A coronavirus variant called B1525 has become one of the most recent additions to the global variant watch list and has been included in the list of variants under investigation by Public Health England.
Scientists are keeping a watchful eye on this variant because it has several mutations in the gene that makes the spike protein - the part of the virus that latches onto human cells. These changes include the presence of the increasingly well-known mutation called E484K, which allows the virus to partly evade the immune system, and is found in the variants first identified in South Africa (B1351) and Brazil (P1).
While there is no information on what this means for B1525, there is growing evidence that E484K may impact how effective COVID vaccines are. But there is no suggestion so far that B1525 is more transmissible or that it leads to more severe disease.
There are other mutations in B1525 that are also noteworthy, such as Q677H. Scientists have repeatedly detected this change - at least six times in different lineages in the US, suggesting that it gives the virus an advantage, although the nature of any benefit has not been identified yet.
The B1525 variant also has several deletions - where "letters" (G, U, A and C) of the virus's RNA are missing from its genome. These letters are also missing in B117, the variant first detected in Kent, England. Research by Ravindra Gupta, a clinical microbiologist at the University of Cambridge, found that these deletions may increase infectivity twofold in laboratory experiments.
As with many variants, B1525 appears to have emerged quite recently. The earliest example in the shared global database of coronavirus genomes, called Gisaid, dates from December 15 2020. It was identified in a person in the UK. And like many variants, B1525 had already travelled the world before it came to global attention. A total of 204 sequences of this variant in Gisaid can be traced to 18 countries as of February 20 2021.
Two countries (Denmark and the UK) account for more than half of the cases, but these two countries are also sequencing lots of coronavirus genomes.
Other countries that have entered at least one genome of this variant in the online database are Nigeria, the US, France, Canada, Ghana, Australia, Japan, Italy, Netherlands, Jordan, Singapore, Finland, Switzerland, Mayotte, Belgium and Spain.
On February 25, the Republic of Ireland reported its first case of B1525.
A total of 31 B1525 genomes have been submitted to Gisaid by Nigeria. In a statement on February 19 2021 on variants of coronavirus from the Nigeria Centre for Disease Control, it was reported that the first detected B1525 genome was from a sample collected on November 23 2020 from a patient in Lagos State, but the sample wasn't immediately updated to the database, hence the UK sample being the first recorded one. So far, the variant has been detected among cases in five states in Nigeria. B1525 cases have also been reported in other countries in travellers from Nigeria. So the mutation may have first emerged in Nigeria.
Knowing if a certain variant is common in a population is useful for public health and policy decisions in a given country. But because the evolution of the coronavirus is occurring worldwide, it's best to avoid relating a variant to a country to avoid stigma.
Different pattern of frequency
Another way of defining the frequency of specific variants is to determine how often they occur compared with other variants in circulation at the same time. Looking at the frequency of B1525 sequences detected since the date that the first example of this variant was detected in that country, a different pattern of frequency emerges.
In Denmark, as of February 20 2021, it accounted for 59 out of 12,222 sequences; in the UK, 57 of 100,063 sequences; and in Nigeria, 31 of 144 sequences. This suggests that the variant is probably quite common in Nigeria, but rare in Denmark and the UK. A lack of sequence data may mask the frequency in other countries. However, these types of calculations can be biased if viruses isolated from travellers are more likely to be sequenced.
Whichever way we choose to measure the frequency of B1525, it remains, at this point, a rare variant. But it joins a growing list of coronavirus variants that need to be studied in detail in the laboratory and in infected people to find out if it's a variant we should be concerned about, and if so, where it sits on the leader-board of variants to watch and respond to.
Author: Sharon Peacock - Director, COVID-19 genomics UK Consortium (COG-UK) and Professor of Public Health & Microbiology, University of Cambridge