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Virology

Introduction


Virological tests are usually costly and labour-intensive, therefore they should be undertaken only when good clinical indications for doing so exist, and after thoughtful consideration of the types of tests to request for.

Virological tests fall into three categories:

  • Culture of virus from infected body fluids or tissues
  • Antibody detection in blood and, where appropriate, CSF
  • Demonstration of the presence of viral antigen in infected tissues or body fluids.

Sample Labelling & Completion of Request Forms


All samples must be clearly labelled with the patient’s name and unique identification number, e.g. NRIC number, as well as the nature, source and date of collection of the sample.

Each sample must be accompanied by a request form that is completed legibly with the patient’s name, unique identification number, location, relevant history, findings and clinical diagnosis, the test(s) required, the nature, source and date of collection of the sample, and the name and for urgent requests, the contact number of the requesting doctor. The form must be signed by the requestor.

It should be ensured that these requirements are met to avoid rejection of the sample by the laboratory or a delay in reporting.

General Guidelines for Virus Isolation

  1. For most viral infections, the causative agents can only be isolated during the first 3 – 4 days of the acute illness.
  2. Although some viruses are slow growing, results can be available from 1 day to 3 weeks.
  3. Viruses are usually very labile, so samples should reach the laboratory within one hour of collection. If this is not possible, the sample must be refrigerated at 2-8°C (for a maximum period of 48 hours) until transport. Do not freeze samples as many viruses are inactivated at –20°C. For samples collected after office hours, refrigerate at 2-8°C until transport to the laboratory. Do not freeze them.
  4. Transport the sample with an ice pack or in a bag of ice cubes. First seal the sample in a plastic specimen bag, then place this bag inside an outer plastic bag containing the ice pack or ice cubes. On no account should the ice cubes come into direct contact with the sample bottle as contamination will occur. Place the accompanying request form into another plastic bag to keep the form dry.
  5. All swabs and tissue samples for virus isolation must be transported in virus transport medium (VTM). Dry swabs will not be accepted by the laboratory because the virus would probably no longer be viable. Blood, CSF, stools and effusions may be sent without VTM. For urine, see special instructions given below.
  6. Dacron or rayon swabs should be used for sampling, not calcium alginate, and the shaft of the swab stick should preferably be of plastic.

Collection Methods for Virus Isolation by Sample Type


Throat Swabs

  1. Depress the tongue for unobstructed access to the back of the throat.
  2. Swab the pharynx and both tonsils vigorously. Avoid touching the tongue and other parts of the oral cavity.
  3. If the patient has an associated rhinitis, collect a nasal swab at the same time, using a separate swab. Place both swabs in the same bottle of VTM.

Nasopharyngeal Aspirates


Nasopharyngeal aspirates are superior to throat swabs for the recovery of viruses. Further, immunofluorescence microscopy can be carried out on exfoliated cells in the aspirate for rapid diagnosis.

  1. Attach a disposable polythene catheter (French catheter 8 for infants) to a mucus trap and a suction pump.
  2. Insert the catheter through the nose for a distance equal to that from the tip of the nose to the angle of the jaw.
  3. Using the suction pump, aspirate mucus into the trap. If secretions are thick and trapped in the catheter, dislodge the mucus by sucking up 1 – 3 mL of VTM.
  4. Disconnect the trap when collection is complete and empty contents into a bottle of VTM. (If necessary, pour the VTM into the mucus trap, swirl the contents, then pour it back into the VTM bottle).
  5. If a suction pump is not available, attach the catheter to a 20 mL syringe, aspirate secretions, then expel secretions into VTM.

Saliva


For mumps isolation, swab the buccal mucosa opposite the upper molars where Stensen’s ducts open, then swab the floor of the mouth at the openings of the submandibular gland ducts. For cytomegalovirus (CMV) isolation, swab the buccal mucosa or aspirate saliva into a mucous trap and send in VTM.

Vesicular Lesions


Sample fresh skin vesicles during the first three days following the appearance of the eruption. Crusted lesions have a lower chance of yielding viable virus. Macules or papules should not be sampled.

  1. Gently clean the surface of the vesicle with sterile saline. Do not use alcohol.
  2. If the vesicle is intact, use a sterile needle to lift off the roof of the vesicle.
  3. Using a sterile swab, soak up all the fluid from the vesicle, then swab the base of the lesion vigorously to dislodge cells on the base (which contain the virus) onto the swab.
  4. Using the same swab, repeat the procedure with a number of vesicles, if present, in order to increase the yield of virus.
  5. Insert the swab into a bottle of VTM, break off the stick and screw-cap the bottle tightly.

Open Lesions


Clean open lesions on the skin and genitalia with sterile saline to remove any pus, then swab firmly to sample the basal cells. For oral lesions, swab the base of the lesions. Insert the swab into a bottle of VTM, break off the stick and screw-cap the bottle tightly.

In the case of keratoconjunctivitis, send scrapings from lesions for virus isolation and/ or immunofluorescence.

Conjunctival Swabs


Using a swab moistened with sterile saline, pull down the lower lid and swab the conjunctiva firmly, then evert the upper lid and swab similarly. Insert the swab into a bottle of VTM, break off the stick and screw-cap the bottle tightly.

For keratoconjunctivitis, send scrapings from lesions for virus isolation and/ or immunofluorescent antigen test.

Cervical Swabs

  1. Use a speculum during collection.
  2. Use one swab to clean the cervix of mucus and discard.
  3. Insert a second swab about 1 cm into the cervical canal.
  4. Rotate and leave for a few seconds to absorb the secretions.
  5. If vesicles or open lesions are present, sample as described above in Collection Methods for Virus Isolation by Sample Type (Virology Section, Vesicular Lesions and Open Lesions).
  6. Transport in VTM.

    Biopsy and Autopsy Samples


    Send fresh samples for virus isolation. Formalinised or fixed tissues cannot be used, as the virus would have been destroyed. Place a piece of the sample about 1 cm in size (or smaller if necessary) directly into the bottle of VTM, and screw-cap the bottle tightly.  Place the bottle in a specimen bag, seal it, and place this bag in an outer plastic bag containing ice or an ice-pack.  Send immediately to the laboratory.

    Urine


    For adults, instruct the patient to clean the urethral/vulval and perineal areas with soap and water, before collecting a mid-stream sample in a sterile bottle. For infants and young children, clean the perineum and genitalia and collect the sample in a sterile bottle. Transfer the urine into a urine culture bottle up to the mark indicated (about 10 mL). This bottle, which contains antibiotics, can be obtained from the Client and Specimen Management Section of the Department of Clinical Pathology.

    Stool


    Stool can be sent for virus culture to diagnose enteroviral infections. The virus is excreted in the faeces for several weeks.

    Most of the viruses that cause gastroenteritis such as rotavirus, the enteric adenoviruses and the caliciviruses, cannot be cultured in tissue cultures at present, and virus isolation is usually non-productive for viral gastroenteritis.

    With CMV enteritis, stool cultures are usually negative and an intestinal biopsy sample is required for virus isolation or antigen detection.

    Stool in amount equivalent to the tip of the little finger should be collected in a sterile bottle without VTM.

    Rectal Swabs


    Collect from cases with suspected enteroviral infections only when stool is difficult to collect, as rectal swabs are inferior to stool.

    Insert a sterile swab at least 3 cm deep into the anal orifice of an adult and rotate it to ensure collection of faeces. Place the swab in a bottle of VTM, break off the swab stick and screw cap the bottle firmly.

    Blood


    Viruses may be isolated from leucocytes and/or plasma so send unclotted blood.

    1. Collect 6 mL blood in EDTA tubes. EDTA is preferred to heparin as an anticoagulant because some viruses are inactivated by heparin.
    2. Mix the sample gently to prevent clotting and lysis of cells.
    3. Do not freeze the sample during transport as this will cause cell lysis.

    CSF


    Collect 1 – 2 mL CSF in a sterile bottle without VTM.

    Effusions


    Collect 3 – 4 mL of fluid in a sterile bottle without VTM.

    General Guidelines for Virus Serology

    1. Collect 3 – 5 mL of blood (6 – 8 mL if a panel of tests is being ordered) in a plain sterile tube without anticoagulants, and send the sample to the laboratory inside a sealed plastic specimen bag. If any delay is anticipated, the sample must be refrigerated at 2-8°C until transport. Do not freeze the sample as this will cause lysis of the cells, which can possibly interfere with some serological tests.
    2. To demonstrate a significant rise in antibody levels, the acute sample should be collected as soon as possible after the onset of illness and the second sample 10 days to two weeks later, and not earlier than seven days. When sending the second sample, label the sample as “second”. The two samples will then be tested in parallel in the same test run.
    3. Tests must be requested by name as well as methodology, if more than one type of test is offered (e.g. measles EIA* or measles CFT†). If in doubt about which to ask for, consult the laboratory.
    4. When an acute viral infection is suspected, the first serum can be tested for IgM antibody. However, IgM antibody may be absent in a sample if it is collected too soon after infection. A convalescent sample taken 7-14 days later will demonstrate IgM seroconversion. False negative IgM results can also occur, especially in infants with congenital infections (e.g. CMV). Conversely, false positive IgM antibody results can occur in patients with rheumatoid factor, autoimmune diseases or, sometimes, with other viral infections.
    5. Great care must be taken to avoid a traumatised, blood-stained CSF sample, as this will present difficulty with interpretation of result. The antibody detected may merely represent that in the blood. When sending CSF, always collect a blood sample at the same time, as this will be useful for determining the significance of any antibody detected in the CSF.
    6. For immunity screening, a single sample will suffice. Results are given as antibody “Present” or “Absent”, or in the case of hepatitis B and rubella antibody, in international units. The complement fixation test (CFT) should not be requested for immunity screening because complement fixing antibody is not long lasting.
    7. Serology for enteroviral infections is not available from this laboratory. For diagnosis, isolation must be carried out (see under Enterovirus Isolation).
    8. For Rubella Serology on female patients suspected of having acute rubella or who are contacts of rubella cases, clinical details and LMP (last menstrual period) dates should be provided.

    * EIA: Enzyme Immunoassay
    † CFT: Complement Fixation Test

    General Guidelines for Viral Antigen Detection

    1. The direct detection of viral antigen in secretions and tissues can provide a rapid diagnosis of viral infections; results are usually available within two hours. However, because a negative antigen result can still be followed by a positive culture result, it is useful to send samples in viral transport medium, so that both antigen detection and isolation can be carried out at the same time.
    2. Where both culture and antigen detection are requested, samples must be sent in Virus Transport Medium (VTM). If only antigen detection is required, the sample can be sent in 1 – 2 mL of sterile saline in a sterile bottle. Do not send dry swab. Place the container in a sealed plastic bag for despatch to the laboratory. If delay is anticipated, refrigerate at 2-8°C but do not freeze as this will cause cell lysis, making antigen detection impossible.
    3. The types of samples that can be sent for antigen detection include:
      1. respiratory secretions such as nasopharyngeal aspirates, bronchoalveolar lavage and sputum (throat swabs are inferior to NPA because of the sparsity of respiratory epithelial cells in such samples)
      2. if throat swab cannot be avoided, then for best diagnostic yield, swab the back of throat and both tonsils.
      3. fluid from skin vesicles, pericardial and pleural fluid
      4. scrapings from the base of vesicle or open skin lesions or the conjunctivae
      5. body fluids such as urine and CSF
      6. white cells in blood (for CMV)
      7. biopsy or autopsy tissue samples

    A Summary of Tests and Samples to Collect for Viral Infections

    Presentation Possible Pathogens Samples for isolation Samples for serology Samples for antigen detection
    Respiratory
    infection

    Influenza, RSV, rhinovirus, adenovirus, parainfluenza,
    CMV, VZV, HSV, enteroviruses, SARS-CoV, Chlamydia & Mycoplasma pneumoniae, hMPV
    TS, NPA, BAL, sputum, ETTA or tissues (lung, brain) in VTM. Pleural fluid without VTM
    Paired sera for CFT (all except rhinoviruses, enteroviruses, SARS-CoV, mycoplasma, hMPV). Serum for SARS-CoV total antibody/IgM/IgG, mycoplasma  NPA, BAL or lung tissue (all except rhinovirus,
    enterovirus, SARS-CoV)
    Neurological diseases (meningitis, encephalitis, paralysis) Enteroviruses, mumps, measles, HSV, VZV, HIV, HTLV 
    CSF, stool, NPA, brain biopsy. (VTM for NPA and biopsy sample)
    Paired sera and CSF for CFT, (excluding HIV & enteroviruses), acute serum for IgM (except enteroviruses), one serum for HIV and HTLV
    NPA for measles, mumps; Vesicle swab in saline for HSV, VZV; Brain biopsy for HSV, VZV, measles, mumps
    Conjunctivitis, keratocon- junctivitis Adenovirus, coxsackie A24, enterovirus 70, HSV, VZV, CMV  Conjunctival swab or scraping in VTM Single serum for VZV IgM; paired sera for VZV, HSV and Adeno CFT Conjunctival
    scraping
    in saline for HSV, VZV, adenovirus
    Viral STD HSV, HIV Penile, vaginal or cervical swab in VTM for HSV Paired sera for CFT for HSV. Single serum for HIV EIA Swab or scraping from lesion in saline for HSV
    Maculopapular
    rashes

    Measles, rubella,
    dengue, chikungunya, HIV, enteroviruses,
    parvovirus B19, CMV, EBV 

    Enteroviruses: throat swab in VTM and stool. Dengue and chikungunya: Blood
    Measles: NPA, TS, sputum, brain, lung, skin in VTM, urine, EDTA blood. Rubella: TS, nasal swab, NPA, placental tissue, lung, brain in VTM, urine, EDTA blood, uncoagulated cord blood, amniotic fluid, CSF

    Measles and rubella: Acute serum for IgM and paired sera for CFT. Dengue: see under “Dengue” heading below. Single serum for HIV EIA, Parvovirus B19 and chikungunya IgG and IgM EIA Measles: NPA for antigen detection
    Vesicular skin
    lesions
    HSV, VZV, enteroviruses Swab and fluid from lesion in VTM Paired sera for CFT (HSV and VZV only). Single serum for VZV IgM Swab or scraping from lesion in saline for HSV and VZV
    Cardiovascular:
    myo- or
    pericarditis,
    pleurodynia
    Enteroviruses, influenza
    Throat swabs and NPA in VTM, stools (enteroviruses only), pericardial fluid
    For influenza: paired sera for CFT
    For influenza: NPA for antigen
    Hepatitis HAV, HBV, HCV, HDV, HEV, CMV, EBV CMV: as below CMV: as below. EBV: one serum for IgM. Rest: one serum for EIA CMV: as below
    Gastroenteritis, colitis 
    Rotavirus, norovirus, adenovirus, CMV, enterovirus (infants) and others Intestinal biopsy for CMV in VTM.
    Stool for enteroviruses, adenoviruses
    Paired sera for CFT (CMV and adenovirus)
    Stool for rotavirus and norovirus antigen
    Parotitis Mumps virus Saliva, urine, CSF  Single serum for IgM. Paired sera for CFT NPA, urine or saliva for mumps antigen
    CMV Infection
    CMV Saliva, NPA, BAL, biopsy in VTM, blood, urine Paired sera for CFT. Acute serum for IgM Blood, urine, NPA, BAL or biopsy tissue
    Dengue or dengue-like syndrome Dengue types 
    1 – 4, chikungunya
    Blood Serum for dengue IgM & IgG, chikungunya IgM & IgG  Blood for dengue antigen
    Nasopharyngeal carcinoma  EBV   Blood for Ea IgA & VCA IgA  
    Note: Bold type indicates preferred samples and test

    BAL : broncho-alveolar lavage
    CFT : complement fixation test
    CMV : cytomegalovirus
    EBV : Epstein-Barr virus
    EIA : enzyme immunoassay
    ETTA : endotracheal tube aspirate
    HAV : hepatitis A virus
    HBV : hepatitis B virus
    HCV : hepatitis C virus
    HDV : hepatitis D (or delta) virus
    HEV : hepatitis E virus
    HI : haemagglutination-inhibition
    HIV : human immunodeficiency virus
    hMPV : human metapneumovirus
    HSV : herpes simplex virus
    HTLV : human T-lymphotropic virus
    IF : immunofluorescence 
    NPA : nasopharyngeal aspirate
    RSV : respiratory syncytial virus
    SARS-CoV : severe acute respiratory syndrome coronavirus
    STD : sexually transmitted diseases
    TS : Throat swab
    VTM : viral transport medium
    VZV : varicella-zoster virus


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    Last Modified Date :16 May 2018