Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand

Geoghegan, Jemma L.; Douglas, Jordan; Ren, Xiaoyun; Storey, Matthew; Hadfield, James; Silander, Olin K.; Freed, Nikki E.; Jelley, Lauren; Jefferies, Sarah; Sherwood, Jillian; Paine, Shevaun; Huang, Sue; Sporle, Andrew; Baker, Michael G.; Murdoch, David R.; Drummond, Alexei J.; Welch, David; Simpson, Colin R.; French, Nigel; Holmes, Edward C.; de Ligt, Joep

Real-time genomic sequencing has played a major role in tracking the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), contributing greatly to disease mitigation strategies. In August 2020, after having eliminated the virus, New Zealand experienced a second outbreak. During that outbreak, New Zealand used genomic sequencing in a primary role, leading to a second elimination of the virus. We generated genomes from 78% of the laboratory-confirmed samples of SARS-CoV-2 from the second outbreak and compared them with the available global genomic data. Genomic sequencing rapidly identified that virus causing the second outbreak in New Zealand belonged to a single cluster, thus resulting from a single introduction. However, successful identification of the origin of this outbreak was impeded by substantial biases and gaps in global sequencing data. Access to a broader and more heterogenous sample of global genomic data would strengthen efforts to locate the source of any new outbreaks.