Journal Article

Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand

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

2021

Overview

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.

• Publisher: U.S. National Center for Infectious Diseases,Centers for Disease Control and Prevention
• Subject: 2019 novel coronavirus disease / Control / coronavirus disease / Coronaviruses / COVID-19 / Datasets / Disease transmission / Epidemics / Genomes / Genomics / Health surveillance / Laboratories / Methods / New Zealand / Outbreaks / Phylogenetics / Public health / Quarantine / SARS-CoV-2 / Sentinel health events / Severe acute respiratory syndrome coronavirus 2 / Statistics / Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand / Viruses / Whole genome sequencing