In the COVID-19 global pandemic over 100,000 viral genomes have now been characterised, and made accessible to the global community. In the context of Aotearoa New Zealand’s pandemic response, the genomic sequencing of positive COVID-19 samples will become an increasingly important tool that must be seamlessly integrated into a holistic health response. The aim of this rapid review is to describe and explore the role genomic sequencing and (phylogenetic) analysis has played and may play, in managing the pandemic across Aotearoa New Zealand.
- Aotearoa New Zealand should continue its innovation in the COVID-19 genomics space. The speed at which samples are shipped and genomes can be sequenced remains a priority if genomic data is going to be useful in real-time contact tracing and cluster analysis.
- A priority system for genomic analysis needs to be embedded in the pandemic response system that can rapidly report viral lineages (and mutations therein) from ‘urgent samples’ to contact tracers.
- Protocols and workflows should be put in place to sequence ALL samples that test positive.
- Aotearoa New Zealand needs to embrace genomic tools and analyses for long-term monitoring of viral evolution. This is not simply an academic exercise, rather there is a pressing need to monitor the viral lineages that are circulating (akin to seasonal influenza tracking).