What is genomic sequencing and how is it being used against Covid-19 in Australia?

Genetic detective work is allowing scientists to map coronavirus clusters and identify ‘superspreaders’ as they work to quell a second outbreak in Victoria

Genomic sequencing has emerged as an increasingly important tool in the effort to contain Covid-19, as governments around the world grapple with the inevitability of continued transmission in lieu of a vaccine.

While contact tracing detectives were praised for their work during the early months of outbreaks around the world, genomic sequencing is now allowing health authorities to study prolonged outbreaks, map coronavirus clusters, identify “superspreaders” and understand behaviours that spread Covid-19.

In Melbourne, capital of the Australian state of Victoria, genomic sequencing showed that more than 90% of the state’s second wave of cases could be linked back to an outbreak from a single family who returned from overseas and served the government-mandated quarantine period in a hotel. Evidence from genomic sequencing is expected to influence the state’s future quarantine policy.

Here’s what you need to know about genomic sequencing.

What is genomic sequencing?

Genomic sequencing analyses the virus sample taken from a diagnosed patient and compares it with other cases.

Prior to Covid-19, genomic sequencing has been used in Australia to trace the source of outbreaks of food-borne bacteria and hospital infections.

After a Covid-19 test (which gathers saliva from the back of the throat and nose) returns a positive result, the swab used goes through several steps to separate the RNA molecules from mucus proteins so they can be captured, then converted into DNA that can be read.

Genomic sequencing analyses the virus sample taken from a diagnosed patient and compares it with other cases.
Genomic sequencing analyses the coronavirus sample taken from a diagnosed patient and compares it with other cases. Photograph: Kai Foersterling/EPA

What does that information show?

As a virus passes from human to human, the virus changes slightly. While the genome of one Covid-19 patient compared with the person they caught it from will appear almost identical, after the virus has been transmitted on to further people, differences between the strands of the virus they carry become more apparent.

Dr Rory Bowden, the head of the Centre for Genomics at the Walter and Eliza Hall Institute of Medical Research in Melbourne, told the Guardian the information allowed scientists “to do detective work to understand patterns of spread of pathogens in populations”.

“The Sars-CoV-2 genome, at more than 30,000 nucleotides, is long for an RNA virus, so while there were few changes initially, there is room for quite a lot of information about each strain’s history to accumulate.”

Using the example of Australia, he said that by the time the virus arrived in the country, the different changes, or mutations, of Covid-19 “define branches on a tree”. Each branch of Covid-19 that exists in Australia could be linked back to China in the original instance, as well as via an outbreak in a foreign country.

Bowden said when Wuhan experienced the first outbreak, the genomes in the city were mostly identical.

He said while genomic testing was particularly informative for tracing current outbreaks in countries that are recording continued and significant transmission, earlier on in the pandemic, the method would not be as useful.

“With Sars-CoV-2, there are still not that many variant positions to tell different branches of the tree apart. The thing that helps us is that in Australia, most cases are linked back, through one or a few generations of transmission, to the virus imported from all around the world by returning travellers,” Bowden said.

“If all we had was community spread from a single source introduction … it is unlikely we would be able to tell the different clusters apart.”

Where is genomic sequencing being used and what has it shown?

While governments around the world, including the UK, are working with local research teams on genomic sequencing programs, Victoria’s genomics regime has been at the forefront of the effort to contain its second wave of Covid-19.

On 18 August, at a parliamentary inquiry into Victoria’s hotel quarantine regime, Dr Charles Alpren, an epidemiologist with the Victorian Department of Health and Human Services, said genomic sequencing had shown that “90% or more” of the state’s current Covid-19 cases could be linked back to an outbreak from a single family.

He said genomic sequencing was able to link 14 of 17 cases in an outbreak at a quarantine hotel for returned Australians – the Rydges Hotel in Melbourne’s CBD – to a family of four that returned to Australia on 9 May.

Alpren said this family, and three other returning travellers who quarantined in another Melbourne hotel – the Stamford Plaza – were likely together responsible for “approximately 99% of current cases of Covid-19 cases in Victoria”.

The Stamford Plaza hotel in Melbourne which has been identified as one of the sources of Victoria’s second coronavirus outbreak.
The Stamford Plaza hotel in Melbourne which has been identified as one of the sources of Victoria’s second coronavirus outbreak. Photograph: James Ross/EPA

Benjamin Howden, who leads the public health epidemiology team at Melbourne University’s Doherty Institute, is currently working with state authorities to use genomic sequencing to track Covid-19 cases.

He said bioinformaticians, who apply information technology to biological and medical research, gathered each patient’s genome data and compared it against other patients in the state.

A genomic epidemiologist then matched the historical data of each strand recorded to the patient that provided the sample.

How does it help contain outbreaks, and how did this identify a ‘superspreader’?

Matching the genomic findings to epidemiological information means authorities can tell if a new patient caught a virus from a known source of the virus, and can work to identify the point or person of transmission.

It also means authorities can divert resources more urgently into understanding and containing a case if genomic testing shows someone has caught a strain previously only recorded in a different geographic area.

In the case of the “superspreader”, the genomic data of all of the patients infected by them would have very few variations. This is because the transmissions originated from just one person, as opposed to several people passing it along and giving a strain further chances to mutate.


Elias Visontay

The GuardianTramp

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