7260 Genome sequencing and genomic clustering to SARS-CoV-2 in Victoria 21 May 2021 | Doherty Website

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Genome sequencing and genomic clustering to SARS-CoV-2 in Victoria 21 May 2021

Report date: 21 May 2021

Report period (4 weeks): 20 April 2021 – 17 May 2021

Published date: 4 June 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 17 May 2021.

As of 21 May 2021 sequence data was available for 15,601 (75.9%) Victorian COVID-19 cases diagnosed up to and including 17 May 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 17 May 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 (20 April 2021 – 17 May 2021) there were 34 successfully sequenced cases of COVID-19 in Victoria, of these 32 (94%) were travel associated and 2 (6%) were interstate acquired local cases.

‘Network 1’, ‘Network 2’, ‘Network 3’, ‘Network 4’,  ‘Network 5’ and ‘Network 6’ 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 locally acquired cases:

  • The sequence from the first case (diagnosed 23 April 2021) was most closely related to publicly available sequences closely related to sequences from two cases identified in Western Australian Hotel Quarantine, shared via the AusTrakka platform.
  • The sequence from the second case (diagnosed 11 May 2021) was most closely related to sequences from two cases identified in South Australian Hotel Quarantine, shared via the AusTrakka platform.

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.

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