Documenting elimination of co-circulating COVID-19 clusters using genomics in New South Wales, Australia

Alicia Arnott; Jenny Draper; Rebecca J Rockett; Connie Lam; Rosemarie Sadsad; Mailie Gall; Elena Martinez; Roy Byun; Jennie Musto; Ben Marais; Sharon C-A Chen; Jen Kok; Dominic E Dwyer; Vitali Sintchenko

doi:10.1186/s13104-021-05827-x

Documenting elimination of co-circulating COVID-19 clusters using genomics in New South Wales, Australia

BMC Res Notes. 2021 Nov 17;14(1):415. doi: 10.1186/s13104-021-05827-x.

Authors

Alicia Arnott^#^{1

2

3}, Jenny Draper^#¹, Rebecca J Rockett^{2

3}, Connie Lam^{2

3}, Rosemarie Sadsad^{3

4}, Mailie Gall¹, Elena Martinez^{1

3}, Roy Byun⁵, Jennie Musto⁵, Ben Marais^{2

6}, Sharon C-A Chen^{1

2

3}, Jen Kok^{1

2

3}, Dominic E Dwyer^{1

2

3}, Vitali Sintchenko^{7

8

9}

Affiliations

¹ Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia.
² Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.
³ Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia.
⁴ Sydney Informatics Hub, Core Research Facilities, The University of Sydney, Sydney, NSW, Australia.
⁵ Health Protection New South Wales, NSW Ministry of Health, Sydney, NSW, Australia.
⁶ Children's Hospital at Westmead, Sydney, NSW, Australia.
⁷ Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia. [email protected].
⁸ Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia. [email protected].
⁹ Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia. [email protected].

^# Contributed equally.

Abstract

Objective: To adapt 'fishplots' to describe real-time evolution of SARS-CoV-2 genomic clusters.

Results: This novel analysis adapted the fishplot to depict the size and duration of circulating genomic clusters over time in New South Wales, Australia. It illuminated the effectiveness of interventions on the emergence, spread and eventual elimination of clusters and distilled genomic data into clear information to inform public health action.

Keywords: Australia; Bioinformatics; Genomic epidemiology; SARS-CoV-2; Whole genome sequencing.

MeSH terms

Australia
COVID-19*
Genomics
Humans
New South Wales
SARS-CoV-2

Abstract

MeSH terms

Grants and funding