Perspective Chapter: SARS-CoV-2 Variants – Two Years Post-Onset of the Pandemic

Abstract

Since the pandemic began in China in December 2019, thousands of variants of SARS-CoV-2 have emerged globally since late 2020. The World Health Organization (WHO) defined the SARS-CoV-2 variant of concern (VOC) as a variant with increased transmissibility, virulence, and decreased response to available diagnostics, vaccines, and therapeutics. Areas of the emerging variant of concern arise from countries like the United Kingdom, South Africa, Brazil, and India. These mutations carry a lineage from N501Y, D614G, N439K, Y453F, and others, which are globally dominated by clades 20A, 20B, and 20C. SARS-CoV-2 VOC emerged after 11 months of evolution since the onset through massive human-to-human transmission with five major VOCs recognized by the WHO, namely Alpha, Beta, Gamma, Delta, and Omicron. Their emergence could be attributed to changing immunological dynamics in the human population, which has resulted in resistance or escape from neutralizing antibodies, or to mutations and/or recombinations that increase transmission or pathogenicity. This literature review intends to identify and report on SARS-CoV-2 variants that have evolved two years post-onset of the pandemic and their disease implications.

1. Introduction

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) a member of the Coronaviridae family emerged in late 2019 in Wuhan, China, and has caused a global pandemic of acute respiratory disease in all ages of the population, ranging from mild symptoms to mortality [1]. It belongs to the family of coronaviruses (CoVs), sharing 79% of the genome sequence with SARS-CoV and 50% with Middle East respiratory syndrome coronavirus (MERS-CoV), while the rest of its structure is shared with other betacoronavirus [1]. In this enveloped positive sense, single-stranded ribonucleic acid (RNA) with crown-like S-shaped spiked proteins virus [2], there is an incubation period of 1–14 days with a median onset time of 8 days [1]. Transmission of SARS-CoV-2 is predominantly via droplets, aerosol, and airborne pathways [1]. It achieves invasion by using angiotensin-converting enzyme 2 (ACE2) receptors and human proteases as entry pathways, eventually fusing with the cell membranes in the lung [1]. Mild clinical presentations of this virus include fever, dry cough, and pneumonia [3]. Most patients with mild manifestations of this infection recover [3]. More severe cases cause other issues besides respiratory problems, such as injury to the myocardial cells and heart arrhythmias [3]. Other reported problems caused by this virus are in the central nervous system (CNS), gastrointestinal tract (GIT), musculoskeletal system, hypercoagulability leading to stroke, and organ failure [3]. In the most critical cases, end-organ failure and acute respiratory distress have led to death, especially in those with comorbidities such as hypertension and obesity [2, 3].

Coronaviruses continuously evolve due to mutations that occur during the replication of their genome [4]. Variants that emerged throughout the pandemic differ from each other due to one or more mutations, such as the number and location of substitutions in the spike (S) protein that makes each unique [4]. The United States SARS-CoV-2 Interagency Group (SIG) defines four classes of SARS-CoV-2 variants which are: variants being monitored (VBM), variants of interest (VOI), variants of concern (VOC), and variants of high consequence (VOHC) [4]. Thirteen variations in the S protein of coronavirus disease 2019 (COVID-19) have been detected by late November 2020 [3]. On November 30, 2021, SIG classified Omicron as a VOC, replacing the Delta variant [4]. Currently, there is no VOI and the VBM are Alpha, Beta, Gamma, Epsilon, Eta, Lota, Kappa, 1.616.3, Mu, and Zeta [4].

Of the two VOCs, Delta and Omicron, the Delta variant has been shown to cause a more severe illness in the unvaccinated as compared to the vaccinated [5]. November 2021, the Omicron variant was first discovered in Botswana [5]. Omicron was designated as a VOC by the World Health Organization (WHO), which stated that early research suggests that it carries a higher risk of reinfection than other variants [5]. Currently, in the United States, the Omicron variant is the most common [5]. In December of 2020, the Delta variant was first found in India but has since spread across 178 countries [5]. Changes to the S protein may render the Delta variant up to 50% more transmissible than other prior COVID-19 variants, according to research [5].

Significant advances have been made toward “real-time” generation and sharing of SARS-CoV-2 data throughout the pandemic [6]. As a result, a computational tool, Phylogenetic Assignment of Named Global Outbreak Lineages (Pangolin) was developed to assign the most likely lineage to a genome sequence for managing and interpreting the rapid generation and sharing of data worldwide, at either a national or regional level [6]. Hence this nomenclature was developed to name and track global transmission lineages of SARS-CoV-2 [6]. Nextstrain and GISAID focus on the prevalence and persistence of a variant by ‘clades’ [6]. Thus, the WHO has established a structure for nomenclature using GISAID, Nextstrain, and Pangolin (Pango) nomenclature, so that the scientific community may be able to name and track the variants of SARS-CoV-2 [7].

According to the WHO situation report as of March 22, 2022, there has been a 7% rise in COVID-19 positive cases for the week of March 14–20, 2022, versus the week before [8]. However, there has been a 23% decrease in mortality in comparison to the week before [8]. About 12 million new cases and slightly below 33 thousand deaths have been reported in this period among the six WHO regions [8]. Approximately 468,000,000 COVID-19 positive cases and slightly over 6,000,000 deaths have been disclosed universally as of March 22, 2022 [8].

COVID-19 has become a continuously evolving disease due to rapid changes in the viral variants and despite mitigation strategies such as facial masks, social distancing, hand hygiene, vaccine therapies, and other therapies [2]. One of the earliest VOCs was the Alpha variant (B.1.1.7), which had a high transmissibility rate [2]. Recently, Omicron (B.1.1.529) appears to be at least two times more transmissible than Delta, with Delta variations being 50–70% more transmissible than earlier variants such as Alpha [2]. VOCs remain prevalent, particularly among unimmunized persons [2]. VBM were more problematic earlier in the pandemic and were more notable for high transmission and increased virulence [2]. These include B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma), and of lesser concern, Epsilon (B.1.427 and B.1.429), Eta (B.1.525), Iota (B.1.526), Kappa (B.1.617.1), 1.617.3, Mu (B.1.621, B.1.621.1), and Zeta (P.2) [2].

The two other categories described by the WHO include VOI, which are variants that are widely circulating within a population or have the potential to have an impact on a population, and VOHC, which are mutations that elude vaccines and current therapies that are in place. Currently, there are no circulating VOI and VOHC [2]. Given the continuous evolution of SARS-CoV-2, the impact of variants on public health may be reclassified based on their attributes and prevalence. VOCs and VOIs may differ from those of other reporting agencies because of the impact the variants may cause by location. The purpose of this paper is to discuss the genetic lineages of SARS-CoV-2 that have emerged as variants and circulated globally during the 2 years since the onset of the COVID-19 pandemic.

2. Methodology

PubMed, Google Scholar, EBSCOhost, Mendeley, and MedLine Plus were used to conduct the electronic literature search. The search was confined to relevant publications and articles published between January 2020 and April 2022. If a manuscript was relevant to the issue of genetic mutations or variations of SARS-CoV-2, it was chosen. To narrow and guide the search process, the listed keywords were sought after. COVID-19, SARS-CoV-2, variants of interest (VOI), variants of concern (VOC), genetic variances, and genetic mutations are among them.

3. Variant being monitored

Viruses are known to change over time. SARS-CoV-2 has undergone multiple modifications since the start of the COVID-19 pandemic in Wuhan in late 2019 [9]. Comparing the SARS-CoV-2 pathogenic S protein sequence to the Wuhan-Hu-1 reference protein sequence showed about 96.5% of the original S protein sequence has undergone mutations [9]. These mutations lead to genetic differences, which results in the emergence of new variants of the virus [9]. Centers for Disease Control and Prevention (CDC), in collaboration with the SIG, added a fourth class of variant classification named VBM on September 21, 2021, as depicted in Table 1 [22]. The other classes include VOI, VOC, and VOHC [22].

Lineage	Predominate Countries Affected	Date of Designation	Description
Alpha; B.1.1.7; Q Lineages	United Kingdom (UK) 24.0%, United States of America (USA) 20.0%, Germany 9.0%, Sweden 6.0%, and Denmark 6.0%	September 3, 2020.	First detected in the UK and has spread to over 52 countries including the USA [10, 11, 12]
Beta; B.1.351	South Africa 18.0%, Philippines 10.0%, USA 9.0%, Sweden 8.0%, and Germany 7.0%	September 9, 2020	South African lineage [10, 11, 13]
Gamma; P.1	Brazil 56.0%, USA 29.0%, Chile 3.0%, Argentina 2.0%, and Spain 1.0%	October 1, 2020	Brazilian lineage with functionally significant spike mutations [10, 11, 13]
Epsilon; B.1.429	USA 98.0%, Mexico 1.0%, Aruba 0.0%, and Argentina 0.0%	January 26, 2020	USA lineage, predominantly in California [10, 11, 14]
Eta; B.1.525	Canada 20.0%, USA 15.0%, Germany 9.0%, France 8.0%, and Denmark 7.0%	March 25, 2020	International lineage [10, 11, 15]
Iota; B.1.526	USA 97.0%, Ecuador 1.0%, Canada 1.0%, Puerto Rico 1.0%, and Spain 0.0%	January 28, 2020,	Predominately in New York, with S mutation E484K [10, 11, 16]
Kappa; B.1.617.1	India 72.0%, UK 6.0%, Canada 6.0%, USA 5.0%, and Ireland 3.0%	March 3, 2020	Indian lineage [10, 11, 17]
N/A; B.1.617.3	India 89.0%, UK 4.0%, USA 3.0%, Malawi 2.0%, and Russia 1.0%	January 1, 2021	Indian lineage [10, 11, 18]
Zeta; P.2	Brazil 56.0%, USA 25.0%, Canada 5.0%, Argentina 2.0%, and Paraguay 2.0%	April 13, 2020	Brazilian lineage [10, 11, 19, 20]
Mu; B.1.621	USA 42.0%, Colombia 27.0%, Chile 9.0%, Spain 5.0%, Mexico 3.0%	December 15, 2020	Predominantly in Columbia [10, 11, 21]

Table 1.

Lineage list.

Note. Researchers and public health authorities globally are using the Pango nomenclature to track the transmission and spread of SARS-CoV-2, including variations of concern and interest. This table contains information on various lineages and their distribution [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21].

The VBM class includes variants under surveillance for mutations leading to increased receptor binding, reduced neutralization by host immune systems, decreased efficacy of treatments, and an increase in disease severity and transmissibility but have not yet been deemed a public health threat by SIG at this time [22]. The VBM class also includes previously designated VOIs and VOCs that are no longer detected or have a decreased prevalence in the population [22]. The variants belonging to the VBM class do not pose a significant risk to public health [22]. Regardless of the minimal risk presented by the VBM class, they are closely monitored for new data [22]. VBM class that warrants more concern can have their classification changed to VOI or VOC if required by SIG [2].

4. Variant of concern

4.1 Delta

Viruses constantly undergo mutations resulting in new variants [23]. Table 2 shows the Delta variant of COVID-19, formally known as B.1.617.2 [4, 19]. Part of the AY lineage, this variant appeared in late 2020 from India and had spread to over 179 countries by late 2021 [4, 24]. By late 2021, the Delta variant was the most transmissible, spreading more easily than the first identified Alpha variant - roughly two times more contagious than the original virus [24]. Mutations of the S protein in the Delta variant have not been analyzed in detail, though the following substitutions identified are T19R, (V70F*), T95I, G142D, E156-, F157-, R158G, (A222V*), (W258L*), (K417N*), L452R, T478K, D614G, P681R, and D950N [4]. The Delta variant is thought to have a distinct receptor-binding interface than the other forms [24]. The replication capacity of the Delta variant has been noted to be more efficient, leading to increased rates of transmission, infectivity, and viral load in comparison to other strains [24].

Lineage	WHO Label	GISAID Clade	Nextstrain Clade
B.1.617.2	Delta	G/478 K.V1	21A, 21I, 21 J
B.1.1.529	Omicron	GR/484A	21 K → BA.1, BA.1.1; 21 L → BA.2; Recombinant lineages → XE, XF, and XD

Table 2.

Circulating variants of concern.

Note. Data extracted and recreated from the WHO.

Antiviral medication has been developed to minimize symptoms and lessen the duration of viral infection. There are no less than 13 vaccines against SARS-CoV-2 being used [25]. Each vaccine has been developed with the aim of the immune system recognizing the immunodominant S protein [26]. Although the development of vaccines has proven successful in decreasing fatalities, reports suggest that mutations continue to increase - proposing that the administration of these vaccines does not eradicate disease spread [24]. Therefore, the attributes for the Delta variant suggest that monoclonal antibody therapies with Emergency Use Authorization (EUA) are effective against nearly all Delta lineages [4]. The AY.1 and AY.2 lineages are resistant to several monoclonal antibody treatments [4]. In addition, research has shown a decrease in post-vaccination sera neutralization [4].

4.2 Omicron

The Omicron variant (B.1.1.529, BA lineages, and other recombinant lineages, respectively depicted in Table 2) of SARS-CoV-2 was initially reported to the WHO in late November 2021, by South Africa [4, 7, 27, 28]. By December 2021, the United States reported its first case of COVID-19 connected to the Omicron variant [4, 27, 28]. Numerous mutations not previously seen in the original SARS-CoV-2 strain have been recognized in Omicron [29]. Omicron possesses greater than 30 mutations on its surface within the S protein, one insertion, and three deletions which allows the virus to infect cells, rendering elusive characteristics [27, 29].

A substantial number of amino acid substitutions are in the receptor-binding domain (RBD) with several alternative changes in other genomic regions [27]. Mutations to the S protein of the Omicron variant increase the affinity of binding to receptors, allowing the virus to circumvent antibodies against previous variants and remain infectious [30]. Factors influencing the transmissibility and infectivity of the Omicron variant are dependent on genetic variability and the location of the mutation [31].

Monoclonal antibody treatments aid the immune system in recognizing and responding more effectively to the virus [32]. The attributes for the Omicron variant suggest that some monoclonal antibody treatments with EUA may reduce neutralization [4]. In addition, post-vaccination sera may also reduce neutralization [4].

A comprehensive list of the lineages can be cross-referenced from Table 1 [4, 7].

5. Discussion

Viruses regularly undergo mutations, sometimes creating a lineage of virus progeny known as variants. SARS-CoV-2 has mutated several times since its discovery. Using the original Wuhan-Hu-1 protein as a reference, researchers discovered that the genes encoding the pathogenic S protein had mutated to the point that just 3.5% of the original coding sequence remains [9]. The SIG was founded by the United States Department of Health and Human Services (HHS). SIG and the CDC collaborated on a report that accounted for these variants and their classification [33]. In terms of population impact, the VBM are quite a minimal risk. Alpha, Beta, Gamma, Epsilon, Eta, Iota, Kappa, Mu, and Zeta are the varieties under the VBM class as of December 2021, with B.1.617.3’s structure being unique when comparing other progenies: B.1617.1 and B.1.617.2 [2]. As per the CDC, the VBM class poses no significant and imminent risk to public health in the United States; in addition, there are no VOI or VOHC for SARS-CoV-2 [4].

Countries such as the United Kingdom, South Africa, Brazil, and India have growing variants of concern [23]. These mutations have a pedigree that includes N501Y (i.e., B.1.1.7 and several lineages), D614G (i.e., B.1 lineage and the initial dominant variant of 2020), N439K (i.e., arising from the B.1 lineage of the mutated D614G), Y453F (i.e., Cluster 5 and mink variant), and additional mutations that are dominated by clades [23]. Clades are classified according to the year they first appeared and are given a new alphabetical letter depending on their discovery: 19A (first emerging in 2019), 19B (appearing after 19A), 20A (new appearance at the start of 2020), 20B, and 20C, so on and so forth [23]. Delta (i.e., of clades 21A, 21I, and 21 J) and Omicron (i.e., of clades 21 K and 21 L) were designated as VOCs by the CDC and SIG in late 2021 [7]. The Delta variant was discovered to be the most infectious version, with an estimated transmission rate double that of the original virus. Its evolved receptor-binding interface may be the reason for its success when compared to the other variants [24]. Where Delta may have been the fastest transmissible variant, Omicron was the most clandestine [27, 29, 34]. First seen in late November of 2021, researchers found over 30 mutations within the S protein. These mutations increased the affinity of receptor binding, allowing the virus to circumvent antibodies against previous variants and remain infectious [30]. It was also reported that monoclonal antibody treatments were found to be effective against Omicron [34].

The S protein is found on the external surface of the virus and is categorized into two subunits, S1 and S2 [24]. The S protein is the main virulence factor that moderates host infection by binding to the ACE2 receptors prominent on type II alveolar epithelial cells found in the respiratory epithelium [24]. Once the S protein binds to the host cell, it undergoes a conformational change in its structure from the inactive “down” state into an active “up” state, which signals a cascade of cleavages to the S1/S2 subunits by the host enzymes and other proteases [24]. This change further alters the S protein into an amino N-terminal S1 subunit containing an RBD and a carboxyl (C)-terminal S2 subunit for virus and host cell membrane fusion [24]. Much of the SARS-CoV-2 genome is made of ORF1ab (one large open reading frame), and when the virus penetrates the host cell, it gets translated into polypeptides pp1a or pp1ab [24]. These polypeptides primarily make non-structural proteins nsp1-nsp16 that mediate ssRNA replication [24]. Approximately one-third of the SARS-CoV-2 genome is responsible for synthesizing structural proteins such as the S (spike) protein, E (envelope) protein, M (membrane) protein, and N (nucleocapsid) protein, as well as accessory proteins ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 [24].

During viral replication, mutations in the ssRNA genome can be classified as synonymous with no changes to the amino acid being synthesized or non-synonymous with modifications to the amino acid [24]. The S protein has two regions that are susceptible to mutation, the N-terminal domain, and the receptor-binding domain, which directly interacts with host ACE2 and is a region that contains a heightened number of amino acid substitutions [24].

5.1 +S: K417N (Delta)

The mutation K417N has lysine (K) being substituted with asparagine (N) [35]. This mutation is found close to the RBD and has displayed the capability of impairing the RBD inactive “down” state [24]. Recent data also indicates that multiple combination mutations are possible and can generate an even more significant decline in neutralization attempts, such as mutation K417N in conjunction with mutations E484K and N501Y [24].

5.2 +S: E484K (Delta)

The mutation E484K has arisen from multiple lineages, such as Beta and Gamma [24]. This variant indicates an amino acid substitution in position 484 with glutamic acid (E) substituting for lysine (K) [35]. In addition, this mutation is close to the tip of the spike [24]. This substitution alters the shape of the S protein and grants resistance to several antibodies and the ability to evade the immune response [24].

5.3 +S: R346K (Omicron)

A recent study conducted by Lu et al., which used transmembrane protease serine 2 (TMPRSS2) to isolate variant Omicron strains HKU691, and HKU344-R346K from patients indicated that the Omicron variant has an extra spike R346K mutation that is seen in 8.5% of strains reported in the GISAID database [36]. The study also indicated that both strains were less susceptible to neutralization, and many patients did not demonstrate neutralizing antibodies to Omicron variant isolates [36]. The R346K mutation is also found in the receptor-binding domain and the mu variant [36].

Coronaviruses often recombine; therefore, a single phylogenetic tree will not necessarily depict SARS-CoV-2’s evolutionary history accurately [10]. While this complicates the phylogenetic analysis, recombination is made possible with the approach of lineage nomenclature and assignment [10]. Conversely, the co-infection of both Delta and Omicron, although rare, happens [34, 36]. If a different recombination event initiates continuous transmission, it will result in the formation of a new viral lineage with a distinct common ancestor. Because this new lineage lacks a specific or clear ancestor, it will be given the next available alphabetical prefix [10]. For example, XE, a cross between two Omicron strains that are now well-known: BA.1 (the original Omicron strain) and BA.2 (the more contagious strain that is now prominent in the United States and other countries) [4, 7, 10].

6. Conclusion

SARS-CoV-2 first appeared in late 2019 in Wuhan, China, as a positive-sense, single-stranded RNA virus with crown-like S-shaped spiking proteins; and has since spread throughout the world, resulting in a global pandemic of acute respiratory illness in people of all ages, with symptoms ranging from mild to fatal. It can undergo mutations, creating a lineage of virus progeny. It has become a continuously evolving disease due to rapid changes in the viral variants. They differ from each other due to one or more mutations, such as the number and location of substitutions in the S protein that makes each unique. This article discusses the genetic lineages of SARS-CoV-2 that have emerged as variants and circulated globally during the two years since the onset of the COVID-19 pandemic. There are four classifications by SIG of which the most alarming is classified as VOC. Important VOCs are Alpha, Beta, Gamma, Delta, and Omicron. Some of the lineages of these mutations are N501Y, D614G, N439K, Y453F, and others, which are globally dominated by clades 20A, 20B, and 20C. Of these, Alpha was the earliest and most infective initially. Variants have mostly emerged from countries like the United Kingdom, South Africa, Brazil, and India. The mutations are thought to appear due to massive human-to-human transmission, which is why prevalence is particularly higher among unimmunized persons. Other classifications are defined as VBM, VOI, VOC, and VOHC but most of these are at lower risk for infectivity, although they are still being monitored for new data. To date, no SARS-CoV-2 variants are designated as VOI or VOHC. Of note, further research is required to fully understand these variants and increase the accuracy of treatments. The public should consider vaccination along with preventative measures, such as wearing a mask, washing hands frequently, and practicing social distancing for the best chance of avoiding contact and increase in the variants.

Conflict of interest

The authors declare no conflict of interest.