Publication of a scientific article as part of the AFROSCREEN project: “CDC Trioplex diagnostic assay underperforms in detection of circulating Chikungunya West African genotype”
Publication of a scientific article as part of the AFROSCREEN project: “CDC Trioplex diagnostic assay underperforms in detection of circulating Chikungunya West African genotype”
Chikungunya virus on the surface of a cell © Institut Pasteur/Thérèse Couderc, Groupe Microorganismes et Barrières de l’Hôte Avenir Inserm U604. Ultrastructural Microscopy Platform – Colorization Jean-Marc Panaud.
Since 2015, as part of the 4S network’s national fever surveillance program; the virology laboratory of Institut Pasteur Dakar has been carrying out molecular tests to detect mosquito-borne viruses, including Chikungunya. At the end of 2023, Senegal recorded its biggest ever epidemic, with 210 cases of Chikungunya confirmed by RT-qPCR.
In view of the spread of this virus (CHIKV) to Gambia and Burkina Faso, and the potential increase in cases in the region, the performance of CDC Trioplex RT-qPCR was evaluated. This system simultaneously detects Zika, Dengue and Chikungunya viruses from serum samples collected at the start of the epidemic.
An average delay of 7 Ct (cycle threshold) values was observed compared with the Institut Pasteur Dakar’s in-house RT-qPCR CHIKV device for 15 CHIKV-positive samples, meaning that it was less sensitive. To understand the reason for this delay, the samples were sequenced and the test sequences analyzed. The analysis revealed mismatches in the target sequences of the Chikungunya West Africa (WA) genotype for the primers and probes used with the CDC Trioplex RT-qPCR, due to mutations in this RNA virus. These incompatibilities can disrupt the efficiency of virus detection.
In addition, previous studies show that genetic variations can lead to false-negative results, particularly when the viral load is intermediate to low (Ct values > 28). In contrast, the CHIKV in-house RT-qPCR at Institut Pasteur Dakar showed reliable detection without mismatches for the WA genotype.
This study highlights the importance of regularly verifying the performance of analyses and monitoring the genomic evolution of viruses during epidemics.
https://www.researchgate.net/publication/381583427_CDC_Trioplex_diagnostic_assay_underperforms_in_detection_of_circulating_Chikungunya_West_African_genotype
Chikungunya virus on the surface of a cell © Institut Pasteur/Thérèse Couderc, Groupe Microorganismes et Barrières de l’Hôte Avenir Inserm U604. Ultrastructural Microscopy Platform – Colorization Jean-Marc Panaud.
Since 2015, as part of the 4S network’s national fever surveillance program; the virology laboratory of Institut Pasteur Dakar has been carrying out molecular tests to detect mosquito-borne viruses, including Chikungunya. At the end of 2023, Senegal recorded its biggest ever epidemic, with 210 cases of Chikungunya confirmed by RT-qPCR.
In view of the spread of this virus (CHIKV) to Gambia and Burkina Faso, and the potential increase in cases in the region, the performance of CDC Trioplex RT-qPCR was evaluated. This system simultaneously detects Zika, Dengue and Chikungunya viruses from serum samples collected at the start of the epidemic.
An average delay of 7 Ct (cycle threshold) values was observed compared with the Institut Pasteur Dakar’s in-house RT-qPCR CHIKV device for 15 CHIKV-positive samples, meaning that it was less sensitive. To understand the reason for this delay, the samples were sequenced and the test sequences analyzed. The analysis revealed mismatches in the target sequences of the Chikungunya West Africa (WA) genotype for the primers and probes used with the CDC Trioplex RT-qPCR, due to mutations in this RNA virus. These incompatibilities can disrupt the efficiency of virus detection.
In addition, previous studies show that genetic variations can lead to false-negative results, particularly when the viral load is intermediate to low (Ct values > 28). In contrast, the CHIKV in-house RT-qPCR at Institut Pasteur Dakar showed reliable detection without mismatches for the WA genotype.
This study highlights the importance of regularly verifying the performance of analyses and monitoring the genomic evolution of viruses during epidemics.
https://www.researchgate.net/publication/381583427_CDC_Trioplex_diagnostic_assay_underperforms_in_detection_of_circulating_Chikungunya_West_African_genotype