Next-Generation Sequencing (NGS) Solutions for Biosecurity Challenges

Background:

The Covid-19 pandemic highlighted the role of international travel in facilitating the global spread of the virus and has prompted considerable research into methods of infectious disease monitoring at points-of-entry, such as international airports. The aim of this project was to deliver a proof-of-concept system for pathogen surveillance at a UK airport. Rather than a targeted approach where samples are screened for a specific pathogen of concern (e.g. SARS-CoV-2 qPCR), the customer instead required a “target-agnostic” approach — the ability to detect previously uncharacterised pathogen sequences that may represent new human health concerns.

Process:

The requirement of the solution to be capable of detecting any pathogenic microorganism present in a sample matrix meant that research and development had to focus exclusively on metagenomic next-generation sequencing (mNGS) approaches and de novo genome assembly techniques. James developed and tested numerous procedures for sample treatment and techniques to improve target capture, including methods to segregate bacterial and viral particles and preferentially filter out genomic sequences of interest while discarding waste material. He also deployed a commercial hybridisation probe capture technique, allowing a single sample to be screened for the entire genomes of 66 human viruses simultaneously. Typically, such techniques detect the presence of microbial genes by capturing short strands of DNA that contain a sequence of nucleotides known to be associated with a particular species, but they can also potentially capture very long DNA strands. When paired with long-read sequencing technologies this approach allowed for a semi-agnostic pathogen detection modality capable of detecting sequences displaying variance from any reference genome for that species.

As part of this ongoing commission, James also undertook an investigation into the design of a completely automated solution for nucleic acid extraction, for incorporation into a fully automated, end-to-end, field-based sequencing workflow.

Outcomes:

1. Novel, target-agnostic wastewater sensing capabilities were deployed as proof of concept for point-of-entry surveillance of pathogens in airplane holding tanks and wet wells at a UK airport (doi: 10.1371/journal.pgph.0001346)