key: cord-0968737-ulls5euy
authors: Zella, Davide; Giovanetti, Marta; Benedetti, Francesca; Unali, Francesco; Spoto, Silvia; Guarino, Michele; Angeletti, Silvia; Ciccozzi, Massimo
title: The variants question: What is the problem?
date: 2021-07-28
journal: J Med Virol
DOI: 10.1002/jmv.27196
sha: bd7a946d6ef4e9398c1256cdb2bd863b4f2c1e6b
doc_id: 968737
cord_uid: ulls5euy

The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) originated in Wuhan, China in early December 2019 has rapidly widespread worldwide. Over the course of the pandemic, due to the advance of whole‐genome sequencing technologies, an unprecedented number of genomes have been generated, providing both invaluable insights into the ongoing evolution and epidemiology of the virus and allowing the identification of hundreds of circulating genetic variants during the pandemic. In recent months variants of SARS‐CoV‐2 that have an increased number of mutations on the Spike protein have brought concern all over the world. These have been called “variants of concerns” (VOCs), and/or “variants of interests” (VOIs) as it has been suggested that their genome mutations might impact transmission, immune control, and virulence. Tracking the spread of emerging SARS‐CoV‐2 variants is crucial to inform public health efforts and control the ongoing pandemic. In this review, a concise characterization of the SARS‐CoV‐2 mutational patterns of the main VOCs and VOIs circulating and cocirculating worldwide has been presented to determine the magnitude of the SARS‐CoV‐2 threat to better understand the virus genetic diversity and its potential impact on vaccination strategy.

origin from a bat-borne virus and the global pandemic represents the first time that the virus has been transmitted into humans. 3, 4 Generally, the rates of nucleotide substitution of RNA viruses are fast, and this rapid evolution is mainly shaped by natural selection. This high error rate and the consequent rapidly evolving virus populations, 5 which could lead to the accumulation of amino acid mutations, might affect the transmissibility of the virus, its cell tropism, and pathogenicity. It would unfortunately also present daunting challenges for the design of effective vaccines and diagnostic assays. Fortunately, however, until now the observed diversity among SARS-CoV-2 sequences has been low.

Coronaviruses such as SARS-CoV-2 are relatively stable thanks to a proofreading mechanism that operates during replication. Many genomic studies have nevertheless revealed changes in their genomes, including mutations and deletions. As the terms mutation, variant, and strain are often used interchangeably in describing the epidemiology of SARS-CoV-2, the distinctions appear to be crucial.

The genetic material of SARS-CoV-2 is RNA. To replicate, and therefore establish the infection, the virus must hijack the host cell and use the cell's machinery to duplicate itself. Errors often occur during this entire process which is the RNA replication. This results in viruses that are similar but not exact copies of the original one.

Those errors are called mutations, and viruses with these mutations are called variants. Variants could differ by a single or many mutations. A variant is referred to as a strain when it starts to present distinct physical properties. Such differences could involve a variant binding to a different cell receptor, or replicating more quickly, or transmitting more efficiently, and enhancement in its virulence. Essentially, all strains are variants, but not all variants are strains.

The first SARS-CoV-2 variant with a D614G substitution in the spike protein emerged early in the pandemic, between January and February 2020. [6] [7] [8] [9] [10] Over a period of several months, the D614G mutation replaced the initial SARS-CoV-2 strain identified in Wuhan, China, and by June 2020 became the dominant form of the virus circulating globally.

Studies highlighted the role of this variant which appears to confer a fitness advantage to the virus possibly associated with the improvement of replication and/or transmission in humans. 8, 11, 12 Currently, four variants (B. shift the dynamics and public health impact of the pandemic. [13] [14] [15] [16] They appear potentially associated with (i) increased transmissibility, (ii) propensity for re-infection, (iii) escape from neutralizing antibodies, and (iv) increased affinity for the human angiotensinconverting enzyme 2 (ACE2) receptor 16, 17 (Figure 1 and Table 1 ).

The Alpha variant contains 23 nucleotide substitutions and it is not phylogenetically related to the SARS-CoV-2 virus circulating in the UK at the time the variant was detected. Recently epidemiological modeling, phylogenetic and clinical findings suggest that the Alpha variant has increased transmissibility due to a mutation called N501Y, which allows SARS-CoV-2 to bind more readily to the human receptor ACE2, the entry point for SARS-CoV-2 to a wide range of human cells. However, preliminary analyses also indicate that there is no change in disease severity or occurrence of reinfection. Another mutation in this variant of concern (VOC), the deletion at position 69/70del, was found to affect the performance of some diagnostic polymerase chain reaction (PCR) assays with an S gene target. However, most PCR assays in use worldwide use multiple targets, and therefore the impact of the variant on diagnostics is not anticipated to be significant. Laboratory evaluation has also demonstrated no significant impact on the performance of antigen-based lateral flow devices ( Figure 1 and Table 1 ).

F I G U R E 1 Schematic representation of S1 and S2 subunits of SARS-CoV-2 with the main mutations indicated for each VOC and VOI. The Recent studies suggest this variant is associated with a higher viral load, which may suggest the potential for increased transmissibility, and or virulence, allowing differential clinical outcomes. Further investigations are needed to understand the impact on transmission, clinical severity of infection, laboratory diagnostics, therapeutics, vaccines, or public health preventive measures ( Figure 1 and Table 1 ).

The Gamma variant, first identified in January 2021 in travelers from the Amazonas state (North of Brazil) who arrived in Japan, 15 harbors a constellation of 17 unique mutations, including three in the RBD of the spike protein (K417T, E484K, and N501Y). It thus immediately raised concerns to public health authorities over the risk of its unknown potential of faster spreading and/or worsening of coronavirus disease 2019 (COVID-19) clinical outcomes ( Figure 1 and Table 1 ).

The Kappa variant, first identified in India in October 2020, has raised global concern, after being reported in many countries worldwide. This variant harbors a constellation of 12 unique mutations, including three in the RBD of the spike protein (T19R, L452R, T478K, P681R, and D950N) ( Figure 1 and Table 1 ).

Since the identification of these VOCs, the combination between the unprecedented number of cases and more than 1. Table 1 ).

The Kappa variant, first identified in India in October 2020, has raised global concern, after being reported in many countries T A B L E 1 List of the main variants of concerns (VOC) and variants of interests (VOI) with the new WHO nomenclature, the old nomenclature based on lineages, the defining SNPs, the earliest documented samples dates, the location of the first detection, and the classification status allow the virus to escape the immune system ( Figure 1 and Table 1 ).

The Eta variant has been described as a VOI for the first time in mid-December 2020 in Nigeria and later then in many other countries. This variant presents a notable group of missense mutations believed to be of particular importance due to their potential for increased transmissibility, virulence, and reduced effectiveness of vaccines. 16 (Figure 1 and Table 1 ). S1 spike is the major SARS-CoV-2 protein allowing virus entry into human cells expressing ACE2 receptor through a defined RBD. 24 It has been shown that antibodies generated against the spike pro- To further support this concept, we note that two common endemic human coronaviruses, HCoV-OC43 16 and HCoV-299E, 27 have extensive deletions in the C-terminal region of Nsp1.

To provide further information about how quickly the virus could potentially increase its genetic variability, we analyzed the Open Reading Frame 1ab gene of SARS-CoV-2 to look for the presence of mutations that could have been caused by selective pressure on the virus and that could influence its ability to infect the host. 28 Sputnik-V (Gam-COVID-Vac). 35 The efficacy seems to be pretty high for all the vaccines, with 70%-95% protection against mild to severe COVID-19 symptoms and almost total protection against death.

However, several strains of SARS-CoV-2 carrying mutations in the spike protein were recently identified, such as the Alpha, 36 There are a number of preliminary studies aimed at evaluating the efficacy of each vaccine against these variants. Preliminary data seem to indicate that some vaccines are still effective, though they may need to be updated periodically. [38] [39] [40] [41] The hope that three vaccines recently approved by the FDA for emergency use could determine the end of the SARS-CoV-2 pandemic has been supported by the evidence that these vaccines showed an efficacy superior to 85%.

This hope has been dampened by the identification of viral variants with mutated spike protein, which in all vaccines is the viral antigen used for active immunization, thus worrying the public opinion with the suspicion that these variants could lower the vaccine's efficacy. The discovery of variants was indeed considered as a sudden event and presented with astonishment when it was an ZELLA ET AL. One year after the outbreak, each country is still struggling to control the pandemic by implementing several different measures.

Identifying variants of concern have now become crucial, even though meaningful epidemiological data are still lacking in many cases. A few of the most advanced countries have developed effective epidemiological surveillance systems, while others are still in the process of expanding their current ones. For this reason, data coming from these few countries with an adequate surveillance system tends to influence all the others.

It thus is clear that only when epidemiological surveillance centers will be developed at the national level and then interconnected globally, it will be possible to control the virus in the appropriate ways. This will also allow us to better manage the spreading of variants of concern, and to adopt targeted measures to contain the contagion.

Adaptive mutations in the SARS-CoV-2 genome could alter its pathogenic potential, and at the same time would increase the difficulty of drug and vaccine development. This contribution will not deal in detail with the mass of molecular information now available for SARS-CoV-2. It will rapidly summarize the information on its evolutionary and structural features that could be useful for the development of vaccines.

Finally, we must remember that identifying these mutations is relevant for the design of antiviral drugs and vaccines updates. For this reason, timely viral detection and sequence analysis, more precise and reliable tracking methods, prompt implementation of measures of social distancing, are fundamental to quickly recognize and contain new emerging clusters of infection.

Open access funding enabled and organized by Projekt DEAL.

All the authors declare that there are no conflicts of interest. 

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