Exploring the depth and breadth of the genomics toolbox during the COVID-19 pandemic: insights from Aotearoa New Zealand

Abstract

Background: Genomic technologies have become routine in the surveillance and monitoring of the coronavirus disease 2019 (COVID-19) pandemic, as evidenced by the millions of SARS-CoV-2 sequences uploaded to international databases. Yet the ways in which these technologies have been applied to manage the pandemic are varied.

Main text: Aotearoa New Zealand was one of a small number of countries to adopt an elimination strategy for COVID-19, establishing a managed isolation and quarantine system for all international arrivals. To aid our response, we rapidly set up and scaled our use of genomic technologies to help identify community cases of COVID-19, to understand how they had arisen, and to determine the appropriate action to maintain elimination. Once New Zealand pivoted from elimination to suppression in late 2021, our genomic response changed to focusing on identifying new variants arriving at the border, tracking their incidence around the country, and examining any links between specific variants and increased disease severity. Wastewater detection, quantitation and variant detection were also phased into the response. Here, we explore New Zealand's genomic journey through the pandemic and provide a high-level overview of the lessons learned and potential future capabilities to better prepare for future pandemics.

Conclusions: Our commentary is aimed at health professionals and decision-makers who might not be familiar with genetic technologies, how they can be used, and why this is an area with great potential to assist in disease detection and tracking now and in the future.

Keywords: COVID-19; Genomic surveillance; Genomics; SARS-CoV-2; Variants; Wastewater surveillance; Whole genome sequencing.

Fig. 1

Percentage of border and community cases sequenced (top panel) and number of daily confirmed COVID-19 cases by reported date (bottom panel) in Aotearoa New Zealand. The timing of public health measures under the elimination (Alert Levels 1–4) and suppression strategies (COVID-10 Protection Framework) are also shown as are the arrival of Delta and Omicron, and national border closures

Fig. 2

The many modes of genomic surveillance