Test Catalog

Test Id : CHIKC

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Chikungunya Virus, PCR, Molecular Detection, Spinal Fluid

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Overview

Test Catalog

Useful For
Suggests clinical disorders or settings where the test may be helpful

Qualitative detection of chikungunya virus in cerebrospinal fluid after early symptom onset (ideally <7 days)

 

This test is not recommended for screening healthy patients.

Highlights

This test provides qualitative detection of chikungunya virus RNA from cerebrospinal fluid collected during the acute phase of infection.

 

This test is intended for evaluation of patients with a clinical history and symptoms consistent with chikungunya virus infection.

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

Method Name
A short description of the method used to perform the test

Real-Time Reverse Transcription Polymerase Chain Reaction (RT-PCR)/DNA Probe Hybridization

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

Chikungunya Virus, PCR, CSF

Aliases
Lists additional common names for a test, as an aid in searching

Chikungunya virus

Togavirus virus

Mosquito Borne Chikungunya

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

Specimen Type
Describes the specimen type validated for testing

CSF

Additional Testing Requirements

Due to the short period in which chikungunya RNA may be detected in cerebrospinal fluid (CSF), testing serum for IgM- and IgG-class antibodies to chikungunya virus is also recommended. See CHIKV / Chikungunya IgM and IgG, Antibody, Serum.

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

Collection Container/Tube: Vial number 2

Submission Container/Tube: Sterile screw cap vial

Specimen Volume: 0.5 mL

Collection Instructions: Do not centrifuge or heat inactivate.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Forms

If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the testing laboratory. The minimum volume is sufficient for one attempt at testing.

0.3 mL

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

Heat-inactivated specimen Reject

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

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

Useful For
Suggests clinical disorders or settings where the test may be helpful

Qualitative detection of chikungunya virus in cerebrospinal fluid after early symptom onset (ideally <7 days)

 

This test is not recommended for screening healthy patients.

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Chikungunya virus (CHIK) is an RNA virus of the genus Alphavirus, family Togaviridae transmitted mainly through the bite of infected mosquitoes in the genus Aedes (Aedes aegypti and Aedes albopictus). This is the same mosquito that transmits dengue, yellow fever, and Zika viruses. Most people infected with chikungunya virus will develop some symptoms, most commonly fever and joint pain. There is no specific antiviral treatment for chikungunya virus infection.

 

Most cases of disease have occurred in Africa, Asia, Europe, and the Indian and Pacific Oceans, but transmission of CHIK has been identified in Caribbean countries and South American regions, as well as foci in the southern United States. Infection with chikungunya virus may be suspected based on symptoms (fever, joint pain, and headache) and recent history of travel. A diagnosis of CHIK infection can be confirmed through laboratory tests on serum or cerebrospinal fluid.

 

This assay is designed to detect only species of clinical significance and is to be used for patients with a clinical history and symptoms consistent with chikungunya infection.

Reference Values
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

Negative

Reference values apply to all ages.

Interpretation
Provides information to assist in interpretation of the test results

A positive test result indicates the presence of chikungunya virus RNA in the specimen.

 

A negative test result with a positive internal control indicates that chikungunya virus RNA is not detectable in the specimen.

 

A negative test result with a negative internal control is considered evidence of polymerase chain reaction inhibition or reagent failure. A new specimen should be collected for testing if clinically indicated.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

This assay is designed to be used for patients with a clinical history and symptoms consistent with chikungunya infection.

 

Negative chikungunya virus real-time reverse transcription polymerase chain reaction results do not preclude infection with chikungunya virus and should not be used as the sole basis for patient treatment or management decisions. All results should be interpreted by a trained professional in conjunction with review of the patient's exposure history and clinical signs and symptoms.

 

False-negative results may arise from degradation of chikungunya virus RNA during incorrect shipping or storage, and specimen collection after the period that chikungunya virus RNA is typically found in the patient (7 days after onset of symptoms).

Supportive Data

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

 

Accuracy/Diagnostic Sensitivity and Specificity:

Clinical specimens, commercial samples, and a blinded panel of positive and negative samples provided by the Centers for Disease Control and Prevention (CDC) were used for the accuracy experiments. Testing was completed per the manufacturer's instructions, using the easy Mag (bioMerieux) for RNA extraction.

-Ninety-five clinical serum specimens received from the Mayo Infectious Disease Serology Laboratory (IDS) were tested using the Altona RealStar (ARS) Chikungunya (CHIK) RT-PCR Kit 2.0 assay. These specimens had been submitted through Mayo Clinic Laboratories and sent to an external laboratory for serology (IgM IFA) and reverse transcription polymerase chain reaction (RT-PCR) testing in 2014.

-Sixteen vials of human plasma from donor units collected in Puerto Rico extracted using the QIAGEN QIAamp Viral RNA Mini Kit.

-Spiking studies: To supplement the results, negative cerebrospinal fluid (CSF) specimens were spiked with viral RNA of CHIK and tested in a blinded fashion. The spiking material was heat inactivated (HI) CHIK culture fluid (CF). The ARS CHIK results were compared to the consensus results of the ARS CHIK, a published assay by Lanciotti(1) and a commercial assay, the Bio-Rad ZDC Multiplex RT-PCR Assay (ZDC). The gold standard was considered the consensus between 2 of the 3 PCR assays.

 

Results:

The ARS CHIK RT-PCR Kit detected 9 more chikungunya virus-positive specimens from the patient samples received from IDS than the Lanciotti and ZDC RT-PCR assays.

-Eight of the nine ARS CHIK+/Lanciotti-/ZDC- results were positive by chikungunya IgM EIA and/or chikungunya RT-PCR at another commercial reference lab, and therefore considered likely true positives. Final consensus sensitivity and specificity were 100% and 98% respectively.

-There was 100% agreement with among the ARS CHIK, Lanciotti, and CDC Trioplex RT-PCR assays using a CDC validation panel.

-The CSF specimens spiked with HI chikungunya virus CF at low concentrations gave expected results in 44/44 specimens.

 

Analytical Specificity:

No cross-reactivity was observed with the ARS CHIK RT-PCR Kit when tested against a comprehensive specificity panel, which included 32 bacterial, fungal, and viral organisms from culture collections along with well characterized laboratory strains causing similar disease states, closely related organisms, or from organisms commonly found in the specimens tested. This included West Nile virus (lineage 1 and 2), dengue virus (types 1, 2, 3, and 4), tick-borne encephalitis virus, yellow fever virus, Japanese encephalitis virus, Zika virus, and poliovirus. The manufacturer tested additional organisms as listed in the package insert.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

1. Lanciotti RS, Kosoy OL, Laven JJ, et.al. Chikungunya virus in US travelers returning from India, 2006. Emerg Infect Dis. 2007;13(5):764-767

2. Johnson BW, Russell BJ, Goodman CH. Laboratory diagnosis of chikungunya virus infections and commercial sources for diagnostic assays. J Infect Dis. 2016;214(suppl 5):S471-S474. doi:10.1093/infdis/jiw274

3. Morrison TE. Reemergence of chikungunya virus. J Virol. 2014;88(20):11644-11647

Method Description
Describes how the test is performed and provides a method-specific reference

The RealStar Chikungunya Virus RT-PCR Kit was developed by Altona Diagnostics to assist in the diagnosis of chikungunya (CHIK) infection by testing cerebrospinal fluid for CHIK RNA. The Altona RealStar Chikungunya (ARS CHIK) RT-PCR Kit 2.0 is a qualitative reverse transcription-PCR (RT-PCR) assay targeting the nonstructural protein 1 (NS1) gene. The assay includes a heterologous amplification system (internal control: IC) to identify possible RT-PCR inhibition and to confirm the integrity of the reagents of the kit. Testing will be performed per the manufacturer's instructions using the LightCycler 480 following extraction with the NucliSENS easyMag (bioMerieux).

 

Real-time RT-PCR technology utilizes a reverse-transcriptase reaction to convert RNA into complementary DNA, PCR for the amplification of specific target sequences, and target specific probes for the detection of the amplified DNA. The probes are labelled with fluorescent reporter and quencher dyes. Probes specific for CHIK RNA are labelled with the fluorophore FAM. The probe specific for the IC is labeled with the fluorophore JOE. Using probes linked to distinguishable dyes enables the parallel detection of CHIK specific RNA and the IC in corresponding detector channels of the real-time PCR instrument.(Package insert: RealStar Chikungunya RT-PCR Kit 2.0. Altona Diagnostics; 01/2017)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Tuesday, Thursday

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

Same day/1 to 5 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

7 days

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
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Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

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

CPT Code Information
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

87798

LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

Test Id Test Order Name Order LOINC Value
CHIKC Chikungunya Virus, PCR, CSF 81153-9
Result Id Test Result Name Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
603832 Chikungunya Virus, PCR, CSF 81153-9

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports