For virus specimen
selection guidelines, refer to Table 4.

In general, specimens for virus isolation should be collected within 4 days after onset of illness as virus shedding decreases rapidly after that time.  With only a rare exception, virus cultures are not worthwhile for specimens collected more than 7 days after the onset of illness.

Except for body
fluids (BAL, CSF, urine, blood), place all viral specimens in UTMa

Most viruses remain stable at 4oC for 2-3 days and almost indefinitely at –70oC.
Do not freeze at –20oC.

To ensure proper evaluation, the following information should accompany the specimen: (1) date of illness onset, (2) date and time specimen was collected, (3) admitting diagnosis, (4) source of specimen.
Collection of acute and convalescent phase sera should always be considered.

Blood

1.  Cleanse venipuncture site with 70% isopropyl alcohol.
2. Starting at the site, swab concentrically with 2% iodine tincture.
3. Allow the iodine to dry (≈ 1 min).
4. Do not palpate the vein at this point.
5. Collect 8-10 ml in an anticoagulant tube (viral transport is not required).
6. After venipuncture, remove iodine from the skin with alcohol.

Heparin tube, 8-10 ml/tube.
You may need to draw 2 or more tubes from patients who are leukopenic.

Submit at RTa

None

Commonly ordered for: CMV.
Collect blood during the early, acute phase of infection. Maintain at RTa. Do not refrigerate.

CSF

1. Disinfect site with 2% iodine tincture.
2. Insert a needle with stylet at L3-L4, L4-L5, or L5-S1 interspace.
3. On reaching the subarachnoid space, remove the stylet and collect 2-5 ml in a sterile leakproof tube. (UTMa not required).

Sterile screw-cap tube, 1.0 ml

Submit immediately at 4oC.

None

Frequently isolated: coxsackievirus (some), echovirus, enterovirus, mumps virus.
Less frequently isolated: arboviruses, HSV, LCMV, rabies virus.

Cervical or vaginal swabb

1. If lesions are present, swab vigorously. Place swab in UTMa.
2. If lesions are not present, remove mucus from the cervix with a swab and discard the swab.
3. Firmly sample the endocervix (≈ 1 cm. into the cervical canal) with a fresh swab by rotating the swab for 5 seconds.
4. Place swab in UTMa.
5. Carry out a vulvar sweep using a second swab; place both swabs in the same transport tube.

Swabb

Immediately place swab in UTMa.
Submit at 4oC.

1/day/
source

Frequently isolated: HSV, CMV
Noncultivable: papillomavirus, molluscum contagiosum virus.
Although a cervical swab sample is the specimen of choice in the monitoring of pregnant women with a history of genital HSV infection, recovery of HSV may be increased by also sampling the vulva.

Conjunctiva swabb

1. Collect material from the lower conjunctiva with a flexible, fine-shafted swab moistened with sterile saline.
2. Place swab in UTMa.

Swabb

Immediately place swab in UTMa.
Submit at 4oC.

None

Frequently isolated: adenovirus;
coxsackievirus A (some), CMV, HSV, enterovirus (including type 70), Newcastle disease virus.

Feces

1. Pass directly into a clean, dry container.
2. 2-4 g of stool to sterile, leakproof container and transport immediately to lab.

Sterile, leakproof, wide-mouth container, at least 2 g or more.

Submit at 4oC.

1/day

Frequently isolated: adenoviruses; enteroviruses.
Less frequently isolated: rotavirus
Rotavirus antigen is detected by EIA.

Nasal swabb

1. Pass a flexible, fine shafted swab into the nostril.
2. Rotate slowly for 5 seconds to absorb secretions.
3. Remove swab and place in UTMa.
4. Repeat for other nostril using a fresh swab. Place both swabs in the same transport tube.

Swabb

Immediately place swab in UTM. Submit at 4oC.

1/day

Frequently isolated; influenza virus, parainfluenza virus, rhinovirus (limited), RSV (nasopharyngeal preferred)
Influenza A virus and RSV are detected by antigen assay (EIA).

Nasopharynx
aspirate or wash

1.  Pass appropriate size tubing or catheter into the nasopharynx.
2. Aspirate material with a small syringe.
3. If material cannot be aspirated, tilt patient’s head back about 70o and instill 4 ml. of sterile PBS until it occludes the nostril.
4. Reaspirate. Place in sterile container.
5. Place specimen at 4oC immediately.

Sterile container.

Submit at 4oC.

1/day

Frequently isolated: influenza virus, parainfluenza virus, rhinovirus (limited), RSV.
Influenza A virus and RSV can be detected by antigen assay.

Nasopharynx swabb

1. Pass a flexible, fine shafted swab into the nasopharynx.
2. Allow secretions to absorb for 5 seconds; then carefully remove swab and place it in UTMa.
3. Repeat for other nostril using a fresh swab. Place both swabs in the same transport tube.

Swabb

Immediately place swab in UTMa.
Submit at 4oC.

1/day

Frequently isolated: influenza virus, parainfluenza virus, rhinovirus (limited), RSV.

Oral swabb

1. Firmly sample base of lesion(s) with a swab.
2. Place swab in UTM.

Swabb

Immediately place swab in UTMa.
Submit at 4oC.

1/day

Frequently isolated: enterovirus (some), HSV.

Rash
  Maculopapular

1. Gently cleanse area with sterile saline.
2. Disrupt the surface of the lesion and firmly sample its base with a swab moistened with sterile saline.
3. Place swab in UTMa.

Swabb

Immediately place swab in UTMa.
Submit at 4oC.

1/day/
source

Frequently isolated: adenovirus, enterovirus, rubella virus, measles virus (rubeola virus)
Less frequently isolated: pox viruses
Noncultivable: parvovirus B19

Vesicular

1.  Sample only fresh vesicles because older crusted vesicles may not contain viable virus.
2. Cleanse area with sterile saline.
3. Carefully open the vesicle with needle or scalpel blade.
4. Using a swab, collect fluid and cellular material by vigorously sampling the base of the lesion.
5. Place in UTMa.

Swabb

Immediately place swab in UTMa.
Submit at 4oC.

1/day/
source

Frequently isolated: enterovirus (some), echovirus, HSV, VZV
Less frequently isolated: poxviruses
The preferred specimen for VZV is a vesicle aspirate placed in 1 ml. UTMa.

Throat swabb

1. Using a tongue depressor, depress the tongue to prevent contamination with saliva.
2. Firmly sample the posterior pharynx, tonsils, and inflamed areas with a sterile swab.
3. Place swab in UTMa.

Swabb

Immediately place swab in UTMa.
Submit at 4oC.

1/day

Frequently isolated: adenovirus, CMV, enterovirus, HSV, influenza A and B viruses, measles virus, mumps virus, parainfluenza virus.
Less frequently isolated: RSV.

Tissue

1. Obtain samples from areas directly adjacent to affected tissue.
2. Place specimen in a sterile vial containing UTMa.

UTMa

Submit at 4oC.

None

Always submit as much tissue as possible. Never submit a swab that has simply been rubbed over the surface. 

Urethral swabb

Patient should not have urinated within 1 h prior to collection.
1.  Express and discard any exudate.
2.  Carefully insert flexible, fine-shafted swab 4 cm. into urethra.
3. Rotate swab 2-3 times to obtain an adequate number of cells.
4. Remove swab and place in UTMa.

Swabb

Immediately place swab in UTMa.
Submit at 4oC.

1/day

Frequently isolated: CMV, HSV

Urine

Refer to specific guidelines for urine collection.
Collect 5 ml. of midstream clean, voided urine in a sterile container (UTMa not required).

Sterile container, 5 ml

Submit at 4oC

1/day

Frequently isolated: adenovirus, CMV, HSV, mumps virus
Less frequently isolated: polyomavirus (JC virus), rubella virus
Two or three specimens on successive days maximize recovery of CMV.

a BAL, bronchoalveolar lavage; CSF, cerebral spinal fluid; UTM, virus, chlamydia, mycoplasma, ureaplasma, transport medium; PBS, phosphate buffered saline, RT, room temperature; CMV, cytomegalovirus; HSV, herpes simplex virus; EBV, Epstein-Barr virus; HIV-1, human immunodeficiency virus type 1: LCMV, lymphocytic choriomeningitis virus: EIA, enzyme immunoassay; RSV, respiratory syncytial virus; ELISA, enzyme-linked immunosorbent assay; VZV, varicella-zoster virus.

b Dacron or rayon with plastic or aluminum shafts are acceptable; calcium alginate swabs or swabs with wooden shafts are not acceptable.