Next Generation Sequencing (NGS) for biological threat preparedness

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

The way ahead

Development of field-ready sequencing technology could be used as part of a real-time response to an alleged bio-attack or an infectious disease outbreak, if the necessary equipment is highly portable/field deployable and the protocols could be simple, rapid and robust.

Real-time data of an outbreak could reveal key indicators of an emerging epidemic including intentional spread of a pathogen. Furthermore, data not considered sensitive can be shared through on-line cloud servers. 

Next stages would require improvements in the following areas:

• Developing of sample preparation and sequencing method for complex field samples. At the moment NGS is best applied when analyzing nearly pure cultures or other non-high background samples.
   
• Development of secure real-time exchange capabilities and platforms for sharing of data and information from the field would allow the bioinformatics analysis to be performed by other laboratories than the ones doing the sequencing. 
   
• There is also a need for improving the accuracy of reference databases which could be used in an investigation.
   
• Developing end user-friendly interface for field sequencing is also required.