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Source: Massey University

Andrea Sajuthi (L), Alyssa Earnshaw, Bhargava Reddy Morampalli. Olin Silander, Stella Pearless, Nikki Freed, Georgia Breckell, Daying Wen, Markéta Vlková (also an author on the genome sequencing paper).

The School of Natural and Computational Sciences’ senior lecturers in genetics Dr Nikki Freed and Dr Olin Silander were awarded $165,471 by the Ministry of Health and Health Research Council of New Zealand in April to create a faster, cheaper way to turn around test results and undertake genome sequencing to track the evolution of the virus among people who have tested positive.

Two months on, the pair say they are building on the existing work that’s taken place around the world and their results and method of sequencing are now gaining international interest.

Genome sequencing looks into the makeup of the virus and Dr Freed says identifying subtle differences in the sequence of the ribonucleic acid can help them to identify the sources of outbreaks. The genome sequence can be determined in a single day.

Their new method decreases the cost of reagents (substance or mixture for use in chemical analysis) for genome sequencing, and results in genome sequences that are more complete than current methods. This has sparked interest in the method from universities and testing labs overseas.

“Genome sequencing lets us understand how the virus is changing over time, which is important for understanding outbreaks,” Dr Freed says.

Their aim is to enable a single person to screen more than 500 samples per day and obtain up to 24 whole genome sequences per day. They are also working closely with health authorities and the Institute for Environmental Science and Research (ESR) to track where new cases of COVID-19 in the Auckland area have come from in an attempt to stop the spread of the virus. “For example, we have had a few people who have arrived into Auckland recently and have tested positive for the virus at the border. We were able to sequence those COVID-19 samples and provide the viral genome sequences to the New Zealand reference laboratory, ESR within 48 hours.”

“We are proud to be building on the work that a lot of people have done. This work has gone from conception to experiment to pre-print and has been accepted in a journal within less than three months. That’s really exciting and quite a quick timeline in terms of research,” Dr Silander says.

Dr Freed agreed, adding that it is a career highlight for her. “This research has the possibility to make the most impact out of all the other research I’ve done in terms of the number of people that might use it.”

Further testing work

Part of the Ministry of Health and Health Research Council of New Zealand funding is earmarked for finding a quicker and cheaper COVID-19 testing method, which the pair say they are still actively working on.

They have partnered with an Auckland-based biotech company, Ubiquitome, to research the use of portable devices for rapid detection of the virus that causes COVID-19

The goal is to try and develop “point of care testing” where a mobile testing device can be taken into a nursing home, airport or hotel, to test a patient using their saliva, rather than have a medical professional have to wear full PPE and do a nasal swab.

“This work takes more time because the stakes are much higher,” says Dr Freed. “You do not want to get that type of test wrong, especially a false negative.”

“It’s going to take a lot of work to make sure a saliva test is sensitive and specific enough. There are a lot of variables,” she says.

Dr Freed acknowledges that much of this work hinges on the herculean efforts from the local diagnostic labs and District Health Boards who are testing thousands of samples for COVID-19. She highlighted Dr. Fahimeh Rahnama from the Auckland District Health Board as a critical partner in providing samples in a timely fashion.