Sequencing the genome of Covid-19

A research team from Massey University are sequencing the genome of the virus strains that causes Covid-19 in New Zealand and developing less invasive and more efficient ways of testing for the illness.

Dr Nikki Freed and Dr Olin Silander tell Bryan Crump their team are working on a new testing procedure using saliva and hope it will replace the often painful nasal swab when its efficacy is proven.

They are also mapping any mutations of the virus in New Zealand, using methods of genome sequencing to study transmission and types of strains coming into the country.

“One of the important things that a genome sequence can give you information on is transmission chains. So, how a virus has been passed from one person to the next," Silander says.

"A concrete example of that is all the people that we have in isolation now - some of them were positive and some of them may pass the virus on to someone else and if we want to figure out which individual has passed that on, then if we have the genome sequences of the viruses for all the individuals that are in isolation then we may be able to figure out which individual passed on that virus.”

Genome sequencing is the process of determining the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. 

Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and DNA are nucleic acids. Along with lipids, proteins, and carbohydrates, nucleic acids constitute one of the four major macro molecules essential for all known forms of life.

Dr Nikki says RNA is part of the Covid virus' genetic constitution, which scientists can map using high-tech equipment.

 “All viruses also have genetic information and in particular the virus that causes Covid-19 actually has RNA as its genetic material. Generally, it’s four different letters to the genetic code and what we do when we sequence the virus, we determine the sequence of the virus. We detect about 30,00 base pairs – these letters are called base pairs – and we can sequence and detect all the base pairs in the genome.”

"We do that at our lab at Massey using hand-held genome sequencers that are cool devices that allow us in real-time and very quickly give that information.”

Because the virus has infected so many people there are many strains with differing genomes, he says. 

“As a virus is transferred from one person to the next it may accumulate one mutation or one change and that’s a DNA sequence and then it will be passed on to another person. It may not change in that person and it will be passed on again – and so over time those changes build up.”

If there is no mutation in the virus picked up by a patient you can’t tell who the virus came from.

The mutation rate is relatively low compared to many other similar RNA viruses. Possibly one out of 10 transfers result in a mutation.

Freed says scientists can tell if the virus has mutated when sequencer records changes in the voltage when observing the DNA and RNA, so can infer there’s been a change.

Part of the mission of the lab is to work out ways of making testing faster, more efficient and cheaper, less invasive, and safer for clinicians, she says. The Massey team are working with colleagues at Yale University in New Haven, Connecticut. 

“Typically, when you go into get a Covid-19 test it’s a swab from the back of your nose. There’s a lot of motivation to change that sampling a little bit.

“We’re working with a group at Yale. A woman named Ann Wyllie, who’s from New Zealand originally, and her group are working on saliva instead of this completely uncomfortable nasal swab and things are looking promising.”

Wyllie is the lead author of a paper released on April 23 suggesting that saliva could be more sensitive to the Covid-19 virus than nasal swabs. Wyllie, an associate research scientist in epidemiology, spent the last six weeks working with saliva samples from healthcare workers and inpatients at Yale New Haven Health to investigate their potential use for testing.

“It’s a virus that seems like it’s going to be around for a while, so anything we can do to make it easier… will help us to get this virus under control,” Freed. says

There remain practical barriers to the new testing.

“We’re trying to develop tests that use samples from saliva – one of the problems with saliva is it’s not easy to pipette in the lab and so this is one simple problem that we’ve tried to address – to add the right kind of chemicals to it that might make it easier to pipette,” she says.

Silander says tackling Covid-19 has involved “rapid communication” between scientists around the world, allowing his team to collaborate on research and other scientific breakthroughs, without waiting to view published scientific papers.

“When doing our research, we are informed about what other people are doing, not because we read articles anymore and not because we wait for publications, but because we’re on Slack channels. So, any lab that makes any progress, very quickly a number of other people will know about it," he says.

Although there is a caveat, he admits. There are limits to the collaboration, as corporate interests compete to market a viable vaccine.

“We’re not trying to make any money off this and most scientists aren’t. Of course, it’s not true that companies are necessarily sharing all their secrets. But there are definitely some companies out there that are sharing some secrets and are willing to collaborate. So, we are talking with one of those companies right now.”

That company is LA-based medtech form Octane.

Nikki says it is important to keep track of the virus and what strains are prominent in a location, to build up a picture as to how it has managed to spread. She says the lab in New Zealand had sequenced the strands identified among those Covid-positive in the country and has been able to determine the virus’ transmission from multiple sources.

“We can also look at specific mutations that seem to be becoming more frequent, so there is a particular variation or mutation called D614G and a particular part of the virus that seems to be spreading predominantly, so it’s a dominant genome type now.”

The information is used to inform those creating vaccines, she says.

So far there is no conclusive evidence suggesting that D614G is a more virulent strand than others, but there’s data on lab-grown D614G variants suggesting it’s more easily spreadable, he says.

“There’s two possibilities. One is yes, it is spreading so fast because it is more virulent. But the other possibility is that it’s just random chance.”

The problem of false negatives and the risk this poses of community transmission is something that a new testing regime involving saliva may not solve. The testing limitations are more to do with what scientists don't know about the nature of the virus at this point.

“The strategy right now, testing at day thee and day 12 is a really good strategy. That’s going to catch the vast majority of cases.

“There are some limits to these tests. Generally speaking, these tests - when we use PCR to test for this virus - these are quite specific and quite sensitive, but we still don’t know that much about different aspects about how you swab the patient and at what progression of the disease they have. So, all of these are variables can contribute to false negatives.

“These tests can even go down to five viral particles per test, so they can pick up very small quantities of the virus. They are quite sensitive but still there is this chance that you have a false negative and that is a real risk, so that’s why we need to remain vigilant and do our contact tracing and continue to do widespread testing in the community.”

With a lack of active cases in New Zealand they are looking to results using patient samples at Yale and Oregon and expect to get a sense of how efficient these tests are in the field within months.