Why genomics is the real MVP in the fight against COVID clusters
As COVID-19 clusters in gyms, restaurants, and aged care centres across NSW and Victoria continue to climb and make headlines, contact tracing efforts and genomic sequencing feature heavily in the media’s reporting of the coronavirus pandemic.
But how exactly is genetics being used for epidemiological tracing purposes and how is it helping researchers and policymakers to respond to these outbreak clusters in real-time?
On Monday, for example, NSW recorded another ten new cases of COVID-19 with four of them linked to the CBD cluster – which has grown to 28 in total over the past month – linked to the City Tattersalls club and gym. The Thai Rock restaurant and Potts Point cluster is a good example of how the scale of infection spread can take off before authorities can trace from where the index case originated.
The cluster was first announced in mid-July after a staff member in the Wetherill Park restaurant tested positive, by the start of August secondary clusters beyond the restaurant stood at 32 cases.
Several weeks later, the ‘supercluster’ as it’s become known has been linked to 153 cases, and genomic sequencing was used to confirm what authorities had long suspected, that the Potts Point and Wetherill Park clusters share a close genomic fingerprint.
NSW Health have said in a statement that genomic sequencing of the virus from the City Tattersalls cases is related to other recent clusters in the state. At the same time, they have also confirmed the virus strain picked up by the Marriott Hotel security guard in Sydney is not of the same mutated strain and appears to have come from an imported overseas case.
Meanwhile in Victoria, the aged care outbreak across Melbourne which has led to more than 1800 cases among elderly Australians, and more than 400 deaths has been genetically linked back to cases recorded in the state’s botched hotel quarantine program for returning travellers. The staff member in whom this outbreak is thought to have originated is still hotly debated, whether by a hotel security guard, or by hotel night manager at Rydges Melbourne.
Using genetics for epidemiological tracing purposes in this way has been especially useful when traditional contact tracing methods have failed to identify a link or source between localised outbreaks.
What is genomic sequencing?
Essentially, genomics is the study of the genetic materials within an organism — DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
What genomic sequencing allows researchers to do is take a ‘genetic fingerprint’ of an organism, such as the SARS-CoV-2 virus and map precisely what the RNA code of that virus looked like at the time it was detected.
It is these mutations, hidden within the 30,000 letters or nucleotides that make up the rapidly replicating virus, that interest researchers because these subtle changes in the RNA code as the virus jumps hosts that tell them about the lineage of the strain circulating within a community at any given time.
Right now, scientists globally are sharing much of this information through global genomic databases such as Nextstrain or the Global Initiative on Sharing All Influenza Data (GISAID).
Interestingly, most agree for the moment these mutations so far haven’t changed how the virus behaves in the host, nor has it affected its infectiousness which is estimated to be less infectious than seasonal influenza – but far more deadly.
It is also mutating at a much more stable rate than influenza strains, estimated to be at a rate of 20 mutations a year. Some early studies have suggested there could be at the moment as many as 30 strains of SAR-CoV-2.
The silver lining of it all is that it appears the gravity of the pandemic has led to an explosion of real-time genome-sequencing of the virus, and unprecedented global sharing of these genetic lineages as they come to light.
Explore the science with STEM Reactor experiments
Sickle Cell Gene Detection
Sickle Cell Anemia is a common genetic disease that causes long rods in red blood cells, giving them a "sickled" appearance. In this experiment, your students will investigate the restriction enzyme that discriminates between HbA (normal) and HbS (disease) genes and perform a simulated test on a patient.
In-da-pendant Genes
In this activity, students will extract DNA from their own cheek cells and leave class wearing their DNA in a stylish glass pendant around their neck. This simple lab activity requires no specialized equipment or stains, yet allows students to conduct a real-world laboratory procedure that is used to extract DNA from a wide variety of organisms.
Related Resources
Article:
How Coronavirus Mutates and Spreads
By Jonathon Coram and Carl Zimmer of the New York Times
Article: Supercluster confirmed as genetic fingerprint links two outbreaks 34km apart
By Kate Aubusson and Pallavi Singhal of SMH
Article: The same coronavirus strain turned up in an Australian and a tiger. How?
By Sherryn Groch and Liam Mannix of SMH
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Blog Sources:
Rockett, R.J., Arnott, A., Lam, C. et al. Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nat Med (2020). https://doi.org/10.1038/s41591-020-1000-7
Mallapaty. S., 2020, How sewage could reveal true scale of coronavirus outbreak, Nature