Specimen Collection Instructions for Clinicians

Key points

Clinicians should collect specimens for AFM as early as possible. Early specimen collection has the best chance to yield a cause of AFM. CSF, respiratory (NP/OP), serum, and stool specimens should be sent to CDC for testing. Contact your health department to coordinate sending of specimens to CDC.

specimen collection tools

Testing Protocols

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.

What You Need to Know‎

The single case of polio – identified in the United States in July 2022 – reinforces the importance of collecting stool from patients with suspected AFM to rule out polio.
  • 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 should include CSF, respiratory swab, serum, and stool specimens.

Clinicians should:

If specimens have not been collected or all of the available specimens have been used and no specimen remains, you should repeat specimen collection, when feasible.

Specimens to Collect from Patients Under Investigation (PUIs) for AFM

Collect the specimens below from patients under investigation (PUIs) for AFM. Work with your health department to coordinate submission of specimens for testing at CDC.

Keep Reading: Reporting Patients Under Investigation for Acute Flaccid Myelitis

Cerebrospinal fluid (CSF)

  • Minimum amount: 0.15 mL, 0.5-2 mL preferred
  • Tube type: Cryovial
  • Processing: Spun and processed; collect at same time or within 24 hours of serum if feasible
  • Storage: Freeze at <-20°C
  • Shipping: Ship on dry ice
  • Results of testing: Results for EV/RV testing will be returned as testing completed (within 14 days); CSF will also be used for special studies

Respiratory - nasopharyngeal (NP) or oropharyngeal (OP) swab

  • Minimum amount: 0.5 mL, 1 mL preferred
  • Tube type: N/A
  • Processing: Store in viral transport medium
  • Storage: Freeze at <-20°C
  • Shipping: Ship on dry ice
  • Results of testing: EV/RV testing and typing will be performed and results returned within 14 days of sample receipt

Serum

  • Minimum amount: 0.5 mL, 1 mL preferred
  • Tube type: Tiger/red top for collection; separate tube for shipping
  • Processing: Spun and processed; send aliquot; collect at same time or within 24 hours of CSF if feasible
  • Storage: Freeze at <-20°C
  • Shipping: Ship on dry ice
  • Results of testing: Results for EV/RV testing will be returned as testing completed (within 14 days); Serum will also be used for special studies

Whole stool

  • Minimum amount: 1 gram, 10 – 20 grams preferred
  • Tube Type: Sterile container; Not a rectal swab.
  • Processing: 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
  • Storage: Freeze at <-20°C
  • Shipping: Ship on dry ice
  • Results of testing: Results for EV/RV and poliovirus testing will be returned as testing completed (within 14 days)

Postmortem testing‎

In the event of death, follow separate instructions for Postmortem Specimen Submission for AFM Testing.

Sending Specimens to CDC

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

Reporting Results

  • 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.
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Content Source:
National Center for Immunization and Respiratory Diseases; Division of Viral Diseases
  • 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.