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Genome sequencing and genomic clustering to SARS-CoV-2 in Victoria - 5 November 2021

eport date: 05 November 2021

Report period (4 weeks): 28 September 2021 – 25 October 2021

Published date: 12 November 2021

The public health genomic sequencing laboratory at the Doherty Institute (the Microbiological Diagnostic Unit Public Health Laboratory) perform genome sequencing of 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 25 October 2021.

As of 12 November 2021 sequence data was available for 22,102 (24.3%) Victorian COVID-19 cases diagnosed up to and including 25 October 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 recent Victorian COVID-19 genomic clusters, including cases diagnosed between 6 May 2021 and 25 October 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 (28 September 2021 – 25 October 2021) there were 46,555 cases reported and 856 (1.84%) were successfully sequenced, of these 853 (99.65%) were locally acquired, and 3 (0.35%) was travel associated.

a‘ ‘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, with genomic diversity arising as the virus has circulated locally. Genomic clusters within these transmission networks have been grouped and collapsed to enable visualisation.

bGenomic clusters with fewer than five cases and cgenomic clusters involving only cases suspected to have acquired their infection overseas have been grouped as ‘Fewer than 5 cases’ and ‘Travel associated’ respectively. dCases 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 most recent local Transmission Networks:

  • Network 7 – Relates to the Victorian Kappa outbreak, genomically linked to a returned traveller that was epidemiologically linked to a Hotel Quarantine breach in South Australia.
  • Network 8 – Relates to the Victorian Delta outbreak, genomically linked to a returned traveller that was in Victorian Hotel Quarantine.
  • Network 9 – Relates to the outbreaks epidemiologically linked to the NSW Delta (B.1.617.2 lineage) outbreak. At least 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.