COVID-19: Alpha’s mutations

provide insight into Omicron

Share on
PinterestStudying mutations in the Alpha variant may help us understand the Omicron variant better.
VICTOR TORRES/Stocksy

 Scientists do not yet fully understand how individual mutations in SARS-CoV-

2 variants influence contagiousness or disease severity.
 To enter a human cell, the SARS-CoV-2’s spike protein must be activated.
This happens following cleavage by an enzyme called furin.
 Scientists have theorized that mutations at the furin cleavage site might play
an important role in a variant’s ability to infect or replicate in human cells.
 Contrary to expectations, the authors of a new study found that this
mutation did not influence the ability of the virus to enter or spread
between cells.
 Some variants of concern, such as Delta and Omicron, also have mutations at
the same furin cleavage site, and this study may help understand the
changes in their contagiousness and ability to produce disease.

The SARS-CoV-2 Alpha variant, once known as B.1.1.7, carries a mutation at the site
where its spike protein is cleaved by an enzyme called furin.
Scientists believed that this mutation might contribute to Alpha’s increased
transmissibility or disease severity.

However, a recent study from researchers at Cornell University, in Ithaca, NY,

suggests that this mutation at the furin cleavage site did not influence Alpha’s ability
to spread between or infect cells.

In other words, mutations other than the ones at the furin cleavage site are
probably responsible for Alpha’s increased abilities to transmit and to cause
disease.

The recently emerged Omicron variant has many mutations that are similar to
Alpha’s, including the mutation at the cleavage site for furin.

Stay informed with live updates on the current COVID-19 outbreak and visit our
coronavirus hub for more advice on prevention and treatment.

The study’s lead author, Dr. Gary Whittaker, a virologist at Cornell, explains,
“Omicron has a lot of the same features as Alpha. So what we learned about Alpha
helps us understand Omicron and possible future variants.”

The increased contagiousness but reduced disease severity of Omicron, compared

with Alpha, are likely due to other genetic differences.

The new study appears in the journal iScience.

Furin cleavage site

Errors during the replication of the SARS-CoV-2 virus result in mutations in its
genome. This produces variants.

Although mutations are constantly produced as SARS-CoV-2 replicates, only a small

number Trusted Sourceof these mutations are responsible for an increase in
transmissibility or disease severity.

Variants of concernTrusted Source, which have increased transmissibility, disease

severity, or ability to evade the immune system, tend to carry multiple mutations in
their genomes.
Experts have yet to understand the precise role of individual mutations in enhancing
the transmission of the virus or causing more severe disease.

The Alpha variant, which was first identified in the United Kingdom in the fall of
2020, was 45–71% more transmissible than the wild-type SARS-CoV-2 that originated
in Wuhan, China. Alpha was also associated with an increase in disease severity.

The Alpha variant had 23 mutations in its genome, including nine in the gene
coding for the spike protein.

Scientists have observed multiple spike protein mutations in the different variants of
concern, and some of these mutationsTrusted Source are associated with increased
transmissibility.

The spike protein is expressed on the surface of SARS-CoV-2, and it allows the virus
to bind to the angiotensin-converting enzyme 2 receptor on the surfaces of human
cells.

The cleavage of the spike protein at a specific site by the enzyme furin, which human
cells express, is thought to be essential to facilitate the entry of the virus into airway
epithelial and lung cells.

One mutation in the spike protein gene of the Alpha variant is at the furin cleavage
site. Changes in the sequence of this site may influence the transmissibility of SARS-
CoV-2.

The present study characterized the ability of this mutation at the Alpha variant’s
furin cleavage site to influence the virus’ ability to infect and replicate in human cells.

Biochemical assays
To understand the impact of this particular mutation, the researchers first used a
bioinformaticsTrusted Source approach. Bioinformatics involves using software tools
to analyze biological data, and it can predict the structure of proteins using genetic
information.
The bioinformatics analysis predicted that the mutation at the furin cleavage site in
the Alpha variant would slightly enhance the cleavage of the spike protein by the
furin enzyme.

The researchers also conducted a biochemical assay in the laboratory to confirm this.
They incubated a short fragment of the spike protein containing the furin cleavage
site from the Alpha variant and wild-type SARS-CoV-2 with furin.

The assay showed that the spike protein fragment from the Alpha variant was
cleaved to a slightly greater extent than the wild-type SARS-CoV-2, but only at a
specific pH.
CORONAVIRUS NEWS

Stay informed about COVID-19

Get the latest updates and research-backed information on the novel coronavirus
direct to your inbox.
Enter your email

SIGN UP
Your privacy is important to us

Cell entry
The researchers then used pseudoparticles to assess the impact of the mutation at
the furin cleavage site on the ability of SARS-CoV-2 to enter human cells.

These pseudoparticles consist of a surrogate virus other than SARS-CoV-2 that

expresses a specific SARS-CoV-2 protein. They have the essential components to
infect a cell but cannot replicate, making them harmless.

In the present study, the researchers used pseudoparticles expressing the spike
protein from wild-type SARS-CoV-2 and the Alpha variant.

The researchers also used a third type of pseudoparticle that expressed a modified
form of wild-type SARS-CoV-2 spike protein that included one particular alteration
found in the Alpha variant.
This modified wild-type SARS-CoV-2 spike protein only had one change at the furin
cleavage site, which was caused by a specific mutation of the Alpha variant, but it
did not have the other changes seen in the Alpha variant’s spike protein.

The researchers compared the ability of these three pseudoviruses expressing

different spike proteins to infect Vero cells, which are laboratory-cultured kidney
cells.

SARS-CoV-2 can enter cells by two main pathwaysTrusted Source. One involves the
fusion of the virus envelope with the membrane of human cells and is mediated by
an enzyme called TMPRSS2, which is on the surface of human cells. In the other
pathway, the virus is engulfed by fluid-filled bodies called endosomes that are
present inside the cells.

The researchers used two types of Vero cells. One expressed TMPRSS2 and favored
entry by fusion. The other cell line favored the entry of the virus by the endosomal
pathway.

There was no difference in the abilities of the pseudoviruses expressing the three
different spike proteins to infect either type of Vero cells.

In other words, the presence of the mutation at the furin cleavage site of the Alpha
variant’s spike protein did not enhance cell entry — through either the TMPRSS2 or
endosomal pathways.

Since Vero cells are derived from the kidney, the researchers then infected
laboratory-cultured cells from the human respiratory tract with the pseudoparticles
expressing the three spike proteins.

The pseudoparticles expressing the spike from the Alpha variant were slightly more
effective at infecting respiratory tract cells than those with the wild-type virus’ spike.

Interestingly, the pseudoparticles carrying the wild-type SARS-CoV-2 spike with the
mutation at the furin cleavage site did not differ from the wild-type virus in their
ability to infect respiratory tract cells.
The results of the experiment with respiratory tract cells suggest that mutations
other than the one at the furin cleavage site are probably responsible for the
increased capacities of the Alpha variant to transmit and to cause disease.

Growth and cell fusion

The researchers then compared the ability of samples of wild-type SARS-CoV-2 and
the Alpha variant to replicate in the two Vero cell lines and human respiratory tract
cells.

Similar viral titers were observed in all three cell types, suggesting that the Alpha
variant did not replicate more quickly than wild-type SARS-CoV-2.

The SARS-CoV-2 spike protein is also known to mediate the fusion of infected cells
with adjacent uninfected cells, thus facilitating the spread of the virus throughout
the lungs.

Because there were no differences between the Alpha variant’s and wild-type SARS-
CoV-2’s abilities to infect or replicate in human cells, the researchers decided to
investigate any differences in the abilities of these spike proteins to induce cell
fusion. The researchers found that the Alpha variant’s spike did not enhance cell
fusion in the two Vero cell lines.

In summary, the study suggests that the specific change at the furin cleavage site in
the Alpha variant’s spike protein may increase its cleavage. But it does not boost
the variant’s ability to infect or replicate in human cells.

As Dr. Whittaker notes, the furin cleavage site may, in fact, “be relatively
inconsequential.”

Furin cleavage and variants of concern

The Delta variantTrusted Source, which was first identified in India in late 2020, was
found to be more contagious than previous variants of concern, including the Alpha
variant. The Delta variant also caused more severe disease.
Like the Alpha variant, the Delta variant has a mutation at the furin cleavage site.
However, this mutation is different from Alpha’s and is associated with increased
cleavage by furin.

This mutation of Delta’s is also associated withTrusted Source enhanced cell entry
and cell-to-cell fusion, and increased disease severity.

However, the Omicron variant that emerged in November 2021 has an identical
mutation to the Alpha variant.

Dr. Whittaker says: “Omicron went back to square one. It returned to the same
genetic change in the furin cleavage site that Alpha had. It essentially took a large
step back in its evolutionary trajectory as a disease agent.”

“Alpha would cause cells to fuse. Delta would fuse cells even more…. but then
Omicron comes along, and its host cells aren’t fusing at all. It has gone completely
backward,” he explains.