Specimen Collection Instructions

CDC continues to search for potential causes of acute flaccid myelitis (AFM) by broadening laboratory approaches that test for potential infectious, noninfectious, and post-infectious causes, including possibly immune-mediated mechanisms or host responses to AFM. To support the updated testing protocols, CDC will prioritize testing of cerebrospinal fluid (CSF) and serum to optimize yield of an etiologic agent or possible mechanism for AFM. CDC will conduct routine testing and typing of CSF, respiratory specimens and stool for enterovirus/rhinovirus, and poliovirus testing of stool specimens to rule out the presence of poliovirus. Additional testing protocols are being developed to look for AFM biomarkers and studies to identify possible mechanisms for AFM are underway. Pathogen-specific testing should continue at hospital or state public health laboratories and may include CSF, sera or whole blood, stool, and respiratory specimens.

Clinicians should collect specimens from patients under investigation (PUIs) for AFM as early as possible in the course of illness, preferably on the day of onset of limb weakness. Early specimen collection has the best chance to yield a cause of AFM. Clinicians should follow the instructions in the table for collecting specimens from PUIs. For more information on how to send information about a PUI, see CDC’s Job Aid for CliniciansCdc-pdf[2 pages]. If specimens have not been collected or all of the available specimens have been used and no specimen is remaining, repeating specimen collection is requested, when feasible.

Since the testing protocols include several assays that are not performed under the Clinical Laboratory Improvement Amendments (CLIA) nor intended for clinical diagnosis, CDC will be unable to provide patient-specific results for certain tests that are performed. Results following testing of samples from multiple cases that may indicate a possible cause of AFM will be rapidly disseminated. Results from certain tests, such as EV/RV testing and typing and stool testing, will be shared with the health department upon completion.

CDC appreciates your assistance and participation in this important endeavor. With your assistance, we hope to gain further insights into the nature of this unusual condition.

Specimens to Collect and Send to CDC for Testing for Patients Under Investigation (PUIs) for AFM

Specimens to Collect and Send to CDC for Testing for Patients Under Investigation (PUIs) for AFM table
Specimen Type Minimum Amount Collection Storage Shipping Comments
Cerebrospinal fluid (CSF) 1 mL Spun and processed; standard cryovial tube; collect at same time or within 24 hours of serum if feasible Freeze at -70°C Ship on dry ice CSF will be used for special studies; EV/RV testing will be batched and results returned as sample amount allows
Serum* 0.4 mL Spun and processed; Tiger/red top tube; collect at same time or within 24 hours of CSF if feasible. Freeze at -70°C Ship on dry ice Serum will be used for special studies; no individual results will be returned
Whole stool ≥1 gram Collect in sterile container, no special medium required. Please do not send a rectal swab†. Freeze at -20°C** Ship on dry ice Two samples total, collected at least 24 hours apart, both collected as early in illness as possible and ideally within 14 days of illness onset. Results for EV/RV and poliovirus testing will be returned as testing completed (within 14 days)
Respiratory – nasopharyngeal (NP) or oropharyngeal (OP) swab 1 ml Store in viral transport medium Freeze at -20°C** Ship on dry ice EV/RV testing and typing will be performed and results returned within 10 days of sample receipt
In the event of death, please send the following specimens, if possible
Fresh-frozen tissue Place directly on dry ice or liquid nitrogen Freeze at -70°C Ship on dry ice Representative sections from various organs are requested, but particularly from brain/spinal cord (including gray and white matter), heart, lung, liver, kidney, and other organs as available.
Formalin-fixed or formalin-fixed, paraffin-embedded tissue Avoid prolonged fixation—tissues should have been fixed in formalin for 3 days, then transferred to 100% ethanol Room temperature Ship at room temperature with paraffin blocks in carriers to prevent breakage See comment above regarding frozen tissue


*If any of the serum samples that you are sending to CDC were collected after the patient had received intravenous immune globulin (IVIG), steroid treatments, or plasmapheresis/plasma exchange, please indicate the date of that therapy on the Patient Summary Form.

† The negative predictive value is very low for rectal swabs since the amount of fecal material collected is much less than for stool.

**All specimens may be stored at -70⁰C for ease of shipping.

Handling and Shipping

CDC advises overnight shipment of available clinical specimens from patients under investigation (PUIs) for AFM to CDC to optimize yield from specialized testing.

State and local health departments and clinicians treating PUIs may contact CDC for further laboratory and epidemiologic support by phone through the CDC Emergency Operations Center (770-488-7100), or by email at AFMinfo@cdc.gov.

Please ship specimens overnight so they arrive at CDC on Tuesday through Friday. Do not ship specimens on Friday or over the weekend.

  • For samples that should be frozen, please freeze them at -20°C (for fresh-frozen tissues, use -70°C) and make arrangements to ship the samples overnight to CDC frozen on dry ice.
  • Samples from each patient should be shipped with completed hard copies of
  • If 10 or more patient specimens are submitted, please provide an electronic line listing by email. Use the following headers in this order: patient ID number; date of birth; sex; onset date; fatal y/n; specimen ID number; specimen collected date; specimen type; if culture isolate—cell line and passage number.
  • Prior to shipping, please email Will Weldon (wweldon@cdc.gov), Heather Jost (ifa2@cdc.gov), and AFMinfo@cdc.gov regarding what is being shipped and include the name, phone number and email address of the shipper.
Shipping Address

Dr. Will Weldon
Centers for Disease Control and Prevention
1600 Clifton Road, NE
Unit 76
Building 17, Room 6124
Atlanta, GA 30329
Office: 404-639-5485; Mobile: 404-216-6183; Email: wweldon@cdc.gov

Page last reviewed: November 8, 2018