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
. 2022 Oct 13;18(10):e1010415.
doi: 10.1371/journal.pgen.1010415. eCollection 2022 Oct.

New rules for genomics-informed COVID-19 responses-Lessons learned from the first waves of the Omicron variant in Australia

Ashleigh F Porter  1 , Norelle Sherry  2 , Patiyan Andersson  2 , Sandra A Johnson  2 , Sebastian Duchene  1 , Benjamin P Howden  1   2
Affiliations

New rules for genomics-informed COVID-19 responses-Lessons learned from the first waves of the Omicron variant in Australia

Ashleigh F Porter et al. PLoS Genet. .
No abstract available

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Epidemiological curve of SARS-CoV-2 in Australia, demonstrating the rapid rise in cases in 2022 upon emergence of the Omicron variant, and the diminishing cumulative proportion of cases sequenced.
Panel A has a reduced scale to visualise the limited case numbers during January 2020 to July 2021 inclusive. Panel B includes data from August 2021 to April 2022 inclusive. The case numbers (Y-axis, left) obtained from PCR tests and rapid antigen tests (RAT) are respectively shown in green and blue. The cumulative percentage of cases sequenced (Y-axis, right) is visualised as an orange line. The emergence of variants of concern (Alpha, Delta and Omicron), as well as the 4 phases of the Victorian Government’s “Roadmap” [2] for easing COVID-19 restrictions, are shown at the top of the curve. The Victorian Roadmap is an example of jurisdiction-managed responses to the COVID-19 pandemic. The roadmap included four phases (A-D) that gradually eased restrictions on travel and social distancing measures, partly based on the percentage of the population fully vaccinated. Phase A focused on returning students to the classroom, whereas Phase B and C guided the return to work and travel upon reaching vaccination targets of 70% and 80% of the population (16+) fully vaccinated, respectively. The final stage, Phase D, was reached when 80% of the population (12+) was fully vaccinated, allowing the restrictions to ease and align with Australia’s National COVID-19 response.
Fig 2
Fig 2. Visualisation of different sources of COVID-19 data, including sequence data and metadata, and how they feed into genomic epidemiology and link to research and policy making decisions.
Here we highlight the flow and collaboration within the Australian COVID-19 pandemic response network, between public and private pathology, public and private pathology laboratories, bioinformatics laboratories, research groups and the health departments. The infographic on the left represents the pipeline of sequence data, sourced from samples collected from the public, feeding into genomic epidemiology and phylogenomic tools. The coloured bubbles on the right represent additional sources of data, such as epidemiological metadata (yellow bubbles) or global surveillance data (orange bubbles).
Fig 3
Fig 3. Illustration of the current “non-strategic” sequencing used for monitoring the COVID-19 pandemic, in comparison to the plan we have outlined as our “ideal dataset”.
The two main streams of sequencing we have described, focused and representative sampling, are represented by the orange and green boxes, respectively. These streams are shown along with surveillance sampling, represented by the blue box. The size of each box represents the proportion of sequenced genomes being generated from each stream. The associated metadata with each stream is represented by a coloured bubble in the right panel. Following the blue arrows, we overview the parameters we can estimate from the “ideal dataset” sequencing strategy, combined with metadata.
See this image and copyright information in PMC

References

    1. Lane CR, Sherry NL, Porter AF, Duchene S, Horan K, Andersson P, et al.. Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study. Lancet Public Health. 2021;6(8):e547–e56. Epub 2021/07/13. doi: 10.1016/S2468-2667(21)00133-X ; PubMed Central PMCID: PMC8270762. - DOI - PMC - PubMed
    1. Victorian Government. Australia. Victoria’s Roadmap: Delivering the National Plan, 2021. [cited 2022 Aug 25]. Available from: https://www.premier.vic.gov.au/sites/default/files/2021-09/210919%20-%20....
    1. Tosif S, Haycroft ER, Sarkar S, Toh ZQ, DL A-h, Donato C, et al.. Virology and immune dynamics reveal high household transmission of ancestral SARS-CoV-2 strain. 2022. - PMC - PubMed
    1. Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, Mumford JA, et al.. Unifying the epidemiological and evolutionary dynamics of pathogens. science. 2004;303(5656):327–32. doi: 10.1126/science.1090727 - DOI - PubMed
    1. Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian phylogeography finds its roots. PLoS computational biology. 2009;5(9):e1000520. doi: 10.1371/journal.pcbi.1000520 - DOI - PMC - PubMed

Publication types

Supplementary concepts