The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand

Abstract

Background Real-time genomic sequencing has played a major role in tracking the global spread and local transmission of SARS-CoV-2, contributing greatly to disease mitigation strategies. After effectively eliminating the virus, New Zealand experienced a second outbreak of SARS-CoV-2 in August 2020. During this August outbreak, New Zealand utilised genomic sequencing in a primary role to support its track and trace efforts for the first time, leading to a second successful elimination of the virus. Methods We generated the genomes of 80% of the laboratory-confirmed samples of SARS-CoV-2 from New Zealand’s August 2020 outbreak and compared these genomes to the available global genomic data. Findings Genomic sequencing was able to rapidly identify that the new COVID-19 cases in New Zealand belonged to a single cluster and hence resulted from a single introduction. However, successful identification of the origin of this outbreak was impeded by substantial biases and gaps in global sequencing data. Interpretation Access to a broader and more heterogenous sample of global genomic data would strengthen efforts to locate the source of any new outbreaks. Funding This work was funded by the Ministry of Health of New Zealand, New Zealand Ministry of Business, Innovation and Employment COVID-19 Innovation Acceleration Fund (CIAF-0470), ESR Strategic Innovation Fund and the New Zealand Health Research Council (20/1018 and 20/1041).