Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand

Jemma L Geoghegan et al. Emerg Infect Dis. 2021 May.

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Sequenced and published genomes of global severe acute respiratory syndrome coronavirus 2 isolates. A) Proportion of global cases sequenced and shared on GISAID (https://www.gisaid.org) from December 2019 through January 2021, for which the second mode was largely driven by COG-UK as illustrated. B) Number of genomes sequenced and number of reported cases per country on a linear scale. Red, New Zealand (NZ); blue, other countries. C) Number of genomes sequenced and number of reported cases per country on a logarithmic scale. COG-UK, COVID-19 Genomics UK Consortium (https://www.cogconsortium.uk); UK, United Kingdom; US, United States.
Figure 2
Figure 2
Genomic sequence analyses of global severe acute respiratory syndrome coronavirus 2 isolates. A) Maximum-clade credibility phylogenetic tree of 2,000 subsampled global genomes (1,996 most recently sampled B.1.1.1. plus 4 non-B.1.1.1. used as an outgroup) with an outer ring colored by sampling region. B) Posterior probability of genomes within the sister clade to that of the August 2020 outbreak in New Zealand, color coded by sampling location. C) Proportion of genomes within lineage B.1.1.1. in the global dataset over time, color-coded by sampling location.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Holmes EC. Novel 2019. coronavirus genome [cited 2021 Jan 20]. https://virological.org/t/novel-2019-coronavirus-genome/319
    1. Shin MD, Shukla S, Chung YH, Beiss V, Chan SK, Ortega-Rivera OA, et al. COVID-19 vaccine development and a potential nanomaterial path forward. Nat Nanotechnol. 2020;15:646–55. 10.1038/s41565-020-0737-y - DOI - PubMed
    1. Stebbing J, Phelan A, Griffin I, Tucker C, Oechsle O, Smith D, et al. COVID-19: combining antiviral and anti-inflammatory treatments. Lancet Infect Dis. 2020;20:400–2. 10.1016/S1473-3099(20)30132-8 - DOI - PMC - PubMed
    1. Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Chall. 2017;1:33–46. 10.1002/gch2.1018 - DOI - PMC - PubMed
    1. Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018;34:4121–3. 10.1093/bioinformatics/bty407 - DOI - PMC - PubMed