How Genetic ‘Fingerprints’ of First COVID-19 Cases Help Manage Pandemic in Australia

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Genomic information from COVID-19 cases in the very first 10 weeks of Australia’s break out showed important to comprehending the trajectory of the illness and has a crucial function to play progressing.

A brand-new research study released today in the world-leading journal Nature Medicine, exposes how genomic sequencing and mathematical modeling offered crucial insights into the ‘parentage’ of cases and most likely spread of the illness in New South Wales.

The information, from a cooperation in between the University of Sydney and NSW Health, were utilized to notify actions that successfully handled the very first wave of COVID-19 infections in the state.

The group of researchers from Westmead Clinical School and NSW Health Pathology is continuing to work behind the scenes, utilizing the exact same method to keep watch on brand-new COVID-19 cases as Australia experiences a revival of infections.

“The high-resolution genomic data we produced across the first Sydney clusters were crucial to identifying the difference between imported cases and local community transmissions,” stated Dr. Rebecca Rockett, lead author, and a virologist at the University of Sydney’s Marie Bashir Institute for Infectious Diseases and Biosecurity at Westmead Hospital.

“Within days of the first confirmed Australian cases, we designed a new process to effectively generate COVID-19 genetic fingerprints from positive cases.”

The University of Sydney group created hereditary information from 209 NSW COVID-19 cases. The information was utilized to supplement public health details from contact tracing and notify public health follow-up.

Key findings

Among the findings, scientists recognized a quarter of COVID-19 favorable samples were regional transmissions and had the ability to recognize institutional clusters such as in health care centers.

The information was highly confirmed by a computational design established by the Centre for Complex Systems which tracked and anticipated the real pandemic spread in Australia.

The design was utilized to notify federal government action to successfully decrease regional neighborhood transmissions.

“Genome sequencing is the key to unlocking the puzzle of local transmission, and it’s critical that we continue to invest in this research to advance our ability to contain the virus in the long-term ” — Dr. Rebecca Rockett

Genomic sequencing discussed

Genomic sequencing develops a ‘genetic fingerprint’ of organisms and maps the order of how chemical foundation of a genome are arranged.

The scientists took a look at how the infection’ hereditary series was arranged by spotting and equating minute distinctions in each brand-new infection. A hereditary ‘family tree’ was produced revealing which COVID-19 favorable cases were linked and to track clusters.

“The more fingerprints we took, and the critical information collected from the contact tracers, the easier it became to identify if someone contracted COVID-19 from a known cluster or case,” stated Dr. Rockett.

“Very early on – we were able to discover cases which weren’t linked to a known cluster or case. This informed state and federal governments that community transmission was happening, and led to the border closures, revision of testing policies and other measures that stopped further spread of the virus.”

Dr. Rockett and her group handled to produce these genomic information so rapidly due to the fact that they leveraged years of experience in utilizing genome sequencing to find food-borne pathogens such as salmonella, throughout gastrointestinal disorder break outs, and transmission of tuberculosis.

Moving forward

The research study is a ‘behind the scenes’ take a look at the complex and collaborated effort by virologists, bioinformaticians and mathematical modelers along with clinicians and public health specialists.

Dr. Rockett’s laboratory is the devoted center hosted by NSW Health Pathology supplying genomic sequencing information to NSW Health specialists operating at the frontline of handling the pandemic.

“Genome sequencing is the key to unlocking the puzzle of local transmission, and it’s critical that we continue to invest in this research to advance our ability to contain the virus in the long-term not just to trace locally acquired cases, but also to identify new cases once border restrictions are lifted and travel resumes,” states Dr. Rockett.


Reference: “Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling” by Rebecca J. Rockett, Alicia Arnott, Connie Lam, Rosemarie Sadsad, Verlaine Timms, Karen-Ann Gray, John-Sebastian Eden, Sheryl Chang, Mailie Gall, Jenny Draper, Eby M. Sim, Nathan L. Bachmann, Ian Carter, Kerri Basile, Roy Byun, Matthew V. O’Sullivan, Sharon C-A Chen, Susan Maddocks, Tania C. Sorrell, Dominic E. Dwyer, Edward C. Holmes, Jen Kok, Mikhail Prokopenko and Vitali Sintchenko, 9 July 2020, Nature Medicine.
DOI: 10.1038/s41591-020-1000-7

This research study was supported by the Prevention Research Support Program moneyed by the NSW Ministry of Health and the National Health and Medical Research Council Centre for Research Excellence in Emerging Infectious Diseases. The funders of this research study had no function in research study style, information collection, information analysis and analysis, or writing of the short article.

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