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  • Collection Procedure







    The UMMC Serology / Virology Laboratory utilizes a variety of methods for identification of infectious agents, including viruses. Methods include, but are not limited to, viral culture, viral nucleic acid amplification testing, shell vial assays, and real time PCR. It is our goal to utilize the most current methods available to provide our patients with accurate and rapid results.

    Specimen Collection Guidelines:

    Valid interpretation of results can be achieved only if the specimen obtained is appropriate for processing. As a result, care must be taken to collect only those specimens that may yield pathogens, rather than colonizing flora or contaminants. Specific rules for the collection of material vary, depending upon the source of the specimen, but several general principles apply:


    Collect specimens as soon as possible after the onset of symptoms. The chance of patient recovery is best during the first 3 days after onset and is greatly reduced beyond 5 days with many viruses. Autopsy samples need to be collected as soon as possible after death before tissues start decomposing.


    Wear appropriate PPE when collecting specimens from sterile sites. Use strict aseptic technique.


    If the specimen is collected in a syringe, remove the needle and replace it with a cap prior to transport. Specimens will NOT be accepted with needles attached.


    Label all specimen containers with identifying information about the patient (name and MRN) and the specimen source and date and time of collection.


    Complete all paper or electronic requisitions completely and precisely, including requested details on patient history, antimicrobial therapy, and specimen source, so that the laboratory can best determine the appropriate method for processing the specimen.


    Place warning labels on specimens from patients suspected of having highly contagious diseases and notify the laboratory supervisor.


    Polymerase Chain Reaction (PCR) and other molecular methods have become the preferred method for detecting viral diseases. Because PCR tests detect extremely small amounts of viral particles and do not depend on the presence or number of live, viable viral organisms for detection, results are definitive and reliable.


    Calcium-alginate tipped swabs, wood swabs, or swabs in transport tubes containing gel are NOT ACCEPTABLE for PCR testing.


    Use only Cobas PCR Female Swab Sample Packet for Chlamydia and Neisseria gonorrhoeae testing for females and urine for males.



    **The collection procedures offered below are guidelines only to provide for the optimum specimen possible.**



    Obtain by standard collection procedure. Refer to the Routine Venipuncture procedure for details. Specimens can also be collected via catheter. 2-4 heparinized tubes (green top) are required for Buffy Coat culture. Place on ice immediately.

    Cerebrospinal Fluid (CSF):

    Collect CSF aseptically from a lumbar puncture into sterile tubes. Send second tube for Microbiology / Virology / Serology testing.


    Cleanse area around eye with mild antiseptic. Pass swab moistened with sterile saline twice over Conjunctiva. Avoid eyelid border and lashes. Conjunctival or corneal scrapings should be collected by ophthalmologist. Specimen must be placed in Viral Transport Media and on ice immediately.

    Fluids (other than Blood, Urine or CSF):

    Joint, Pericardial, Peritoneal, Pleural: Aspirate using needle and syringe. Remove needle and replace with cap, or dispense fluid into a sterile container. Place on ice immediately.

    Gastrointestinal Tract:

    Feces: Collect directly into clean container. Avoid contamination with urine, soap, etc. May also be obtained from a diaper. Do not allow specimen to sit at room temperature. Refrigerate or place on ice immediately.

    Rectal Swab: Insert swab 4-6 cm into rectum and roll swab against mucosa. Place swab in viral transport media and refrigerate or place on ice immediately.

    Genital Tract - Female:

    Cervix: Clean cervix of vaginal secretions and mucus using the larger cleaning swab provided in kit. Use speculum without lubricants. Gently compress cervix with blades of speculum and use a wringing motion with smaller collection swab. Place swab in transport media tube. Pap smear for HPV must be collected in ThinPrep collection device, with a minimum of 4 mL ThinPrep solution.

    Endometrium: Collect as for cervix. If swabs are to be used, collection through a sterile tube sheath may avoid contamination with vaginal flora.

    Urethra: One or more hours after urinating, clean the area with sterile gauze or swab. Express and discard any exudate. Use thin wire swabs to collect material from 2-4 cm inside urethra.

    Vagina: Collect as for cervix. Can collect through aspiration or swabbing.

    For Group B Strep testing, insert one swab from the COPAN Venturi System into the distal third of the vagina and sample secretions from the mucosa. Rotate the swab for 30 seconds to ensure adequate sampling. Carefully withdraw the swab and place into transport container. Insert second swab approximately 2-3 cm beyond the anal sphincter. Gently rotate at least one full turn to sample anal crypts. Carefully withdraw the swab and place into the same transport container.

    Genital Tract - Male:

    Penis: One or more hours after urinating, clean area with a non-alcohol, non-iodine antiseptic. Vesicles must be opened and secretion collected as aspirate, or as a swab. Alcohol and iodine are lethal to enveloped viruses.

    Semen: Collect in sterile container and place on ice immediately.

    Urethra: Same as for female.

    Respiratory Tract:

    Bronchoalveolar/Bronchotracheal secretions, washings or brushings: Collect 3-5 mL via bronchoscopy into a sterile container. Place on ice and deliver to lab immediately.

    Nasopharyngeal Swab: Insert sterile cotton, rayon, foam or nylon tipped swab with flexible shaft into the nares. Swab the posterior nasopharynx and any visible lesions. Put swab in viral transport media and place on ice. Specimens for Flu and RSV are to be collected only with foam tipped swabs provided by the laboratory.

    Nasopharyngeal Washings: Clean nares of excess mucous and debris. Using syringe, rapidly flush 5-7 mL sterile saline into the nares then pull back on the syringe to recollect the fluid. Cap syringe or put fluid in sterile container and place on ice.

    Nose: Insert COPAN swabs 1-2 cm into nasal passage and rotate against nasal wall while applying pressure with a finger to the outside of the nose. Repeat in the second nostril with the same swabs. Place swabs back in the transport container and deliver to lab. This collection is for MRSA by PCR only.

    Sputum: Instruct patient to produce lung material, not saliva, into sterile container. Expectoration can be assisted by saline nebulization, postural drainage or physiotherapy. Specimens can also be collected according to the Bronchoscopy Protocol by Respiratory Therapy. If specimen is to have routine bacteriology in addition to virus culture, collect separate specimen for routine bacteriology and place only the specimen for virus culture on ice.

    Throat Swab: Depress tongue with blade. Using swab from M4 media collection system, rub areas of exudation or inflammation. Use caution if epiglottis is inflamed, as sampling may cause serious respiratory obstruction. Put swab in viral transport media if for viral testing and place on ice. Swabs for testing other than viral can be transported in a dry, sterile container. Use green shaft rayon tipped swab for Group A Strep collection and place back in plastic sleeve. Must be tested within 4 hours of collection, or stored at 2-8° C for up to 24 hours.

    Throat Washing: Instruct patient to gargle with small amount of saline 10-20 seconds and expectorate into sterile container. Put container on ice and transport immediately to the laboratory.


    Collect surgically or through needle biopsy and put in sterile container. Place on ice and deliver to lab immediately.


    Clean voided urine: Instruct patient to clean area well and void for 2-3 seconds into toilet then stop. They can begin voiding again into the sterile container until approximately half full. Females should hold labia apart, and uncircumcised males should hold foreskin back while collecting specimen. First morning urine is preferable specimen.

    Catheter urine: Disinfect the catheter tube’s sampling port with 70% alcohol or iodine. Aspirate urine through sampling port with needle, or syringe if using a needle-free system, and place in sterile container. First morning urine is preferable specimen.


    Open: Gently swab base of the lesion to sample the fresh border. Put swab in viral transport media and place on ice. Do NOT use alcohol or iodine to clean the area as these are lethal to enveloped viruses.

    Closed: Gently unroof the vesicle and swab debris and cellular material. Because the sensitivity of viruses decrease with healing, fresh or open vesicles should be sampled in preference to closed, crusted ones. Do NOT use alcohol or iodine to clean the area as these are lethal to enveloped viruses.