‘New kid on the block’ finds source of COVID-19 infections within hours

The source of coronavirus infections could be uncovered within four hours using a new genome sequencing strategy developed by Sydney researchers.

Collaborating with NSW Health Pathology, researchers at St Vincent's Hospital's Garvan Institute of Medical Research and UNSW's Kirby Institute have adapted an existing sequencing technology to trace coronavirus infections more quickly.

Nanopore genome sequencing allowed for the source of an infection in a cleaner at the Novotel Darling Harbour to be uncovered within a day.Credit:Brook Mitchell

The technology, known as Nanopore, was used last week to determine a cleaner at a quarantine hotel had caught an overseas variant of the virus within a day. Previously, genome sequencing of an infection has taken two to three days.

"If you want to know what the whole sequence of the virus is you will need to wait a couple of days, but if you just want to know where it sits with other viruses in the world, you can have that same day or even within a few hours," said Professor Bill Rawlinson, senior medical virologist at NSW Health Pathology’s Prince of Wales lab.

The quick discovery that the woman had likely not caught the virus in the community provided relief for contact tracers, Professor Rawlinson said.

Further testing using the established "shotgun sequencing" method of genome sequencing and other inquiries led health authorities to deduce her infection was from US airline crew staying at the hotel.

Genome sequencing is a process of mapping changes in a virus, to determine where it was acquired.

The technique was used to link the Crossroads Hotel outbreak in south-west Sydney to cases in Victoria and a recent string of cases in Adelaide to a returned traveller from the UK staying at a quarantine hotel.

But while these results took days, Nanopore can return results within four hours as the technology has no upper limit on the length of DNA fragments that can be sequenced.

In a paper published in Nature Communications on Thursday, the researchers presented an analytical validation and best practice guide for using the technology in coronavirus tracing.

The COBAS instrument processing coronavirus samples lights up the virology laboratory as a technical officer carries out general testing. Credit:Kate Geraghty

"Nanopore is kind of the new kid on the block in genomics," Dr Ira Deveson, head of Garvan's genomic technologies group, said.

He said the process of genome sequencing using Nanopore is largely the same as shotgun sequencing in that the virus is isolated from a sample and then amplified.

However, while shotgun sequencing requires shorter fragments of 100 to 150 genetic letters to be "stitched" together for analysis, Nanopore feeds DNA strands continually through a port, creating electronic currents which can be measured over time.

"The steps involved in preparing that experiment and running that experiment are much faster and, ultimately, reduce the turnaround time, which is pretty critical in coronavirus research and contact tracing," Dr Deveson said.

The instruments used in Nanopore sequencing are also the size of a smartphone and can be used with just a laptop, presenting an opportunity to conduct sequencing in hospitals rather than sending material to a lab.

Nanopore was previously used by researchers in response to the Ebola outbreak in west Africa.

Although previous research has questioned the accuracy of the technology, the new research found Nanopore to be highly accurate in a coronavirus context, detecting virus variants with greater than 99 per cent sensitivity and accuracy in 157 COVID-19 patient specimens.

Professor Rawlinson said he believed the method was less accurate than shotgun sequencing but would have a place in NSW Health Pathology's coronavirus tracing in tandem with other genome sequencing.

He said he expects the technology will be most useful in situations like that at the Novotel, where a quick and rough understanding of the source of a mystery case is needed.

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