Rapidly mutating coronavirus creates risk of unreliable testing: U of Manitoba researchers

Researchers at the University of Manitoba warn that unless scientists continually track changes in the rapidly mutating virus that causes COVID-19, testing could produce false negative results and efforts to produce a vaccine could be thwarted.

The Manitoba researchers compiled data from patients around the world in order to detect genetic variations in the coronavirus, technically known as SARS-CoV-2, across geographic regions. They found 146 variants, or "genetic footprints."

When countries around the world locked down their borders in order to slow the spread of the pandemic, the virus began to evolve differently within those countries, said Dr. Carlos Farkas, a U of M post-doctoral researcher who led the study.

The variants are significant, because the tests used to detect the novel coronavirus use small pieces of DNA, called primers, that bind to the viral sequence and amplify the signal of any genetic material in the patient sample. 

"The problem is, you can still have the virus but with variants, and probably these primers will fail to amplify this different strain of the virus," said Farkas. 

"That's a problem, and could explain the false negative that actually we're seeing worldwide."

New primers needed

For example, the researchers found that in Washington state, one of the first U.S. states where the virus was detected, the virus had a distinct footprint, different from samples taken in Europe or Asia. 

"Because SARS-CoV-2 is changing rapidly, researchers should be aware of its current local viral footprints in order to design DNA primers that don't bind to regions of the virus that have changed," Dr. Jody Haigh, a co-author of the study, said in a news release. 

"Other regions of the virus that don't show these changes should be used for designing primers."

The researchers found two specific variants of the virus that could go undetected by the common test developed by the U.S. Centers for Disease Control, which Farkas called the "gold standard."

The variations could mean that a vaccine used to prevent the virus in one country might not work on a virus from a different region, he said.

One of the reasons the coronavirus mutates so rapidly is because of what it's made of.

Rather than consisting of DNA, like a papillomavirus, the novel coronavirus is made of RNA, which is less stable, said Farkas.

"So the mutation rate is higher than DNA viruses," he said. "It mutates, evolves very rapidly, and that's the problem.… You can't capture a single virus, or a single vaccine."

Maintaining physical distancing

In the absence of a viable vaccine, Farkas said it is important for people to maintain physical distancing to limit the spread of the virus, because the more people it spreads to, the more chances it has to mutate and pass on its variants.

The number of variants included in this study represent only about 50 datasets from early in the pandemic, up until March 27.

Farkas and his team are currently going through 8,000 new datasets and he expects the total number of variants of SARS-CoV-2 to be much higher, and continually growing.

The peer-reviewed study, which was conducted in collaboration with a virology lab in Chile, was published in PeerJ — the Journal of Life and Environmental Sciences. 

The study team recently received funding to develop online tools to track genetic variations and develop new testing primers that avoid sections of the genetic sequence prone to change.