Spit not yet polished for coronavirus testing

Saliva may prove useful for screening for Covid-19, but it has limitations

A nurse takes a sample from a man’s throat to test for coronavirus. Photograph:   Peter Komka/Pool/AFP via Getty Images

A nurse takes a sample from a man’s throat to test for coronavirus. Photograph: Peter Komka/Pool/AFP via Getty Images

 

There can be few people who like having a swab pushed up their nose to get a test for the Covid-19 virus, SARS-CoV-2. Wouldn’t it be easier if we could have our saliva tested for the virus instead?

Several projects in Ireland are looking at using saliva for screening (to identify people who may need a more definitive diagnostic test) but the “messy” nature of saliva means it’s not always as easy as it sounds.

Messy specimens

“We don’t routinely use saliva to test for respiratory viruses,” says medical virologist Dr Cillian de Gascun, who directs the National Virus Reference Laboratory at University College Dublin.

“That’s partly because saliva can be a messy sample to work with. It contains enzymes that can impact on PCR – the method that amplifies genetic material from the virus in a sample, so it can be more easily measured – and saliva can be quite viscous and gloopy, so it is difficult for some of the automated liquid-handling machines in the lab to handle.”

There’s another issue too, according to de Gascun. “At the moment we believe that saliva testing would be less sensitive than the current swabs we are taking [to test for the Covid-19 virus],” he says.

“So I don’t envisage saliva replacing swab samples, but saliva testing might be useful for particular situations, such as testing children, people in nursing homes or where a person needs to take serial tests. If saliva has an acceptable sensitivity, it might be an additional specimen type to consider, given that it would be better than no sample at all.”

Saliva screens

Prof Cliona O’Farrelly sees value in saliva testing, with the emphasis on screening. “We need to screen lots of people, lots of the time, many, many times,” says O’Farrelly, professor of comparative immunology at Trinity College Dublin. “So we need something much quicker, simpler and cheaper than swabs and PCR. This is where saliva can come in. Then we will need to diagnose a small proportion of all the people we screen, as most [people] will likely be negative. This is when swabs and PCR can come in useful for diagnosis.”

Despite its limitations, Prof Kingston Mills at Trinity College Dublin believes saliva could be used to screen and perhaps even diagnose large numbers of people. “The big benefit of saliva would be that it obviates the need for testing centres, because a person could drool into a tube and send that off for analysis,” he says.

Mills leads the Trinity Covid-19 Immunology Project, where Prof Orla Sheils is screening saliva samples from students by using loop-mediated isothermal amplification (LAMP) rather than PCR.

“The LAMP assay is quick, it takes 30 minutes, it doesn’t require sophisticated equipment and if there is virus present it shows up as a colour change,” says Mills. “The test we are carrying out is not a diagnostic test, but I think the LAMP assay could be a game changer, especially using saliva, to diagnose as well as screen.”

Detergent to preserve

One way to preserve a saliva sample is to store and transport it in a detergent that inactivates the virus but preserves the genetic material. Dr John Mac Sharry from APC Microbiome Ireland and colleagues were recently awarded Science Foundation Ireland funding to explore the impact of detergent on SARS-CoV-2 in saliva samples.

“My area of research is lung microbiology, and before Covid-19 we had been looking at levels of bacteria and fungi in the saliva of patients with asthma,” explains Mac Sharry, a lecturer in medical microbiology at University College Cork.

“Then, when the pandemic started, we decided to look for viruses in saliva. We are adding detergent to the saliva when it is collected, to see what happens to the virus. Accumulated scientific knowledge through history suggests the detergent will help to preserve the genetic material [of] SARS-CoV-2, but we need the evidence.”

The project will also compare saliva samples and swabs from the same patients to see how the saliva test protocol matches up, though he admits the saliva specimens have their limitations.

“No test is perfect,” he says. “And it’s important that people don’t eat or drink anything or smoke for a period before the test is taken, as this can introduce more variability into the sample.”

On-the-spot colour change

Dr Niamh Gilmartin, a biochemistry lecturer at TU Dublin, echoes the need for saliva to be as “clean” as possible when providing a sample. “Food particles in saliva are a big problem,” she says. “And there is probably more sample preparation needed compared to, say, blood or urine, which are easier samples to handle from a laboratory perspective.”

Gilmartin, Dr Steve Meaney and colleagues are developing a colour-based kit to immediately screen for the virus in saliva. AptaGold uses aptamers – short pieces of DNA – that have been designed to bind to a protein on the surface of SARS-CoV-2. The aptamers are coated onto nanoparticles of gold, then if they bind to the virus in a sample, the particles clump and change the colour of the liquid from blue to red.

The technology looks for a protein on the virus, rather than for genetic material that can be amplified by PCR. But Gilmartin anticipates the sensitivity level of the AptaGold assay will be fit for purpose. “The idea is to make Covid-19 screening accessible outside of a lab,” she explains. “But the emphasis is on screening, this would not be a diagnostic test.”

Not the optimum for diagnosis

While the Covid-19 pandemic is changing how we do many things, de Gascun does not believe it will push saliva testing beyond the realm of screening and into routine diagnostics. “It is not like people haven’t thought of this before, and there are logisitic and sensitivity reasons why saliva is not the optimum specimen for definitive diagnosis,” he says.

“[Saliva] may have a role to play in certain situations, but I don’t see it changing the way we do diagnostics for respiratory viruses, and in 12 months’ time, next winter, I would be surprised if we are using saliva as the preferred specimen type for routine diagnostic testing.”