The emergence of more transmissible variants has been one of the biggest drivers of new scientific unknowns. The way that we will begin to chart our course to a less dangerous relationship with SARS-CoV-2 is based in part on access to information that researchers will have about emerging variants of concern.
A country’s ability to sequence genomic data could play a major role in its ability to respond to potentially more dangerous and emerging outbreaks and mutations. A virus’s genome includes molecules called RNA that allows virologists and other scientists to understand its basic characteristics and how it behaves. As the virus is transmitted, its genomic sequence changes and can result in different characteristics and the emergence of new variants. Many of these will not have any sort of evolutionary advantage over others and will consequently disappear quite quickly. But when a genomic mutation results in a change that is beneficial to the virus – for example, its improved capacity to spread to new hosts – that variant is likely to become dominant. This is what happened with the now widespread Delta variant.
For University of British Columbia’s COVID-19 Research Lead Jeffrey Joy, it’s still too soon to say whether Sars-CoV-2 will evolve to become more dangerous. Joy says that he is keeping close watch on two other emerging variants of concern: the Lambda variant that is widespread in South America and another variant that currently doesn’t have a WHO label but has recently been responsible for a growing number of deaths among vaccinated members of a care home in Belgium. This B.1.621 variant first emerged in Colombia in February and has a number of the same mutations in the spike protein as other known variants, but seems to be better able to dodge our immunity. Although we still need more information about these variants to know how big of a concern they should be, Joy says “it’s something I’m keeping my eye on.”
Joy says there are a few ways in which the virus could mutate that could become more harmful to humans. The virus can evolve with common smaller mutations that accumulate over time – researchers believe this is likely the way the Alpha and Delta variants emerged. Joy says another way that viruses mutate is through a process called recombination.
Recombination is the transfer of genetic information between different viruses and can generate new genetic variants. This happens frequently among betacoronaviruses like MERS-CoV and the original 2003 SARS. If someone already infected with one variant of SARS-CoV-2 becomes infected with another strain, there is a chance that recombination could occur and, notes Joy, it is not as unlikely as it may sound.
“We have an extremely large pool of people. Each one of those is an opportunity for viral evolution to happen,” says Joy. “Within a cell, you have the two genomes and then what happens is the polymerase (an enzyme that is responsible for making new copies of RNA in the form of nucleic acid molecules) that is replicating the two, jumps from one genome to the other.”
This could, for example, result in the genome of a more transmissible variant coming into contact with the genome of one that is more virulent, resulting in a new variant that is able to spread more quickly and is more dangerous to humans.
Despite Canada’s capacity to test and sequence viruses producing high-quality data that would help reveal information about the virus – for example, the emergence of new Canadian variants – there are restrictions that impact the quality of information that is being collected, says David Earn, a professor and researcher of mathematical epidemiology at McMaster University as well as a member of Health Canada’s Expert Group on Modelling Approaches. He notes that many of the current limitations around improved access to genomic data centre around privacy concerns.
“That sort of attention to privacy, which in principle is a very good thing, is sometimes a barrier to releasing good quality data that helps with modelling and could improve our projections,” Earn says. “You can imagine if we have good collection procedures with a lot of information about each sample circulated to people like me … we might be able to identify a new variant more quickly. That can make all the difference. If you discover there’s, for argument’s sake, two weeks before a variant takes off, for some provinces in Canada that could make all the difference in terms of our ability to prevent it from spreading widely.”
To isolate and predict the emergence of variants of concern effectively, experts stress the need to be able to track emerging variants as close to real time as possible. But to track and contain them in the longer term, we will have to be able to sequence data across the world, says Arinjay Banerjee, research scientist at the University of Saskatchewan’s Vaccine and Infectious Disease Organization.
“We need to be able to know which variants are circulating in which areas of the planet,” says Banerjee. “When you’re looking at low- and middle-income countries you’re also looking at the availability of the infrastructure to begin sequencing to begin with. That’s a huge problem if you’re starting to open up economies and travel again.”
Issues relating to costs emerge quickly when discussing mass viral surveillance across the globe, and that is going to be a big question moving forward, says Banerjee. “We have to sequence. There’s absolutely no other way to identify which variants are circulating without going in and sampling and sequencing. And who pays for that? Who supplies the infrastructure and how do you coordinate this?”
Moving forward, controlling the global spread of new and emerging variants is going to rely heavily on our ability to sequence data across the globe and ensure widespread international access to vaccines.
For Banerjee, moving on from SARS-CoV-2 is going to rest on getting as many people vaccinated as possible. “There’s a lot of uncertainty but vaccines are our hope out of this pandemic. That is really it.”