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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
Emerging infectious diseases, 05/2021, Volume: 27, Issue: 5Journal Article
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.
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