Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand

Details

• Alternative Title:
  Emerg Infect Dis
• Personal Author:
  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
• Description:
  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.
• Subjects:
  Coronavirus Infections Covid-19 Disease Outbreaks Genomics Humans Sars-Cov-2
• Source:
  Emerg Infect Dis. 27(5):1317-1322
• Pubmed ID:
  33900175
• Pubmed Central ID:
  PMC8084492
• Document Type:
  Journal Article
• Place as Subject:
  New Zealand
• Location:
  Oceania
• Volume:
  27
• Issue:
  5
• Collection(s):
  Emerging Infectious Diseases
• Main Document Checksum:
  urn:sha256:2f5ab39dc1911fa5275c4e3b701ad649c174e0e2da6d5301b2c627da8417c2ba
• Download URL:
  https://stacks.cdc.gov/view/cdc/106023/cdc_106023_DS1.pdf
• File Type:
  [PDF - 3.66 MB ]