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Genome sequencing and genomic clustering to SARS-CoV-2 in Victoria 23 July 2021

Report date: 23 July 2021

Report period (4 weeks): 22 June 2021 – 19 July 2021

Published date: 30 July 2021

The public health genomic sequencing laboratory at the Doherty Institute (the Microbiological Diagnostic Unit Public Health Laboratory) aims to perform genome sequencing of all COVID-19 cases in Victoria. Identifying genomic clusters and linking this information with epidemiological data captured by the Department of Health (DH) can help identify outbreaks, potential sources of infection, and determine which people are more likely to have transmitted the virus to each other. Sharing the data internationally can help understand the evolution of the virus globally.

Figure 1: Epidemic curve of Victorian COVID-19 cases diagnosed between 15 January 2020 and 19 July 2021.

As of 23 July 2021 sequence data was available for 15,853 (76.2%) Victorian COVID-19 cases diagnosed up to and including 19 July 2021 are included in the following analysis.

Not Available - Recently identified cases without available sequence data may include those currently undergoing and/or pending sequencing, and the proportion of cases with available sequence data may increase as sequencing is completed. Cases from the first and second waves where sequence data is not available are unlikely to become available.


Figure 2: Timeline of Victorian COVID-19 genomic clusters, including cases diagnosed between 15 January 2020 and 19 July 2021.

A group of genome sequences that are more closely related to each other and represent a group of cases more likely to have transmitted it to each other, is referred to as a ‘genomic cluster’.

In the past 4 weeks (22 June 2021 – 19 July 2021) there were 100 successfully sequenced cases of COVID-19 in Victoria, of these 73 (33%) were locally acquired and 27 (27%) were travel associated.

‘Network 1’, ‘Network 2’, ‘Network 3’, ‘Network 4’,  ‘Network 5’, ‘Network 6’, ‘Network 7’, ‘Network 8’ and ‘Network 9’ are discrete transmission networks. In this context, a transmission network represents a group of very closely related genomic clusters. Each transmission network is thought to represent a separate but single importation of the virus into Victoria, with genomic diversity arising as the virus has circulated locally. Genomic clusters within these transmission networks have been grouped and collapsed to enable visualisation.

Genomic clusters with fewer than five cases and genomic clusters involving only cases suspected to have acquired their infection overseas have been grouped as ‘Fewer than 5 cases’ and ‘Travel associated’ respectively. Cases not currently found within a genomic cluster grouped as ‘Not clustered’.

Genomic cluster names are arbitrary and do not reflect relationships between clusters.

Of the two new Transmission Networks:

  • Network 7 – Relates to the Kappa (B.1.617.1 lineage) outbreak. The sequence from the initial case detected in Victoria was most closely related to sequences from two cases identified in South Australian Hotel Quarantine, shared via the national AusTrakka platform.
  • Network 8 – Relates to the Victorian Delta (B.1.617.2 lineage) outbreak. After identification of local cases of the Delta Lineage, additional investigations identified a genomic link to a returned traveller who had been in Hotel Quarantine in early May 2021. An epidemiological link between the Hotel Quarantine case and any of the locally acquired cases has not yet been identified.
  • Network 9 – Relates to the outbreaks epidemiologically linked to the NSW Delta (B.1.617.2 lineage) outbreak. Three separate introductions of cases epidemiologically and genomically linked to the NSW Delta outbreak resulting in onwards transmission within Victoria.

AusTrakka is a secure platform utilised by public health laboratories in all Australian states and territories for real-time national genomic surveillance of priority public health pathogens such as SARS-CoV-2.