Clinical comparison, standardization and optimization of Zika virus molecular detection

Objective Molecular Zika virus (ZIKV) detection is key to patient diagnostics during the current outbreak. Here, we address standardization and diagnostic performance of widely used realtime RT-PCR (qPCR) protocols for ZIKV detection. Methods Two novel qPCR protocols covering the currently known ZIKV genetic variability were analyzed together with all six published qPCR protocols. The performance of all assays was compared using a newly constructed universal control RNA (ucRNA) that contains the target regions of all compared assays on one strand of synthetic RNA. Findings Up to 10 oligonucleotide mismatches with ZIKV outbreak strains existed in published qPCR protocols. The analytical sensitivity of most assays was around 5 copies per reaction, whereas three assays showed a 3-250-fold decreased sensitivity. The novel ucRNA enabled uniform ZIKV quantification, whereas comparisons of PCR threshold cycles (CT-values) resulted in up to 20-fold misquantification between protocols. Mean ZIKV loads in 33 outbreak samples were 10 4 RNA copies/mL of blood (range; 10 2 -4x10 5 ) and 5x10 3 RNA copies/ mL of urine (range; 4x10 2 -5.9x10 4 ) within two weeks after symptom onset. Conclusion Several ZIKV qPCR protocols show limited sensitivity and incompatibility with ZIKV outbreak strains. ZIKV infection results in low virus concentrations close to the technical limit of detection irrespective of sample type, implying that 20%-80% of patients may go undiagnosed due to limited sensitivity of molecular tests. We provide updated protocols for ZIKV detection that are suitable for all ZIKV strains. The ucRNA will enable coordinated implementation of ZIKV molecular diagnostics across regions and within multicentric clinical