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COVID-19 (or Coronavirus Disease of 2019) is caused by the SARS-CoV-2 (or severe acute respiratory syndrome coronavirus 2) virus. The genetic code of this virus is a single-stranded RNA that has 11 protein coding regions that encode for viral proteins such as S, E, M, and N proteins. Of these proteins, the Spike protein (or S-protein) binds to the ACE-2 receptor of host cells, enters the host cells, and uses the host’s machinery to make copies of itself. The S-protein is a large type I transmembrane protein containing two subunits, S1 and S2. S1 contains a receptor binding domain, which is responsible for recognizing the cell surface receptor. S2 contains basic elements needed for the membrane fusion. The S-protein plays a key part in the induction of neutralizing-antibody and T-cell responses, as well as protective immunity. Variants of SARS-CoV-2 arise due to mutations in its genome. While a vast majority of variants do not have a distinct clinical behavior, a small minority show differences in transmissibility and resistance to immune response. Intended for the practicing pathologist and medical laboratory scientist, this article provides a basic overview of mutations, variant nomenclature, and variant classification of SARS-CoV-2. The information included herein is collated from publicly available information and readers are advised to review the Center for Disease Control and Prevention (CDC) website for the most updated information.

SARS-CoV-2 mutations

The genetic sequence of viruses is constantly changing, and these changes are called mutations. These mutations are present in both coding and non-coding regions of the RNA genome. Mutations that involve regions that encodes the S-protein of the coronavirus are especially important since a modified S-protein can increase the transmissibility of the virus and help the virus evade existing antibodies. While several mutations have been described in the SARS-CoV-2 genome, following is a select list of mutations that have been shown to modify transmissibility and immune evasion.

The D614G mutation is characterized by an aspartic acid (D) to glycine (G) shift at the amino acid position 614 of the S-protein. It is thought that since glycine is less bulky than aspartic acid, it makes the hinge region on the S-protein more flexible. Studies have shown that a D614G makes the virus more infectious and transmissible. Further, it is also believed that anosmia (that is loss of sense of smell) is associated with the D614G mutation.

The N501Y mutation is characterized by an asparagine (N) to tyrosine (Y) shift at the amino acid position 501 of the S protein. The N501 mutation enhances ACE-2 receptor binding.

The E484K mutation is characterized by a glutamic acid (E) to lysine (K) shift at the amino acid position 484 of the S-protein. The E484K mutation enhances ACE-2 receptor binding and interferes with the binding of existing antibodies.

The P681H mutation is characterized by a proline (P) to Histidine (H) shift at the amino acid position 501 of the S protein. This mutation affects the S-protein adjacent to the furin cleavage site. It has been believed that the P681H mutation interferes with the binding of existing antibodies.

The E484Q mutation is characterized by a glutamic acid (E) to glutamine (Q) shift at amino acid position 484 of the S protein. This mutation enhances ACE2 receptor binding and interferes with the binding of existing antibodies.

The L452R mutation is characterized by a leucine (L) to arginine (R) shift at amino acid position 452 of the S-protein. This mutation enhances ACE-2 receptor binding and interferes with the binding of existing antibodies. Additionally, the L452R mutation is postulated to confer resistance to T-cells.

SARS-CoV-2 variants

A virus with one or more new mutations is referred to as a “variant.” Several variants of the SARS-CoV-2 virus have been documented across the globe during the COVID-19 pandemic. Sometimes new variants emerge and disappear within weeks. Other times, new variants emerge and persist for months.

Variant nomenclature

While names based on the region where the variant was first isolated (for example, ‘UK variant’ and ‘South African variant’) are popular in lay media, they increase the risk of stigma for communities residing in those areas. In late 2020, a nomenclature system based on evolutionary relationships was proposed by Oliver Pybus and Andrew Rambaut, of the University of Edinburgh. They have proposed a system where major lineage labels begin with letter(s) and each descendent variant is assigned a numerical value. In this system, alphabets A and B refer to the earliest cases that were isolated in Wuhan, China. The early January 2020 outbreak in the state of Washington (imported from Wuhan, China) was designated as lineage A.1. The B lineage in Wuhan gave rise to B.1 and B.2 lineages that caused the large outbreaks in Italy and Europe, and B.3 lineage that caused an outbreak in the United Kingdom. B.1.1 is a major European lineage that gave rise to several variants, including the B.1.1.7 variant or the ‘U.K. variant.’

Variant classification

A vast majority of variants do not have a clear clinical or public health relevance, only a minority do. Mutations may influence the transmissibility and pathogenicity of the virus. Several variants can share the same mutation. The L452R mutation is present in B.1.526.1, B.1.427, and B.1.429. The E484K mutation is present in B.1.525, P.2, P.1, and B.1.351, and few strains of B.1.526 and B.1.1.7. To efficiently track these variants, a US government interagency group has developed a variant classification scheme that defines three variant classes: variants of interest, variants of concern, and variants of high consequence.

A variant of interest is a variant with specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity. As of mid-May of 2021, there are eight variants of interest, including B.1.525 (first detected in United Kingdom/Nigeria), B.1.526 and B.1.526.1 (first detected in New York), P.2 (first detected in Brazil), and B.1.617, B.1.617.1, B.1.617.2, and B.1.617.3 (first detected in India). The B.1.617 genome has several mutations including two specific mutations in the S-protein, these are E484Q and L452R. It is believed that the combination of these two mutations (often referred as ‘double mutant’ in lay media) gives B.1.617 variant a survival advantage that may help it rapidly spread in a community and evade a timely and sufficient immunological response in certain individuals, including a subset of previously vaccinated individuals.

A variant of concern is a variant for which there is evidence of an increase in transmissibility, more severe disease (increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures. As of mid-April of 2021, there are five variants of concern.

·      B.1.1.7 variant: Commonly known as ‘U.K. variant’ has 50 percent increased transmission. B.1.1 is a major European lineage that was exported in early to mid-2020. Arising from the B.1.1 lineage, the B.1.1.7 variant was first identified in the Southeastern United Kingdom in late 2020 and quickly spread to several countries, including the United States. As of mid-May of 2021, this variant is the predominant variant in the United States. The B.1.1.7 variant has a mutation in the receptor binding domain of the spike protein at position 501, where the amino acid asparagine has been replaced with tyrosine, the shorthand for this mutation is N501Y. The B.1.1.7 variant also has several other mutations, including 69/70 deletion and P681H mutation.

·      P.1 variant (or the B.1.1.28.1 variant): Commonly known as the ‘Brazilian variant,’ this variant was first detected in Japan from passengers arriving from Brazil. This variant was discovered in Michigan in 2021. It has 10 defining mutations in its S-protein, including N501Y and E484K. Please note that in the Pango lineage designation, when the lineage hierarchy reaches a depth of 5, the lineage is given an alias. Therefore, P.1 is an alias for B.1.1.28.1.

·      B.1.351 variant: Commonly known as the ‘South African variant,’ this variant has 50 percent increased transmission. There are three mutations of particular interest in the spike region of the B.1.351 genome: K417N, E484K, and N501Y. According to an Israeli study, this variant may be able to break through certain vaccines.

·      B.1.427 and B.1.429: Both these variants have been isolated in California and have a 20 percent increased transmission. B.1.429 was first observed in July 2020 by researchers in Los Angeles and its prevalence has been fluctuating on the west coast.

A variant of high consequence has clear evidence that prevention measures or medical countermeasures have significantly reduced effectiveness relative to previously circulating variants. A variant of high consequence would require notification to WHO (World Health Organization) under the International Health Regulations, reporting to CDC, an announcement of strategies to prevent or contain transmission, and recommendations to update treatments and vaccines. As of mid-May of 2021, there are no SARS-CoV-2 variants that rise to the level of high consequence.

Summary

We hope this overview was useful in providing you with an overview of the evolving landscape of SARS-CoV-2 variants. A virus with one or more new mutations is referred to as a variant. Mutations involving the S-protein of the coronavirus are significant since a modified S-protein can increase the virus's transmissibility and help the virus evade existing antibodies. Variants can be tracked and named according to their evolutionary relationships. In this system, major lineage labels begin with a letter, and each descendent variant is assigned a numerical value, for example. B.1.1.7. In the United States, a government interagency group has developed a variant classification scheme that defines three variant classes: variants of interest, variants of concern, and variants of high consequence. The CDC website has the most up-to-date information of each class. Practicing pathologists and medical laboratory scientists should keep abreast with the evolving information on SARS-CoV-2 variants.

References

·      Center for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html. Retrieved 17 May 2021.

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