What’s the difference between mutations, variants and strains? A guide to COVID terminology



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Lara Herrero, Griffith University and Eugene Madzokere, Griffith University

Living through a global pandemic over the past year has seen all of us expanding our vocabularies. We now understand terms like PPE, social distancing and contact tracing.

But just when perhaps we thought we had a handle on most of the terminology, we’re faced with another set of new words: mutation, variant and strain.

So, what do they mean?

The genetic material of SARS-CoV-2, the coronavirus that causes COVID-19, is called ribonucleic acid (RNA). To replicate, and therefore establish infection, SARS-CoV-2 RNA must hijack a host cell and use the cell’s machinery to duplicate itself.

Errors often occur during the process of duplicating the viral RNA. This results in viruses that are similar but not exact copies of the original virus. These errors in the viral RNA are called mutations, and viruses with these mutations are called variants. Variants could differ by a single or many mutations.

Not all mutations have the same effect. To understand this better, we need to understand the basics of our genetic code (DNA for humans; RNA for SARS-CoV-2). This code is like a blueprint on which all organisms are built. When a mutation occurs at a single point, it won’t necessarily change any of the building blocks (called amino acids). In this case, it won’t change how the organism (human or virus) is built.

On occasion though, these single mutations occur in a part of the virus RNA that causes a change in a particular building block. In some cases, there could be many mutations that together alter the building block.




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A variant is a referred to as a strain when it shows distinct physical properties. Put simply, a strain is a variant that is built differently, and so behaves differently, to its parent virus. These behavioural differences can be subtle or obvious.

For example, these differences could involve a variant binding to a different cell receptor, or binding more strongly to a receptor, or replicating more quickly, or transmitting more efficiently, and so on.

Essentially, all strains are variants, but not all variants are strains.

A diagram depicting the evolution from mutation to variant to strain.
Viruses with mutations become variants. If the variant displays different physical properties to the original virus, we call it a new strain.
Lara Herrero, created using BioRender, Author provided

Common variants (which are also strains)

Three of the most common SARS-CoV-2 variants are what we’ve come to know as the UK variant (B.1.1.7), the South African variant (B.1.351) and the Brazilian variant (P.1). Each contains several different mutations.

Let’s look at the UK variant as an example. This variant has a large number of mutations in the spike protein, which aids the virus in its effort to invade human cells.

The increased transmission of the UK variant is believed to be associated with a mutation called N501Y, which allows SARS-CoV-2 to bind more readily to the human receptor ACE2, the entry point for SARS-CoV-2 to a wide range of human cells.

This variant is now widespread in more than 70 countries, and has recently been detected in Australia.

While we commonly call it the “UK variant” (which it is), it’s also a strain because it displays different behaviours to the parental strain.

We’ve got lots more to learn

There is some confusion around how best to use these terms. Given all strains are variants (but not all variants are strains), it makes sense the term variant is more common. But when the science shows these variants behave differently, it would be more accurate to call them strains.

Pleasingly, the World Health Organisation and health departments in Australia appear to be using the terms correctly in the context of SARS-CoV-2.




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The big question everyone is asking at the moment is how the new variants and strains will affect the efficacy of our COVID vaccines.

The scientific community is uncovering more information about emerging mutations, variants and strains all the time, and leading vaccine developers are testing and evaluating the efficacy of their vaccines in this light.

Some recently licensed vaccines appear to protect well against the UK variant but recent data from Novavax, Johnson & Johnson and Oxford/AstraZeneca indicates possible reduced protection against the South African variant.

Health authorities in South Africa recently paused their rollout of the Oxford/AstraZeneca vaccine for this reason. However, its too early to tell what impact, if any, this will have on Australia’s vaccine plans.

The vaccine rollout in Australia will assess all information as it comes to light and ensure optimal available protection for the population.




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The Conversation


Lara Herrero, Research Leader in Virology and Infectious Disease, Griffith University and Eugene Madzokere, PhD Candidate in Virology, Griffith University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Are vaccines already helping contain COVID? Early signs say yes, but mutations will be challenging


Maximilian de Courten, Victoria University; Maja Husaric, Victoria University, and Vasso Apostolopoulos, Victoria University

More than 130 million COVID vaccine doses have been administered worldwide already, according to the University of Oxford’s “Our World in Data” vaccination tracker.

Israel, the United Kingdom, the United States, the United Arab Emirates and China are leading this huge global effort.

COVID vaccines were initially tested and approved on their ability to reduce the severity of the disease.

However, the long-term goal of vaccination is to decrease infection rates and eliminate the virus.

Excitingly, early signs suggest vaccines are already helping drive down infection rates in some countries, including Israel and the UK.

In saying that, it’s early days, and some preliminary data suggest countries might have to update their vaccine strategies to deal with emerging variants of the virus.

Israel is leading the way

The US (43 million doses), China (40 million) and the UK (13 million) have administered the most doses in total.

However, these numbers don’t take into account population size, so looking at the number of doses injected per 100 people is more meaningful.

Here, the league table is currently topped by Israel, with around 67 vaccination doses administered per 100 people.

Almost 25% of the population are fully vaccinated with both doses. And all this in just five weeks.

Israel aims to vaccinate everyone over the age of 16 and reach at least 80% of its nine million people by May this year.

Reaching at least 70% of the population via vaccination (and/or natural infection) is needed for herd immunity for COVID, according to initial modelling by University of Chicago researchers in May last year.

However, given more infectious variants of the virus have emerged, we may need to vaccinate an even higher proportion of the population to reach herd immunity.

Infection rates are falling

So far, Israel is solely using the Pfizer/BioNTech vaccine. Interim reports from the country suggest the vaccine rollout is linked to a fall in infections in people over 60 years old.

It can be tricky to separate the effects of public health measures such as lockdowns versus the effects of vaccination.

But because the fall is most pronounced in older people who were first in line to receive the vaccine, data suggest this is also partly due to the vaccine, and not just the country’s current restrictions. A team of Israeli researchers found larger falls in infections and hospitalisations after the vaccinations than occurred during previous lockdowns.

Only 0.07% of the 750,000 over-60s vaccinated tested positive for COVID, according to Israeli Ministry of Health data released last week. And only 38 people, or 0.005%, fell ill and required hospitalisation. The chance of testing positive for COVID two weeks after receiving the first dose was 33% lower than in those not vaccinated.

The UK is also showing positive signs

The UK has administered 19.4 doses per 100 people. Around 13.2 million people (or one in five adults) have received the first dose, and 0.5 million have received the second dose.

It’s currently using both the Pfizer/BioNTech and Oxford University/AstraZeneca vaccines in its rollout.

The infection rate appears to be decreasing substantially. The current daily infection growth rate is falling by between 2-5%, and the R number is estimated to be between 0.7 and 1 (an R number of less than 1 means daily new cases will decrease over time).

However, it’s difficult to determine whether these numbers are due to the lockdown or vaccinations. It’s too early to tell whether vaccines are slowing transmission, but the signs are encouraging.

According to data from the Oxford/AstraZeneca vaccine group, released as a preprint with The Lancet last week and yet to be peer reviewed, its vaccine is showing signs of reducing transmission. The shot was associated with a 67% reduction in transmission among vaccinated volunteers in clinical trials in the UK.

It’s early days, but authors of the study suggest the vaccine may have a “substantial” effect on reducing rates of transmission in the future.

In saying that, preliminary data suggest it offers minimal protection against mild or moderate illness caused by the South African variant.




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What threatens the successful rollout of vaccines?

There are three main problems that might hinder the success of this global vaccination drive.

1. Vaccine development, manufacturing, distribution and delivery

The world’s population over the age of five is currently estimated at seven billion people. If we need to vaccinate at least 70% of them to achieve herd immunity, we need to reach around five billion people.

This is an enormous undertaking, so vaccine production and availability are crucial. Many countries face the massive challenge of producing or securing enough vaccines to immunise all their citizens.

Generally, wealthier countries that could afford to make advanced purchase agreements with vaccine producers — or who could manufacture a vaccine domestically — have been the first to start COVID vaccinations.

Unfortunately, partial vaccination of the world’s population won’t achieve herd immunity. One modelling study suggests if high-income countries exclusively acquire the first two billion doses without regard for vaccine equity, the number of COVID deaths could double worldwide.

2. Administering, monitoring, and reporting adverse effects

Vaccinating a large number of citizens quickly can’t be done with existing health institutions alone.

It’s urgent we enable alternative sites such as halls and sporting venues to be used as mass vaccination sites. We also need to allow a range of health professions such as medical students, public health officials and pharmacists to administer doses to help speed up the process.

And once vaccines have been administered, it’s crucial we monitor efficacy and report on any adverse effects, which will require additional resources.




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3. Vaccine effectiveness and virus mutation

The effectiveness of vaccines can be hindered by mutations of the virus. COVID variants originating in Brazil, South Africa, and the UK have triggered huge concern worldwide.

There’s early evidence some of our current crop of COVID vaccines respond less effectively to certain variants, though most of these data are preliminary and are still emerging.




Read more:
UK, South African, Brazilian: a virologist explains each COVID variant and what they mean for the pandemic


If vaccines become less effective, new vaccines will need to be developed either including a booster dose incorporating the region of the mutated virus, or reformulating existing vaccines to include the mutated strains.

This, however, isn’t uncommon — flu vaccines are required to be updated regularly in order to increase protective capacity against new mutated strains.The Conversation

Maximilian de Courten, Professor in Global Public Health and Director of the Mitchell Institute, Victoria University; Maja Husaric, Senior Lecturer; MD, Victoria University, and Vasso Apostolopoulos, Professor of Immunology and Pro Vice-Chancellor, Research Partnerships, Victoria University

This article is republished from The Conversation under a Creative Commons license. Read the original article.