Closer Look: What are the Covid-19 variants of concern?

Photo by CDC on Unsplash

The press is struggling to describe the new mutations and variants that have been discovered in South Africa, Kent, Brazil, etc and what they might mean. The variants have incomprehensible names like B.1.1.7 and preliminary vaccine tests against them have been misreported. So what’s going on?

What can mutations do?

Most mutations will be neutral, some will make the virus less successful, and others will make the virus more successful. Some combinations of mutations will also be more successful than others. In general we are interested in mutations that can…

  • Increase transmission in a population
  • Increase or decrease disease severity
  • Decrease effectiveness of natural or vaccine-induced immunity
  • Decrease detectability by viral tests

What mutations we have already appeared?

There are hundreds of mutations in covid19 worldwide that are being tracked, with the majority being apparently neutral. There are a few combinations of mutations that that have arisen in so called variants of concern. It becomes a lot easier to understand if we describe the actual mutations. So, meet Nelly, Eeek, and Ken.

UK (Kent) Variant B.1.1.7

So let’s start with the UK variant (B.1.1.7) that we first described in November in Kent. It has been seen in lots of other countries as well. This variant has a gene change that we can call “Nelly” [1], which affects the way the virus can “unlock” human cells. This gene makes the covid-19 virus about 50% more transmissible [2]. In the UK it took this variant four weeks to go from 20% of the cases to 80% of the cases, clearly dominating against original covid-19 virus when given the chance [3].

There is not much evidence this variant is better at evading antibodies or immunity. Oxford/AstraZeneca vaccine, for example, is just as effective against Nelly variants than the original covid-19 virus [4]. However, there is some evidence this variant may lead to higher hospitalisation and deaths, although more research is ongoing.

South African Variant B.1.351

So next we have the South Africa variant (B.1.351), which scientists have been watching carefully since December and has since been detected around the world. It has Nelly, which it gained completely independently to the UK variant.

It also has two mutations where the spiky outside of the virus has slightly changed. The two mutations are called “Eeek” and another called K417N which doesn’t have an official silly name yet, so I’ll call it “Ken”.

In flu, the spikes change so much and so rapidly it is very difficult to gain long-term immunity, and so in comparison these two mutations are a very small change. However, it means the covid-19 virus can evade the immune system a bit better. There have been about 105 cases of this variant in the UK so far.

Some preliminary studies have estimated that antibodies for the original covid-19 virus are about 10–60 times less effective against the variants with Eeek [5]. Some preliminary tests have found the Oxford/AstraZeneca vaccine is not very effective against this strain in preventing minor illness [6a], and Pfizer vaccine efficacy against disease is also slightly reduced [6b]. More on this later!

UK (Bristol) Variant 202102/02

In February, it’s been discovered a UK variant with Nelly has now independently gained Eeek as well (found in Bristol). There are very low numbers of this variant so far, about 61 cases, but this is still a variant of concern as it could provide antibody escape like other variants with Eeek.

Brazilian Variant P.1

Next, the Brazilian variant (P.1), first spotted in December and has recently arrived in the UK. This has Nelly and Eeek, and Ken. There’s no evidence it makes the disease more deadly/serious nor more transmissible. Vaccines haven’t been tested against this variant yet, but similar results to the South Africa variant are expected. There is evidence that people who are immune to covid-19 could get symptomatic disease from this variant .See this article for more information:

Other Variants and Mutations

China D614G mutation

Before all these mutations arose, this first mutation D614G or “Doug” appeared in East China in early 2020. This mutation is so successful it completely replaced all the covid-19 viruses without this mutation, and so it likely improves transmission and ability for the virus to replicate in human cells. We can consider this the main covid-19 variant.

California Variant B.1.427

A variant with a mutation called L452R has been found in California, and now makes up over half the cases there. It is unknown how L452R affects transmission or vaccine escape.

New York Variant B.1.526

A variant has been found in 30% of cases in New York, with the Eeek mutation and another called S477N, where the effects of this mutation are currently unknown.

I heard that over time, viruses evolve to become more transmissable but less deadly…

…so covid-19 should eventually become just another flu we all have to live with.

The first part is mostly true but not necessarily the second part. If we imagine a very successful virus, it would by highly transmissable but also spread asymptomatically and silently. If the humans feel sick or notice symptoms, they are less likely to mix with other humans and spread the virus. So it is a good strategy to be as innocuous as possible. Killing the human host quickly is also a bad strategy because they can’t spread it to more humans. That’s why the most widespread and successful human viruses on the planet are herpes viruses and the common cold, both are silent enough to spread unnoticed.

However, it’s reasonably difficult for a virus to be fully asymptomatic, particularly those making use of the respiratory system to spread through coughs and sneezes and breathing. Eventually the immune system will be alerted and the human will get a fever, aches, chills, and feel very unwell. The act of the virus replicating in human cells also causes tissue damage, which is why uncontrolled spread of any virus, even a common cold, would kill the victim. Luckily the immune system works to stop this happening.

So while no symptoms at all is best, any virus that spreads well before symptoms kick in will be just as successful at infecting humans globally. This is why covid-19 has been so devastating, even though the death rate is pretty low, when compared to Ebola or the previous coronavirus pandemic SARS. The problem with both Ebola and SARS is that the victim gets very sick and doesn’t spread the disease well before becoming symptomatic. Isolating the sick and those in contact with the sick is effective, as it is an easier disease to trace.

As covid-19 is already excellent at asymptomatic spread, it is unlikely there will be a high selection pressure to make the virus to less deadly. Time alone does not make viruses less deadly, it’s also about whether it can silently spread. Measles and polio are so infectious they are highly successful and their severity has not reduced even after generations. The timeline for evolution is also not really very comforting, it’s thought the black plague took 7 years to become “harmless” and killed 1/3 of the world population. Spanish flu was quicker, but again killed 40 million people in the meantime.

So going back to the original statement, virus strains/variants that spread better will outcompete and win, but as long as the virus can spread asymptomatically then there is a much lower chance it will become fully harmless. It’s possible, but not inevitable.

References:

https://undark.org/2020/11/11/coronavirus-evolve-less-deadly/

https://www.bmj.com/content/372/bmj.n359

https://www.annualreviews.org/doi/abs/10.1146/annurev-micro-090110-102833?journalCode=micro

https://www.nytimes.com/interactive/2021/health/coronavirus-variant-tracker.html

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Postdoctoral Zoology researcher at the University of Oxford

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Lydia France

Lydia France

Postdoctoral Zoology researcher at the University of Oxford

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