Rapid Molecular Assays for the Detection of Yellow Fever Virus in Low-Resource Settings

Abstract

Background

Yellow fever (YF) is an acute viral hemorrhagic disease transmitted by Aedes mosquitoes. The causative agent, the yellow fever virus (YFV), is found in tropical and subtropical areas of South America and Africa. Although a vaccine is available since the 1930s, YF still causes thousands of deaths and several outbreaks have recently occurred in Africa. Therefore, rapid and reliable diagnostic methods easy to perform in low-resources settings could have a major impact on early detection of outbreaks and implementation of appropriate response strategies such as vaccination and/or vector control.

Methodology

The aim of this study was to develop a YFV nucleic acid detection method applicable in outbreak investigations and surveillance studies in low-resource and field settings. The method should be simple, robust, rapid and reliable. Therefore, we adopted an isothermal approach and developed a recombinase polymerase amplification (RPA) assay which can be performed with a small portable instrument and easy-to-use lyophilized reagents. The assay was developed in three different formats (real-time with or without microfluidic semi-automated system and lateral-flow assay) to evaluate their application for different purposes. Analytical specificity and sensitivity were evaluated with a wide panel of viruses and serial dilutions of YFV RNA. Mosquito pools and spiked human plasma samples were also tested for assay validation. Finally, real-time RPA in portable format was tested under field conditions in Senegal.

Conclusion/Significance

The assay was able to detect 20 different YFV strains and demonstrated no cross-reactions with closely related viruses. The RPA assay proved to be a robust, portable method with a low detection limit (<21 genome equivalent copies per reaction) and rapid processing time (<20 min). Results from real-time RPA field testing were comparable to results obtained in the laboratory, thus confirming our method is suitable for YFV detection in low-resource settings.

Author Summary

Despite the use of a safe and effective vaccine, yellow fever virus is still causing hundreds of thousands of infections and tens of thousands of deaths every year. The disease is widespread in South America and Africa where several outbreaks have occurred in the past years. As the disease is difficult to distinguish from other illnesses during its early stage, it is necessary to develop reliable, rapid and simple diagnostic methods to confirm YF cases to be able to respond effectively to outbreaks through vaccination and vector control. In this study, we describe the development a diagnostic method for YFV, using an isothermal technology called recombinase polymerase amplification which allows detection of the virus within 20 minutes, using a portable and easy-to-use device. The YFV RPA assay proved to be a specific and sensitive detection method during testing in the laboratory and under field conditions in Senegal.