Ever since WHO declared the novel coronavirus 2019 (COVID-19) a pandemic on March 2020, the pandemic is continuing to devastate the world with high numbers of cases and deaths and continual cycles of lockdowns and re-openings. The COVID-19 pandemic will continue well into the future as COVID-19 vaccines slowly trickle to low- and middle-income countries to fully immunise the global population against COVID-19.
Like all bacteria and viruses, the SARS-CoV-2 virus, the virus that causes COVID-19 infection, can mutate. These mutations can confer new properties to the SARS-CoV-2 virus, making them more capable in spreading to other people and causing severe disease and death. With uncontrolled, widespread infection of the virus during the pandemic, the virus can mutate at a faster rate, producing a series of variants that are different from the Wuhan strain that emerged in December 2020. In this blog post, I will explain in detail what SARS-CoV-2 variants are and how they arise. Following this, I will describe the various mutations that are present in SARS-CoV-2 variants and explain how they contribute to enhanced virus transmission and infection severity.
How do viral variants arise?
DNA or RNA inside the virus encodes genetic information that serves as the blueprint for producing viral proteins. The sequence of nucleotides in viral DNA or RNA can be translated into a sequence of amino acids (called a polypeptide) that, when combined, forms a protein. These proteins adopt particular conformations, with folds in specific parts of the protein that can affect how viral proteins interact with host proteins.
DNA and RNA polymerases are enzymes that can copy, or replicate, DNA or RNA. They use existing DNA or RNA strands as a template to form new DNA or RNA strands by bringing together and fusing complementary nucleotides. However, compared to human DNA and RNA polymerases, viral DNA and RNA polymerases are more susceptible to making mistakes. They are not only more likely to join the wrong nucleotide onto the new DNA or RNA strand, but they are also less likely to correct them. These mistakes, called mutations, can have a massive effect on the protein’s conformation and how it functions or interacts with other host and viral proteins.
Most mutations substitute one nucleotide with another nucleotide, changing the amino acid that is added to the protein. These substitution mutations are defined by the notation XNY, where amino acid X in position N is replaced with amino acid Y. For example, the mutation D614G represents a substitution mutation where D (aspartate) in position 614 of the protein is replaced with G (glycine). Other mutations may insert or delete a nucleotide which can massively affect what amino acids get added onto the protein. These mutations are represented by ins or del after the position number which represent insertion and deletion mutations respectively (relevant examples include 64ins and 157-158del).
Most mutations either do not affect the virus’ ability to transmit or cause disease or may even be detrimental, reducing its ability to infect and replicate inside cells. Some mutations; though, can enhance the SARS-CoV-2 virus’ ability to transmit and/or cause severe disease. These mutations are what contributes to the emergence of SARS-CoV-2 variants.
What is a SARS-CoV-2 variant?
SARS-CoV-2 variants are SARS-CoV-2 viruses that are different from their initial form (the Wuhan strain). These variants arise as a result of uncontrolled, widespread transmission of the SARS-CoV-2 virus, where the virus has more chances to mutate and become more effective in infecting and transmitting between humans.
The most notable SARS-CoV-2 variants are defined as either variants of interest (VOIs) or variants of concern (VOCs) by health organisations such as the World Health Organisation (WHO). According to the WHO, a VOI is a SARS-CoV-2 variant:
- with genetic changes that are predicted or known to affect virus characteristics such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape; AND
- identified to cause significant community transmission or multiple COVID-19 clusters, in multiple countries with increasing relative prevalence alongside increasing number of cases over time, or other apparent epidemiological impacts to suggest an emerging risk to global public health.
In other words, VOIs have mutations that increase the ability of SARS-CoV-2 viruses to transmit between humans and/or cause more severe infection.
In contrast, a VOC, according to the WHO, are SARS-CoV-2 variants that:
…meets the definition of a VOI and, through a comparative assessment, has been demonstrated to be associated with one or more of the following changes at a degree of global public health significance:
- Increase in transmissibility or detrimental change in COVID-19 epidemiology; OR
- Increase in virulence or change in clinical disease presentation; OR
- Decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.
In other words, VOCs have mutations that increase the ability of SARS-CoV-2 viruses to transmit between humans and/or cause more severe infection which significantly impact on the number of cases, hospitalisations or deaths nationally and globally (defined under global public health significance). Note that SARS-CoV-2 variants can transition between VOIs and VOCs depending on how prevalent they are nationally or globally.
As of 8th November 2021, current VOIs include the Lambda and Mu variants, while current VOCs include the Alpha, Beta, Gamma and Delta variants. These VOCs possess certain mutations that contribute to the increased transmissibility and infection severity of the SARS-CoV-2 virus.
Where are most SARS-CoV-2 mutations located?
The S protein is a surface protein on the SARS-CoV-2 virus that can contribute to the enhanced infectivity and transmissibility of SARS-CoV-2 variants. The S protein binds to ACE2 which can be found on many different human cells, giving the virus the ability to enter and infect different cells around the body. On exposure to a SARS-CoV-2 virus or a COVID-19 vaccine, the human body produces antibodies, most of which bind to the S protein. These antibodies neutralise or block the S protein’s ability to bind to ACE2, leaving these viruses outside the body to be engulfed and degraded by phagocytes such as macrophages and DCs.
Mutations on the S protein can change its conformation which can strengthen its binding to ACE2 and/or reduce antibody binding. One such mutation that “kickstarted” the pandemic is the D614G mutation, located on the interface between two S protein subunits bound together by a hydrogen bond. The D614G mutation, which replaces aspartate (D) with glycine (G), abolishes this hydrogen bond, opening the S protein more. Although this mutation did not increase COVID-19 infection severity, it did speed up viral replication in human lung cells, leading to increased amounts of virus in the upper airways of hamsters and humans. The D614G mutation first emerged in Europe around late February – early March 2020 and became prominent in the early stages of the pandemic, being present in 78% strains circulating globally in mid-May 2020.
What are important mutations of SARS-CoV-2 VOCs?
The Alpha, Beta and Gamma variants share three mutations on the S protein. These mutations enhance the variants’ ability to transmit and/or cause more severe infection in humans by reducing binding of antibodies to the S protein and strengthen S protein binding to ACE2.
The first such mutation is N501Y, a substitution mutation found on the receptor binding domain of the S protein that interacts with ACE2. This mutation replaces asparagine (N) with tyrosine (Y) in position 501 of the S protein. The N501Y mutation has been shown to increase replication of the SARS-CoV-2 virus in both human airway epithelial cells (a cellular model) and the upper airways of hamsters (an animal model). This is thanks to the mutation increasing the number of interactions and strengthening the bonds between the S protein and ACE2. The mutation also reduces antibody binding to the S protein, allowing the virus to evade the immune response and to continue replicating and infecting cells.
The second mutation is E484K, another substitution mutation found on the receptor binding domain of the S protein. Glutamate (E) in position 484 is an important amino acid as its side chain interacts with many antibodies. Replacing glutamate with lysine (K) changes the conformation of the receptor binding domain of the S protein, impeding the binding of antibodies to the S protein. Again, this allows the virus to escape the immune response and to continue replicating and infecting cells, perpetuating COVID-19 infection.
The last mutation is K417N/T/V. This mutation replaces lysine (K) at position 417 of the S protein with asparagine (N), threonine (T) or valine (V). Even though this mutation decreases the strength of binding between the S protein and ACE2, it does reduce antibody binding and neutralisation of the S protein. Again, this allows the virus to evade the immune response and to continue infecting and transmitting between humans.
These mutations, when taken together, can contribute to the increased spread of SARS-CoV-2 variants and increased severity of COVID-19 infection, possibly leading to death. When the Alpha variant first emerged in England in September 2020, it was estimated to be 43% to 90% more transmissible compared to the previously dominant strain. This has resulted in the Alpha variant becoming the most dominant strain in the UK a few months after its emergence and its spread to at least 114 countries. In addition, being infected with the alpha variant is associated with an increased risk of hospitalisation and possibly increased death rates. These results show the effects of mutations on SARS-CoV-2 variants transmitting more rapidly among humans.
The Delta variant: a different beast altogether
The Delta variant is a different SARS-CoV-2 variant to the Alpha, Betta and Gamma variants. Besides the D614G mutation, it possesses different mutations to other variants that enhance its ability to replicate, transmit and cause severe disease in humans. Overall, the Delta variant has eight mutations:
- Four in the N-terminal domain: T19R, G142D, 156-157del and R158G. These mutations, whose residues are important for antibody binding to the N-terminal domain, may be important in allowing the Delta variant to evade antibody responses against its N-terminal domain.
- Two in the receptor binding domain: L452R and T478K. These mutations are shown to be involved in the delta variant escaping antibody responses from monoclonal antibodies that target the receptor binding domain.
- One mutation close to the furin-cleavage site: P681R. This mutation is critical to Delta’s potent spread and infection as it can speed up the fusion of viral and cell membranes, an important step for releasing viral RNA and proteins into the host cell.
- One in the S2 region: D950N. This mutation opens the S2 protein more to affect interactions between the S protein and ACE2.
With these mutations, the Delta variant is not only more able to evade immune responses, being less likely to be neutralised by antibodies, but it also spreads more quickly between humans compared to other variants, becoming the predominant strain globally in 2021. Once inside the human body, the Delta strain can replicate to higher viral levelsand stay in the human body longer than other variants. Infection with the Delta variant is also shown to increase the risk of hospitalisation, ICU admission and death, highlighting the increased severity of COVID-19 infection from the Delta variant.
Nevertheless, receiving a COVID-19 vaccine can still protect people against being infected with, hospitalised and dying from infection by the Delta variant. A New England Journal of Medicine study has found that receiving two doses of the AstraZeneca or Pfizer vaccine can decrease the risk of showing symptoms of Delta variant infection by 67% and 88% respectively. This translates to reduced risk of being infected with the Delta variant, as well as being hospitalised and dying from infection. Additionally, in an epidemiology study across 13 US states conducted by the CDC, people who were unvaccinated were 4.6-times more likely to be infected, 10.4 times more likely to be hospitalised and 11.3 times more likely to die of Delta variant infection compared to those who were vaccinated. These results are possible because COVID-19 vaccines can still stimulate the production of antibodies that bind to and neutralise the Delta strain, allowing it to be eliminated by the immune system. However, to induce strong antibody responses, the person needs to receive two doses of the vaccine; receiving only one dose induces weak antibody responses, if any.
Conclusion
SARS-CoV-2 variants are generated as a result of mutations that confer the original virus enhanced abilities to infect and transmit between humans as well as cause severe COVID-19 infection. Many of these variants arose from uncontrolled, widespread infection of the SARS-CoV-2 virus in millions of humans, increasing the rate that the virus can produce mutations that benefit them. While the pandemic is continuing and much of the global population is unimmunised, the SARS-CoV-2 virus will continue to mutate and adapt, producing new, potentially more devastating variants that may spread to the global population. To reduce the risk that new SARS-CoV-2 variants will emerge, it is imperative that people continue to follow measures that slow down the spread of the virus such as social distancing. This will buy time for everyone globally to receive the COVID-19 vaccine which has been shown to reduce the risk of infection, hospitalisation and death by the SARS-CoV-2 virus, halting transmission of the virus and ending the pandemic.