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Test ID: WNCSF West Nile Virus, RNA, PCR, Molecular Detection, Spinal Fluid

Specimen Required

Collection Container/Tube:

Preferred: Vial number 2

Acceptable: Any vial number

Submission Container/Tube: Sterile screw cap vial

Useful For

Rapid testing for West Nile virus (WNV) RNA (lineage 1 and lineage 2) using cerebrospinal fluid specimens


An adjunctive test to serology for detection of early WNV infection (ie, first few days after symptom onset)


This assay should not be used for screening asymptomatic individuals and should only be used to test patients with signs and symptoms of WNV disease.

Method Name

Real-Time Polymerase Chain Reaction (PCR)

Reporting Name

West Nile Virus RNA, PCR, CSF

Specimen Type


Specimen Minimum Volume

0.3 mL

Specimen Stability Information

Specimen Type Temperature Time Special Container
CSF Refrigerated (preferred) 7 days
  Frozen  7 days

Clinical Information

West Nile virus (WNV) is a mosquito-borne flavivirus (single-stranded RNA virus) that primarily infects birds but occasionally infects horses and humans.(1,2,3) Until the virus was recognized in 1999 in infected birds in New York City, WNV had been detected only in the Eastern hemisphere with a wide distribution in Africa, Asia, the Middle East, and Europe. There are 2 distinct lineages of WNV: lineage 1 has the broadest distribution worldwide, including North America and Europe, whereas lineage 2 is found only in Africa and parts of Europe.


Most people who are infected with WNV do not experience symptoms. It is estimated that about 20% of those who become infected will develop West Nile fever with mild symptoms, including headache, myalgia, and, occasionally, a skin rash on the trunk of the body. About 1 of 150 WNV infections (<1%) results in meningitis or encephalitis. Fatality rates among patients hospitalized during recent outbreaks have ranged from 4% to 14%. Advanced age is the most important risk factor for death, and patients older than 70 years are at particularly high risk.


Laboratory diagnosis is best achieved by demonstration of specific IgG- and IgM-class antibodies in serum specimens. However, polymerase chain reaction (PCR) testing can be used to detect WNV RNA in serum, whole blood, and urine specimens from patients with recent WNV infection (ie, 3-5 days following infection) when specific antibodies to the virus are not yet present. It may also be useful for patients who are immunocompromised when an antibody response is minimal or absent. Finally, PCR can be useful for supporting a serologic diagnosis, given the known cross-reactivity of WNV serology with other flaviviruses.


Studies indicate that whole blood testing by PCR may provide higher sensitivity when testing patients with acute WNV disease (up to 87%) compared to serum, plasma, urine, and cerebrospinal fluid testing.(4) However, viral RNA may be detected for a longer period of time (≥10 days after symptom onset) in urine than in other sources.(5) Serum testing offers lower sensitivity (26%) but may be used when it is the only specimen type available.

Reference Values


Reference values apply to all ages.


A positive result indicates the presence of West Nile virus RNA and is consistent with early infection.

Clinical Reference

1. Petersen LR, Brault AC, Nasci RS: West Nile virus: review of the literature. JAMA. 2013 Jul 17;310(3):308-315

2. Colpitts TM, Conway MJ, Montgomery RR, Fikrig E: West Nile virus: Biology, transmission, and human infection. Clin Microbiol Rev. 2012 Oct;25(4):635-648

3. Centers for Disease Control and Prevention (CDC), National Center for Emerging and Zoonotic Infectious Disease (NCEZID), Division of Vector-Borne Diseases (DVBD): West Nile Virus: Information for Healthcare Providers. CDC; Reviewed December 10, 2018. Accessed January 3, 2023. Available at

4. Lustig Y, Mannasse B, Koren R, et al: Superiority of West Nile virus RNA detection in whole blood for diagnosis of acute infection. J Clin Microbiol. 2016 Sep;54(9):2294-2297

5. Barzon L, Pacenti M, Franchin E, et al: Excretion of West Nile virus in urine during acute Infection. J Infect Dis. 2013 Oct;208(7):1086-1092

Day(s) Performed

Monday through Friday

Report Available

Same day/1 to 5 days

Test Classification

This test was developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information


LOINC Code Information

Test ID Test Order Name Order LOINC Value
WNCSF West Nile Virus RNA, PCR, CSF 34461-4


Result ID Test Result Name Result LOINC Value
608435 West Nile Virus RNA, PCR, CSF 34461-4
Mayo Clinic Laboratories | Microbiology and Infectious Disease Catalog Additional Information: