What question did this study set out to answer?

The aim is to develop a rapid assay to differentiate between vaccine-derived and wild-type chikungunya virus strains.

May 15, 2026Emerging Microbes & Infections0 citationsOpen Access

Rapid differentiation of VLA1553 and wild-type ECSA chikungunya strains in the context of an IXCHIQ vaccination campaign

LPLaura PezziInserm ÉFÉtienne FrumenceUniversity of Reunion Island KWKonrad WesselmannAix-Marseille Université

Key Points

The aim is to develop a rapid assay to differentiate between vaccine-derived and wild-type chikungunya virus strains.
Developed a duplex real-time RT-qPCR assay targeting specific regions of the chikungunya virus.
Assessed analytical performance using various chikungunya isolates and specific viral strains.
Evaluated clinical performance with samples from vaccinated individuals and patients infected with ECSA-2 strains.
The duplex assay achieved LOD95 values of 0.9 and 1.1 copies/µL for vaccine-specific and wild-type targets, respectively.
All clinical samples were classified accurately, including those with simultaneous infections, as confirmed by sequencing.
The assay demonstrated high specificity and sensitivity, with no cross-reactivity observed.

Abstract

In 2024-2025, Réunion Island experienced a large outbreak driven by East-Central-South African (ECSA)-2 lineage of chikungunya virus (CHIKV), leading to the implementation of a vaccination campaign using live-attenuated IXCHIQ (VLA1553). Currently, distinguishing vaccine-derived viremia from wild-type infection relies on genomic sequencing, which is resource-intensive and not routinely available in many diagnostic laboratories. To address this gap, we developed a duplex real-time RT-qPCR assay specifically designed to differentiate VLA1553 from wild-type ECSA strains circulating in La Réunion. The assay targets the non-structural protein 3 hypervariable region, including the 61-amino-acid deletion characteristic of the VLA1553 backbone. Analytical performance was assessed using a panel of CHIKV isolates representing different lineages and a VLA1553-like strain generated using an Infectious Subgenomic Amplicon system. Clinical performance was evaluated using samples from recently vaccinated individuals and patients infected with ECSA-2 strains, and compared with two RT-qPCR assays routinely used by the French National Reference Centers for arboviruses. The duplex assay proved to be specific, detecting wild-type ECSA strains exclusively in the FAM channel and the vaccine strain exclusively in the HEX channel, with no cross-reactivity. It demonstrated high sensitivity, with LOD95 values of 0.9 and 1.1 copies/µL for the vaccine-specific and wild-type-specific targets, respectively. All clinical samples were correctly classified, including one vaccinated individual simultaneously infected with a circulating wild-type strain, as confirmed by sequencing. This duplex assay provides a rapid and reliable method to distinguish vaccine-derived from naturally-acquired CHIKV viremia, supporting more accurate clinical and epidemiological investigations in settings where vaccination and viral circulation overlap.

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