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

Nicola Stephens; Michelle Mcpherson; Louise Cooley; Rob Vanhaeften; Mathilda Wilmot; Courtney Lane; Michelle Harlock; Kerryn Lodo; Natasha Castree; Torsten Seemann; Michelle Sait; Susan Ballard; Kristy Horan; Mark Veitch; Fay Johnston; Norelle Sherry; Ben Howden

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

Author: Nicola Stephens ^{1
,

2} ; Michelle McPherson ^{1
,

2} ; Louise Cooley ^{1
,

3} ; Rob Vanhaeften ⁴ ; Mathilda Wilmot ^{5
,

6} ; Courtney Lane ^{5
,

6} ; Michelle Harlock ⁷ ; Kerryn Lodo ⁷ ; Natasha Castree ⁷ ; Torsten Seemann ^{5
,

6} ; Michelle Sait ^{5
,

6} ; Susan Ballard ^{5
,

6} ; Kristy Horan ^{5
,

6} ; Mark Veitch ⁷ ; Fay Johnston ^{7
,

8} ; Norelle Sherry ^{5
,

6} ; Ben Howden ^{5
,

6}
Author Information

1. Tasmanian School of Medicine, University of Tasmania, Tasmania, Australia
2. Public Health Services, Tasmanian Department of Health, Tasmania, Australia
3. Tasmanian Health Services, Tasmanian Department of Health, Tasmania, Australia
4. Tasmanian Health Services, Tasmanian Department of Health, Tasmania, Australia
5. Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology &
6. Immunology, University of Melbourne at the Doherty Institute, Victoria, Australia
7. Public Health Services, Tasmanian Department of Health, Tasmania, Australia
8. Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
Publication Type:Journal Article
From: Western Pacific Surveillance and Response 2021;12(4):93-101
CountryWHO-WPRO
Language:English
Abstract: Objective:We undertook an integrated analysis of genomic and epidemiological data to investigate a large healthcare-associated COVID-19 outbreak and to better understand the epidemiology of all 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 SARS-CoV-2 samples or extracted RNA from those cases, were included. Sequencing was conducted by tiled amplicon PCR using ARTIC v1 or v3 primers and Illumina sequencing. Consensus sequences were generated, sequences were aligned to a reference sequence, and phylogenetic analysis performed. Genomic clusters were determined and integrated with epidemiologic data to assess any additional insights.
Results:All COVID-19 cases notified in Tasmania during the study period (n=231) and 266 SARS-CoV-2 positive samples, representing 217/231 (94%) of notified cases, were included in the study; 182/217 (84%) were clustered, 21/217 (10%) were unique, 12/217 (6%) could not be sequenced. Genomics confirmed the presence of seven epidemiological clusters, clarified transmission networks where epidemiology was unclear and additionally identified another genomic cluster which had not been identified by epidemiology alone.
Discussion
Full text:wpsar.2021.12.4.878 Stephens v2.pdf