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.
【초록키워드】 COVID-19, coronavirus disease, SARS-CoV-2, Coronavirus disease 2019, coronavirus, Epidemiology, Sequencing, Transmission, severe acute respiratory syndrome Coronavirus, Genomics, RNA, polymerase chain reaction, Phylogenetic analysis, Surveillance, outbreak, Cluster, community transmission, Genomic analysis, epidemiological data, respiratory, information, Illumina, genomic, imported cases, reference sequence, Evidence, Analysis, evidence of, Chain Reaction, source of infection, acute respiratory syndrome, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, confirmation, COVID-19 case, sequences, study period, sequence, epidemiological links, consensus sequences, primer, epidemiological link, positive sample, objective, polymerase chain, Seven, Result, collected, sequenced, conducted, provided, was performed, unique, representing, aligned, 【제목키워드】 genomic, Public health intervention,