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ColumnFor people who want to easily understand the new coronavirus variant (May 2021)

For people who want to easily understand the new coronavirus variant (May 2021)

For people who want to easily understand the new coronavirus variant

By reading this article, you will find it easier to understand primary information about the novel coronavirus from public research institutions and papers.
With reliable sources of information, you will be able to make accurate judgments and choices.

Table of Contents

This article provides highly reliable information

"What information about the novel coronavirus should I trust?"

"I don't understand the meaning of N501Y or E484K."

This article solves these concerns.

Specifically,

  • Words used commonly by healthcare workers, researchers, and the media that are difficult to understand
  • Reliable information as of May 2021, referenced from public research institutions and papers
  • Mutations that vaccines are less effective against as of May 2021

will be explained.

If you do not obtain reliable information, rumors and media with low credibility and validity will be your only sources. You may be misled by inaccurate information and sweet words, and you may be unable to make your own judgments and choices. The likelihood of being controlled by others and falling victim to scams will also increase.

However, by reading this article, you will find it easier to understand primary information about the novel coronavirus from public research institutions and papers. With reliable sources of information, you will be able to make accurate judgments and choices.

Variant viruses have different surfaces

When a virus undergoes mutation, the structure of the spike protein on the virus surface changes. The spike protein is the bridge between us and the novel coronavirus. Without the spike protein, the virus cannot infect us.

According to a report from the National Institute of Infectious Diseases, when the spike protein changes due to mutations, it can lead to:

  • Increased infectivity
  • Reduced vaccine efficacy
  • Higher likelihood of severe illness

Mutation means changes in genetic information

A mutation occurs when the genetic information changes, altering even the proteins that the virus produces.

The genetic information of the novel coronavirus is called RNA, which is composed of:

  • Adenine (A)
  • Guanine (G)
  • Uracil (U)
  • Cytosine (C)

These nucleotides are randomly arranged in approximately 300,000 units. RNA is often compared to a blueprint for proteins, as proteins are produced based on this blueprint. Therefore, if the blueprint is rewritten due to a mutation, the resulting proteins will also change.

For example, let's say the sequence AAUUG is the blueprint for a protein that increases the virus's survival ability.

(Note: AAUUG is not actually the blueprint for a protein that increases the virus's survival ability. This is a hypothetical example for easier understanding.)

Now, a mutation occurs, changing AAUUG to AAUGG.

If AAUGG is the blueprint for a protein that reduces the virus's survival ability, the virus's survival ability has weakened.

N501Y and E484K are amino acid mutations

How mutations occur

The symbols like N501Y and E484K reported in the news represent specific mutations.

N501Y means that the 501st amino acid of the spike protein has changed from N (asparagine) to Y (tyrosine).
E484K indicates that the 484th amino acid has changed from E (glutamic acid) to K (lysine).

If RNA changes, amino acids change too

"Wasn't the mutation about the replacement of RNA's genetic information?"
Some of you might be thinking this.

In conclusion, RNA mutations directly lead to amino acid mutations.

RNA is the blueprint for proteins. Proteins are made up of amino acids.

Due to RNA mutations, the amino acids that are produced change, resulting in different proteins being created.

For example, not just limited to proteins, if the materials change, the final product will also be different.

What is the difference between types like 〇〇 and N501Y?

The UK variant, South African variant, and Brazilian variant are general terms for combinations of multiple mutations.

The UK variant includes the N501Y mutation.

However, having the N501Y mutation does not necessarily mean it is the UK variant. The UK variant (B.1.1.7) also has the following mutations:

  • H69/V70 deletion
  • Y144 deletion
  • A570D 
  • P681H

In other words, it is the combination of multiple mutations that defines the UK variant.

The South African variant (B.1.351) also has the N501Y mutation, along with:

  • 242-244 deletion
  • K417N
  • E484K 

This combination of mutations is what defines the South African variant.

VOC and VOI indicate the degree of danger

The severity of novel coronavirus variants is classified into VOC (Variants of Concern) and VOI (Variants of Interest). This classification is based on differences in transmissibility and the likelihood of causing severe illness.

VOC are more dangerous than VOI and are considered worrisome variants. These viruses are more likely to exhibit changes such as increased transmissibility, increased severity, and reduced vaccine efficacy.

The following variants are classified as VOC:

  • UK variant B.1.1.7
  • South African variant B.1.351
  • Brazilian variant P1

The U.S. Centers for Disease Control and Prevention (CDC) designated the variant discovered in California, 452R.V1 (B.1.427+B.1.429), as a VOC on March 16, 2021.

Furthermore, the Indian variant was reported to have been elevated from VOI to VOC on May 11, 2021.

VOI are noteworthy variants. They are likely to affect transmissibility, severity, and vaccine efficacy. The R1 strain is classified as a VOI.

The Philippine variant is not classified as a VOC in the Philippines but is considered a VOC in Japan.

Variant viruses around the world and in Japan

The UK variant spreading worldwide

Among the novel coronavirus variants, those with the highest global share are:

  • UK variant (130 countries)
  • South African variant (80 countries)
  • Brazilian variant (45 countries)

(As of March 28, 2021, from the WHO COVID-19 Weekly Epidemiological Update, March 28, 2021, 10 am)

According to GISAID, an organization tracking new coronavirus variants:

  • The variant discovered in California, 452R.V1 (B.1.427 + B.1.429)
  • The newly discovered variant in the UK, 484K.V3 (B.1.525)
  • The Indian variant, 452R.V3 (B.1.617)

In addition to the three variants mentioned above, these variants have also been found worldwide.

What about in Japan?

It has been reported that the UK variant has the highest share. In the future, it is expected that existing viruses will transition to the UK variant.

The South African, Brazilian, and Indian variants have also been confirmed domestically. Additionally, there have been cases of the Philippine variant, known as P3, and the R1 strain, whose origin is unknown.

Which types are less affected by vaccines?

In May 2021, the vaccine jointly developed by Pfizer and BioNTech was being administered in Japan. The Japanese government has also agreed to administer the vaccines from AstraZeneca and Moderna, with approval expected by the end of May 2021.

Based on data from the National Institute of Infectious Diseases, let's explain how the neutralizing ability of the vaccines changes against the globally prevalent variants:

  • UK variant
  • South African variant
  • Brazilian variant
  • Philippine variant
  • Indian variant

※1 Neutralizing ability: The capacity to eliminate the effectiveness of the virus. For instance, a high neutralizing ability makes it easier to prevent infection and the onset of illness.

The South African and Brazilian variants reduce vaccine efficacy

As of May 2021, despite minor differences, all vaccines demonstrate similar levels of effectiveness.

It has been reported that the three vaccines are effective against the UK variant. The neutralizing ability of the vaccines against the UK variant is either unchanged or only slightly reduced compared to the original coronavirus.

However, it has been announced that the neutralizing ability of the three vaccines decreases to a medium to high extent for the South African and Brazilian variants.

E484K and N501Y mutations reduce vaccine efficacy

The variants that possess both N501Y and E484K are:

  • Brazilian variant
  • South African variant
  • Philippine variant

Additionally, the R1 strain, which is classified as a VOI, also has E484K. However, since the R1 strain does not have N501Y, the impact of E484K alone on vaccine efficacy is still considered a possibility rather than a certainty.

A study published in Nature Medicine in March 2021 also found that E484K reduces the efficacy of the Pfizer/BioNTech vaccine.

This study tested the neutralizing capacity of blood (which contains antibodies) from recovered individuals and the Pfizer/BioNTech vaccine against the following variants:

  • UK variant
  • Brazilian variant
  • South African variant

Neutralization in this experiment refers to the phenomenon of eliminating the virus's effect.

The results showed that the UK variant was neutralized with a similar amount of antibodies as the original novel coronavirus. However, for the South African and Brazilian variants, it was reported that 3.5 to 4 times the amount of antibodies were needed to achieve neutralization compared to the original novel coronavirus.

All three variants (UK, Brazilian, South African) have N501Y. However, only the Brazilian and South African variants have E484K.

Therefore, it is thought that the presence of both E484K and N501Y in these variants may be what is reducing the effectiveness of the vaccines.

Is the vaccine less effective against the Indian variant?

LineageMain mutations in spike protein
B.1617
(Indian variant)		G142D, E154K, L452R, E484Q, D614G, P681R, Q1071H
B.1617.2T19R, G142D, 157/158 deletions, L452R, T478K, D614G, P681R, D950N
B.1617.3T19R, L452R, E484Q, D614G, P681R, D950N

The Indian variant (B.1.617) includes B.1.617.1, B.1.617.2, and B.1.617.3. The mutations common to all three subtypes are:

  • L452R
  • D614G
  • P681R

Additionally, B.1.617.1 also has the E484Q mutation.

The anticipated impacts of these mutations are:

  • Vaccine efficacy reduced to one-third
  • The effectiveness of antibodies in recovered individuals reduced by half

However, it is important to note that these evaluations are based on laboratory experiments, so they should be interpreted with caution.

References