Two new variants of SARS-CoV-2, the virus that causes COVID-19, have been detected and are spreading. The first is the Kent variant (B.1.1.7 strain), which emerged in the UK, and has already spread to many other countries including the US. It is also now the dominant strain in the UK, responsible for more than 50% of new cases. The second variant emerged in South Africa (E484K strain), and the BBC reports:
It is already the dominant virus variant in the Eastern and Western Cape provinces of South Africa. Other countries including Austria, Norway and Japan, have also found cases.
What are the implications of these new strains? Are they more infectious, or more deadly, and will the current vaccines work against them?
How do new variants emerge?
The emergence of new strains or variants of a virus occurs through natural mutations in the virus as it replicates. Different viruses mutate at different rates. The flu virus, for example, mutates rather quickly, with many infectious strains identified. Each flu season, in fact, new strains are likely to be circulating from the previous year. The coronavirus, however, has error-correction abilities that reduce the number of mutations while it replicates, and so it mutates much more slowly than the flu virus. It still mutates, however.
This is a significant long-term risk to allowing the pandemic to spread for as long as it has. The emergence of new variants is inevitable. In fact, there are thousands of strains of the virus circulating, and this is partly how scientists track the spread of the virus. Most mutations are inconsequential – they either don’t alter the amino acid sequence of proteins or any changes does not affect the overall structure and function of the protein. Occasional mutations may make structural changes to a viral protein without a dramatic effect on its properties.
But occasionally a mutation will change an important structural protein and alter the virus’s ability to infect hosts, to spread, or the severity of the illness they produce. This is always the worry, and why we don’t like to let epidemics or pandemics simmer for a long time. The more the virus replicates, the greater the opportunity for chance mutations that will give rise to a more serious strain.
The Kent variant
The new strain that arose in Kent in the UK was first detected on September 20th. Researchers were investigating a surge in COVID cases in Kent, and tracing variants to map the spread. They found the dominant variant had a cluster of 23 new mutations, which itself is unusual. Later study found that this variant is more infectious than previously identified variants. Eight of these mutations are on the infamous spike protein that gives the coronavirus family its name, and is what allows the virus to enter and infect cells.
Scientists are still trying to sort out the effect of these mutations, but so far it seems that the Kent variant has a greater ability to infect and to spread. Patients with this variant may remain infectious longer, and the virus seems to have a greater ability to infect cells. This is why this variant quickly dominates once it spreads to a region.
The good news, however, is that this variant does not appear to be more deadly. Also, it appears to be as vulnerable to neutralizing antibodies produced by the approved vaccines – so the vaccines will protect against this variant.
How this variant emerged is also still under investigation, but the current hypothesis is that chronically ill patients, with an active COVID infection for months, gave the virus an opportunity to accumulate multiple mutations. Specifically, patients with compromised immune systems provide fertile ground for the virus to replicate and mutate. Also, patients treated with partially effective treatments, that allowed them to survive for a long time but did not eradicate the infection, gave the virus the opportunity to mutate.
The South African variant
The second new variant of concern was first detected in South Africa, and is now also in other countries, with cases detected as far as the UK. This variant also has mutations on the spike protein, including some of the same mutations found in the Kent variant. These are almost certainly independent mutations, and not due to a common source. Because it has some of the same mutations, and ones specifically that confer greater infectivity, this variant is also more infectious and will tend to dominate once it spreads to a region.
However, the South Africa variant has a new property that is extremely concerning – the mutations to its spike protein allow it to partially evade antibodies produced by prior infection or vaccination. So far it seems that such antibodies have some effect against this new strain, just diminished. Researchers will have to specifically study how effective existing vaccines are against this strain, but they are likely to be less effective (although not worthless).
Fortunately it will not take much time to reformulate existing vaccines to cover this new variant. The mRNA vaccines in particularly could be created in a matter of days, once they have the genome of the new variants. This will definitely complicate vaccination efforts, however. It may mean that people need to get vaccinated every year or so, not only to maintain immunity but also to cover new emerging strains.
What does all this mean?
The fact that SARS-CoV-2 mutates relatively slowly was considered reassuring by epidemiologists. If we could get this pandemic under control quickly enough, we could stop it before any new and worse strains emerge. However, mutating slowly is still mutating, and new strains have been emerging at a steady rate. It was inevitable that new strains would emerge that possess greater infectivity or deadliness or that have properties that allow them to evade the immune system. This is evolution in action.
In fact, our attempts at treating patients with COVID-19, which we have to do, provides further evolutionary pressure, and even further opportunity (by allowing some patients to survive for a long time with an active infection) for new strains to emerge. This is just a microcosm of the bigger picture – that humanity is engaged in an evolutionary war against a host of infectious agents. This is just one battle in that never-ending war.
Further, the pandemic itself, and the emergence of these new strains, highlight the fact that fighting infections is a global species-wide problem, and we have to face it together with a coordinated response. We simply don’t have the option of allowing pandemics to spread, to ride them out and take the hit. This is one more reason why public health measures aimed at stopping the pandemic are so important. The longer the pandemic is allowed to continue, the greater the chance that new and deadlier strains will emerge. These new strains can emerge from any part of the world and wind up on our shores.
This is also one more reason why mask denialism and anti-vaxxer propaganda is so deadly. These choices affect everyone.
One might reasonably argue that we are fighting a losing war against infectious disease. New germs are evolving faster that we can deal with them. Pandemics are emerging at an increasing rate. The World Health Organization warned that the COVID-19 pandemic, as bad as it is, might not be “The big one”. We likely have more deadly pandemics in our future.
The good news is that science is steadily advancing. The ability to produce multiple highly effective vaccines in less than a year is testimony to that. But this is coupled with serious bad news – the pandemic has revealed that politically we do not have our stuff together. It has revealed weaknesses in the system, and if we don’t fix them science will not save us in the future. One of those weaknesses is the ease with which pseudoscience and misinformation are spread. Misinformation is perhaps the most deadly pandemic, and we have no system in place for dealing with it.
