Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study

Abstract

Background A cornerstone of Australia's ability to control COVID-19 has been effective border control with an extensive supervised quarantine programme. However, a rapid recrudescence of COVID-19 was observed in the state of Victoria in June, 2020. We aim to describe the genomic findings that located the source of this second wave and show the role of genomic epidemiology in the successful elimination of COVID-19 for a second time in Australia.Methods In this observational, genomic epidemiological study, we did genomic sequencing of all laboratoryconfirmed cases of COVID-19 diagnosed in Victoria, Australia between Jan 25, 2020, and Jan 31, 2021. We did phylogenetic analyses, genomic cluster discovery, and integrated results with epidemiological data (detailed information on demographics, risk factors, and exposure) collected via interview by the Victorian Government Department of Health. Genomic transmission networks were used to group multiple genomic clusters when epidemiological and genomic data suggested they arose from a single importation event and diversified within Victoria. To identify transmission of emergent lineages between Victoria and other states or territories in Australia, all publicly available SARS-CoV-2 sequences uploaded before Feb 11, 2021, were obtained from the national sequence sharing programme AusTrakka, and epidemiological data were obtained from the submitting laboratories. We did phylodynamic analyses to estimate the growth rate, doubling time, and number of days from the first local infection to the collection of the first sequenced genome for the dominant local cluster, and compared our growth estimates to previously published estimates from a similar growth phase of lineage B.1.1.7 (also known as the Alpha variant) in the UK.

Prospective characterisation of SARS-CoV-2 infections among children presenting to tertiary paediatric hospitals across Australia in 2020: a national cohort study

“…Importantly, these data reflect infection predominantly with lineage D.2, which was responsible for over 98% of cases during Melbourne, Victoria’s second wave in 2020. 34 The PAEDS network is continuing surveillance with comprehensive data on a large delta variant point-source outbreak in Eastern Australia in 2021. This will afford opportunities to compare the severity of these two variants over time in children.…”

Towards equitable access to public health pathogen genomics in the Western Pacific

“… [4] Genomic analysis has been critical to support detection of outbreaks and importation events, enhanced understanding of transmission dynamics, surveillance of emerging mutations and variants of concern, and estimation of disease spread across the Western Pacific region. [4] , [5] , [6] , [7] Access to genomic sequencing has allowed for contribution of data from the region to global SARS-CoV-2 genomic surveillance efforts, resulting in better understanding of disease spread worldwide. In Australia, where there is high sequence coverage and a relatively low burden of COVID-19, genomics has played a critical role in identifying the source of disease outbreaks, and measuring the impact of public health interventions.…”

“…In Australia, where there is high sequence coverage and a relatively low burden of COVID-19, genomics has played a critical role in identifying the source of disease outbreaks, and measuring the impact of public health interventions. [5] …”

Outcomes for emergency department patients with suspected and confirmed COVID‐19: An analysis of the Australian experience in 2020 (COVED‐5)

“…1 , 2 , 3 While Australia has been relatively successful in containing the spread of the virus, sporadic outbreaks continue to place pressure on the healthcare system. 4 , 5 , 6 …”