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

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.