Next-Generation Sequencing for Biodefense: Biothreat Detection, Forensics, and the Clinic

Abstract

BACKGROUND Next-generation sequencing (NGS) is revolutionizing a variety of molecular biology fields including bioforensics, biosurveillance, and infectious disease diagnostics. For pathogen detection, the ability to sequence all nucleic acids in a sample allows near limitless multiplexability, free from a priori knowledge regarding an etiologic agent as is typically required for targeted molecular assays such as real-time PCR. Furthermore, sequencing capabilities can generate in depth genomic information, allowing detailed molecular epidemiological studies and bioforensics analysis, which is critical for source agent identification in a biothreat outbreak. However, lack of analytical specificity, inherent to NGS, presents challenges for regulated applications such as clinical diagnostics and molecular attribution. CONTENT Here, we discuss NGS applications in the context of preparedness and biothreat readiness. Specifically, we investigate current and future applications of NGS technologies to affect the fields of biosurveillance, bioforensics, and clinical diagnostics with specific focus on biodefense. SUMMARY Overall, there are many advantages to the implementation of NGS for preparedness and readiness against biowarfare agents, from forensics to diagnostics. However, appropriate caveats must be associated with any technology. This includes NGS. While NGS is not the panacea replacing all molecular techniques, it will greatly enhance the ability to detect, characterize, and diagnose biowarfare agents, thus providing an excellent addition to the biodefense toolbox of biosurveillance, bioforensics, and biothreat diagnosis.

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

“…Hlai, which is one important branch of the Tai-Kadai language, is widely spoken by more than 1.51 million Hainan Li for daily communications at present [31,32].In the field of massively parallel sequence (MPS), for the past decade, there are tremendous advances had been made in the aspect of accuracy, speed, read length, and throughput, as well as the substantial cost reduction. Together, these progresses democratized this technology and laid a solid foundation for the future development of abundant applications in basic subjects and translational research areas, such as clinical diagnostics, agrigenomics, and forensic sciences [33][34][35][36][37][38][39]. The ForenSeq™ DNA Signature Prep Kit, as the first commercial MPS-based and forensic related kit formally released in 2015, made full use of the MPS method's advantages by means of the simultaneous and compound amplification of either greater than 150 loci including various types of genetic markers.…”

On DNA Signatures, Their Dual-Use Potential for GMO Counterfeiting, and a Cyber-Based Security Solution

“…Yet, as with microbial forensics, “resolving with high confidence whether or not the outbreak” - or the occurrence of illicit or manipulated GMOs - “manifested as a result of a natural, accidental, or deliberate event is crucial” (Murch, 2015). While more difficult to realize, the above denial part may effectively complement previous efforts to assign molecular attribution (see also Minogue et al, 2019).…”

A Survey of Antimicrobial Resistance Determinants in Category A Select Agents, Exempt Strains, and Near-Neighbor Species

“…Provided suitable sensitivity can be achieved and data processing simplified, this is where rapidly evolving technologies such as next generation sequencing (NGS) may find tremendous application [56]. Several excellent studies have recently demonstrated use of targeted pyrosequencing and next generation sequencing approaches to rapid detect and identify both horizontally and vertically transmitted AMR determinants within Select Agent strains [57][58][59].…”