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.
| Virus | Real-Time PCR Winter Panel Dec-May (Test Catalog ID 693) | Real-Time PCR Summer Panel June-Nov (Test Catalog ID 686) | Validated Sample Types* | Note |
|---|---|---|---|---|
| Adenovirus | X | X | CSF, respiratory swabs, urine, rectal swabs, and stool | |
| Cytomegalovirus | X | X | CSF, nasopharyngyl swabs, blood, and bronchial wash | |
| Epstein Barr Virus | X | X | CSF | |
| Enterovirus (all serotypes, including Coxsackievirus and echovirus) | X | X | CSF, respiratory swabs, rectal swabs and stool | |
| Herpes Simplex virus 1 | X | X | CSF, genital, rectal, and lesion swabs | |
| Herpes Simplex virus 2 | X | X | CSF, genital, rectal, and lesion swabs | |
| Human Herpes virus 6 | X | X | CSF | |
| Varicella Zoster Virus | X | X | CSF, genital, rectal, and lesion swabs | |
| Eastern Equine Encephalitis virus | X | CSF, serum | ||
| St. Louis Encephalitis Virus | X | CSF, serum | ||
| West Nile Virus | X | CSF, serum | ||
| California Sero-group Viruses (including LaCrosse & Jamestown Canyon) | X | CSF | Requires NPL approval | |
| Cache Valley Virus | X | CSF | Requires NPL approval | |
| Powassan Virus | X | CSF, serum | ||
| Heartland | X | CSF, serum, whole blood |
*Submission of a different specimen type will require an approved Non-permitted Laboratory Test Form.
Specimen Submission
If an arbovirus is suspected, always include serum with the CSF. Serum is tested by serology, PRNT and PCR. Additionally, urine and whole blood are highly recommended to improve the opportunity for detection and identification of suspected arboviral infections. Published studies have shown that molecular detection is improved by the inclusion of these additional specimen types for flavivirus testing. WNV and Zika virus reach higher titers and are present longer in urine and whole blood than in CSF.
Refer to the Virology Specimen Collection and Shipping page for information.
Contact Information for Encephalitis testing at the Wadsworth Center:
Amy Dean, PhD, 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 (<0°C) 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 (15-25°C) 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.