Virology Specimen Collection Guide

TEST	SPECIMEN	COLLECTION INSTRUCTIONS	TRANSPORT
Chlamydia/Gonorrhea and/or Trichomonas nucleic acid amplification	Genital swab - Females	Aptima Unisex Swab Specimen Collection Kit: Use the white shaft swab with red printing to remove excess mucus from the cervical os and surrounding mucosa and discard. Insert the specimen collection swab (blue shaft swab in the package with green printing) into the endocervical canal and gently rotate clockwise for 10 to 30 seconds to ensure adequate sampling. Withdraw the swab carefully by avoiding any contact with the vaginal mucosa. Remove the cap from the swab specimen transport tube and immediately place the specimen collection swab into the transport tube. Discard and replace the tube if the contents are spilled. Carefully break the swab shaft at the score line against the side of the tube and discard the top portion of swab shaft. Re-cap the swab specimen transport tube tightly.	After collection, transport and store the swab in the swab specimen transport tube at 2°C to 30°C until tested. Specimens must be tested within 60 days of collection.
Chlamydia/Gonorrhea nucleic acid amplification	Rectal swab	Aptima Multitest Collection Kit: Use the small-tipped specimen swab only (DO NOT USE THE LARGE-TIPPED SWAB FOR SPECIMEN COLLECTION). Do not touch the soft tip or lay the swab down. Hold the swab, placing your thumb and forefinger in the middle of the swab shaft covering the score line. Do not hold the swab shaft below the score line. Carefully insert the swab into the rectum about 1-2 inches past the anal margin and gently rotate the swab clockwise for 5-10 seconds. Withdraw the swab without touching the skin. Unscrew the tube cap while holding the swab. Place the small-tipped swab into the transport vial, making sure that there is fluid in the bottom of the vial. If contents of the tube are spilled, use a new collection kit. Break the swab at the score line and replace the screw cap securely. Discard the top portion of the swab shaft. Tightly screw the cap onto the tube.	After collection, transport and store the swab in the swab specimen transport tube at 2°C to 30°C until tested. Specimens must be tested within 60 days of collection.
Chlamydia/Gonorrhea nucleic acid amplification	Throat swab	Aptima Multitest Collection Kit: Peel open the swab package and remove the blue shaft small tipped swab (DO NOT USE THE LARGE-TIPPED SWAB FOR SPECIMEN COLLECTION). Do not touch the soft tip or lay the swab down. Hold the swab, placing your thumb and forefinger in the middle of the swab shaft covering the score line. Do not hold the swab shaft below the score line. Carefully insert the swab into the throat ensuring contact with bilateral tonsils (if present) and the posterior pharyngeal wall, then withdraw the swab without touching the inside of the cheeks or tongue. Unscrew the tube cap while holding the swab. Place the small-tipped swab into the transport vial, making sure that there is fluid in the bottom of the vial. If contents of the tube are spilled, use a new collection kit. Break the swab at the score line and replace the screw cap securely. Discard the top portion of the swab. Tightly screw the cap onto the tube.	After collection, transport and store the swab in the swab specimen transport tube at 2°C to 30°C until tested. Specimens must be tested within 60 days of collection.
Chlamydia/Gonorrhea nucleic acid amplification	Urine	Aptima Urine Specimen Collection Kit: Patient should not urinate at least one hour prior to collection of specimens. Collect the first 20-30 ml of voided urine (the first part of the stream) in a sterile, plastic, preservative-free, urine collection cup. Remove the cap and transfer 2 mL of urine into the urine specimen transport tube using the disposable pipette provided. The correct volume of urine has been added when the fluid level is between the black fill lines on the urine specimen transport tube label (SPECIMENS OUTSIDE THESE LINES WILL NOT BE ACCEPTED). Re-cap the urine specimen transport tube tightly.	Urine specimens in Urine Collection Kit can be transported and stored at 2-30°C. Specimens must be tested within 30 days of collection.
Chlamydia/Gonorrhea and/or Trichomonas nucleic acid amplification	Vaginal swabs	Aptima Multitest Swab Specimen Collection Kit: Remove the swab aseptically. Discard and use a new swab if contaminated. Do not touch the soft tip or lay the swab down. Hold the swab, placing your thumb and forefinger in the middle of the swab shaft covering the score line. Do not hold the swab shaft below the score line. Insert the swab into the vagina about 2 inches past the introitus and gently rotate the swab for 10-30 seconds. Make sure the swab touches the vaginal wall. Remove the swab without touching the skin. Unscrew the tube cap while holding the swab. Discard and replace with a new transport tube if the contents are spilled. Place the swab into the tube and the break off the swab at the black score line against the side of the tube. Discard the top portion of the shaft. Screw the cap tightly and label the tube.	After collection, transport and store the swab in the swab specimen transport tube at 2°C to 30°C until tested. Specimens must be tested within 60 days of collection.
HSV & VZV nucleic acid amplification	Lesion	Collect specimens of vesicle fluids from the bases of lesions before crusting and healing have begun. Use a swab to obtain both fluid and cells from open lesions and break swab into a screw capped vial with 2-3 ml of viral transport medium.	Transport to the laboratory as soon as possible, no later than 72 hours, at 2-8°C. Specimens that cannot be transported within 72 hours should be frozen at -70°C and transported on dry ice.
Influenza PCR	Bronchial wash	Bronchial and bronchoalveolar washes are usually collected from hospitalized patients using specialized (invasive) procedures. Specimen should be transferred to a sterile leak proof container before transporting to the laboratory.	Transport to the laboratory as soon as possible, no later than 72 hours, at 2-8°C. Specimens that cannot be transported within 72 hours should be frozen at -70°C and transported on dry ice.
Influenza PCR	Nasal swabs	Use a dry synthetic fiber swab to swab each nostril. Do not touch the soft tip or lay the swab down. Carefully insert the swab in the first nostril 1/2-3/4 inches. Rotate with moderate pressure against as much of the wall of the anterior nares regions as possible in a large circular path inside the nose at least 4 times (~10-15 seconds). Using the same swab, repeat on the other nostril. Place swab in a sterile, screw-capped vial with 2-3 ml of viral transport medium.	Transport to the laboratory as soon as possible, no later than 72 hours, at 2-8°C. Specimens that cannot be transported within 72 hours should be frozen at -70°C and transported on dry ice.
Influenza PCR	Nasal washings	While the patient's head is tilted back slightly, instill several milliliters of sterile saline into each nostril; bring the head forward and allow the saline to drain into a small sterile container held beneath the nose. A small catheter with suction may be used with infants. Pour the contents into a sterile, screw-capped vial.	Transport to the laboratory as soon as possible, no later than 72 hours, at 2-8°C. Specimens that cannot be transported within 72 hours should be frozen at -70°C and transported on dry ice.
Measles PCR Or Influenza PCR	Pharyngeal/Throat swabs (PCR)	Using a synthetic fiber swab (cotton or calcium alginate swabs or swabs with wooden shafts are not acceptable), dry or moistened with viral transport medium, rub the tonsils and posterior pharynx and place in sterile, screw capped vial with 2-3 ml of viral transport medium.	Transport to the laboratory as soon as possible, no later than 72 hours, at 2-8°C. Specimens that cannot be transported within 72 hours should be frozen at -70°C and transported on dry ice.
Measles PCR	Urine	Clean, voided urine specimens collected in sterile conventional containers, while not the specimen of choice, are acceptable for some viruses. No special collection requirements are needed. Specimens should be kept refrigerated until transported to the laboratory. If unable to transport to the laboratory within 24 hours, process urine by centrifuging at 2500 x g for 15 minutes at 4°C. Remove supernatant and resuspend pellet in 2-3 mL of UTM/VTM. Refrigerate until transport to the laboratory.	Transport to the laboratory as soon as possible, within 24 hours, at 2-8°C. Processed specimens in UTM/VTM should be transported at 2-8°C as soon as possible not later than 72 hours. Processed specimens that cannot be transported to the lab within 72 hours should be frozen at -70°C and transported on dry ice.
Mumps PCR	Buccal Swab	To obtain a buccal specimen, massage the parotid gland area (the space between the cheek and teeth inside the mouth just below the ear) on each side of the face for about 30 seconds prior to collection of the buccal secretions. Using a Dacron or other polyester swab (cotton or calcium alginate swabs or swabs with wooden shafts are not acceptable), rub the inside of each cheek with the same swab for about 10 seconds. Sweep the swab between the upper and lower molar areas of each side of the mouth. Ensure the swab is moist with saliva when finished swabbing. Place the swab in a tube containing 2-3 ml of viral transport media (VTM) or universal transport media (UTM).	Transport to the laboratory as soon as possible, no later than 72 hours, at 2-8°C. Specimens that cannot be transported within 72 hours should be frozen at -70°C and transported on dry ice.
Norovirus PCR	Stool	Collect a 2-5 gram portion of stool (formed or liquid) and place in a sterile leakproof container. No transport medium is required.	Transport to the laboratory as soon as possible, no later than 72 hours, at 2-8°C.
SARS-CoV-2 NAAT/PCR and/or Influenza PCR	Nasopharyngeal (NP) swab	Use a dry synthetic fiber swab. Tilting the head back 70 degrees, gently and slowly insert swab through the nostril parallel to the palate until resistance is encountered. The nasopharynx is contacted when the distance inserted is equivalent to that from the nostril to the ear. Gently rub and roll swab, leaving it in place for several seconds to absorb secretions. Slowly remove swab while rotating it and place in a sterile, screw-capped vial with 2-3 ml of viral transport media.	Transport to the laboratory as soon as possible, no later than 72 hours, at 2-8°C. Specimens that cannot be transported within 72 hours should be frozen at -70°C and transported on dry ice.