RT-PCR on Urine Samples: Added Value for the Diagnosis of Chikungunya Virus Infection

Retrospective laboratory evaluation of the detection rate of CHIKV infection by real-time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) on urine. Urine and serum samples from patients with confirmed CHIKV infections from an endemic area (Aruba) and from ITM will be analyzed. The results will be evaluated on a case-by-case basis: time since onset, patient characteristics, severity of symptoms, serology results.

The positivity in-time of CHIKV RNA in urine will be evaluated in comparison with viremia. Patients with suspected acute CHIKV infection will be asked (by written informed consent; annex 1) to provide urine samples within 72 hours after onset of disease, followed by urine samples on day 7, day 10, day 14 and three urine samples 3, 4 and 12 weeks after onset. They will be asked to provide serum samples within 72 hours after onset of disease, followed by serum samples on day 7, day 10, day 14. In total, twenty patients with an initial positive result of CHIKV RT-PCR on serum will be included for follow-up. The number of urine samples that will be tested is 140.

Objectives

1. To assess the added value of RT-PCR for CHIKV on urine samples for diagnosing CHIKV infection in comparison to the reference methods.
2. To describe the kinetics of RT- PCR for CHIKV on urine samples for diagnosing CHIKV infection over time.

Study design, population, materials and methods:

Prospective cohort study of patients with a confirmed CHIKV infection (positive RT-PCR for CHIKV on the sample at the time of inclusion or seroconversion defined as positive anti-CHIKV Immunoglobulin M (IgM) antibody assay on day 14), who attend the outpatient clinic of the Institute of Tropical Medicine in Antwerp and the Horacio Oduber Hospitaal in Aruba within 72 hours after fever onset. After signing informed consent, clinical and epidemiological data will be recorded in a standardized Case Record Form. Baseline blood and urine samples will be collected as required for routine clinical evaluation of the individual case; sampling will include serum CHIKV serologic assays, CHIKV E1 (or similar rapid test), as well as serum and urine for RT-PCR for CHIKV. After the initial evaluation, suspected CHIKV cases are scheduled for biweekly serum and urine collection for RT-PCR for CHIKV for a duration of 2 weeks, then after 3, 4 and 12 weeks. Serum at 4 weeks will be used for second serologic assay. Suspected cases that test negative for CHIKV by RT-PCR on serum will be excluded.

Study population : patients with confirmed CHIKV infection Sample size : panel of 20 CHIKV confirmed cases Data analysis and reporting : The percentages of positive urine RT-PCR (over different time-points of duration of the CHIKV infection) will be calculated. Proportions of positivity rates will be tested by χ²-test for equality of proportions. Ct-values between two different sample types (serum/urine) will be compared by calculation of Spearman's rank correlation coefficient (ρ). The Ct-values measured will be subtracted (indicated by ∆Ct) and the mean of all ∆Ct-values (± 95% confidence interval) will be calculated. Reporting in accordance with Standards for Reporting of Diagnostic Accuracy (STARD) guidelines.

Endpoints: diagnostic sensitivity of CHIKV RT-PCR on urine samples in patients with a confirmed CHIKV infection, comparison of analytical sensitivity (based on Ct-values) with RT-PCR on serum, positivity rates of RT-PCR urine samples over time Ethical issues: Informed consent will be obtained from study participants. Demographic, geographic, clinical and laboratory data will be obtained; the data are de-identified and stored in an encoded database (code known to the principal investigators). Ethical approval through the ITM/ University Hospital Antwerp (UZA) Ethics Committee (EC) and the EC in Aruba.

Expected results and relevance :

Evaluation of the sensitivity of RT-PCR on urine samples for diagnosing CHIKV infection in the post-viremic phase in both endemic and non-endemic settings. Possible advantages of the use of PCR on urine over serological assays are:

1. a shift in timeframe for accurately diagnosing CHIKV infection that could benefit returning travelers who consult after the acute phase.
2. the use of single specimens that are obtained by non-invasive procedures
3. high specificity
4. the opportunity for typing of CHIKV strains.

Eligibility Criteria:
Inclusion Criteria:

* Age 18 years or older
* clinical suspicion of CHIKV infection, i.e.
* fever (≥38°C) AND arthralgia OR rash
* Confirmation of CHIKV infection by RT-PCR on serum or seroconversion (defined as positive anti-CHIKV IgM antibody assay on day 14)
* living within 50 kilometer of either study site (ITM Antwerp, on Aruba)
* Willing and able to provide written informed consent (assent for minors).

Exclusion Criteria:

* Alternative diagnosis at the time of evaluation
* Unable to produce urine sample by spontaneous micturition