Test Catalog

Test ID: CHIKS    
Chikungunya Virus, PCR, Molecular Detection, Serum

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

Qualitative detection of chikungunya virus in serum 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.

See Mosquito-borne Disease Laboratory Testing in Special Instructions.

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, and is transmitted mainly through the bite of infected mosquitoes in the genus Aedes (A aegypti and A 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.


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 PCR 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 (RT)-PCR 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 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 Clinical Laboratories and sent to an external laboratory for serology (IgM IFA) and 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.



-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 had 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 May;13(5):764-767. Available at www.cdc.gov/eid

2. Johnson BW, Russell BJ, Goodman CH: Laboratory Diagnosis of Chikungunya Virus Infections and Commercial Sources for Diagnostic Assays. J Infect Dis 2016 Dec 15;214(suppl 5):S471-S474. Available at https://doi.org/10.1093/infdis/jiw274

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

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