Chikungunya virus (CHIKV) is a re-emerging flavivirus that poses a significant public health threat. CHIKV exhibits a wide array of non-vector borne human transmission routes, such as sexual transmission, trans-placental transmission and blood transfusion. Detection and surveillance of CHIKV is highly crucial in preventing and controlling major outbreaks. With the majority of cases reported in low-resource locations, simple, low-cost detection methods are considered highly desirable. Here we have developed a sensitive and specific CHIKV diagnostic using reverse transcription recombinase-aided amplification (RT-RAA) coupled with lateral flow strip detection (LFD) targeting the CHIKV E1 gene. This diagnostic provides rapid and robust detection of CHIKV without compromising sensitivity and specificity, when compared to the gold-standard diagnostic techniques such as qRT-PCR.
Our sample preparation results demonstrate that we are able to fully inactivate live CHIKV in 2 mins at RT whilst successfully extracting viable viral RNA. As such, we show that our Iso-CHIKV-Dx can detect live (Mauritius strain) CHIKV in urine samples down to 25,000 FFU/ml. Specificity testing confirmed that our test did not detect closely related Alphaviruses (Ross River, O’nyong-nyong, Semliki Forest, Sindbis or Barmah Forest virus. Contrary to conventional RT-PCR our Iso-CHIKV-Dx does not require expensive machinery, specialised laboratory settings or extensively trained personnel.
Collectively, our data suggested that our Iso-CHIKV-Dx diagnostic has the potential to become a sensitive and specific RT-PCR alternative by offering a promising diagnostic tool for resource-limited settings, where CHIKV and several other arboviruses are endemic.