Validation of the easyscreen flavivirus dengue alphavirus detection kit based on 3base amplification technology and its application to the 2016/17 Vanuatu dengue outbreak
Open Access
- 17 January 2020
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 15 (1), e0227550
- https://doi.org/10.1371/journal.pone.0227550
Abstract
The family flaviviridae and alphaviridae contain a diverse group of pathogens that cause significant morbidity and mortality worldwide. Diagnosis of the virus responsible for disease is essential to ensure patients receive appropriate clinical management. Very few real-time RT-PCR based assays are able to detect the presence of all members of these families using a single primer and probe set. We have developed a novel chemistry, 3base, which simplifies the viral nucleic acids allowing the design of RT-PCR assays capable of pan-family identification. Synthetic constructs, viral nucleic acids, intact viral particles and characterised reference materials were used to determine the specificity and sensitivity of the assays. Synthetic constructs demonstrated the sensitivities of the pan-flavivirus detection component were in the range of 13 copies per PCR. The pan-alphavirus assay had a sensitivity range of 10–25 copies per reaction depending on the viral strain. Lower limit of detection studies using whole virus particles demonstrated that sensitivity for assays was in the range of 1–2 copies per reaction. No cross reactivity was observed with a number of commonly encountered viral strains. Proficiency panels showed 100% concordance with the expected results and the assays performed as well as, if not better than, other assays used in laboratories worldwide. After initial assay validation the pan-viral assays were then tested during the 2016–2017 Vanuatu dengue-2 outbreak. Positive results were detected in 116 positives from a total of 187 suspected dengue samples. The pan-viral screening assays described here utilise a novel 3base technology and are shown to provide a sensitive and specific method to screen and thereafter speciate flavi- and/or alpha- viruses in clinical samples. The assays performed well in an outbreak situation and can be used to detect positive clinical samples containing any flavivirus or alphavirus in approximately 3 hours 30 minutes.This publication has 29 references indexed in Scilit:
- West Nile Virus, Texas, USA, 2012Emerging Infectious Diseases, 2013
- Quantitative real-time PCR detection of Zika virus and evaluation with field-caught MosquitoesVirology Journal, 2013
- The global distribution and burden of dengueNature, 2013
- Epidemiological and laboratory characterization of a yellow fever outbreak in northern Uganda, October 2010–January 2011International Journal of Infectious Diseases, 2012
- Epidemiologic update on the dengue situation in the Western Pacific Region, 2010Western Pacific Surveillance and Response Journal, 2011
- Male-female differences in the number of reported incident dengue fever cases in six Asian countriesWestern Pacific Surveillance and Response Journal, 2011
- A microbial detection array (MDA) for viral and bacterial detectionBMC Genomics, 2010
- Comparison of a novel HPV test with the Hybrid Capture II (hcII) and a reference PCR method shows high specificity and positive predictive value for 13 high-risk human papillomavirus infectionsJournal of Clinical Virology, 2008
- Risks for Ross River virus disease in tropical AustraliaInternational Journal of Epidemiology, 2005
- Association of Tonate Virus (Subtype IIIB of the Venezuelan Equine Encephalitis Complex) with Encephalitis in a HumanClinical Infectious Diseases, 2000