Researchers develop rapid genomics strategy to trace coronavirus
Garvan Institute of Medical Research
Thanks to cutting-edge 'Nanopore' genome sequencing technology, researchers at the Garvan Institute of Medical Research and the Kirby Institute at UNSW Sydney have developed the most rapid coronavirus genome sequencing strategy in Australia to date.
The technological advance has the potential to provide critical, timely clues on how cases of SARS-CoV-2 infection are linked.
The researchers today published an
analytical validation and best practice guidelines for Nanopore sequencing of
SARS-CoV-2 in Nature Communications, which they hope will enable a
greater uptake of the fast sequencing technology for health initiatives in Australia
and overseas.
"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. 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," says co-first author A/Prof Rowena Bull, from UNSW's Kirby Institute.
A/Prof Bull says genomic testing is
crucial for tracking virus transmission in cases where the source remains
unclear from investigating known epidemiological contacts alone.
"By reconstructing the virus's
evolutionary history, or 'family tree', we can understand the behaviours that
help spread COVID-19 and identify so-called 'super-spreaders'," she says.
"When a new 'mystery'
coronavirus case is identified, every minute counts. At Garvan, we have
repurposed our genomic sequencing capabilities to enable a rapid analysis of a
coronavirus genome in just a few hours," says senior author Dr Ira
Deveson, Head of the Genomic Technologies Group at Garvan's Kinghorn Centre for
Clinical Genomics.
"We've been thrilled to
collaborate with the Garvan and Kirby Institutes to develop unparalleled speeds
of coronavirus genome testing. Rapid methods such as this provide a way
forward, as a potential future option for contact tracing through real time
genomic transmission studies," says Prof Bill Rawlinson AM, from UNSW
Sydney and NSW Health Pathology Randwick.
"This technical advance is a
testament to what's possible when public pathology collaborates with Research
Institutes for a common goal," says Prof Sebastiaan van Hal, from NSW
Health Pathology -- Royal Prince Alfred Hospital.
Pioneering rapid genomics
Pinpointing SARS-CoV-2 transmission quickly is crucial. NSW Health Pathology has collaborated with the Garvan Institute and Kirby Institute to develop faster SARS-CoV-2 genome sequencing capabilities, potentially enhancing the ability of contact tracers to take rapid action to quarantine and monitor potential contacts.
Garvan researchers
have fine-tuned the protocols for cutting-edge Oxford Nanopore Technologies to
sequence SARS-CoV-2 in less than four hours. Garvan's Kinghorn Centre for
Clinical Genomics is the first facility in Australia to establish and apply
this Nanopore technology for genomic surveillance of SARS-CoV-2.
Highly accurate emerging
technologies
The current gold-standard method
reads short genetic sequences of just 100-150 genetic letters at a time,
whereas Nanopore technologies have no upper limit to the length of DNA
fragments that can be sequenced and are able to more rapidly determine the
complete sequence of a viral genome.
"However, as with many emerging
technologies, there have been concerns about the accuracy of Nanopore
sequencing. We addressed these concerns in our paper where we report the
outcomes of a rigorous analytical evaluation of our protocols for sequencing
the coronavirus genome," says Dr Deveson.
The researchers' analysis revealed
the Nanopore sequencing method to be highly accurate (variants were detected
with >99% sensitivity and >99% precision in 157 SARS-CoV-2-positive
patient specimens) and provides best practice guidelines, which the researchers
hope will promote the uptake of the technology by other teams globally.
The researchers say Nanopore
sequencing even has the potential to enhance SARS-CoV-2 surveillance by
enabling point-of-care sequencing and improved turnaround times for critical
cases.
"Nanopore devices are cheaper,
faster, portable and don't require the lab infrastructure needed by current
standard pathogen genomics tools," says Dr Deveson. "We hope our
validation of this protocol will help other public health teams around the
world adopt this technology."
The research published in Nature
Communications was supported by a UNSW COVID-19 Rapid Response
Research Initiative, the Medical Research Future Fund (Investigator Grant
APP1173594), Cancer Institute NSW and The Kinghorn Foundation.