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

Abstract

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.

Keywords: Australian Capital Territory; COVID-19; SARS-CoV-2; genomic epidemiology; pandemic.

Fig. 1.

Epidemic curve and timeline of public health interventions for SARS-CoV-2 in the Australian Capital Territory, August to November 2021. The number of reported cases (left y-axis) per day is shown as a bar chart. The cumulative percentage of the total population receiving two vaccine doses (right y-axis) is shown as a grey area curve. A timeline of the major public health interventions is shown below the charts.

Fig. 2.

Incursions and onward spread of SARS-CoV-2 B.1.617.2 (Delta) in the Australian Capital Territory (ACT), 12 August to 11 November 2021. Sequencing of SARS-CoV-2 was attempted on 80% of ACT cases reported during the study period and an additional 30 non-ACT cases. A time-structured phylogeny was estimated based on consensus sequences with ≤10% ambiguous bases (a). Tips are coloured by ACT genomic lineage. Each lineage reflects a separate incursion event with subsequent local spread, as defined by phylogenetic analysis and corroborating epidemiological information. Sequences where onwards transmission within the community was not identified within the ACT are coloured grey. The density plot shows the relative proportion of ACT genomic lineages over time, based on all sequences with ≤20% ambiguous bases (b). Both (a) and (b) are scaled to the same x-axis.

Fig. 3.

Resolution of a complex transmission chain using genomic epidemiology. Dots represent individual cases and are coloured by exposure setting. Primary, secondary and tertiary cases are marked by braces. The ACT genomic sublineage of each case is specified. Directionality of transmission, inferred from epidemiological contact tracing, laboratory information and/or genomic sequencing, is indicated by arrows. Boxes delineate separate cohorts. n.s., Not sequenced; i.s., case diagnosed interstate.

Fig. 4.

Genomic sequencing revealed two independent incursions into a social housing complex over a 3-week period. Dots represent individual cases and are coloured by ACT genomic sublineage. Primary, secondary and tertiary cases are marked by braces. Directionality of transmission, inferred from epidemiological contact tracing, laboratory information and/or genomic sequencing, is indicated by arrows. Boxes delineate separate cohorts.