Diagnosis of Viral Families Using a Nucleic Acid Simplification Technique

Abstract

We have developed a novel strategy to simplify microbial nucleic acids termed 3base™. This technology uses the chemical sodium bisulphite to reduce the genome from adenine, cytosine, guanine, and thymine or uracil, in the case of RNA containing viruses, to adenine, guanine and thymine thus reducing genome complexity. The method has been applied to the detection of high-risk human papilloma virus (HPV), gastrointestinal pathogens, alphaviruses, flaviviruses, dengue and more recently coronaviruses. Currently, there are very few real-time RT-PCR based assays that can detect the presence of all members of these viral families using conventional approaches. This strategy allows the design of assays that are capable of pan-family detection. The pan-viral assays provide a sensitive and specific method to screen and thereafter speciate viral families in clinical samples. The assays have proven to perform well using clinical samples and additionally during an outbreak of dengue fever that occurred in 2016/17 on the islands of Vanuatu. The 3base™ assays can be used to detect positive clinical samples containing any viral family generally in less than 3 hours making them ideally suited to viral surveillance and perhaps the discovery of emerging viruses in families without prior sequence knowledge of the pathogen.