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Tracking the COVID-19 pandemic in Australia using genomics

Our take —

This preprint, non peer-reviewed study combined epidemiological and genomic data to provide a detailed picture of the emergence and limited onward spread of SARS-CoV-2 in Australia. The researchers show, using both epidemiological and genomic data, that most of the cases in Australia were travel-related. The use of genomic data enabled the researchers to resolve community transmissions of unknown origin and identified high-risk social areas that were responsible for community spread of SARS-CoV-2. The study demonstrates how genomics-based COVID-19 surveillance can help implement targeted interventions to control COVID-19 spread.

Study design

Retrospective Cohort

Study population and setting

This study analyzed 903 SARS-CoV-2 virus sequences and associated epidemiological data collected from 1,333 COVID-19 positive individuals in Victoria, Australia. These cases are from January 25 to April 14, 2020, representing the first 1,333 cases in the country. The purpose of the study was to demonstrate the integration of genomics-based COVID-19 surveillance into public health response.

Summary of Main Findings

Active case-finding and contact tracing identified a total of 1,333 COVID-19 laboratory confirmed cases in Victoria over the study period. 62% of these cases were from travelers returning mostly from the Americas and Europe. Sequence data from this cohort showed that the sequences were representative of the global diversity at that time, consistent with the epidemiological information. Over 10% of cases with associated epidemiological data were from an unknown source in Australia, but analysis of their sequences identified potential transmission routes. Additionally, analysis of the 903 sequences generated in this study revealed clusters of cases associated with specific social venues in Melbourne, Australia, providing genomic evidence for community transmission. The authors also examined within-patient virus diversity (in cases where multiple samples were available from the same patient) and found limited evidence for viral evolution during the course of infection.

Study Strengths

A key strength of this study is that the large number of genomes generated (903) represents a large fraction of the first cases detected in Victoria, Australia. This dense sampling allows the authors to draw more specific conclusions about transmission of COVID-19. Additionally, the authors also describe epidemiological data for a large number of the sequenced samples, and use the combination of genetic and epidemiological information to support and confirm findings. The methodology is also clear and very detailed, and all data were made publicly available.

Limitations

This study would be improved by providing more information about the published sequences used to compare to the generated sequences from Australia, as this impacts inferences related to the source of viral importations. Additionally, the within-host section of the paper is limited due to the small number of patients from whom multiple sequences were available, so additional studies are needed to fully characterize within-host evolution.

Value added

The study was part of a national public health surveillance program that combined epidemiology and viral genomics analyses. There was strong concordance between epidemiological and genomic data, and most of the community acquired transmissions and of unknown source were identified using genomic data. This was useful in providing information on how community acquired transmissions occurred and how to implement appropriate interventions. The report demonstrated how integration of genomics-based COVID-19 surveillance into public health response aided targeted intervention programs by identifying high-risk areas (like large social venues in Melbourne) responsible for community transmission of SARS-CoV-2.