Research Areas

Tackling COVID-19

As soon as we heard about a novel coronavirus, the virus later named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), and the disease/infection caused by this virus named Coronavirus Disease 2019 (COVID-19), in early January 2020, the team at GCEID started to follow the situation closely and began to prepare in case diagnostic support or research activities were required.

For this, we initially checked that our pan-coronavirus PCR would be likely to detect the novel virus and in addition, worked with our main commercial collaborator, ThermoFisher, to source the reagents/kits required to conduct diagnostic/research PCR testing to back-up any needed local or expanded testing. Consequently, we are available as a back-up diagnostic testing capacity.

We also geared up to be able to conduct full genome sequencing of the virus directly from patient samples, and have thus far sequenced the virus from 3 local cases of COVID-19. GCEID has also continued our laboratory function in order to provide scientific advice as well as research support, such as sample storage. In addition, GCEID has also helped the local testing laboratory with needed equipment and have provided testing components to Barwon Health. The activities are supported by internal GCEID funds and a special allocation for laboratory preparedness from Barwon Health and Deakin University.

Investigating a virus that causes meningitis-/sepsis-like illness in infants

We are sequencing the virus genomes of a human picornavirus (human parechovirus 3) that caused an outbreak of meningitis-/sepsis-like illness in young infants in Australia in 2013, 2015, 2017 and 2019-2020.

The research focuses on identifying the gene sequence of this virus from cases in and around Geelong, Melbourne, Sydney, Adelaide, Darwin and Brisbane to provide greater understanding of the severe disease observed and the spread and epidemiology of this infection.

Additionally, our research is exploring the development of a serological test and the very first steps required to develop and test possible pilot vaccine candidates.

This project has recently been expanded to include other human viruses of interest, such as rhinovirus, influenza virus and metapneumovirus as well as detection/rule out of unknown pathogens to support clinical decision making and to see if next generation sequencing can be made that has direct relevance for clinicians.

The work is a collaborative project with Barwon Health clinicians and scientists at GCEID, Deakin University, CSIRO-AAHL, Australian Clinical Labs, the Victorian Infectious Diseases Reference Laboratory (VIDRL) and with other collaborators from the APPRISE NHMRC CRE (www.apprise.org.au).

Next generation sequencing of clinical samples

Next generation sequencing of clinical samples to detect and characterise known and unknown pathogens or to substantiate absence of pathogens to inform treatment.

Investigating antimicrobial resistance (AMR) genes in clinically healthy humans and animals

Antimicrobial resistance (AMR) is a significant global public health threat. Drug-resistant bacteria are widespread among humans, animals and the environment, and contain antimicrobial resistance genes known as the “resistome”. Some of these bacteria may cause disease, but many do not cause disease, and indeed are helpful to the health of the host (these are known as commensal bacteria).

However, AMR in commensal (non-disease causing) bacteria is of great concern due to the potential for the resistance genes in these ‘good’ bacteria to spread to disease-causing bacteria.

This research project investigates the AMR resistome in healthy humans and animals. This work will contribute towards better understanding of AMR genes in commensal bacteria and the potential risks of transfer of resistance between different bacteria and different hosts. This project is supported by a PhD-fellowship from Deakin University.

Animal influenza and other animal viruses

This is a collaborative project with the University of Copenhagen under the Deakin University agreement with them. The project focus on animal influenza virus, including swine influenza virus, and other animal viruses of One Health interest.

This project is supported by a PhD-fellowship from Deakin University together with funds from University of Copenhagen.

The screening of wild birds for the presence of coronaviruses

Coronaviruses are responsible for the emergence of epidemics/outbreaks of the Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) and most recently COVID-19 resulting in significant human disease and mortalities. In these cases an intermediate mammal, such as bats and civets (“civet cats”) for SARS and for MERS likely dromedary camels (and for COVID-19 still unknown), was/is responsible for the transfer of the virus into human hosts. Several types of coronavirus are specific to mammals and birds while some relatively closely related ones, in particular the newly discovered deltacoronaviruses, may infect both. There is limited understanding of their presence world-wide and as Australia is a regional hub for a diverse range of wild birds this project is investigating the potential presence of coronaviruses in wild birds. If such viruses are detected, they will be characterized in detail genetically. This project is a collaboration with Deakin University’s Centre for Integrative Ecology and the WHO Collaborating Centre for Reference and Research on Influenza at VIDRL in Melbourne.

In addition, we have a PhD-project ongoing, supported by Deakin University, using metagenomics to detect and characterise unknown/known/novel viruses in wild birds. Wild birds are potential hosts of many viruses such as Murray Valley encephalitis virus, Kunjin virus, and Ross River virus. The introduction or transmission of viruses to novel hosts or habitats can have significant health and economic consequences. We currently have limited knowledge of the avian host-associated virus communities including both pathogenic and non-pathogenic viruses, yet they are potential carriers with a risk of zoonotic disease emergence. In addition, as birds can fly over large distances, they may also passively carry other viruses e.g. insect and plant viruses present in their sources of food. This research project aims to address the lack of knowledge through method development for virus community detection and characterisation using metagenomics to identify the virome of birds. This research will also help to understand the prevalence, transmission routes and associations of virus types with disease or health status. It will provide insight into the wild bird virome with relation to ecology and contribute towards better understanding of the risks from potentially zoonotic viruses in wild birds.

In addition, we are working on a collaborative project led by the Deakin University Centre for Integrated Ecology to look at genomic diversity, tolerance and ecology of wildlife disease, specifically at an infection caused by a circovirus, beak and feather disease virus, in Crimson rosellas.

Overall these projects are supported by internal funds to GCEID, by PhD Fellowships from Deakin University and with funds from ARC.