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


Posted: 2021-11-18 20:00:00
BMC Res Notes . 2021 Nov 17;14(1):415. doi: 10.1186/s13104-021-05827-x. Alicia Arnott # 1 2 3 , Jenny Draper # 1 , Rebecca J Rockett 2 3 , Connie Lam 2 3 , Rosemarie Sadsad 3 4 , Mailie Gall 1 , Elena Martinez 1 3 , Roy Byun 5 , Jennie Musto 5 , 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 Expand 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. Vitali.Sintchenko@health.nsw.gov.au. 8 Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia. Vitali.Sintchenko@health.nsw.gov.au. 9 Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia. Vitali.Sintchenko@health.nsw.gov.au. # Contributed equally. Item in Clipboard Alicia Arnott et al. BMC Res Notes. 2021. Show details Display options Display options Format 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 Gall 1 , Elena Martinez 1 3 , Roy Byun 5 , Jennie Musto 5 , 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. Vitali.Sintchenko@health.nsw.gov.au. 8 Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia. Vitali.Sintchenko@health.nsw.gov.au. 9 Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia. Vitali.Sintchenko@health.nsw.gov.au. # Contributed equally. Item in Clipboard CiteDisplay options Display options Format 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. © 2021. The Author(s). References Rockett RJ, Arnott A, Lam C, Sadsad R, Timms V, Gray KA, et al. Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modelling. Nat Med. 2020;26(9):1398–404. https://doi.org/10.1038/s41591-020-1000-7 . - DOI Eden J-S, Rockett RJ, Carter I, Rahman H, de Ligt J, Hadfield J, et al. An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evol. 2020. https://doi.org/10.1093/ve/veaa027 . - DOI - PubMed - PMC Miller CA, McMichael J, Dang HX, Maher CA, Ding L, Ley TJ, et al. Visualizing tumor evolution with the fishplot package for R. BMC Genomics. 2016;17(1):880. https://doi.org/10.1186/s12864-016-3195-z . - DOI - PubMed - PMC Draper, J. Epifish package for R, https://github.com/learithe/epifish McAnulty JM, Ward K. Suppressing the Epidemic in New South Wales. N Engl J Med. 2020;382: e74. https://doi.org/10.1056/NEJMc2011592 . - DOI - PubMed Show all 8 references Grant support

参考サイト PubMed: covid-19



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