Tweet
Emerg Infect Dis
. 2021 May;27(5):1317-1322.
doi: 10.3201/eid2705.204579.
Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand
Jemma L Geoghegan, Jordan Douglas, Xiaoyun Ren, Matthew Storey, James Hadfield, Olin K Silander, Nikki E Freed, Lauren Jelley, Sarah Jefferies, Jillian Sherwood, Shevaun Paine, Sue Huang, Andrew Sporle, Michael G Baker, David R Murdoch, Alexei J Drummond, David Welch, Colin R Simpson, Nigel French, Edward C Holmes, Joep de Ligt
- PMID: 33900175
- DOI: 10.3201/eid2705.204579
Abstract
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.
Keywords: 2019 novel coronavirus disease; COVID-19; New Zealand; SARS-CoV-2; coronavirus disease; genomics; infectious disease; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.