The researchers behind the study say 20C-US has been spreading rapidly through the US since June, and predict it could soon become the dominant variant of Covid-19 in the US.
In early January, another closely related new variant appeared in California, called CAL.20C. There were more than 1,000 cases of this variant reported at the start of February and in Los Angeles accounts for a quarter to one third of all Covid-19 cases. There are also reports of this variant infecting people who have already been infected with a different variant of the virus last year. One of the mutations carried by CAL.20C, called L452R, is found on the spike protein and has been associated with a decreased sensitivity to antibodies, suggesting it may be able to evade parts of the immune system.
Recently, scientists at the University of Manitoba, in Winnipeg, Canada, also identified two emerging variants that have been spreading around the world and are associated with “high fatality rates” compared to the earlier virus. One features a mutation called V1176F in the spike protein, which occurs alongside another mutation called D614G.
The first letter in these mutation names indicates the amino acid that has been replaced, the number is its location on the protein, and the final letter is the new amino acid that has appeared at that site. The D614G mutation alone appeared relatively early on in the pandemic in Europe and caused a dramatic increase in how much virus was shed by patients it infected, helping it to spread more quickly. The addition of the V1176F mutation may alter this behaviour further, the Canadian researchers say, and it has appeared in several countries independently, suggesting it gives the virus an advantage.
The other variant they identified appeared rapidly in Australia and carries a S477N mutation, which seems to have increased the virus’s ability to bind to human cells.
The researchers warn that these two new mutations “may pose significant public health concerns in the future” if they continue to spread and provide the virus with an advantage. They add that Covid-19 appears to be “evolving non-randomly and human hosts shape emergent variants with positive fitness that can easily spread into the population”.
Researchers in the UK have also recently noticed a mutation called E484K – which is thought to reduce the virus’s vulnerability to antibodies in the South African and Brazilian variants – has appeared in some samples of the British variant B117. Although only in a handful of cases so far, it is raising concerns that the faster spreading British variant may also now pick up some ability to escape the immune systems of those who have been vaccinated or already infected.
Another variant of concern found to be circulating in New York in February 2021 has also worried scientists. This variant, designated B1.526, has been increasing in numbers and by mid-February accounted for 12.3% of the viruses analysed. It contains two key mutations – E484K and N501Y – that were also seen in the variants of concern from Brazil and South Africa.
These signs of adaptation by the virus are not entirely surprising to scientists. In most viruses and disease-causing bacteria, the use of treatments and vaccines causes them to evolve ways of escaping them so they can continue to spread. Those that develop resistance to a treatment or can hide from the immune system will survive for longer to replicate and so spread their genetic material.
“I do not see a reason that this evolutionary selective process would differ in a pandemic such as Sars-CoV-2 [the Covid-19 virus], compared to a geographically contained epidemic,” says Carolyn Williamson, head of the division of virology at the University of Cape Town and one of the researchers who identified a rapidly spreading South African variant in December. “One could speculate that the virus being exposed to different selective pressures in different regions of the world, together with rapid spread, may see these more favourable properties emerge more quickly, but we really don’t know.”