Specimen collection basics
- Samples should be collected using a proper container based on the type of sample to be collected
- Samples should be collected as soon as possible following the onset of the disease (acute phase of infection when viral concentration is at its maximum) – for the virus, isolation should be within 4 days as virus shedding decreases rapidly after that time.
- The specimen should reflect the system(s) involved in clinical disease
- All specimens must be properly identified and labeled – Indicate animal ID, sample ID, laboratory number, or name of the specimen
- The specimens for virus isolation should be collected aseptically, refrigerated promptly, and sent to the laboratory as soon as possible after collection
-If the samples cannot be sent within 24 hours, freeze them at -70˚C to -80˚C if possible
-Do not freeze samples for virus isolation at -20˚C
What types of specimens are collected for viral diagnosis?
All specimens should be collected immediately upon the onset of clinical symptoms or the death of the animal.
- Feces: Place 2-4 grams inside a sterile sealed container. A leakproof, wide-mouth container should be used and transported immediately to the laboratory. Specimens should be stored at 4 ˚C. Frequently isolated viruses in feces include adenoviruses and enteroviruses while less frequently isolated viruses include rotaviruses.
- Rectal swab: Insert swab 4-6 cm and roll against the mucosa. Place swab in 1-2 ml of sterile saline or viral transport media.
- Vesicle or lesion swab: Open the lesion carefully using a sterile instrument. Moisten a sterile swab with sterile saline or other transport media and collect cells from the open lesions. Place swab in 1-2 ml of sterile saline or viral transport media.
- Ocular/conjunctiva swab: Collect from the lower conjunctiva using a swab moistened with sterile saline. Place swab in 1-2 ml of sterile saline or viral transport media. Immediately place the swab in Universal Transport Medium (UTM) and store it at 4 ˚C. Frequently isolated viruses include adenovirus; coxsackievirus A (some), CMV, HSV, enterovirus (including type 70), and Newcastle disease virus.
- Corneal or conjunctiva scraping: Place scraping in 1-2 ml of sterile saline or viral transport media.
- Nasal swab: Swab nostrils separately using a flexible swab while rotating slowly for 5 seconds to absorb secretions. Remove and immediately place both swabs in the same 1-2 ml sterile transport tube containing saline or viral transport media (UTM) at 4 ˚C. Frequently isolated viruses include influenza virus, parainfluenza virus, rhinovirus (limited), and RSV (nasopharyngeal preferred).
- *Nasopharyngeal swab: Insert a sterile swab through the nostril into the nasopharynx and rotate several times. Remove and place the swab in 1-2 ml of sterile saline or viral transport media.
- Oropharyngeal/Throat swab: Swab posterior throat and tonsil area and place swab in 1-2 ml of sterile saline or viral transport media. Frequently isolated viruses include enterovirus (some), HSV, adenovirus, CMV, HSV, influenza A, and B viruses, measles virus, mumps virus, and parainfluenza virus while less frequently isolated viruses are RSV.
- Cervical or vaginal swab: If lesions are present, swab vigorously. Place swab in UTM. If lesions are not present, remove mucus from the cervix with a swab and discard the swab. Firmly sample the endocervix (≈ 1 cm into the cervical canal) with a fresh swab by rotating the swab for 5 seconds. Carry out a vulvar sweep using a second swab; place both swabs in the same transport tube. The swab must be immediately placed in UTM and stored at 4 ˚C. Frequently isolated viruses include HSV, and CMV while noncultivable viruses include papillomavirus and 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.
- Nasopharynx aspirate or wash: Insert a suction device through the nostrils into the nasopharynx. Aspirate fluid while removing the suction device. A flush the device with sterile saline and collect it in a sealed container. Store the specimen at 4 ˚C. Frequently isolated viruses include influenza virus, parainfluenza virus, rhinovirus (limited), and RSV.
- Serum: Collect in a red top tube. Centrifuge and remove from clot if possible.
*Note: When requesting antibody titers, send paired samples for the most accurate results.
- Whole blood: Collect in EDTA (purple-top) tube. Collect 8-10 ml in an anticoagulant tube such as EDTA (purple-top) or Heparin tube (viral transport is not required). Collect blood during the early, acute phase of infection. Depending on the purpose, the blood may be kept at room temperature (Do not refrigerate) or kept at 4 ˚C refrigerated).
- CSF: Collect in the sterile container. 1. Disinfect site with 2% iodine tincture. Insert a needle with stylet at L3-L4, L4-L5, or L5-S1 interspace. On reaching the subarachnoid space, remove the stylet and collect 2-5 ml in a sterile leakproof tube. (UTM not required). Frequently isolated viruses include coxsackievirus (some), echovirus, enterovirus, and mumps virus while less frequently isolated viruses include arboviruses, HSV, LCMV, and rabies virus.
- Tissue: Obtain samples from areas directly adjacent to the affected tissue. Place in a sterile container or plastic bag with a small amount of sterile saline or viral transport media to keep moist and keep at 4 ˚C. Always submit as much tissue as possible. Never submit a swab that has simply been rubbed over the surface.
- Semen: Collect in semen straw and transfer immediately into liquid nitrogen.
- Urine: Collect 5 ml of midstream clean, voided urine in a sterile container (UTM not required) but kept at 4 ˚C. Frequently isolated viruses include adenovirus, CMV, HSV, and mumps virus while less frequently isolated viruses include polyomavirus (JC virus) and rubella virus. Two or three specimens on successive days maximize recovery of CMV.