeficiency virus (HIV) type 1 If HIV-2 is suspected, please notifiy laboratory	AIDS, mononucleosis, acute retrovirus syndrome	Blood (red top)	Antibody (EIA screen, Western blot for all positive EIA samples)	Note: All HIV tests require documentation of consent. HIV-2 w.blot sent out	1-7 days (EIA daily , W. blot weekly)
	To guide antiretroviral therapy *Use PCR with caution to diagnose HIV infection in antibody-negative window	Whole blood (2 lavender top)	Quantitiative plasma RNA by RT-PCR 1) Standard PCR 2) Ultrasensitive PCR	Order ultrasensitive PCR only if HIV is not detectable by standard PCR assay (i.e.<400 copies/mL)	2-5 days
			Resistance genotype	Requires 1000 HIV copies/mL	2-4 weeks
	To diagnose infection in neonates and agammaglobulinemics	Whole blood (2 lavender top)	PCR	HIV-1 RNA can be detected in plasma in PBMCs	2-14 days (sent out)
Human herpesvirus type 6 (HHV-6)	Roseola infantum, febrile seizures, infectious mono, hepatitis, pneumonitis	Blood (red top)	Antibody, IgM and IgG	Sent out	1-2 weeks
		Blood (lavender top)	PCR	Special request (sent out)	1-2 weeks
HTLV I/II	Tropical spastic paraparesis or HTLV associated myelopathy; human T cell leukemia/lymphoma	Blood (red top)	Antibody (EIA screen; all positives tested by Western blot)	EIA done in-house; does not distinguish HTLV-I from II	2-7 days
				Western blot sent out	7-10 days
		Blood (2 lavender)	PCR on PBMCs	PCR useful if antibody tests are indeterminate	7-14 days
Influenza A, B	Influenza syndrome, URI, bronchitis, pneumonia, bronchiolitis in infants	Nasopharynx (NP) swab, wash, or aspirate,endotracheal aspirate, BAL (throat swab can be used for culture)	Respiratory screen immunostain (DFA)	Sufficient respiratory epithelial cells required (NP>>>throat)	2-4 hours
			Virus isolation	For all methods, collect specimens within first 48 hrs of illness for maximal virus titers	1-14 days
JC virus (Polyomavirus)	Progressive mulitfocal leukoencephalopathy	Brain biopsy	Histopathology; EM to detect viral particles	Sent to Pathology	2-5 days
		CSF	PCR	Special request (sent out)	4-14 days
Measles	Coryza, conjunctivitis, rash, Koplik's spots; giant cell pneumonia or respiratory symptoms without rash in compromised hosts; encephalitis; atypical measles in previously immunized	Throat swab, NP swab, urine	Virus isolation	Samples must be collected early in disease; requires special test- please notify the laboratory prior to sample collection	2-14 days
		Blood (red top) acute and convalescent	Antibody, IgM and IgG	IgM sent out	1-7 days
Mumps	Partotitis, orchitis, meningitis, encephalitis	Saliva, CSF, urine	Virus isolation	Requires special test; please notify the laboratory	3-14 days
		Blood (red top), acute and convalescent	Antibody		1-7 days
Norwalk virus	Gastroenteritis, winter vomiting disease, outbreaks on cruise ships or associated with contaminated food or water	Blood (red top) acute and convalescent	Antibody titers	Special request; sent out	7-14 days
		Stool collected within 48 hours of onset of symptoms	Detection of virus by RT-PCR	Performed only when outbreak; Special request- sent out	7-14 days
Papillomavirus (over 70 types)	Warts, cervical dysplasia	Cervical swab or biopsy	Hybridization	Tests for genital types only Sent to Pathology	7 days
Parainfluenza types 1-4	URI, croup, bronchitis, pneumonia	NP swab or aspirate, tracheal aspirate, BAL, lung tissue	Respiratory screen (DFA)	DFA for types 1-3 only	2-4 hours
			Virus isolation	Also detects type 4	3-14 days
Parvovirus	Erythema infectiosum (fifth's disease), arthralgias, various exanthems and enanthems, aplastic crisis, chronic anemia in compromised hosts, nonimmune hydrops fetalis	Blood (red top)	Antibody, IgG and IgM	Immunocompromised hosts may not develop antibody	3-7 days
		Serum; bone marrow in congenital anemia	PCR	Special request (sent out)	3-7 days
		Bone marrow	Bone marrow examination	Done in Hematology	2 days
Rabies	Clinical rabies, ascending paralysis, rapidly progressive encephalitis Note: In U.S., half of rabies cases give no history of animal bite	Brian biopsy, skin biopsy from nape of neck (to include hair follicles)	Rabies antigen (immunostain of tissue)	Sent to State Lab and/or CDC	2-14 days
		Blood (red top) and CSF	Antibody	Special request; sent out; serum test invalid if rabies immune globulin has been given	7-14 days
Respiratory syncytial virus	Bronchiolitis, pneumonia, URI	NP aspirate or NP swab, BAL, lung tissue	Respiratory screen immunostain (DFA)	Need adequate respiratory epithelial cells or test invalid; NP aspirate gives best results	2-4 hours
		NP aspirate or swab	Virus isolation		3-14 days
Rhinovirus	URI; lower tract disease in infants, asthma, COPD, ICH	NP swab or aspirate; BAL	Virus isolation		3-14 days
Rotavirus groups A, B	Infantile gastroenteritis (group A) ; diarrhea in adults (group B)	Stool	Rotavirus antigen (ELISA)	ELISA detects only group A and may yield false positive results in neonates	4 hours
			EM to visualize virus	Special request; call lab	1-2 weeks
Rubella	Rubellifrom rash, post-auricular adenopathy, arthralgias, congenital rubella syndrome	Blood (red top) acute and convalescent	Antibody	IgG done in-house, IgM sent out	3-7 days
		Tissue, throat swab and urine	Virus isolation	Special request; please notify laboratory	3-14 days
Varicella-zoster virus (VZV)	Chicken pox, herpes zoster, pneumonia, neurologic syndromes, retinal necrosis Notify laboratory immediately if exposure (health care worker or VZIG candidate)	Skin lesion swabs	VZV antigen (immunostain of skin lesion smears); virus isolation	Need vigorous swab of lesion to dislodge cells for examination; antigen test is most sensitive test for skin lesions if sample is properly collected.	4 hours
		BAL, tissues	Virus isolation	Rapid shell vial centrifugation culture available upon request	3-14 days
		CSF, (1-2 ml)	PCR or antigen	Special request	1-7 days
		Blood (red top)	Antibody, IgG (specify if post-vaccination test)	Collect serum promptly after exposure to determine immune status	7 days

III. CLINCAL SYNDROMES: Associated Viruses, Specimens to Collect and Diagnostic Test of Choice
(Back to Table of Contents)

Clinical Syndrome	Viruses Associated	Specimens to collect	Test method of choice
Respiratory
Pneumonia	Influenza A, B	NP aspirate or swab, BAL, lung tissue	DFA, Culture
	Adenovirus	NP aspirate or swab, BAL, lung tissue	DFA, Culture
	Respiratory syncytial virus	NP aspirate or swab, BAL, lung tissue	DFA, Culture
	Parainfluenza	NP aspirate or swab, BAL, lung tissue	DFA, Culture
	Rhinovirus	NP aspirate or swab, BAL, lung tissue	Culture
	Cytomegalovirus	BAL, lung tissue; blood	Culture; antigenemia
	Varicella-zoster	BAL, lung tissue	Culture; DFA
	Herpes simplex	BAL, lung tissue	Culture; DFA
	Hantavirus*	Lung tissue serum	Serology, PCR, Culture
URI/pharyngitis	Rhinovirus	NP aspirate or swab	Culture
	Respiratory syncytial virus	NP aspirate or swab	DFA, Culture
	Adenovirus	NP aspirate or swab	DFA, Culture
	Parainfluenza	NP aspirate or swab	DFA, Culture
	Influenza A,B	NP aspirate or swab	Culture, DFA
	Enterovirus	Throat and/or NP swab	Culture
	EB virus	Serum	Serology
Pleurodynia	Enterovirus	TS, NP swab	Culture
Ocular
Conjunctivitis/ keratitis	Enterovirus	Conjunctival/corneal swab, TS	Culture
	Adenovirus	Conjunctival/corneal swab, NP	Culture, DFA
	Herpes simplex virus	Conjunctival/corneal swab, lesion swab	Culture, DFA
	Varicella-zoster virus	Conjunctival/corneal swab, lesion swab	DFA, Culture
	Measles	Conjunctival/corneal swab, NP, serum	Culture, DFA, serology
Infectious mononucleosis	EB virus	Serum	Serology
	Cytomegalovirus	Blood , urine, saliva; serum	Antigenemia, culture; serology
	Adenovirus	NP swab, TS, urine	Culture, DFA
	HIV	Serum; blood	Serology; PCR
	HHV-6	Serum	Serology
Cutaneous and mucous membrane
Vesicular/ ulcerative	Herpes simplex virus	Lesion swab	DFA, Culture
	Varicella-zoster virus	Lesion swab	DFA, Culture
	Enterovirus	TS, stool, lesion swab	Culture
	Cytomegalovirus (ICH)	Lesion swab	Culture
	Adenovirus (ICH)	Lesion swab	Culture, DFA
Papillomas, papules	Papillomavirus	Biopsy	Hybridizaton, EM
	Molluscum contagiosum	Biopsy	EM (Note: clinical exam usually sufficient)
Exanthematous	Measles	NP swab or TS, urine; serum	Culture; serology
	Rubella	Serum; NP swab or TS, urine, tissue	Serology; culture (on special request)
	Enterovirus	TS, stool	Culture
	Parvovirus	Serum	Serology
	Human herpesvirus type 6	Serum	Serology
	Dengue, West Nile	Serum	Serology
	Epstein-Barr virus	Serum	Serology
	Adenovirus	NP swab or TS, urine; stool	Culture, DFA
	Cytomegalovirus	Blood, urine, saliva	Antigenemia, culture; serology
Cardiovascular
Myocarditis/ Pericarditis	Enterovirus	TS, stool,endocardial biopsy	Culture
	Cytomegalovirus	Blood, urine, endocardial biopsy	Culture, antigenemia
	Influenza	NP swab, endocardial biopsy	Culture, DFA
	Adenovirus	NP swab or TS, urine; stool	Culture, DFA
Digestive tract
Gastroenteritis	Rotavirus	Stool	ELISA , EM
	Norwalk virus	Stool, acute and convalescent serum	RT-PCR; IEM*
	Adenovirus	Stool	ELISA , EM
	Enterovirus	Stool	Culture; Nasba
Colitis	Cytomegalovirus	GI biopsy, stool;blood	Culture; antigenemia
Proctitis	Herpes simplex virus	Lesion swab, rectal swab	Culture; DFA (lesion swab only)
	Papillomavirus	Lesion biopsy	Histology; hybridization
Hepatitis	Hepatitis A	Serum	Serology
	Hepatitis B	Serum	Serology
	Hepatitis C	Serum	Serology; RT-PCR
	Hepatitis D	Serum	Serology
	Hepatitis E	Serum	Serology**
	EB virus	Serum	Serology
	Cytomegalovirus	Liver tissue, blood	Culture; antigenemia
	Adenovirus	Liver tissue	Culture
	Herpes simplex virus	Liver tissue	Culture
	Varicella-zoster virus	Liver tissue	Culture, PCR
Hematologic
Bone marrow suppression	EBV	Serum, bone marrow	Serology, PCR
	Cytomegalovirus	Blood, bone marrow	Antigenemia, culture
	Human herpes virus type 6	Serum, bone marrow	PCR, serology
	Hepatitis A, B, C	Serum	Serology
	Parvovirus B19	Serum, bone marrow	Serology, PCR
	Influenza	NP aspirate or swab	DFA, culture
	Adenovirus	Throat, stool,, bone marrow	Culture, DFA
Virus associated hemophagocytic syndrome	EBV	Serum, bone marrow	Serology, PCR
	Cytomegalovirus	Blood, bone marrow	Antigenemia, culture
	Varicella-zoster	Skin lesions, bone marrow	DFA, culture
	Herpes simplex	Skin lesions, bone marrow	DFA, culture
	Adenovirus	Throat, stool,, bone marrow	Culture, DFA
	Human herpes virus type 6	Serum, bone marrow	PCR, serology
	Parvovirus B19	Serum, bone marrow	Serology, PCR
Hemolytic anemia	EBV	Serum, bone marrow	Serology, PCR
	Cytomegalovirus	Blood, bone marrow	Antigenemia, culture
	Hepatitis B	Serum	Serology
	Measles	Serum, throat and urine	Serology, culture
	Mumps	Serum, throat and urine	Culture, serology
	Rubella	Serum, throat and urine	Serology, culture
Atypical lymphocytes	EBV	Serum, bone marrow	Serology, PCR
	Cytomegalovirus	Blood, bone marrow	Antigenemia, culture
	Hepatitis A,B,C	Serum	Serology
	Measles	Serum, throat and urine	Serology, culture
	Mumps	Serum, throat and urine	Culture, serology
	Rubella	Serum, throat and urine	Serology, culture
	Respiratory syncytial	NP aspirate or swab	DFA, culture
	Parvovirus B19	Serum	Serology, PCR
Neutrophilia	Mumps	Serum, throat and urine	Culture, serology
	Hepatitis B	Serum	Serology
	Viral hemorrhagic fevers	Serum (biosafety precautions)***	Serology, PCR
Aplastic anemia	Hepatitis C	Serum, bone marrow	Serology, PCR
Pure red cell aplasia	Parvovirus B19	Serum, bone marrow	Serology, PCR
	Hepatitis C	Serum, bone marrow	Serology, PCR
Neurologic
Encephalitis	Herpes simplex virus	CSF ; brain biopsy	PCR; culture
	Cytomegalovirus	CSF, autopsy tissue	PCR, culture, antigen
	Varicella-zoster	CSF, lesion swab	PCR, antigen
	EBV	Serum, CSF	Serology; PCR
	Arbovirus (EEE, WEE, SLE, West Nile, POW,etc)	CSF and serum	Serology; RT-PCR
	Adenovirus	CSF, TS, stool	Culture
	Measles, Rubella	NP swab, urine, serum	Serology; DFA, culture
	Mumps	CSF, urine; serum	Culture; serology
	Influenza	NP swab or TS, CSF	DFA, Culture
	Enterovirus	CSF, TS, stool (CSF, serum in neonates)	Nasba or RT-PCR; Culture
	HIV	CSF; serum	PCR; serology
	BKV	CSF; urine	Culture; PCR
	Rabies**	Brain biopsy; Skin biopsy	DFA, (for antigen)
		Saliva; serum, CSF	Culture; serology
Meningitis	Enterovirus	CSF, stool, TS (CSF, serum in neonates)	Nasba or RT-PCR; Culture
	Herpes simplex virus	CSF, lesion swab	PCR; Culture; DFA if skin lesions
	Varicella-zoster	CSF, lesion swab	PCR, DFA
	EBV	Serum, CSF	Serology; PCR
	Mumps	CSF, urine; serum	Culture; serology
	Jamestown Canyon (Arbovirus)	Serum	Serology
	Lymphocytic choriomeningitis virus (LCM)	Serum	Serology
Progressive multifocal leukoencephalopathy	Polyimavirus (JC)	CSF; Brain tissue	PCR; histopathology; EM

Abbreviations:
Specimens: NP, nasopharyngeal swab or aspirate (provides results superior to TS for respiratory pathogens); TS, throat swab; BAL, bronchoalveolar lavage; CSF, cerebrospinal fluid.

Test Methods: ELISA, enzyme linked immunosorbent assay; DFA, direct immunofluorescence assay; EM, electron microsopy; IEM, immune electron microscopy (requires mixing of immune serum with stool filtrate to aggregate virus particles); Nasba, nucleic acid sequence based amplification; RT-PCR, reverse transcriptase polymerase chain reaction

Please Note:
Acute and convalescent serum should be collected for antibody studies. However, serologic testing is not practical for enteroviruses, rhinoviruses and papovaviruses.

*For Hantavirus diagnosis, serum samples and required form are sent to the State Laboratory. Samples for PCR are sent to the CDC.
**Rabies testing is done at the State Laboratory or CDC; call the Virology Laboratory for details.
***Notify Health Department and CDC.

IV. INTERPRETATION OF TEST RESULTS
(Back to Table of Contents)

VIRUS ISOLATION

Please Note: Please Note: Clinical information and/or virus suspected are needed to select proper culture systems.
EBV is diagnosed by serology, NOT culture.

Viruses routinely isolated in cell culture	Special request required	Interpretation of positive culture
Adenovirus, cytomegalovirus, enteroviruses, herpes simplex, influenza A and B, parainfluenza types 1-4, rhinoviruses, RSV, varicella-zoster virus	Arboviruses, BK virus, measles, mumps, rubella	Varies with virus, specimen source and clinical setting. For example, latent viruses an reactivate with or without symptoms (e.g. CMV, HSV, adenovirus). Isolation of other viruses occurs only with acute infection e.g. measles, influenza).

VIRAL ANTIGEN

Virus	Sample	Test	Sensitivity* / specificity	Interpretation of positive result
CMV antigenemia	Blood leukocytes Collection times must be provided! For quantitative results, sample must be processed within 6 hrs of collection.	DFA	95% / > 99%	No. positive cells per 300,000 leukocytes examined < 10 Low positive > 50 High positive High positive results are more likely associated with clinical disease. However, clinical information and patient risk factors must be considered in interpreting test results. A low positive in a high risk patient or a non-immunosuppressed host may be associated with disease. A negative blood antigenemia test result does not exclude CMV end-organ infection.
Influenza**	NP aspirate or swab	DFA	>95%/ 99%	Acute infection; detects type A and B
RSV**	NP aspirate or swab	DFA	99%/ > 99%	Acute infection; can remain positive longer than culture
Adenovirus**	NP aspirate or swab, eye swab	DFA	60%/ 99%	Acute infection; culture more sensitive for adenovirus
Para 1-3**	NP aspirate or swab	DFA	>90%/ 99%	Acute infection; parainfluenza type 4 not included
Rotavirus	Stool	EIA	>99%/ 98%	Acute infection; false positives reported in neonates; detects group A only
VZV	Skin lesions	DFA	95%/ > 99%	Active infection
HSV	Skin lesions	DFA	95%/ > 99%	Active infection. Use culture to detect asymptomatic shedding.
	Mucosal lesions	DFA	80%/ > 99%	DFA only 80% sensitive for mucosal lesions (mouth, vulva, eye) Use culture to detect asymptomatic shedding.

NP = nasopharynx, IF = immunofluorescence, EIA = enzyme immunoassay
*Sensitivity compared with culture of the same sample. If sample poorly collected or collected late in illness, results of all tests will be poor.
**Order Respiratory Screen DFA (Influenza A and B, RSV, parainfluenza types 1-3 and adenovirus included)

CLOSTRIDIUM DIFFICILE TOXIN

Method	Toxin detected	Results	Interpretation
Cytotoxicity in cell culture, followed by neutralization with specific antitoxin	Toxin B (cytotoxin)	Negative Positive titer 1:10 to > 1:10,000	Toxin not present. Toxin present; titer correlates in general with severity of disease

VIRAL ANTIBODY

Please note: Administration of blood products or immunoglobulin may result in passive transfer of antibody and transiently positive antibody test results. False negative antibody results may occur in immunocompromised hosts or agammaglobulinemic patients.

IMMUNE STATUS TESTING

Sensitivity and sepcificity of these assays ranges from 97-99% in various studies

Virus	Method	Result	Interpretation
Cytomegalovirus, Herpes simplex, Measles, Rubella, Varicella-zoster(a)	EIA or latex agglutination(a)	Negative	No antibody detected
		Positive	Antibody present
		Equivocal	Non-specific reaction or low level antibody. Submit second sample.

a) Note: VZV vaccine-induced antibody may only be detected by latex agglutination; must be specified when ordering

DIAGNOSIS OF ACUTE INFECTION

Virus	Method	Result		Interpretation
Cytomegalov