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

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.

Lessons learnt from the first large outbreak of COVID-19 in health-care settings in Tasmania, Australia.

PROBLEM: One month after the initial case of coronavirus disease 2019 (COVID-19) in Tasmania, an island state of Australia, two health-care workers (HCWs) from a single regional hospital were notified to public health authorities following positive tests for SARS-CoV-2 nucleic acid. These were the first recognized cases in an outbreak that overwhelmed the hospital's ability to function. CONTEXT: The outbreak originated from two index cases. Both had returned to Tasmania following travel on a cruise ship and required hospital admission for management of COVID-19. A total of 138 cases were subsequently linked to this outbreak: 81 HCWs (most being nurses) and 23 patients across three hospitals, one resident of an aged-care facility and 33 close contacts. ACTION: The outbreak was controlled through the identification and isolation of cases, identification and quarantining of close contacts and their household members, closure of the affected facilities and community-level restrictions to reduce social mixing in the affected region. LESSONS LEARNT: Factors that were likely to have contributed to ongoing transmission in this setting included workplace practices that prevented adequate physical distancing, attending work while symptomatic, challenges in rapidly identifying contacts, mobility of staff and patients between facilities, and challenges in the implementation of infection control practices. DISCUSSION: Many commonly accepted hospital practices before the COVID-19 pandemic amplified the outbreak. The lessons learnt from this investigation changed work practices for HCWs and led to wider public health interventions in the management of potential primary and secondary contacts.