When India's Delta strain of SARS-CoV-2 was discovered in Melbourne last week, it had authorities scrambling.
The cluster of seven cases was unrelated to others in the Victorian capital — so where had the strain come from?
Then, earlier this week, a link was found between the outbreak and a returned traveller who had been in hotel quarantine in Melbourne.
This detective work was done using genomic sequencing — a technique that analyses the viral genome and compares its make-up with the genetic material from other cases.
"Genome sequencing has become the gold standard of disease surveillance, outbreak detection, and response," said Benjamin Howden, director of the Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL).
Underpinning Australia's SARS-CoV-2 genomic sequencing efforts is AusTrakka, a national online platform that allows public health laboratories around the country to share their sequencing data across states.
"This allows us to take advantage of this genomic data to really respond to public health emergencies," said Anders Gonacalves Da Silva, a bioinformatician at the Doherty Institute, and co-lead for AusTrakka.
How does genetic sequencing work?
Analysing SARS-CoV-2 sequences is like detective work, allowing researchers to detect changes in the virus's genetic make-up across the country.
When a nose or throat test is sent to a public health lab, all COVID-positive samples are genetically sequenced.
The SARS-CoV-2 genome is made up of nearly 30,000 building blocks called nucleotides.
Each building block is assigned a letter — A, T, C or G.
To compare sequences from various cases, researchers line them up and look for differences in how the letters are arranged.
The quality of these sequences can vary, depending on the infection stage a person is at when they get a swab test.
In cases where virus levels are low, such as during the early stages of infection, there is not enough genetic material to sequence.
In Victoria, around 80 per cent of cases result in good quality genomic sequences.
This sequence data is uploaded to AusTrakka, where it can be compared with sequences from other parts of the country.
Each night, AusTrakka generates a phylogenetic tree — a branched diagram that shows how different SARS-CoV-2 genetic sequences are related.
The position of the sequences on the tree can reveal the origin of a COVID case, how it was transmitted, and its link to other outbreaks.
Branches of sequences that are closer together indicate they are more closely related, often revealing a cluster of cases in the community.
Sequences that are more genetically distinct sit further apart on the tree, signifying their arrival from other regions.
For instance, if a case crops up in Victoria and the sequence is similar to those seen in cases in NSW, it's likely that the virus crossed the border.
"We're trying to find the perfect matches that might suggest there is an epidemiological link that is worth pursuing as early as possible, to catch an outbreak before it becomes a public health nuisance."
How did AusTrakka help reveal the origin of the Victorian outbreak?
When the Delta variant was detected in Melbourne last week, the team ploughed through the sequences stored in the database to try and find a match in Victoria.
"We could not find a match anywhere in the country that might explain the source of this disease," Professor Howden said.
Supplied: Guy Cleeves
)So AusTrakka's network of labs across Australia agreed to upload their lower quality sequences to the database to help find a match.
Around 20,000 SARS-CoV-2 sequences have been uploaded to the database, representing over 50 per cent of all COVID-19 cases in Australia.
"Within about 12 hours, we got all the data from around the country into a single location," Professor Howden said.
Because Australia has eight jurisdictions that each manage their own public health activities, sharing sequences between states isn't as straightforward as it seems.
"Traditionally, everything has been done at the state level, but COVID-19 isn't a state-level problem," said Torsten Seemann, a bioinformatician at the Doherty Institute who co-leads AusTrakka.
Having national SARS-CoV-2 sequencing data under one roof makes it easier to detect outbreaks early, leading to a faster response to slow the spread.
This means that researchers are able to get a clear answer quickly, allowing them to change their approach early, such as retesting samples.
Understanding the genetic links between cases can help authorities decide on the best course of action, such as enforcing border closures or snap lockdowns.
"Genomic data in Australia is now informing decisions on a daily basis," Professor Howden said.
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2021-06-09 19:00:00Z
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