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Updated: Jul 13, 2026
Multiplexed Isothermal Amplification Based Diagnostic Platform to Detect Zika, Chikungunya, and Dengue 1
Published on: March 13, 2018
Molecular diagnosis and analysis of Chikungunya virus
Carolyn J Edwards1, Stephen R Welch, John Chamberlain
1Novel and Dangerous Pathogens Department, Centre for Emergency Preparedness and Response, Health Protection Agency, Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom. carolyn.edwards@hpa.org.uk
Background:
In March 2005 a Chikungunya fever outbreak began on the islands of the Indian Ocean. The number of cases of this disease dramatically rose amongst these islands before affecting over a million people in India. Travellers to these regions have returned to the UK with the disease leading to a greater than 15-fold increase in the annual number of Chikungunya virus (CHIKV) sero-positive samples in 2006.
Objectives:
A real-time RT-PCR test was developed for CHIKV and designed to detect currently circulating strains of virus as well as other genotypes. Its sensitivity was compared with an existing standard RT-PCR assay and a previously published real-time assay.
Study Design:
A real-time RT-PCR assay was optimised and evaluated using a panel of 55 clinical serum samples and a synthetic RNA transcript as a positive control. Nucleotide sequencing of part of the E1 gene of CHIKV was used to investigate the relatedness of the samples.
Results:
The real-time RT-PCR was 10-fold more sensitive than a conventional block-based RT-PCR and could detect as low as 20 copies of RNA transcript. The assay also had 10-fold improved sensitivity in detecting the outbreak strain of virus when compared to another published TaqMan assay. Analysis of sequences from patients that had travelled to India, Mauritius or the Seychelles showed high similarity with published sequences from the Indian Ocean island of Réunion.
Conclusions:
A sensitive and rapid real-time RT-PCR assay has been developed for CHIKV and tested against current isolates.
Insights
A new real-time RT-PCR assay offers a highly sensitive method for detecting Chikungunya virus (CHIKV). This rapid diagnostic tool is crucial for identifying the virus, especially during outbreaks.
Area of Science:
- Medical Virology
- Molecular Diagnostics
- Epidemiology
Background:
- Chikungunya fever outbreak on Indian Ocean islands in 2005, spreading to over a million in India.
- Increased CHIKV cases in the UK due to returning travelers, with a 15-fold rise in sero-positive samples in 2006.
Purpose of the Study:
- Develop a real-time RT-PCR assay for Chikungunya virus (CHIKV).
- Ensure detection of currently circulating strains and other genotypes.
- Compare the new assay's sensitivity against existing standard and real-time RT-PCR methods.
Main Methods:
- Optimized and evaluated a real-time RT-PCR assay using 55 clinical serum samples.
- Utilized a synthetic RNA transcript as a positive control.
- Performed nucleotide sequencing of the CHIKV E1 gene to analyze sample relatedness.
Main Results:
- The real-time RT-PCR assay demonstrated 10-fold higher sensitivity than conventional RT-PCR, detecting as low as 20 RNA copies.
- Achieved 10-fold improved sensitivity in detecting the outbreak strain compared to a published TaqMan assay.
- Sequence analysis revealed high similarity between samples from travelers and the Réunion island CHIKV strain.
Conclusions:
- A sensitive and rapid real-time RT-PCR assay for CHIKV has been successfully developed.
- The assay is effective in detecting current viral isolates, including outbreak strains.
