COVID-19 in health care workers, Australia 2020.

BACKGROUND: Health care workers are at increased risk of SARS-CoV-2 infection due to potential exposure to patients or staff in health care settings. Australian health care services and health care workers experienced intense pressure to prepare for and respond to SARS-CoV-2 infections. We summarise national data on health care worker infections and associated outbreaks during 2020. METHODS: We collected aggregated data on infected health care workers and outbreaks in health care facilities from all jurisdictions. Health care workers working solely in residential aged care and outbreaks in residential aged care facilities were excluded. Jurisdictions provided data on the number of health care setting outbreaks, confirmed cases, hospitalisation, source of infection, and health care worker role. We analysed data for two periods that aligned with two distinct peaks in the epidemic relative to 1 June 2020, referred to here as the first wave (23 January - 31 May 2020) and the second wave (1 June - 18 September 2020). RESULTS: Jurisdictions reported a total of 2,163 health care worker infections with SARS-CoV-2 during the surveillance period. Source of acquisition was known for 81.0% of cases (1,667/2,059). The majority of cases in the first wave were acquired overseas, shifting to locally-acquired cases in the second wave. The odds of infection in the second wave compared to the first wave were higher for nurses/midwives (odds ratio, OR: 1.61; 95% confidence interval (95% CI): 1.32-2.00), lower for medical practitioners (OR: 0.36; 95% CI: 0.28-0.47) and did not differ for 'other' health care workers (OR: 1.07; 95% CI: 0. 87-1.32). The odds of infection in the second wave were higher in a health care setting (OR: 1.76; 95% CI: 1.28-2.41) than in the community. There were 120 outbreaks in health care settings with 1,428 cases, of which 56.7% (809/1,428) were health care workers. The majority (88/120; 73.8%) of outbreaks in health care settings occurred in the second wave of the epidemic, with 90.9% of these (80/88) occurring in Victoria. CONCLUSIONS: In the second wave of the epidemic, when there was heightened community transmission, health care workers were more likely to be infected in the workplace. Throughout the epidemic, nurses were more likely to be infected than staff in other roles.

Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study.

BACKGROUND: A cornerstone of Australia's ability to control COVID-19 has been effective border control with an extensive supervised quarantine programme. However, a rapid recrudescence of COVID-19 was observed in the state of Victoria in June, 2020. We aim to describe the genomic findings that located the source of this second wave and show the role of genomic epidemiology in the successful elimination of COVID-19 for a second time in Australia. METHODS: In this observational, genomic epidemiological study, we did genomic sequencing of all laboratory-confirmed cases of COVID-19 diagnosed in Victoria, Australia between Jan 25, 2020, and Jan 31, 2021. We did phylogenetic analyses, genomic cluster discovery, and integrated results with epidemiological data (detailed information on demographics, risk factors, and exposure) collected via interview by the Victorian Government Department of Health. Genomic transmission networks were used to group multiple genomic clusters when epidemiological and genomic data suggested they arose from a single importation event and diversified within Victoria. To identify transmission of emergent lineages between Victoria and other states or territories in Australia, all publicly available SARS-CoV-2 sequences uploaded before Feb 11, 2021, were obtained from the national sequence sharing programme AusTrakka, and epidemiological data were obtained from the submitting laboratories. We did phylodynamic analyses to estimate the growth rate, doubling time, and number of days from the first local infection to the collection of the first sequenced genome for the dominant local cluster, and compared our growth estimates to previously published estimates from a similar growth phase of lineage B.1.1.7 (also known as the Alpha variant) in the UK. FINDINGS: Between Jan 25, 2020, and Jan 31, 2021, there were 20 451 laboratory-confirmed cases of COVID-19 in Victoria, Australia, of which 15 431 were submitted for sequencing, and 11 711 met all quality control metrics and were included in our analysis. We identified 595 genomic clusters, with a median of five cases per cluster (IQR 2-11). Overall, samples from 11 503 (98·2%) of 11 711 cases clustered with another sample in Victoria, either within a genomic cluster or transmission network. Genomic analysis revealed that 10 426 cases, including 10 416 (98·4%) of 10 584 locally acquired cases, diagnosed during the second wave (between June and October, 2020) were derived from a single incursion from hotel quarantine, with the outbreak lineage (transmission network G, lineage D.2) rapidly detected in other Australian states and territories. Phylodynamic analyses indicated that the epidemic growth rate of the outbreak lineage in Victoria during the initial growth phase (samples collected between June 4 and July 9, 2020; 47·4 putative transmission events, per branch, per year [1/years; 95% credible interval 26·0-85·0]), was similar to that of other reported variants, such as B.1.1.7 in the UK (mean approximately 71·5 1/years). Strict interventions were implemented, and the outbreak lineage has not been detected in Australia since Oct 29, 2020. Subsequent cases represented independent international or interstate introductions, with limited local spread. INTERPRETATION: Our study highlights how rapid escalation of clonal outbreaks can occur from a single incursion. However, strict quarantine measures and decisive public health responses to emergent cases are effective, even with high epidemic growth rates. Real-time genomic surveillance can alter the way in which public health agencies view and respond to COVID-19 outbreaks. FUNDING: The Victorian Government, the National Health and Medical Research Council Australia, and the Medical Research Future Fund.

Tracking the COVID-19 pandemic in Australia using genomics.

Genomic sequencing has significant potential to inform public health management for SARS-CoV-2. Here we report high-throughput genomics for SARS-CoV-2, sequencing 80% of cases in Victoria, Australia (population 6.24 million) between 6 January and 14 April 2020 (total 1,333 COVID-19 cases). We integrate epidemiological, genomic and phylodynamic data to identify clusters and impact of interventions. The global diversity of SARS-CoV-2 is represented, consistent with multiple importations. Seventy-six distinct genomic clusters were identified, including large clusters associated with social venues, healthcare and cruise ships. Sequencing sequential samples from 98 patients reveals minimal intra-patient SARS-CoV-2 genomic diversity. Phylodynamic modelling indicates a significant reduction in the effective viral reproductive number (Re) from 1.63 to 0.48 after implementing travel restrictions and physical distancing. Our data provide a concrete framework for the use of SARS-CoV-2 genomics in public health responses, including its use to rapidly identify SARS-CoV-2 transmission chains, increasingly important as social restrictions ease globally.