Lay summary
New Zealand’s interventions to control COVID-19 have eliminated respiratory viruses that ordinarily circulate annually. An essentially immunologically-naïve population, New Zealand will likely experience larger, unseasonal, and more severe outbreaks in future - like the 2021 respiratory syncytial virus (RSV) outbreak following borders being opened briefly to Australia. As New Zealand reconnects internationally through quarantine-free travel, we will have a unique opportunity to understand how respiratory infections re-enter and become re-established - generating a complete picture of their spread in New Zealand. To do so, we will generate whole viral genomes from patient samples diagnosed with respiratory infections such as RSV and influenza viruses; and extend our genomics-informed surveillance to undiagnosed respiratory infections using a meta-transcriptomics approach. Our world-leading team of infectious disease experts will collaborate to enhance pathogen surveillance and diagnostics in New Zealand and build a genomic pathogen framework, augmenting our ability to respond to future disease outbreaks.