London Calling 2023: The value of real-time, long-read sequencing for public health

Real-time, whole-genome sequencing using the Oxford Nanopore Midnight protocol was used to support the COVID-19 response in Aotearoa New Zealand by providing an additional line of evidence to contact tracers and policy officials. The data were successfully used to demonstrate the airborne nature of SARS-CoV-2 and enhance mitigation measures in quarantine settings. In addition to the real-time nature of Oxford Nanopore long-read sequencing, it also offers further public health value as demonstrated by the generation of local reference genomes and their use in pangenome graphs for reliable outbreak detection without reference bias. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves the mapping rates and variant calling (of both simple and complex variants) for simulated and real datasets of Neisseria meningitidis.