In December, the UK reported a Covid-19 variant of concern, commonly referred to as the B117 variant, which appeared to be more transmissible. Since then, scientists have established that B117 is somewhere between 50% to 70% more transmissible than other variants. If more people are getting sick, there is more pressure on health systems, and in the UK health services are so overloaded a country-wide lockdown has been enforced.
While many scientists say B117 does not appear more deadly, researchers on the UK government’s New and Emerging Respiratory Virus Threats Advisory Group found it may increase the death rate by 30% to 40%, though their sample size was small and they said more research is needed. With B117 now detected in more than 50 countries, understanding the variant is urgent.
But other variants of concern have also been identified, including in California, South Africa and Brazil.
So exactly what is a variant, and how many are there? And why are some variants of more concern than others?
An associate professor with the University of New South Wales, Stuart Turville, who works with the Kirby Institute’s immunovirology and pathogenesis program, says although many people have referred to some of these variants as new “strains” of the virus, it is most accurate to say the virus strain causing Covid-19, known as SARS-CoV-2, has thousands of variants, which can also be described as subtypes, isolates or lineages.
However, some of these variants have more changes in their genetic instructions, known as a genome, than others. Turville says the genome of Covid-19 has around 30,000 base pairs. Base pairs are the molecules on opposite strands of the virus’s genetic material, which form chemical bonds with one another. These chemical bonds act like rungs in a ladder and help hold the strands together.
“In the context of the variant identified in the UK [B117], there are about 24 changes among that 30,000, so if you look at that in the context of the whole of genome of the virus, it’s not a huge change from what it was at the beginning at 2020,” Turville says. However that is still a higher amount of changes than usual; other variants have just one or two changes, also called mutations, to the genome.
The variant identified in South Africa, referred to as B1351, also has an unusually high number of mutations, including some of those seen in B117. Again, there is no evidence to suggest that this variant increases disease severity, but it has become the dominant variant in Zambia and is therefore likely more transmissible, though investigations are ongoing.
“There have been thousands of different variants,” Turville has told Guardian Australia.
“One of the things virologists and molecular virologists say is that it’s easier to break something than to turn it into something bigger, better, and faster. There are lots of virus variants out there that have come and gone. If you take out one key element it falls apart, and it’s actually a very fragile virus.
“The key mutants we are talking about are the ones that survive the change and continue. They’re the ones that start to overgrow the variants in the past, and that’s what we are currently seeing in the UK and elsewhere.”
Another variant of concern, known as P1 or B1128, was first detected in January in travellers who arrived in Japan from Brazil. It shares some of the same mutations as B1351, and overall has more than 20 changes, deletions, mutations and insertions in its genome. A report from Brazilian researchers said it is “potentially associated with an increase in transmissibility or propensity for reinfection of individuals”.
In other words, there is some concern that it may evade the antibody response in people with existing immunity to the virus, but a lot more work needs to be done to establish this. But given the researchers said P1 seems to be associated with a rapid increase in cases in locations where previous attack rates are thought to be very high, “it is essential to rapidly investigate whether there is an increased rate of reinfection in previously exposed individuals”.
Then, on 17 January, the California Department of Public Health in the US revealed a variant known as L452R is increasingly being identified by genomic sequencing in multiple counties across the state. However, the department said in a statement: “It’s too soon to know if this variant will spread more rapidly than others”.
“The fact that this variant was identified in several large outbreaks in our county is a red flag and must be investigated further,” said Santa Clara County health officer, Dr Sara Cody.
Australia’s health officials are concerned the variants currently wreaking havoc in the UK, South Africa and Brazil may leak out of hotel quarantine, where returned travellers are required to isolate for 14 days and undergo testing.
On Friday, the deputy chief medical officer, Michael Kidd, said if someone tested positive for the variants they would have to undergo a further 14 days of isolation before being released, up from the 10 days for people diagnosed with less concerning variants.
There are a couple of theories as to why some variants managed to take hold while others died out, Turville said.
“In terms of the variants identified in Brazil and the UK and how they have turned up, there is evidence that people infected with the virus for longer accumulate more changes in the virus.”
People who are immunocompromised, such as those who have cancer, are infected for longer as their bodies can’t fight off the virus as quickly. The theory is this gives the virus an environment to linger and develop mutations, before then being transmitted to someone else.
But Turville said that in countries where Covid-19 is out of control, the sheer number of people infected makes it more likely that there will be a rare event that leads to a “burst in changes in the virus you wouldn’t otherwise see”.
“It may boil down to the fact that in really hard-hit areas, there is more opportunity for a rare virological event,” he said. Turville and other researchers are hoping to learn more about these variants in work they are doing in the Kirby Institute’s containment lab, a high-security laboratory that receives swabs of the virus from international travellers in Australia’s hotel quarantine system.
Turville then uses these swabs to grow the virus. Each time someone enters the lab, they dress in multiple layers of clothing covered by full personal protective equipment including respirator masks, gumboots and overalls over the top. Turville walks through a series of negative pressure chambers before entering the containment lab, which he can only work in for short periods of time to avoid overheating.
“We get swabs coming in from quarantine of all the new virus flavours that are seen there, then we grow them up, and we need to see how they’re behaving in the lab. That helps us learn whether someone who had an antibody response after being infected by a different variant in March will display a similar response to one of the newer variants.”
Turville said the good news was that although some of the new variants may take the edge off an antibody response or a vaccine response, none to date could completely evade the immune response.
“To date, we have yet to see a single virus mutant with complete immune evasion that would make a vaccine useless,” he said.