Why it matters
Novel sequencing technologies provide new opportunities in infectious disease detection and diagnostics, such as rapid sequencing in response to the early phase of an epidemic or the determination of genotypes during the investigation of a bio-threat event. Portable near-future sequencing instruments should be low cost to use and widely deployable.
NGS, also often referred to as High-Throughput DNA Sequencing (HTS) methods, will enable a paradigm shift. Biological field detection is currently based on PCR1-related methods which rely on customised reagents targeting only a limited set of B agents, while NGS targets any B agent (‘wide-spectrum’ or ‘agnostic’ method). It also enables strain-level identification without a priori information on the investigated B-agent (which PCR does not) which is useful for forensics purposes. The use of NGS in the defense context can be wider than just biodefense (general water and food quality control, sanitary medical purposes etc).
One of the key challenges in investigating alleged use of biological weapons is the ability to differentiate intentional spread from naturally-occurring biological events through a scientific assessment, including molecular characterisation of the suspected pathogen. Presence of a pathogen outside its natural area of occurrence or changes in its genetic sequence may indicate deliberate spread. Therefore, molecular characterisation of a pathogen is an important part of a strong response to biological threats as the origin(s) of the outbreak can be identified and an appropriate course of action followed. Genetic sequencing identifies the exact genetic code of the pathogen, thus identifying the species and/or strain in question. Currently, sequencing requires massive hardware, although the recent, next generation sequencing methods, especially their portable/field deployable applications, have become a strong alternative for detection and typing of bio-threat agents. Novel sequencing technologies however require special expertise such as advanced bioinformatics.
1. Polymerase Chain Reaction targeting a specific genetic motif in a genome