Viral encephalitis encompasses a group of inflammatory diseases of the brain caused by a variety of viral agents and exhibiting common clinical symptoms. Symptoms may include headache, confusion, or other alterations in sensorium and / or behavior, nausea, or vomiting. Signs may include evidence of elevated intracranial pressure or meningeal irritation, cranial nerve palsies, paresis or paralysis, altered reflexes, or convulsions. The Viral Encephalitis Laboratory offers a molecular test panel for health care providers to assist in the diagnosis of hospitalized viral encephalitis cases.

Test Menu

The table below lists the Test Menu of polymerase chain reaction (PCR) assays that are performed for Viral Encephalitis testing.  Cerebrospinal fluid (CSF) specimens from hospitalized encephalitis patients are automatically tested for the first eight viruses all year.  The last seven viruses (all arboviruses) are automatically added from June 1st through November 30th or when travel history or mosquito exposure history warrants.

VirusReal-Time PCR Winter Panel Dec-MayReal-Time PCR Summer Panel June-NovValidated Sample Types*Note
AdenovirusXXCSF, respiratory swabs, urine, rectal swabs, and stool 
CytomegalovirusXXCSF, nasopharyngyl swabs, blood, and bronchial wash 
Epstein Barr VirusXXCSF 
Enterovirus (all serotypes, including Coxsackievirus and echovirus)XXCSF, respiratory swabs, rectal swabs and stool 
Herpes Simplex virus 1XXCSF, brain suspension, genital, rectal, and lesion swabs 
Herpes Simplex virus 2XXCSF, brain suspension, genital, rectal, and lesion swabs 
Human Herpes virus 6XXCSF 
Varicella Zoster VirusXXCSF, brain suspension, genital, rectal, and lesion swabs 
Eastern Equine Encephalitis virus XCSF 
St. Louis Encephalitis Virus XCSF 
West Nile Virus XCSF and Serum 
California Sero-group Viruses (including LaCrosse & Jamestown Canyon) XCSFRequires NPL approval
Cache Valley Virus XCSFRequires NPL approval
Powassan Virus XCSF, Serum 
Heartland XCSF, Serum and Whole Blood 

*Submission of a different specimen type will require an approved Non-permitted Laboratory Test Form.

Travel Related Viral Testing 

Mosquito exposure while traveling to countries where the following viruses are circulating may warrant testing when symptoms are present. Please include relevant countries, travel dates and dates of symptom onset. 

Virus Travel to Country of IntrestValidated Speciman Types
Dengue YESSerum, Plasma
ChikungunyaYESSerum, CSF
Yellow FeverYESSerum, Whole Blood, Urine
ZikaYESSerum, Whole Blood, Urine

Specimen Submission

Specimens shipped through the US Postal Service, UPS, Fed Ex, or other commercial courier services should be sent to the address listed on the right.

Laboratory Requirements for PCR Tests

  • Specimens
    • A minimum of 1 ml CSF (frozen at -70°C, no preservatives), please consult the laboratory at (518) 474-4177 regarding tests on smaller volumes.
  • Collect > 1.5 mL CSF for PCR and serology, minimum 300 uL for PCR only (frozen at -70 °C, no preservatives).
  • ALSO Collect 5-10 ml blood in a serum separator tube (SST). Spin to separate and aliquot. Please send >2.5 ml serum to allow for complete testing. A minimum of 1000 µL is needed for PCR only.
  • If an arbovirus is suspected also include urine and whole blood
  • Collect > 2.5 ml urine for PCR testing. A minimum of 1000 µL is needed.
  • Collect > 0.5 ml whole blood (EDTA) for PCR testing. A minimum of 200 µL is needed.
  • Testing of brain tissue may be performed under special circumstances, but must be fresh frozen (-70°C, no preservatives) not formalin fixed or paraffin embedded. Submitter should contact the VEL Director prior to submitting this specimen.
  • A complete Infectious Diseases Requisition Form must be completed with each specimen.
    • Either fill out the form by hand or electronically and print or print the Remote Order Requisition
    • Incomplete information will delay testing.
  • Shipping
    • It is the shipper's responsibility to ensure that appropriate shipping materials are used with regard to safety and transportation regulations, and to ensure that the specimen is still frozen on arrival at the laboratory. Please contact your carrier for shipping and packaging information. Patient specimens must be shipped as "Diagnostic Specimens".
    • Specimens should only be shipped Sunday-Thursday "Priority Overnight" so that appropriate laboratory personnel can be present to receive and accession specimens Monday-Friday.
    • Specimens may also be hand couriered.
    • CSF specimens must be shipped frozen on dry ice (suggested minimum weight 2 kg or 5 lbs of dry ice).

Contact Information for Encephalitis testing at the Wadsworth Center:

Amy Dean, Ph.D., Director

Amy Dean, Ph.D., Director
P: (518) 474-4177
F: (518) 473-1326

Laboratory Requirements for Arbovirus Serology, Acute and Convalescent Serum

Acute sera may be submitted with CSF specimen(s) when the latter is sent for PCR testing. Regardless of whether accompanied by CSF or not:

  • Collect acute serum specimens at the onset of symptoms. 
  • Obtain blood specimens (red top/SST or equivalent tube) aseptically using approved venipuncture techniques by qualified personnel.
  • Allow specimens to clot at room temperature and then centrifuge.
  • Transfer serum to screw-top, plastic tubes and store at 2 - 8°C before shipment.
  • Submit frozen serum with PCR specimen(s) to the Viral Encephalitis Laboratory.
  • Include collection dates for CSF and serum specimens on the Infectious Diseases Requisition Form.

Obtain a convalescent specimen two to four weeks after the acute specimen collection date, as follows:

  • Obtain blood specimens (red top/SST or equivalent tube) aseptically using approved venipuncture techniques by qualified personnel.
  • Allow specimens to clot at room temperature and then centrifuge.
  • Transfer to screw-top, plastic tubes and store at 2 - 8°C before shipment.
  • Submission Form (must accompany specimen).
  • Paired specimens will be tested together.
  • Shipping: Serum specimens can be sent on cold packs directly to the Diagnostic Immunology Laboratory, New York State Department of Health, David Axelrod Institute, 120 New Scotland Avenue, Albany, NY 12208

For questions on serology other than rabies please contact the Diagnostic Immunology Laboratory at (518) 486-3845.

Rabies Tests

Prospective submitters must contact the Rabies Laboratory Director at (518) 485-6464 or (518) 527-7369 prior to sending samples for testing. Specimens should not be sent to the Viral Encephalitis Laboratory.