Next-Generation Sequencing Initiative in Nigeria and Papua New Guinea Highlights Lessons for Field-Based Biothreat Detection
In the summer of 2019, a team of GSSHealth technical experts assembled a portable, miniaturized off-grid laboratory for rapid, next-generation sequencing (NGS) of DNA and RNA. The miniaturized laboratory comprised a selection of existing, off-the-shelf technologies and batteries to facilitate robust environmental testing in remote field environments. The GSSHealth team organized all necessary items in a “Lab-in-a-Backpack format operable by a single user (see Figure 1).
Figure 1. The GSSHealth “Lab-in-a-Backpack.”
Taking their creation to a location near the GSSHealth office in Maryland, the team collected environmental samples from riverbank soil for sequencing as an initial field test and proof of concept (see Figure 2). The findings of this first deployment were then used to refine the composition of the “Lab-in-a-Backpack” prior to deployments in remote field locations in Nigeria and Papua New Guinea.
“People often want to deploy new technologies in resource-limited settings, but technology alone isn’t a magic bullet,” says Martin Adams, GSSHealth Senior Biosecurity Specialist and co-coordinator of the NGS project. “We take pride in ensuring that laboratory staff in remote settings have a voice. Local scientists—whose input is often ignored—know how to solve context-specific challenges and are critical partners in the successful implementation of new technology.”
The team conducted pre-deployment activities including determining feasible field locations and conducting risk assessments to mitigate potential complications, including safety and security issues. In parallel, the team conducted a desk review to evaluate and compare 10 new and emerging biothreat detection technologies, ultimately selecting the MinION for its field suitability. For the GSSHealth team, these initial evaluation, planning, and collaboration-building steps—and associated development of the “Lab-in-a-Backpack”—were just the beginning.
Conducting international field work that included the training of local scientists on NGS technology and coordination of environmental sample collection and testing, GSSHealth and project stakeholders successfully analyzed NGS data to identify signatures of potential pathogens and antimicrobial resistance (AMR) markers. Local laboratory professionals continued deploying NGS technology following the GSSHealth field visits, testing soil samples at sites of interest to make new discoveries. One participating site used the NGS technology to identify a local Shigella outbreak in real time, working in parallel with the local health system and offering a further proof of concept of the ability of NGS and other new technologies to contribute to outbreak response.
As shown in the COVID-19 response, evolving equipment are rapidly becoming essential tools for the rapid detection, characterization, and control of emerging diseases, allowing health authorities to accurately forecast and respond to threats.
This work was conducted as part of a US government funded project to evaluate the feasibility of the field implementation of new and innovative technologies to detect and forecast the presence of harmful biological agents. Genetic sequencing has seen a revolution in recent years, with instrument size and technical barriers being greatly reduced. With this in mind, GSSHealth identified the Oxford Nanopore MinION as a model NGS technology to fully identify usage gaps in field settings.
During the development and testing of the “Lab-in-a-Backpack,” the GSSHealth team identified local partner universities and assessed the geo-socio-political landscape in Nigeria and Papua New Guinea. Building trust and commitment with potential scientific collaborators at partner universities would be crucial to project success. The GSSHealth team engaged in informal and formal communications with on-the-ground laboratory scientists and their leadership, building consensus and sharing resources on key partnership considerations including data rights, intellectual property, ethical concerns, benefit-sharing, and requirements for IRB approval.
Figure 2. Field sample for sequencing.
“We take pride in ensuring that laboratory staff in remote settings have a voice. Local scientists know how to solve context-specific challenges and are critical partners in the successful implementation of new technology.”
Over the past several years, an increasing number of novel technologies have provided field-deployable, pathogen-agnostic, and potentially game-changing solutions for disease detection in austere environments. However, as Martin Adams stresses, platforms need to be evaluated and selected with the field application and end users in mind. Successful technology selection and implementation are based not only on platform robustness and transportability, but also on considerations such as reagent cost, sample type, sample preparation or extraction protocol, additional equipment needed, data analysis complexities, and training and technical support requirements.
While NGS and other emerging technologies are currently restricted to research use, it is essential that the global health community begin planning for eventual clinical applications of biothreat detection technologies, considering their potential utility and challenges to uptake in resource-constrained settings.
The global NGS market is expected to continue expanding over the next few years. In June 2020, an NGS diagnostic device for COVID-19 was approved for use in the US. Allowing for high-volume disease screening for more effective outbreak surveillance, the technology represents just one example of innovation contributing to more effective and scalable biothreat detection.
With further advancements in technology, the increasing availability of field appropriate and cost-effective NGS platforms will allow scientists and public health practitioners to improve global health security through enhanced biothreat detection and response systems.
For more information on GSSHealth’s recent NGS project in Nigeria and Papua New Guinea, watch Martin Adams’ lightning presentation from the Nanopore Community Meeting 2019 in New York (see Figure 3). If you are interested in partnering with us on a technology innovation project, please reach out at email@example.com
Figure 3. GSSHealth Senior Biosecurity Specialist Martin Adams, speaking on NGS field implementation at the 2019 Oxford Nanopore Community Meeting.