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. 2021 Dec 22;12(4):1-9.
doi: 10.5365/wpsar.2021.12.4.878. eCollection 2021 Oct-Dec.

COVID-19: Integrating genomic and epidemiological data to inform public health interventions and policy in Tasmania, Australia

Nicola Stephens  1   2 , Michelle McPherson  1   2 , Louise Cooley  1   3 , Rob Vanhaeften  3 , Mathilda Wilmot  4 , Courtney Lane  4 , Michelle Harlock  2 , Kerryn Lodo  2 , Natasha Castree  2 , Torsten Seemann  4 , Michelle Sait  4 , Susan Ballard  4 , Kristy Horan  4 , Mark Veitch  2 , Fay Johnston  2   5 , Norelle Sherry  4 , Ben Howden  4
Affiliations

COVID-19: Integrating genomic and epidemiological data to inform public health interventions and policy in Tasmania, Australia

Nicola Stephens et al. Western Pac Surveill Response J. .

Abstract

Objective: We undertook an integrated analysis of genomic and epidemiological data to investigate a large health-care-associated outbreak of coronavirus disease 2019 (COVID-19) and to better understand the epidemiology of COVID-19 cases in Tasmania, Australia.

Methods: Epidemiological data collected on COVID-19 cases notified in Tasmania between 2 March and 15 May 2020, and positive samples of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or RNA extracted from the samples were included. Sequencing was conducted by tiled amplicon polymerase chain reaction with ARTIC v1 or v3 primers and Illumina sequencing. Consensus sequences were generated, sequences were aligned to a reference sequence and phylogenetic analysis was performed. Genomic clusters were determined and integrated with epidemiological data to provide additional information.

Results: All 231 COVID-19 cases notified in Tasmania during the study period and 266 SARS-CoV-2-positive samples, representing 217/231 (94%) notified cases, were included; 184/217 (84%) were clustered, 21/217 (10%) were unique and 12/217 (6%) could not be sequenced. Genomics confirmed the presence of seven clusters already identified through epidemiological links, clarified transmission networks in which the epidemiology had been unclear and identified one cluster that had not previously been recognized.

Discussion: Genomic analysis provided useful additional information on COVID-19 in Tasmania, including evidence of a large health-care-associated outbreak linked to an overseas cruise, the probable source of infection in cases with no previously identified epidemiological link and confirmation that there was no identified community transmission from other imported cases. Genomic insights are an important component of the response to COVID-19, and continuing genomic surveillance is warranted.

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Figures

Figure 1
Figure 1
Epidemic curve of Tasmanian COVID-19 cases by genomic cluster
Figure 2
Figure 2
Tasmanian COVID-19 cases by epidemiological link, genomic cluster and putative source of acquisition, 2 March–15 May 2020
See this image and copyright information in PMC

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