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Test Code LABWNPCR West Nile Virus (WNV), Molecular Detection, PCR, Plasma

Additional Codes


Test Name in EPIC EPIC Test Code Mnemonic Mayo Test ID


Reporting Name

West Nile Virus PCR, P

Useful For

Rapid testing for West Nile virus (WNV) RNA


As an adjunct in the diagnosis of early WNV virus infection

Method Name

Real-Time Polymerase Chain Reaction (PCR)/RNA Probe Hybridization

Performing Laboratory

Mayo Medical Laboratories in Rochester

Specimen Type

Plasma EDTA

Specimen Required

Collection Container/Tube: Lavender top (EDTA)

Submission Container/Tube: Screw-capped, sterile container

Specimen Volume: 1 mL

Collection Instructions: Spin down promptly

Specimen Minimum Volume

0.3 mL

Specimen Stability Information

Specimen Type Temperature Time
Plasma EDTA Refrigerated (preferred) 7 days
  Frozen  7 days

Reject Due To


Mild OK; Gross reject






Plasma gel tube

Reference Values


Day(s) and Time(s) Performed

Monday through Saturday; Continuously 7 a.m.-8 p.m. (June through November)

Monday, Wednesday, Friday; 6 a.m. (December through May)

CPT Code Information


LOINC Code Information

Test ID Test Order Name Order LOINC Value
WNVP West Nile Virus PCR, P In Process


Result ID Test Result Name Result LOINC Value
56072 West Nile Virus PCR, P 34892-0


The likelihood of detection of West Nile virus RNA by PCR is relatively low. In cerebrospinal fluid, the clinical sensitivity is approximately 55%, and in blood, about 10%. Specificity of the assay in either matrix is approximately 100%.(6)


This assay should not be used for screening asymptomatic individuals, and should only be used to test patients with signs and symptoms of West Nile virus (WNV) disease.


The sensitivity of the assay is very dependent upon the quality of the specimen submitted.


A negative test does not exclude infection with WNV. Therefore, the results obtained should be used in conjunction with clinical findings to make an accurate diagnosis.


This assay detects both viable and nonviable virus. Test performance depends on viral load in the specimen and may not correlate with cell culture performed on the same specimen.


Possible cross-reactivity with other flaviviruses (eg, Dengue virus, St. Louis encephalitis virus, and Japanese encephalitis virus) may occur.

Supportive Data

The following validation data supports the use of this assay for clinical testing.


Accuracy/Diagnostic Sensitivity and Specificity:  

To determine the ability of the assay to detect RNA from clinical specimens, 30 negative whole blood, serum, plasma, and cerebrospinal fluid (CSF) samples (120 total) were spiked with West Nile virus (WNV)-positive control material at the limit of detection (approximately 10 targets/microliter). The specimens were run in a blinded manner along with 30 negative (nonspiked) specimens for each matrix. 100% of the specimens were positive and 100% of the nonspiked specimens were negative.


To supplement the above data, blinded proficiency panels were tested with this assay and demonstrated 100% concordance. In addition, 8 patient samples that were positive for WNV RNA by this assay were tested with an alternative reference lab assay. Results showed 75% concordance.


Analytical Sensitivity/Limit of Detection (LoD):  

The LoD of this assay is approximately 10 targets/microliter.



Interassay precision is 100% and intraassay precision is 100%.


Reference Range:

Fifty CSF samples from normal donors were tested and found to be negative for targeted WNV RNA.   


Reportable Range:  

This is a qualitative assay and the results are reported as either negative or positive for targeted WNV.

Method Description

This LightCycler PCR assay has been optimized to detect common conserved sequences in the nonstructural protein of West Nile virus (WNV). Viral nucleic acid is extracted by the MagNA Pure automated instrument (Roche Applied Science) from cerebrospinal fluid, or plasma. Primers directed to the nonstructural protein amplifies a specific sequence of the virus. For the test, WNV genomic RNA is transcribed to cDNA. The LightCycler instrument amplifies and monitors the development of target nucleic acid sequences after the annealing step during PCR cycling by fluorescence assay. This automated PCR system utilizes stringent air-controlled temperature cycling and capillary cuvettes to rapidly detect (30-40 minutes) amplicon development. The detection of amplified products is based on the fluorescence resonance energy transfer (FRET) principle. For FRET product detection, a hybridization probe with a donor fluorophore, fluorescein, on the 3'-end is excited by an external light source and emits light that is absorbed by a second hybridization probe with an acceptor fluorophore, LC-Red 640, at the 5'-end. The acceptor fluorophore then emits a light of a different wavelength that can be measured with a signal that is proportional to the amount of specific PCR product. Analysis of the PCR amplification and probe melting curves are accomplished through the use of LightCycler software.(Cockerill FR III, Uhl JR: Applications and challenges of real-time PCR for the clinical microbiology laboratory. In Rapid Cycle Real-Time PCR Methods and Applications. Edited by U Reischel, C Wittwer, F Cockerill. Berlin, Germany, Springer-Verlag; 2002, pp 3-30)

Analytic Time

Monday through Thursday: 2 days Friday, Saturday: 3 days

Specimen Retention Time

1 week

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. Until the virus infection was recognized in 1999 in birds in New York City, WNV was found only in the Eastern hemisphere, with a wide distribution in Africa, Asia, the Middle East, and Europe.(1-3) 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%) result in meningitis or encephalitis. Case 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 of age are at particularly high risk.


Laboratory diagnosis is best achieved by demonstration of specific IgG and IgM class antibodies in serum or cerebrospinal fluid (CSF) specimens (WNV / West Nile Virus [WNV] Antibody, IgG and IgM, Serum or WNVC / West Nile Virus [WNV] Antibody, IgG and IgM, Spinal Fluid).


The specific identification of WNV by detection of IgM in CSF is the recommended test to document central nervous system disease, but this test may be falsely negative in CSF collected <8 days after the onset of symptoms. Alternatively, experiences in nucleic acid testing for WNV RNA in blood prior to transfusion have indicated that PCR can detect viremic target RNA from patients with known West Nile infection when specific antibodies to the virus are not present (ie, from 2-8 days after onset of symptoms).(4,5)

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 U.S. Food and Drug Administration.