Public health interventions successfully mitigated multiple incursions of SARS-CoV-2 Delta variant in the Australian Capital Territory.

The COVID-19 pandemic has presented a unique opportunity to understand how real-time pathogen genomics can be used for large-scale outbreak investigations. On 12 August 2021, the Australian Capital Territory (ACT) detected an incursion of the SARS-CoV-2 Delta (B.1.617.2) variant. Prior to this date, SARS-CoV-2 had been eliminated locally since 7 July 2020. Several public health interventions were rapidly implemented in response to the incursion, including a territory-wide lockdown and comprehensive contact tracing. The ACT has not previously used pathogen genomics at a population level in an outbreak response; therefore, this incursion also presented an opportunity to investigate the utility of genomic sequencing to support contact tracing efforts in the ACT. Sequencing of >75% of the 1793 laboratory-confirmed cases during the 3 months following the initial notification identified at least 13 independent incursions with onwards spread in the community. Stratification of cases by genomic cluster revealed that distinct cohorts were affected by the different incursions. Two incursions resulted in most of the community transmission during the study period, with persistent transmission in vulnerable sections of the community. Ultimately, both major incursions were successfully mitigated through public health interventions, including COVID-19 vaccines. The high rates of SARS-CoV-2 sequencing in the ACT and the relatively small population size facilitated detailed investigations of the patterns of virus transmission, revealing insights beyond those gathered from traditional contact tracing alone. Genomic sequencing was critical to disentangling complex transmission chains to target interventions appropriately.

Hepatitis A outbreak in Australia linked to imported Medjool dates, June-September 2021.

Abstract: Imported, minimally processed food products have been historically associated with several hepatitis A outbreaks in Australia. Here, we report the first known hepatitis A outbreak in Australia linked to consumption of imported fresh Medjool dates. Between June and September 2021, six genetically identical hepatitis A cases were notified in New South Wales and the Australian Capital Territory. All cases reported date consumption during their exposure period. The implicated dates were positive for hepatitis A virus (HAV) by reverse transcription polymerase chain reaction. Rapid detection of this outbreak and the swift implementation of control measures was facilitated by two key factors. Firstly, Australian international border closures implemented in response to the COVID-19 pandemic meant that a common locally-acquired, as opposed to travel-acquired, source for cases was strongly suspected. Secondly, prompt awareness of a hepatitis A outbreak in the United Kingdom (which was found to be associated with date consumption) allowed for early hypothesis generation and investigation. This paper details the epidemiological and microbiological factors involved in this outbreak investigation and the actions taken to mitigate public health risk.

Vaccine breakthrough infections in a highly-vaccinated Australian population during a SARS-CoV-2 Delta outbreak.

Abstract: Over 80% of residents in the Australian Capital Territory were fully vaccinated within 10 weeks of a SARS-CoV-2 Delta variant outbreak. Of the outbreak's 1,545 cases, 10% were breakthrough infections. The incidence of infections among fully- and partially-vaccinated people was 98.5% and 90% lower, respectively, than for unvaccinated people.

Travel-associated SARS-CoV-2 transmission documented with whole genome sequencing following a long-haul international flight.

BACKGROUND: Multiple instances of flight-associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission during long-haul flights have been reported during the COVID-19 pandemic. However, comprehensive investigations of passenger risk behaviours, before, during and after the flight, are scarce. METHODS: To investigate suspected SARS-CoV-2 transmission during a flight from United Arab Emirates to Australia in July 2020, systematic, repeated polymerase chain reaction (PCR) testing of passengers in hotel quarantine was linked to whole genome sequencing. Epidemiological analyses of in-depth interviews covering behaviours during the flight and activities pre- and post-boarding were used to identify risk factors for infection. RESULTS: Seventeen of the 95 passengers from four different travel origins had PCR-confirmed infection yielding indistinguishable genomic sequences. Two of the 17 passengers were symptomatic within 2 days of the flight, and classified as co-primary cases. Seven secondary cases were seated within two rows of the co-primary cases, but five economy passengers seated further away and three business class passengers were also infected (attack rate = 16% [15/93]). In multivariable analysis, being seated within two rows of a primary case [odds ratio (OR) 7.16; 95% confidence interval (CI) 1.66-30.85] and spending more than an hour in the arrival airport (OR 4.96; 95% CI 1.04-23.60) were independent predictors of secondary infection, suggesting travel-associated SARS-CoV-2 transmission likely occurred both during and after the flight. Self-reported increased hand hygiene, frequent aisle walking and using the bathroom on the plane did not independently affect the risk of SARS-CoV-2 acquisition. CONCLUSIONS: This investigation identified substantial in-flight transmission among passengers seated both within and beyond two rows of the primary cases. Infection of passengers in separate cabin classes also suggests transmission occurred outside the cabin environment, likely at the arrival airport. Recognizing that transmission may occur pre- and post-boarding may inform contact tracing advice and improve efforts to prevent future travel-associated outbreaks.

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.

The Healthy Crew, Clean Vessel, and Set Departure Date Triad: Successful Control of Outbreaks of COVID-19 On Board Four Cargo Vessels.

BACKGROUND: A variety of infectious diseases can cause outbreaks on board vessels, with both health and economic effects. Internationally, Coronavirus Disease 2019 (COVID-19) outbreaks have occurred on numerous cruise and cargo vessels and the containment measures, travel restrictions, and border closures continue to make it increasingly difficult for ship operators world-wide to be granted pratique, effect crew changes, and conduct trade. An effective outbreak management strategy is essential to achieve the outcome triad - healthy crew, clean vessel, and set departure date - while maintaining the safety of the on-shore workers and broader community and minimizing disruption to trade. This report describes the principles of COVID-19 outbreak responses on four cargo vessels, including the successful use of one vessel as a quarantine facility. METHODS: Established principles of management and the experiences of COVID-19 outbreaks on cruise ships elsewhere informed a health-lead, multi-agency, strict 14-day quarantine (Q) regime based on: population density reduction on board; crew segregation; vessel cleaning and sanitation; infection risk zones, access, and control measures; health monitoring; case identification and management; food preparation and delivery; waste management control; communication; and welfare and security. FINDINGS: Sixty-five crew were diagnosed with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection (range 2-25; attack rate 10%-81%; 15 asymptomatic). No deaths were recorded, and only one crew was hospitalized for COVID-19-related symptoms but did not require intensive care support. Catering crew were among the cases on three vessels. All non-essential crew (n-EC) and most of the cases were disembarked. During the vessel's Q period, no further cases were diagnosed on board, and no crew became symptomatic after completion of Q. The outbreak response duration was 15-17 days from initial decision.No serious health issues were reported, no response staff became infected, and only two Q protocol breaches occurred among crew. INTERPRETATION: Despite increasing risk of outbreaks on cargo vessels, maritime trade and crew exchanges must continue. The potential consequences of COVID-19 outbreaks to human life and to trade necessitate a balanced response. The principles described can offer health, financial, operational, and safety advantages.