Guide to Viral Diagnosis05.09.pdf | Infection | Public Health


Department of Laboratory Medicine, Yale New Haven Hospital
Director: Marie L. Landry, M.D. (beeper 1-888-631-0112) Laboratory Manager: David Ferguson, M.T., A.S.C.P. (beeper 412-0981) Location: CB 521 (across from the Chemistry Laboratory) Phone number: 688-3524 Standard Hours of Operation: Mon-Fri 7:00 a.m.-to 8:30 p.m.; Sat and Sun 8:00 a.m.-4:30 p.m. During Winter Respiratory Season (December-March), extended hours are in effect. Call Laboratory for schedule. TABLE OF CONTENTS 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 NOTE: SPECIMENS THAT ARE NOT LABELLED WILL BE REJECTED A. Test ordering For HIV antibody testing, the test request (via computer or paper requisition) must indicate that consent was obtained, or the laboratory cannot do the test. This is CT State Law. When ordering cultures, provide clinical information and/or virus suspected so that the laboratory can select the proper test systems. B. Viral antibody studies For immune status testing, a single serum sample is sufficient. PLEASE NOTE: During acute infection, virus is present but antibody is often negative. To detect acute infection, both acute and convalescent sera are generally required to detect an antibody rise or a seroconversion. Virus infections whose clinical symptoms are immune-mediated are exceptions (e.g. EBV, HBV, parvovirus B19). Reactivation of latent or persistent viruses may or may not be associated with rise in IgM and/or IgG. C. Specimen collection All containers that are not labeled will be rejected. Collect specimens for culture, PCR or antigen early in illness when viral shedding is maximal. Updated 5/09 PAGES 1-2

Clinical Virology Laboratory

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Unroof vesicles or remove crusts. For infants and small children NP aspirate preferred. Nasopharynx aspirate Use suction pump connected to a catheter through a mucus trap. Sample must be processed within 4-6 hrs of collection. tongue or palate. Small wire shaft swab for urethral samples NP aspirate Body fluids. remove and place in transport medium. do not dilute sample with saline unless necessary. Throat swabs are suboptimal for DFA testing due to predominance of squamous instead of respiratory epithelial cells obtained. Lesion swab Rectal swab . Collect as much of NP secretions as possible. catheter should be French gauge 8 for infants. After sample collection. Specimen collection instructions for selected specimens Nasopharynx swab Insert large swab into nasopharynx.2 Sample Collection device* Virus isolation. Throat swab Swab posterior pharyngeal wall. lesion. BAL. swab of rectal mucosa can be done for proctitis. Stool specimen required for enteric pathogens. Specimen should be taken from posterior part of nasopharyngeal mucosa which is lined with respiratory epithelium. PCR or antigen test: Swabs Use viral transport medium Large swabs for NP. etc. Refrigerate Refrigerate Blood (leukocytes or plasma) Viral antibody test: Blood (serum) Room temperature Room temperature D. and not from anterior part which is lined with squamous epithelium. Firmly swab base and margins of the lesion. Gently rub nasal turbinate or rotate to dislodge respiratory epithelial cells. Insert catheter as far into nose as possible. obtaining fluid and cells. Do not use disinfectant prior to sample collection or virus may be inactivated.* (Stockroom #108145) Do not dilute body fluids or BAL in transport medium. tonsils. Viral transport medium can be obtained from hospital storeroom. just past point of resistance. Swab firmly and thoroughly. stool Tissues Use sterile trap Use sterile leakproof containers Place in tubes containing liquid viral transport media to keep tissue moist Collect 2 lavender top tubes Collection time required Collect 1 red top tube Holding temperature Refrigerate Comments Viral transport medium with swabs can be obtained from hospital storeroom. Clean lesion with sterile saline soaked gauze pad. clean lesion thoroughly with betadine. throat. not buccal mucosa. French gauge 12 for adults.

Virus isolation Human CoV OC43.cdc. tubulointerstitial nephritis. West Note: Acute and convalescent antibody most sensitive test Not offered outside research setting at present Days to weeks Plasma. call laboratory. Encephalitis/ meningitis form must be filled out for State. Jamestown Canyon. Virus isolation PCR. Plasma levels of >10. Brain biopsy Urine PCR. febrile illness in summertime Note: Different arboviruses are prevalent in other parts of the world. For most recent CDC recommendations. WEE. acute and convalescent Tests Virus isolation or PCR Special instructions and comments Virus isolation can detect the “unexpected”. paralytic disease. NL 63. epidemiologic risk factors must be present. pneumonia. diarrhea. ARDS Gastroenteritis Encephalitis. pneumonia. hepatitis.000 copies/ml associated with risk of nephropathy Sent to State Laboratory. BAL. to monitor renal transplants Deep respiratory samples. quantitative RT-PCR Virus isolation (BSL3) Throat swab eye swab. PCR is more sensitive and more rapid DFA detects only 60% of culture positives Viral load in plasma can be monitored Time to result 1-14 days Immunostain (DFA) 2 hrs Quantitative PCR PCR IgM and IgG antibody in CSF and serum 1-3 days 1-3 days WNV done in-house. Note: Mutations can lead to falsely 1-3 days low or negative results. eye swab Plasma (lavender) Stool CSF Serum (red top). stool AND Paired sera collected early and at >28 days Coronavirus SARS CoV Antibody RT-PCR. intussusception. POW) See also Dengue BK virus (Polyomavirus) Hemorrhagic cystitis in bone marrow transplants. see www.41 Arboviruses (EEE. cough. WNV IgM positives and all other arbovirus requests sent to State Lab. VIROLOGY TEST SELECTION ORGANIZED BY VIRUS Virus suspected Clinical symptoms Specimens Adenovirus types 1-51 URI. keratoconjunctivitis. pharyngitis. gastroenteritis. URI.3 II. Travel history is key. CSF. LaCrosse. hemorrhagic cystitis. conjunctivitis. Early samples can be falsely negative. 229E. needs approval. HKU1 Common cold viruses NP swab or aspirate . 2-21 days WNV IgM positives confirmed by State Lab Special arrangements may be Variable possible. ureteral stenosis post kidney transplant. tonsilitis SARS CoV: fever. tissue. urine. Cross-reactions can give false positives. Louis encephalitis. aseptic meningitis. dyspnea. genital infections Disseminated (severely compromised host) Enteric adenovirus types 40. qualitative or quantitative PCR. stool NP aspirate or swab. St.

Positives after 3 wks can reflect perinatal infection.4 Virus suspected Cytomegalovirus (CMV) Clinical symptoms Fever. do NOT use to follow seropositive patients. skin vesicle swab. Serum sent to State Laboratory. hepatitis. collection times required. myocarditis. virus isolation done at CDC Collect stool. myalgias. for best results Note: Diagnosis by antibody titer is not practical or reliable. neurologic syndromes Specimens BAL. encephalitis. pneumonia. herpangina. stool. Genome copy numbers >>> than number CMV–positive leukocytes. paralytic disease Neonatal “sepsis” Serum Throat swab. CSF and urine . pleurodynia Aseptic meningitis. Time to result 1-21 days 1-3 days Blood samples must be processed 2-24 hrs within 6 hrs of collection. rash. 1-3 days Blood (red top).2 days Blood. urine. mononucleosis. hand-foot-mouth disease. Antibody mainly useful to confirm primary infection or to determine immune status. hemorrhagic fever Summer rashes. biopsy tissue CSF (1-2 mL) Antibody Virus isolation Virus isolation or PCR (coxsackie A viruses may not grow in routine cell cultures) RT-PCR (Virus isolation can be used as back-up) RT-PCR 7-14 days 1-14 days 7 hrs -2 days 7 hrs. Note: CMV in blood can contaminate CSF and give positive PCR To diagnose congenital infection urine must be obtained within 3 wks of birth. esophageal and gastrointestinal ulcerations. acute and convalescent Encephalitis Congenital CMV CSF (1-2 ml) PCR 1-3 days 1-21 days Urine collected at birth Virus isolation Dengue Enterovirus Fever. saliva Viral load options: a) Plasma (lavender tube) b) Blood leukocytes (2 lavender tubes) Tests Virus isolation Order culture if drug resistance suspected Quantitative PCR Replaced antigenemia as main test June 2009 CMV antigenemia Performed as special request Antibody (IgM and/or IgG) Special instructions and comments Both conventional culture and rapid centrifugation culture (1-3 day turnaround) are performed Plasma PCR viral load still valid if leukopenia or delayed processing. not rectal swab. parechovirus and cardiovirus are not detected. Preferred test for CSF. tissue biopsies. however. oral. leukopenia.

chronic hepatitis or hepatitis B virus panels Quantitation of HBV DNA should be done prior to therapy and to monitor response 2-7 days 1-4 days Biopsy tissues Hepatitis A Acute hepatitis. VCA IgM. and EBNA antibodies Special instructions and comments Positive in 90% of adults and <50% of children with I. anti-HBs. must be filled out. relapsing hepatitis Blood (red top) Virus isolation and PCR Antibody (anti-HAV IgM) Antibody (anti-HAV total) HBsAg. Greg Howe (ext. neurologic syndromes. EDTA blood-PBMC Blood (red top) Nucleic acid hybridization or quantitative PCR EBV antibody panel and VCA IgA antibody Note: EBV in lymphocytes can 1-3 days give positive CSF PCR in absence of EBV-associated disease By special arrangement with Dr. Elevated VCA IgA antibody useful in early NPC detection and monitoring for recurrence 7 days 3-7 days Lymphoproliferative disease (PTLD) Nasopharyngeal carcinoma (NPC) Hantavirus Pulmonary Syndrome (HPS) Pneumonia.M. tissue Biopsy tissue. Sent to CDC via State Health Dept Weeks to months Order only in cases of acute 1-3 days infectious hepatitis Specify "immune status" Can be ordered as single tests. 74237) EBV VCA IgA available by special request (sent out). polyarteritis nodosa Blood (red top) 7-10 days . anti-HBc total and IgM. chronic Blood (red top) hepatitis.) Also hepatitis. thrombocytopenia. pneumonitis. 3-7 days available in the virology laboratory. Request if heterophile antibody is negative or if unusual clinical presentation Time to result 1 day 3-7 days CSF (CNS lymphoma) PCR plasma. for travelers to HAV endemic areas Acute hepatitis. hepatocellular carcinoma. as part of acute hepatitis. hemolytic anemia. hemophagocytic syndrome Specimens Blood (red top) Blood (red top) Tests Heterophile antibody (monospot) EBV antibody panel: VCA IgG.5 Virus suspected Epstein-Barr virus (EBV) Clinical symptoms Infectious mononucleosis (I.M. form. cirrhosis. ARDS in previously healthy individual Blood (red top) Antibody Sent to State Health Dept. HBeAg and anti-HBe PCR Hepatitis B See test interpretation on page 16 Immune status.

joint pain. cirrhosis. if DFA positive. BAL. IgG) Virus isolation 1 week 7 days Hepatitis E Herpes simplex virus (HSV) types 1 and 2 Lesion swab. and at recommended time points to monitor response Used to guide therapy Patient must be HBsAg positive to be infected with HDV. Tests sent out. cholestasis. skin lesions. routine for all lesion swabs. gingivostomatitis. chronic Blood (red top) hepatitis. mucosal swab. porphyria Specimens Blood (red top) Tests Antibody (anti-HCV EIA) Antibody (anti-HCV RIBA) Special instructions and comments Can be ordered as a single test. 1-2 weeks 3-7 days HCV RNA (RT-PCR) Hepatitis D (Delta) Acute hepatitis. retinitis CSF (1-2 mL). esophagitis. Rarely detectable in serum. Test sent out. 17 Clinical symptoms Acute hepatitis. blood. genital lesions. hepatitis. biopsy tissue. proctitis. and asymptomatic shedding. recurrent meningitis. BAL. Must have adequate cells for valid result. with pruritus. hepatocellular carcinoma. chronic hepatitis. pneumonia Blood (red top) HCV genotype Antibody (anti-HDV or anti-Delta) Delta antigen Antibody (anti-HEV IgM. HCV RNA test should be used to confirm high positive EIA results instead of RIBA. as part of acute hepatitis or chronic hepatitis panels Time to result 1-3 days HCV RIBA is reflexively performed 2-7 days only for samples with low-positive EIA values. deterioration of chronic HBsAg carrier Acute hepatitis. neonatal HSV. BAL Lesion swab.6 Virus suspected Hepatitis C See test interpretation on pages 16. fulminant hepatitis. Quantitation of HCV RNA should be done when therapy is initiated. culture or PCR not done Viral load can be done in disseminated HSV Immune status (carrier state) HSV-2 carrier state 1-7 days HSV/VZV DFA 2 hrs Encephalitis. essential mixed cryoglobulinemia. meningitis. RIBA or PCR is done only if requested. tissue (touch prep) PCR can also be used for tissues. If EIA value is high. ocular fluid Serum PCR Type-common antibody HSV2-specific antibody 1-2 days 1-7 days 7 days . 20% mortality in pregnant women Cold sore.

please notify laboratory Clinical symptoms Specimens Tests Antibody (EIA) Rapid HIV-1/2 antibody HIV-1 Western blot To guide antiretroviral therapy To diagnose HIV infection in antibody-negative window when viral load is high To diagnose infection in neonates Roseola infantum. pneumonitis. endotracheal aspirate. URI. endotracheal aspirate. Time to result 1 day 30 min Done once a week 2-5 days No symptoms. encephalitis in HSCT To confirm primary infection URI. requires BSL3 safety precautions. myopericarditis. plasma Whole blood (2 lavender top tubes) Quantitative plasma RNA by RT-PCR (Roche TaqMan) Resistance genotype Human herpesvirus type 6 (HHV-6) DNA PCR PCR (quantify plasma) Requires 1. wash. hepatitis. failure to thrive Plasma (lavender) allows faster result 2-4 weeks HIV-1 DNA detected in PBMCs 2-14 days Some patients have stable high 1-3 days levels of HHV-6 DNA in blood. mononucleosis. early 1-3 days spring). neurologic disease Nasopharynx (NP) swab. human T cell leukemia/lymphoma Blood (2 lavender) Influenza A. HIV-2 sent out. ARDS. IgM and IgG HMPV DFA RT-PCR if hospitalized Antibody (EIA screen. throat swab (not NP swab) PCR useful if antibody tests are 7-14 days indeterminate (sent out) Respiratory screen DFA Sufficient respiratory epithelial 2 hrs cells required (NP >>> throat) Virus isolation or PCR if For best results. initial tests may be negative.7 Virus suspected Human immunodeficiency virus (HIV) types 1 and 2 If HIV-2 suspected. pneumonia. brnochiolitis Whole blood (2 lavender top) CSF. bronchiolitis in infants. repeat testing needed 1-3 days 4-24 hrs H1N1 (swine) Avian influenza (H5N1) . collect specimens hospitalized DFA-negative within first 48 hrs of illness 1-14 days Request Subtype by PCR for novel viruses H5N1-specific RT-PCR Subtype also for drug resistance Notify lab. serology is rarely helpful HHV-6 antibody tests sent out 1-2 wks Consider if respiratory screen DFA 2 hrs negative (peak late winter. swab.000 HIV copies/mL Special instructions and comments Note: All HIV tests require documentation of consent. B Influenza syndrome. BAL Same as above BAL. submit separate sample EIA done in-house. diarrhea. infectious mono. BAL Antibody. pneumonia. Serum (red top) acute retrovirus syndrome. does not distinguish HTLV-I from II Western blot (sent out) 2-7 days 7-10 days Human metapneumovirus HTLV I/II Blood (red top) NP aspirate. all positives need confirmation by Western blot) PCR on PBMCs Tropical spastic paraparesis or Blood (red top) HTLV associated myelopathy. due to universal infection by age 2. bronchitis. febrile seizures. AIDS. or aspirate. myositis Influenza syndrome Pneumonia. Call lab to facilitate rapid result All positives require Western blot confirmation.

infection may be persistent. urine Tests PCR Histopathology. BAL. requires special testplease notify the laboratory prior to sample collection IgM sent out Requires special test. chronic anemia in compromised hosts. especially in compromised hosts Done in Hematology 1-7 days 3-14 days 3-7 days 1-3 days Blood (red top). encephalitis. common source outbreaks (food. aplastic crisis. meningitis.8 Virus suspected JC virus (Polyomavirus) Measles Clinical symptoms Progressive mulitfocal leukoencephalopathy (PML) Coryza. rash. croup. giant cell pneumonia or respiratory symptoms without rash in compromised hosts. bone marrow. samples should be collected early in illness for best results Tests only available for genital HPV Sent to Yale Pathology Lab DFA for types 1-3 only Can detect type 4 Immunocompromised hosts may not develop antibody PCR can be positive for months after infection. acute and convalescent Saliva. NP swab. IgG and IgM PCR 2 hrs 3-14 days 3-7 days 1-3 days Bone marrow Bone marrow examination 2 days . atypical measles in previously immunized Parotitis. EM to detect viral particles Virus isolation Special instructions and comments False negative PCRs can occur Sent to Pathology Time to result 1-3 days 4-14 days Samples must be collected early 2-14 days in disease. nonimmune hydrops fetalis Respiratory screen DFA Virus isolation Antibody. orchitis. CSF. IgM and IgG Virus isolation Antibody RT-PCR (detects genogroups I and II) Mumps Norovirus Papillomavirus (over 70 types) Parainfluenza types 1-4 Parvovirus B19 Cervical swab or biopsy NP swab or aspirate. acute and convalescent Stool collected within 48 hrs of onset of symptoms Antibody. please notify the laboratory IgM sent out Genetic variation in virus strains can lead to falsely negative results. urine Blood (red top). encephalitis Gastroenteritis. penumonia Erythema infectiosum (fifth disease). contaminated water or ice) Warts. bronchitis. cervical dysplasia Specimens CSF Brain biopsy Throat swab. various exanthems and enanthems. amniotic fluid Hybridization 7 days URI. conjunctivitis. Koplik's spots. shellfish. lung tissue Blood (red top) Serum. tracheal aspirate. arthralgias.

half of rabies cases report no history of animal bite. antigen test is more sensitive for skin lesions than culture if sample is properly collected. lower tract disease in infants. call lab IgG done in-house. retinal necrosis EM or PCR Blood (red top). skin biopsy from nape of neck (to include hair follicles). postauricular adenopathy. Bats are main source in U.cdc. acute Antibody and convalescent Tissue. corneal scrapings . neurologic syndromes. saliva Blood (red top) and CSF NP aspirate or NP swab. lung tissue NP swab or aspirate. IgG Collect serum promptly after (specify if post-vaccination exposure to determine immune test) status . DFA fastest (2 hrs). ocular fluid Notify laboratory immediately if Blood (red top) exposure (health care worker or VZIG candidate) DFA. herpes zoster.notify laboratory Special request.S. PCR or virus isolation PCR 1-14 days 1-3 days 1-14 days Antibody.9 Virus suspected Rabies Clinical symptoms Clinical rabies.htm) Time to result 2-14 days Respiratory syncytial virus Rhinovirus Rotavirus groups A. cases. B URI. BAL Tests Rabies antigen (immunostain of tissue) RT-PCR. pneumonia. please notify laboratory Need vigorous swab of lesion to dislodge cells for examination. culture Antibody Respiratory screen DFA RT-PCR if hospitalized Virus isolation RT-PCR if hospitalized Virus isolation Rotavirus antigen (ELISA) Note: Serum test invalid if rabies immune globulin has been given Need adequate respiratory epithelial cells or test invalid.. diarrhea in adults (group B) Rubella Rubelliform rash. arthralgias. ICH Infantile gastroenteritis (group Stool A). IgM sent out if rubella high Professional/professi. BAL. pneumonia. Bronchiolitis. COPD. NP aspirate gives best results RT-PCR and DFA >> RSV culture RT-PCR much more sensitive than culture ELISA detects only group A and may yield false positive results in neonates Special request. congenital rubella syndrome Chicken pox. throat swab and urine Skin lesion swabs Virus isolation HSV/VZV DFA 1-2 wks 3-7 days 3-14 days 2 hrs Varicella-zoster virus (VZV) BAL. rapidly progressive encephalitis Note: In U.S. tissues CSF (1-2 ml). asthma. PCR is more sensitive 7-14 days 2 hrs 1-3 days 3-14 days 1-2 days 3-14 days 4 hrs Special instructions and comments Sent to CDC Rabies Lab (www. ascending paralysis. URI Specimens Brain biopsy.

lung tissue. RT-PCR EB virus Serum Serology Pleurodynia Enterovirus TS. lesion swab Culture. Culture SARS CoV* Deep respiratory sample. RT-PCR retinitis Adenovirus Conjunctival/ corneal swab. serology Infectious EB virus Serum Serology mononucleosis Cytomegalovirus Blood. PCR . RT-PCR Parainfluenza NP aspirate or swab. blood Culture. saliva. Culture Herpes simplex BAL. paired sera Serology. blood Culture. Specimens to Collect and Diagnostic Test of Choice Clinical Syndrome Viruses associated Specimens to collect Test method of choice Respiratory Influenza A. Culture Human metapneumovirus NP aspirate or swab. BAL. Culture Cytomegalovirus BAL. BAL. PCR Varicella-zoster virus Conjunctival/ corneal swab. ocular fluid Culture. Culture Rhinovirus NP aspirate or swab. lung tissue RT-PCR. RT-PCR. PCR Adenovirus (ICH) Lesion swab. Culture Hantavirus* Lung tissue. DFA. Culture Respiratory syncytial virus NP aspirate or swab DFA. NP swab Culture Ocular Conjunctivitis/ keratitis/ Enterovirus Conjunctival/ corneal swab. lesion swab Culture Measles Conjunctival/ corneal swab. lung tissue DFA. lung tissue DFA. Culture Enterovirus TS. stool Culture. TS.B NP aspirate or swab Culture. PCR Cytomegalovirus Ocular fluid PCR Vaccinia Conjunctival/ corneal swab. Culture. Culture Varicella-zoster virus Lesion swab DFA. Culture.10 III. lung tissue DFA. throat. DFA. Culture Adenovirus NP aspirate or swab DFA. serum Serology. BAL. PCR. lung tissue DFA. stool. DFA. PCR Cutaneous and mucous membrane Vesicular/ ulcerative Herpes simplex virus Lesion swab DFA. CLINICAL SYNDROMES: Most Commonly Associated Viruses. PCR. RT-PCR. TS Culture. PCR. Culture Influenza A. RT-PCR Vaccinia Lesion swab Culture Cytomegalovirus (ICH) Lesion swab. serum PCR. ocular fluid DFA. Respiratory syncytial virus NP aspirate or swab. stool. NP Culture. serology Adenovirus NP swab. PCR HHV-6 Serum Serology. B NP aspirate or swab. blood Serology. Culture URI/pharyngitis Rhinovirus NP aspirate or swab RT-PCR. PCR. BAL. Culture Pneumonia Adenovirus NP aspirate or swab. RT-PCR. urine. PCR Herpes simplex virus Conjunctival/ corneal swab. BAL. lung tissue DFA. NP. PCR Parainfluenza NP aspirate or swab DFA. RT-PCR Enterovirus Throat and/or NP swab Culture. PCR HIV Serum. PCR (blood) Varicella-zoster BAL. DFA. DFA. BAL. lung tissue DFA. urine Culture. RT-PCR. lung tissue DFA. DFA. Culture. serum Culture.

culture (special request) Culture. blood Liver tissue Liver tissue Test method of choice Hybridizaton. serology RT-PCR. Culture. PCR RT-PCR PCR Culture. PCR Culture. West Nile Epstein-Barr virus Adenovirus Cytomegalovirus Cardiovascular Myocarditis/ Pericarditis Enterovirus Cytomegalovirus Influenza Adenovirus Rotavirus Norovirus Adenovirus Enterovirus Cytomegalovirus Herpes simplex virus Papillomavirus Hepatitis A Hepatitis B Hepatitis C Hepatitis D Hepatitis E EB virus Cytomegalovirus Adenovirus Herpes simplex virus Specimens to collect Biopsy Biopsy NP swab or TS. NP swab or TS. RT-PCR Serology Serology Serology. Culture Exanthematous Digestive tract Gastroenteritis Colitis Proctitis Hepatitis . endocardial biopsy NP swab. endocardial biopsy Blood.11 Clinical Syndrome Papillomas. stool. DFA. Culture Culture. urine. stool Serum Serum Serum Serum NP swab or TS. endocardial biopsy NP swab or TS. urine. stool Stool Stool Stool Stool GI biopsy. stool Blood. rectal swab Lesion biopsy Serum Serum Serum Serum Serum Serum Liver tissue. urine. serology Serology. PCR in special cases Serology. Culture PCR. DFA. urine. blood Lesion swab. serum Serum. PCR PCR. RT-PCR Culture. saliva TS. PCR ELISA. urine. PCR Serology Serology Serology Culture. PCR PCR. RT-PCR Culture. tissue TS. stool. PCR PCR (blood). papules Viruses associated Papillomavirus Molluscum contagiosum Measles Rubella Enterovirus Parvovirus B19 Human herpesvirus type 6 Dengue. urine. RT-PCR Serology. EM EM (Note: Clinical diagnosis usually sufficient) Culture. DFA. hybridization Serology Serology. DFA. DFA (lesion swab only) Histology. Culture Culture. DFA.

throat and urine Serum Serum (biosafety precautions)** Serum. culture DFA. throat and urine NP aspirate or swab Serum Serum. culture PCR. serology Serology. culture Culture. PCR Serology. culture Serology. PCR PCR. PCR Serology. B. bone marrow Serum. throat and urine Serum. culture DFA. bone marrow Blood. Culture. culture Culture.12 Clinical Syndrome Hematologic Bone marrow suppression Viruses associated EBV Cytomegalovirus Human herpesvirus type 6 Hepatitis A. throat and urine Serum. bone marrow Serum. plasma Serum. B. PCR Virus associated hemophagocytic syndrome Hemolytic anemia Atypical lymphocytes Neutrophilia Aplastic anemia Pure red cell aplasia . bone marrow Serum. bone marrow Throat. PCR. bone marrow Serum Serum. throat and urine Serum. bone marrow Serum. PCR Serology. PCR PCR. throat and urine Serum. culture PCR. stool. serology Serology. serology Serology Serology. PCR DFA. bone marrow Serum. bone marrow Skin lesions. stool. PCR. culture. C Parvovirus B19 Influenza Adenovirus HIV EBV Cytomegalovirus Varicella-zoster Herpes simplex Adenovirus Human herpesvirus type 6 Parvovirus B19 EBV Cytomegalovirus Hepatitis B Measles Mumps Rubella EBV Cytomegalovirus Hepatitis A. culture Culture. DFA PCR. RT-PCR Serology. DFA. throat and urine Serum. bone marrow Serum. serology Serology. culture DFA. bone marrow Blood. plasma Serum. PCR PCR. PCR Serology. bone marrow Serum. bone marrow Skin lesions. bone marrow NP aspirate or swab Throat. RT-PCR Culture. bone marrow Blood. culture Serology. C Measles Mumps Rubella Respiratory syncytial Parvovirus B19 HIV Mumps Hepatitis B Viral hemorrhagic fevers** Hepatitis C Parvovirus B19 Hepatitis C Specimens to collect Serum. bone marrow Blood. PCR PCR. bone marrow Test method of choice Serology. culture Serology Serology. PCR Serology. serology Serology. bone marrow Serum Serum. EM (BSL 3 or 4) Serology. PCR Serology. bone marrow Serum Serum. culture Serology Serology. blood.

serum. PCR (sent out) Serology Serology PCR. serum NP swab or TS. stool (CSF. urine. culture Serology. DFA Serology. throat swab. lesion swab Serum. serology PCR. papillomaviruses. serology Serology.13 Clinical Syndrome Neurologic Encephalitis Viruses associated Herpes simplex virus type 1>>2. BAL. reverse transcriptase polymerase chain reaction Please Note: Acute and convalescent serum should be collected for antibody studies. serology DFA. Culture. West Nile. CSF CSF. electron microsopy. TS. enzyme linked immunosorbent assay. Culture. DFA. histopathology. PCR Serology. DFA. CSF CSF. TS (CSF. urine CSF Brain biopsy. Test Methods: ELISA. Culture PCR. nasopharyngeal swab or aspirate (provides results superior to TS for respiratory viruses). CSF CSF and serum CSF. Skin biopsy Saliva. EM. RT-PCR RT-PCR. lesion swab Serum. SLE. Brain tissue Test method of choice PCR. EM Meningitis Progressive multifocal leukoencephalopathy Abbreviations: Specimens: NP. Jamestown Canyon* Lymphocytic choriomeningitis virus (LCMV) Polyomavirus (JC) Specimens to collect CSF. DFA Serology. (for antigen). lesion swab CSF. serum in neonates) CSF. call the Virology Laboratory for details and to fill out required forms **Notify Health Department and CDC. etc)* Adenovirus Measles. except neonatal HSV type 2> 1 Cytomegalovirus Varicella-zoster EBV Arbovirus (EEE. RT-PCR PCR. stool NP swab. Serologic testing is not practical for enteroviruses. DFA if skin lesions PCR. Rubella Mumps Influenza Enterovirus HIV BKV HHV-6 Rabies* LCMV (transplant) Enterovirus. serum in neonates) CSF. culture Culture. serum CSF. TS. serology. CSF Serum . serum CSF. polymerase chain reaction’ RT-PCR. Culture PCR. blood CSF. urine. PCR RT-PCR. PCR Culture. brain biopsy CSF. RT-PCR RT-PCR. Culture PCR DFA. bronchoalveolar lavage. serology Culture. urine. CSF Plasma. * Testing is done at the State Laboratory and/or CDC. WEE. culture PCR. autopsy tissue CSF. rhinoviruses. cerebrospinal fluid. direct fluorescence assay. . parechovirus Herpes simplex virus type 2>> 1 Varicella-zoster EBV HIV (acute infection) Mumps WNV. DFA. stool. POW. CSF CSF. CSF. Serum Serum. and polyomaviruses. TS. serum CSF. CSF CSF. PCR. culture PCR PCR.

parainfluenza types 1-4. DNA copies/ml are MUCH higher. parainfluenza type 4 not included HMPV NP aspirate or swab DFA >85%/ 99% Acute infection Rotavirus Stool EIA >99%/ 98% Acute infection. adenovirus). of collection. NOT culture. herpes simplex. Isolation of other viruses occurs only with acute infection (e. varicellazoster virus Arboviruses. A negative blood antigenemia test result does not be provided! exclude CMV end-organ infection. Note: HMPV DFA is separate test. CMV.000-2. latent viruses can reactivate with or without symptoms (e.000 DNA copies/ml plasma 50 antigen positive cells = 5.000-10. enteroviruses. cytomegalovirus. DFA 60%/ 99% Acute infection. A low positive in a high risk patient or a non-immunosuppressed host may Collection times must be associated with disease. However. eye) Mucosal lesions 80%/ >99% Use culture to detect asymptomatic shedding. YNHH transitioned from antigenemia to PCR as the main viral load test. influenza). . detects types A and B RSV** NP aspirate or swab DFA 99%/ >99% Acute infection. For example. can remain positive longer than culture Adenovirus** NP aspirate or swab. BK virus.000 for bone marrow/stem cell transplant. results of all tests will be poor.000 leukocytes examined Antigenemia <10 Low positive For quantitative results. INTERPRETATION OF TEST RESULTS VIRUS ISOLATION Clinical information and/or virus suspected are needed to select proper culture systems. The relationship between CMV antigen-positive neutrophils and genome copies free in plasma is inconsistent. to 10.g. CMV VIRAL LOAD by real-time TaqMan PCR In June 2009. DFA only 80% sensitive for mucosal lesions (mouth. HSV. *Sensitivity compared with culture (or PCR for HMPV) of the same sample. If sample poorly collected or collected late in illness. RSV. vaccinia. vulva. Significant DNA copy numbers can vary from 1. measles.g. clinical information and patient risk factors must be considered in interpreting test results. measles. Rapidly rising titers may be more predictive of disease than a single point in time.000 for low risk transplant or HIV+ patients. >50 High positive Requires sample must be special request processed within 6 hrs High positive results are more likely associated with clinical disease. to 4. EBV is diagnosed by serology. rubella Varies with virus. parainfluenza types 1-3 and adenovirus included). Treatment varies with risk factors. RSV. NP = nasopharynx DFA= direct fluorescent antibody (immunostain) EIA= enzyme immunoassay **Order Respiratory Screen DFA (Influenza A and B. influenza A and B. It is important that patients are not over-treated due to misinterpretation of results. culture more sensitive for adenovirus eye swab Paraflu 1-3** NP aspirate or swab DFA >90%/ 99% Acute infection. false positives reported in neonates. Viruses isolated in routine cell cultures Special request required Interpretation of positive culture Please Note: Adenovirus. Greatly simplified correlation: 0-1 antigen positive cell = 100-200 DNA copies/ml plasma 10 antigen positive cells = 1. rhinoviruses.000 DNA copies/ml plasma VIRAL ANTIGEN Virus Sample Test Sensitivity*/ Interpretation of positive result specificity CMV Blood leukocytes DFA 95%/ >99% No. positive cells per 300. specimen source and clinical setting. detects group A only VZV Skin lesions DFA 95%/ >99% Active infection HSV Skin lesions DFA 95%/ >99% Active infection.14 IV. Influenza** NP aspirate or swab DFA >95%/ 99% Acute infection.000 for D+/Rsolid organ transplant. mumps.

To link EBV serologic reactivation with clinical disease requires tissue EBV PCR or hybrdization. Submit second sample. Rubella. IF POSITIVE DO CYTOTOXIN For Bacterial Antigen Positives: Toxin detected Result Interpretation Cytotoxicity in cell culture. Positive Toxin present.15 CLOSTRIDIUM DIFFICILE BACTERIAL GDH ANTIGEN SCREEN by ELISA. Herpes EIA or latex Negative -No antibody detected a simplex. or false positive Past infection with flavivirus. positive IgM make take 8 days Parvovirus West Nile Virus EIA EIA PATTERNS OF EBV-SPECIFIC ANTIBODY RESULTS AT DIFFERENT STAGES OF INFECTION: b Antibody to EBV antigens: Uninfected Primary Past Reactivation Viral capsid antigen (VCA)-IgG ++ ++ +a Viral capsid antigen (VCA)-IgM + + or Epstein-Barr nuclear antigen (EBNA) + + a. must be specified when ordering DIAGNOSIS OF ACUTE INFECTION Virus Method Cytomegalovirus EIA IgG Result + + + or – + . If neutralization with specific antitoxin patient severely ill. High titers to EBV VCA IgG may persist for years after primary infection in healthy individuals. IMMUNE STATUS TESTING Sensitivity and specificity of these assays ranges from 97-99% in various studies. VIRAL ANTIBODY Please note: Administration of blood products or immunoglobulin may result in passive transfer of antibody and transiently positive antibody test results. high viral load by PCR in blood may also be helpful . continue therapy. and vice versa) Past infection No antibody detected Acute infection Past infection No antibody detected Acute infection (must be confirmed by State Lab). NOTE: VZV vaccine-induced antibody may only be detected by latex agglutination. cross reaction with CMV or enterovirus Uninfected or early in infection. a. Measles. Repeat test. Treat. False negatives can occur. agglutination Positive -Antibody present a Varicella-zoster Equivocal -Non-specific reaction or low level antibody. Virus Method Result Interpretation Cytomegalovirus. b. followed by Toxin B (cytotoxin) Negative Toxin not detected.or + + IgM Result + + + + Interpretation Primary infection (or false positive) Primary or reactivation infection ( Note: CMV IgM rise can be due to EBV. False negative antibody results may occur in immunocompromised hosts or agammaglobulinemic patients.

or passive antibody via hepatitis B immune globulin. Anti-HBe appears prior to loss of HBsAg and signals reduced level of infectious virus. Marker of recovery and immunity. acute hepatitis. If anti-HBc is the only positive HBV test. Indicates infection with hepatitis C. and chronic HBV infection. Serum contains HBV e antigen. May persist longer than anti-HBs and be the only marker for past HBV infection. Occasionally present in chronic active hepatitis. Positive result is consistent with current or past hepatitis A. it may indicate past infection. Positive test indicates recent infection with HAV. IgM anti-HAV persists for about 4-6 months after acute infection. Test should only be ordered in cases of acute infectious hepatitis. Test done routinely on all samples positive for anti-HBc but negative for anti-HBs. Negative results do not exclude infection with HCV. non-specific result. Delta is a defective virus causing hepatitis only in association with HBV. but anti-HBs is not yet detectable. Persistence beyond 6 months indicates chronic infection. Delta can be acquired simultaneously with HBV (coinfection) or as a superinfection in HBV carriers. Detectable during incubation period. Low positive results can be non-specific. Consistent with recent hepatitis B infection.16 Positive Result HBsAg Anti-HBs Anti-HBc (total antibody) HEPATITIS TEST RESULTS Interpretation Active hepatitis B infection. immunization with HBV vaccine. This suggests that the patient is highly infectious. Detection or quantitation of HCV RNA in serum can be helpful in assessing disease activity. Patient is considered infectious. or low-level chronic HBV infection. Antibody usually persists 4-6 months after acute stage. immunization or passive antibody from immune globulin. Detectable 1-3 months after HBsAg disappears. but may also be seen in HBsAg carrier state. Persistence beyond 10 weeks suggests chronic liver disease. since antibody levels may be below assay detection limits. Present during the "window" period when HBsAg has disappeared. Detects both IgG and IgM. Suggests early convalescence or past infection with HBV. Detects both IgG and IgM. Patients with delta virus infection have anti-delta antibody in their serum. Patients with anti-HAV are usually immune to further HAV infection and are not infectious. COMMON HEPATITIS B SEROLOGY PATTERNS HBsAg Anti-HBc IgM Total anti-HBc + + + + + + + + Anti-HBs + + Anti-HBc IgM HBeAg Anti-HBe Anti-Delta Anti-HAV total Anti-HAV IgM Anti-HCV No evidence of HBV infection Acute HBV infection Chronic HBV (if HBsAg+ for > 6 months) "Window" period during acute HBV Previous HBV infection HBV vaccine response . Indicates current or past hepatitis B infection. Indicates previous hepatitis B. Not associated with recovery or immunity.

This result can be indicative of a nonspecific reaction. Another specimen should be submitted for repeat testing if clinical findings in this patient are contrary to these laboratory results.17 HEPATITIS C VIRUS (HCV) ANTIBODY TEST INTERPRETATION EIA-3 RIBA-3 Interpretation N. direct detection of HIV-1 by PCR may be useful. Please notify the laboratory if patient has risk factors for HIV-2 or HTLV-I/II. but can also be associated with early HIV infection. This specimen is HIV-1 antibody positive. + Indeterminate + + . Negative results may be seen early during the course of infection. Another sample should be submitted in 2-6 weeks. The patient should be followed for at least 6-12 months for increased RIBA reactivity and/or tested by PCR for HCV RNA. passive transfer of antibodies. RIBA is recommended in low risk patients. If you would like a RIBA or RT-PCR performed on this sample. blot Interpretation N. PCR is recommended in high risk patients. Positive for HCV antibodies and indicative of past or present infection with HCV. please notify the laboratory.D. Antibodies are not detectable for 6-7 weeks after initial infection or may not develop in compromised hosts. this could be a false positive result. A negative EIA result does not absolutely exclude HCV infection. This specimen is antibody negative. This sample is indeterminate for HCV antibodies. Recommend repeat antibody testing in 2-6 months and/or HCV RNA PCR. A negative RIBA does not exclude the possibility of HCV infection. If this patient has had serial samples with indeterminate W. Another sample should be submitted in 2-6 weeks. in advanced AIDS and in agammaglobulinemic patients. but can also be associated with early HIV infection. Over 95% of samples strongly positive by EIA are RIBA positive. In high risk individuals. repeat antibody testing and/or HCV RNA PCR should be considered. This sample was strongly positive for HCV antibodies by EIA and was not tested by RIBA. This result can be a nonspecific reaction or can indicate early seroconversion. Repeat testing should also be considered if this is the first positive result in this patient. Low positive Low positive Indeterminate + Low positive HUMAN IMMUNODEFICIENCY VIRUS (HIV) ANTIBODY TEST INTERPRETATION ELISA W. This result could represent a false positive EIA or an early seroconversion. immunosuppression or infection with other human retroviruses. passive transfer of antibodies. + This result can be indicative of a nonspecific reaction.D. If this result is not compatible with the patient's clinical picture. if this patient has no evidence of hepatitis and does not have risk factors for HCV. However. Please notify the laboratory if patient has risk factors for HIV-2 or HTLV-I/II. repeat antibody testing in 2 months and/or HCV RNA PCR should be considered.D. This is indicative of HIV-1 infection. A negative test does not exclude the possibility of infection with HIV. Strong positive N. immunosuppression or infection with other human retroviruses. blot results.

mumps.D. Mon-Fri Location: Building 5.. to 4:30 p. ext 2908 Hours of Operation: 7:30 a. 3379. and RSV) Influenza (during flu season only) CMV (for non-blood samples) Viral serology . respiratory syncytial virus (RSV). VA Connecticut Health System Acting Director: Sheldon Campbell. 2nd floor.m. .HIV-1/2 . herpes simplex virus (HSV). C) Molecular assays RT-PCR for HIV-1 RNA HIV-1 antiviral resistance genotyping Multiplex PCR for HSV. cytomegalovirus (CMV). HSV-2 and VZV in lesions PCR for norovirus in stools RT-PCR for HCV RNA (qualitative and quantitative) HCV genotyping PCR for Chlamydia trachomatis and Neisseria gonorrhoeae . 2. parainfluenza viruses. VZV. Ph. parainfluenza viruses 1. 3380 SERVICES OFFERED Conventional and rapid culture assays . VA-CT Virology Reference Laboratory. SERVICES OFFERED AT THE VIROLOGY REFERENCE LABORATORY. EBV.18 V. and varicella zoster virus (VZV).D.Rapid limited viral cultures (for the detection of specific viruses only) Respiratory viral culture (for adenovirus.m. rhinovirus. measles. CMV and HHV-6 in CSF Real-time PCR for detection of HSV-1. or 932-5711. M. ext. Room C-202 Lab Phone numbers: 937-3441 (outside direct dial). B.Hepatitis viruses (A. enterovirus. influenza A and B. and 3. influenza viruses. 932-5711.Comprehensive viral cultures for the detection of adenovirus.

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