FEB 02, 2021 8:00 AM PST

Keeping an Eye on COVID Clusters With Rapid Sequencing

WRITTEN BY: Tara Fernandez

Contact tracing is a powerful tool used by public health authorities to help slow the spread of infectious diseases such as COVID-19. Those in close contact with infected individuals can swiftly be informed, tested, and advised to self-isolate, thus lowering the risk of the COVID-19 virus spreading further.

Not every case cluster is so easy to track, however. Scientists have found a way of mapping case networks more efficiently, by leveraging one of the virus’s hallmark flaws. 

“Every time the SARS-CoV-2 virus passes from person to person, it may make copying errors that change a couple of its 30,000 genetic letters”, explains Rowena Bull, a researcher from Australia’s University of New South Wales.

“By identifying this genetic variation, we can establish how different cases of coronavirus are linked – to know where a case was potentially picked up from and who they may have given it to.” 

Bull and colleagues have spearheaded the development of a superior method of contact tracing by employing next-generation genome sequencing technologies. This method provides quick answers as to how COVID cases are linked, enabling improved pandemic-control initiatives.

These guidelines, published in Nature Communications, take advantage of nanopore sequencing. Here, subtle changes in an electric current as DNA or RNA traverses a nano-scale hole in a protein called a nanopore are measured. The signals read by this passage of nucleic acids through the nanopore are then decoded and translated into a sequence. 

One of the main benefits of this platform is its speed. Using this technology, developed by Oxford Nanopore Technologies, the entire 30 kilobase-long SARS-CoV-2 genome can be sequenced in just under four hours.

 

 

The new-and-improved form of viral tracking can help trace the origins of variants (such as the highly-contagious UK variant) and bridge the gaps left by traditional epidemiological investigations. It can also be useful in identifying so-called COVID “super-spreaders” in the community. 

Among the concerns around using this relatively new technology for COVID-tracking applications was whether or not it was accurate enough. In their publication, Bull and colleagues demonstrate this not to be the case, detecting variants with >99% sensitivity and >99% precision in a cohort of 157 COVID-positive patient samples.

“Nanopore devices are cheaper, faster, portable and don’t require the lab infrastructure needed by current standard pathogen genomics tools,” said senior author of the study, Ira Deveson, Head of the Genomic Technologies Group. 

“We hope our validation of this protocol will help other public health teams around the world adopt this technology.”

 

Sources: UNSW Sydney, Nature Communications.


 

About the Author
  • Tara Fernandez has a PhD in Cell Biology and has spent over a decade uncovering the molecular basis of diseases ranging from skin cancer to obesity and diabetes. She currently works on developing and marketing disruptive new technologies in the biotechnology industry. Her areas of interest include innovation in molecular diagnostics, cell therapies, and immunology. She actively participates in various science communication and public engagement initiatives to promote STEM in the community.
You May Also Like
JAN 08, 2021
Neuroscience
Can We Identify Alzheimer's from Routine Eye Exams?
JAN 08, 2021
Can We Identify Alzheimer's from Routine Eye Exams?
As people with diabetes age, they are more likely than those without the condition to develop cognitive disorders such a ...
FEB 03, 2021
Immunology
Severely Ill COVID-19 Patients may have Longer Immunity Against the Virus
FEB 03, 2021
Severely Ill COVID-19 Patients may have Longer Immunity Against the Virus
Researchers are still studying how long a person can stay immune against COVID-19 following infection. A new study by a ...
FEB 23, 2021
Genetics & Genomics
New Insight Into Genetic Basis of IBD From African-American Patients
FEB 23, 2021
New Insight Into Genetic Basis of IBD From African-American Patients
The small variations in the genome that lead to differences in biology, including risk for diseases, can't be assumed to ...
MAR 23, 2021
Clinical & Molecular DX
AI Test Distinguishes Cancer Cells From Healthy Ones Based on Acidity Levels
MAR 23, 2021
AI Test Distinguishes Cancer Cells From Healthy Ones Based on Acidity Levels
Researchers have developed a new way of differentiating cancer cells from healthy ones—by how acidic they are. The ...
APR 03, 2021
Drug Discovery & Development
Why Are Some Cancer Therapeutics Ineffective?
APR 03, 2021
Why Are Some Cancer Therapeutics Ineffective?
Why don’t some cancer therapeutics not work in humans when they were successful in mice? The answer to this questi ...
APR 19, 2021
Genetics & Genomics
Better Disease Risk Predictions May Come From Ancestry Data, Not Race
APR 19, 2021
Better Disease Risk Predictions May Come From Ancestry Data, Not Race
Researchers have suggested that it's time for medicine to move away from demographic labels that are too narrow to captu ...
Loading Comments...