key: cord-0901337-naxctvlp
authors: Kumar, Ashutosh; Parashar, Rakesh; Kumar, Sujeet; Faiq, Muneeb A; Kumari, Chiman; Kulandhasamy, Maheswari; Narayan, Ravi K.; Jha, Rakesh K.; Singh, Himanshu N.; Prasoon, Pranav; Pandey, Sada N.; Kant, Kamla
title: Emerging SARS‐CoV‐2 variants can potentially break set epidemiological barriers in COVID‐19
date: 2021-11-29
journal: J Med Virol
DOI: 10.1002/jmv.27467
sha: a8bf927857d255be624f465c29465e1da3263ef2
doc_id: 901337
cord_uid: naxctvlp

Young age, female sex, absence of comorbidities, and prior infection or vaccination are known epidemiological barriers for contracting the new infection and/or increased disease severity. Demographic trends from the recent coronavirus disease 2019 waves, which are believed to be driven by newer severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants, indicate that the aforementioned epidemiological barriers are being breached and a larger number of younger and healthy individuals are developing severe disease. The new SARS‐CoV‐2 variants have key mutations that can induce significant changes in the virus‐host interactions. Recent studies report that, some of these mutations, singly or in a group, enhance key mechanisms, such as binding of the receptor‐binding domain (RBD) of the viral spike protein with the angiotensin‐converting enzyme 2 (ACE2) receptor in the host‐cells, increase the glycosylation of spike protein at the antigenic sites, and enhance the proteolytic cleavage of the spike protein, thus leading to improved host‐cell entry and the replication of the virus. The putative changes in the virus–host interactions imparted by the mutations in the RBD sequence can potentially be the reason behind the breach of the observed epidemiological barriers. Susceptibility for contracting SARS‐CoV‐2 infection and the disease outcomes are known to be influenced by host‐cell expressions of ACE2 and other proteases. The new variants can act more efficiently, and even with the lesser availability of the viral entry‐receptor and the associated proteases, can have more efficient host‐cell entry and greater replication resulting in high viral loads and prolonged viral shedding, widespread tissue‐injury, and severe inflammation leading to increased transmissibility and lethality. Furthermore, the accumulating evidence shows that multiple new variants have reduced neutralization by both, natural and vaccine‐acquired antibodies, indicating that repeated and vaccine breakthrough infections may arise as serious health concerns in the ongoing pandemic.

Since the onset of the coronavirus disease 2019 (COVID-19) pandemic a large number of variants of the causative agent, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), have arisen, of which some have raised serious epidemiological concerns.

The successive COVID waves triggered by emerging variants are presenting with varying epidemiological characteristics than the first wave caused by wild-type (WT) strain and the early mutants. [1] [2] [3] [4] WT strain was known to cause greater fatality among the aged, male sex, and those with comorbidities. [5] [6] [7] In contrast, the data coming out from the recent preclinical/clinical and epidemiological studies are giving clear indications that multiple newer variants, more particularly the variants of concerns (VOCs), can potentially breach the set epidemiological barriers and are capable of causing significant fatality across the demographic categories. [1] [2] [3] [4] Moreover, a gain of resistance against the natural and vaccine acquired, and multiple therapeutically used monoclonal antibodies have been noted in multiple variants, [8] [9] [10] [11] which may make the gain of herd immunity against the SARS-CoV-2 infection far-reaching goal. In this perspective, we examine the strength of the empirical evidence available for the increased trans- Figure 1 ). 12, 13 To infect a host cell, SARS-CoV-2 requires binding to the cell-surface receptor, angiotensin-converting enzyme-2 (ACE2), through the receptor-binding domain (RBD) present on its spike (S) protein. 13, 14 As a prerequisite to binding to ACE2, it is necessary that the viral spike protein (S) gets cleaved by a set of host proteases-an event called "priming or activation" which is considered essential for the fusion of the virus with the host cell-membranes. 13, 14 The known host proteases for SARS-CoV-2 are transmembrane serine protease 2 (TMPRSS2) and furin, are expressed in the cytoplasmic membrane, and Cathepsin B or L (CTS-B or L) is expressed in the endosomal membranes of the host cells ( Figure 1 ). 14-16 ACE2 has been a hostcell entry receptor for a few other CoVs causing acute respiratory illness as well, such as SARS-CoV-1 and HCoV-NL-63. 13, 14 The hostcell entry receptor ACE2 and entry associated proteases are not limited only to the respiratory system, but are widely expressed across the human tissue types, which is a stated reason why beyond the respiratory system pathology COVID-19 leads to multiorgan involvement and a systemic illness. 17 Notably, ACE2 is an interferon (IFN) stimulated gene 18 hinting that SARS-CoV-2-receptor binding mediated dysregulation of ACE2 expression may be a likely molecular mechanism responsible for prominent IFNs-dysregulation characteristically observed in COVID-19 patients. 19 SARS-CoV-2 has a close genomic sequence resemblance to a bat CoV RaTG3 (~96%) and to SARS-CoV-1 (~79%) indicating an evolutionary linkage among these viruses. 20 Of note, virus-host interactions are very similar for the WT strains of SARS-CoV-1 and SARS-CoV-2, however, the later has gained multiple advantageous mutations within the RBD encompassing receptor binding interface. 21, 22 The recent studies examining the strength of virus RBD:ACE2 complex have established that SARS-CoV-2 has a more efficient binding to ACE2 than the SARS-CoV-1, 21,23 thus imparting it higher transmissibility and virulence than the later. Interestingly, the inclusion of furin in the list of entry associated protease also seems an evolutionary gain in SARS-CoV-2 as it is not present in SARS-CoV-1 or other SARS-related viruses. 14 The furin cleavage site (FCS) of SARS-CoV-2 is a small stretch of peptide (PRRAR) inserted at the intersection of spike segments S1 and S2 (681-685 aa residues), facilitating proteolytic cleavage of the viral spike protein at that point 14 ( Figure 1 ). Noteworthy, FCS is not present in SARS-CoV-1 and other SARS-related viruses (although it is present in a number of other human coronaviruses, including MERS-CoV, HKU1-CoV, and OC43-CoV) and is considered as an evolutionary gain in SARS-CoV-2 towards imparting it higher virulence. 14 Furin cleavage also improves further proteolytic cleavage by another host-proteases TMPRSS2 at S1-S2 intersection-an event essential for the priming of the virus membrane for host-cell fusion. [24] [25] [26] Apart from the spike protein, multiple nonstructural proteins (NSPs) have been linked to higher virulance and excessive immunological dysregulations by SARS-CoV-2 in comparison to SARS-CoV-1 and other CoVs, and influenza viruses. Of note, SARS-CoV-2 manipulates the host immune cells to ensue a delayed and excessive IFNs response, which is a key innate defense mechanism for the protection against new viral infections (reviewed in Kumar et al. 19 and country of origin, and current evidence for an increase in transmissibility, lethality, or immune escape, is presented in Table 1 .

The SARS-CoV-2 strain with D614G (B.1) was the first noticeable variant having a significant edge over the WT strain. 29 The variant was found to be more transmissible 29 and by the end of 2020 it almost replaced the WT strain globally. However, there had been no substantial evidence suggesting that it had increased virulence. there is no evidence whether it had increased lethality. 32 Furthermore, a F I G U R E 1 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): host-cell entry mechanisms. Entry of SARS-CoV-2 into host cell depends on binding of receptor-binding domain (RBD) of viral spike (S) protein to the cell surface receptor angiotensin-converting enzyme-2 (ACE2). For a successful binding to ACE2, "S" protein is required to be cleaved by the host proteases, TMPRSS2 and Furin. Another host protease CTSL is involved in a pH-dependent cleavage of the S protein inside the endosomes. The binding to ACE2 leads to endocytosis and allows for replication of the virus inside the host cell. The newly formed virions are released after bursting of the infected cell and spread further. Viral infection of the host-cell subsequently leads to activation of innate host defense mechanism, recruitment of the immune cells by the infected tissue, and synthesis and release of the cytokines 

The spike mutations are enriched at the regions which bear epitopes for the natural, vaccine acquired, and monoclonal antibodies, primarily at the receptor-binding domain (RBD) and N-terminal of spike (S) protein ( Figure 3 ). It appears that these mutations are imparting the emerging variants a selection advantage over the WT strain (and early variants), making them more suitable for the spread in a population that has developed only partial herd immunity. 37 

Increased transmissibility and virulence have been speculated for nearly all of the VOCs based on the analysis of the structural and functional changes imparted by the mutations. 44 The emerging variants are accumulating mutations in the spike protein-which encompasses the binding site for the host-cell entryreceptor and is also the most antigenic region of the virus, towards which natural and acquired antibodies are targeted. 44 Key mutations in the spike protein (Table 1) 

Recent studies have shown that most of the emerging variants, primarily VOCs, have gained a certain level of resistance against the natural and vaccine-acquired antibodies (Table 1) . 9, 58, 66 Resistance has been also reported against the multiple monoclonal antibodies currently being used in the treatment of COVID-19. 8,67,68 A significant fall in antibody-mediated neutralization has been observed in most of the variants ( Table 1 ). The most likely mechanisms for the gain of immune escape by variants are (i) inclusion or deletion of amino-acid residues at immunogenic epitopes, thus bringing conformational changes at the binding interface, (ii) remodeling of the electrostatic surface potential, and (iii) gain of additional glycosylation sites thus shielding the binding site for the neutralizing antibodies. 10, 37, 39, 44, 56, 69 Gain of an extra glycosylation site at spike region has been reported for P1 variant in a preprint study. 70 In Moreover, increasing incidences of severe disease and poor outcomes in individuals with no significant co-morbidity are concerning and should be considered alarming. 2, 35, 51 Also, repeated and vaccine breakthrough infections have been reported frequently with the new variants. 31, 35 The changing epidemiological characteristics of the COVID-19

pandemic with the emergence of more transmissible and virulent variants give clear indications that an increasing number of younger and healthy individuals, irrespective of sex, may develop severe COVID-19 as these variants dominate over the global population.

Increasing immune escape against natural, vaccine acquired and therapeutically administered monoclonal antibodies in the emerging variants is a grave public health concern threatening of possible future COVID-19 waves (Table 1) . 85 

Authors express their sincere gratitude to GISAID (https://www. gisaid.org/) and Outbreak.info (https://outbreak.info/) databases, which were utilized for generating data graphs and/or mutation landscapes for SARS-CoV-2 variants.

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The authors declare that there are no conflict of interests.

The concept was developed by Ashutosh Kumar