Elsevier

Gene

Volume 814, 10 March 2022, 146134
Gene

From delta to Omicron: S1-RBD/S2 mutation/deletion equilibrium in SARS-CoV-2 defined variants

https://doi.org/10.1016/j.gene.2021.146134Get rights and content

Highlights

  • SARS-CoV-2 demonstrates a continuous tendency for new variants emergence.

  • Differences in those variants regarding their mutations/deletions/insertions in spike genomic sequence leads to altered transmissibility/infectivity/re-infection/morbidity/mortality rates.

  • Omicron variant is characterized by an ‘’exotic’’ genomic profile due to the increased number of host mutations and the combination of deletions/insertion in S1-RBD/S2 domains.

  • Delta to Omicron transition is the next step for SARS-CoV-2 adjustment regarding its effort to survive in human affected cells.

Abstract

Coronavirus-related Severe Acute Respiratory Syndrome (SARS-CoV) in 2002/2003, Middle-East Respiratory Syndrome (MERS-CoV) in 2012/2013, and especially the current 2019/2021 Severe Acute Respiratory Syndrome-2 (SARS-CoV-2) affected negatively the national health systems’ endurance worldwide. SARS-Cov-2 virus belongs to lineage b of beta-CoVs demonstrating a strong phylogenetic similarity with BatCoVRaTG13 type. Spike (S) glycoprotein projections -consisting of two subunits S1/S2- provide a unique crown-like formation (corona) on virion’s surface. Concerning their functional role, S1 represents the main receptor-binding domain (RBD), whereas S2 is involved in the virus-cell membrane fusion mechanism. On Nov 26th 2021, WHO designated the new SARS-CoV-2 strain – named Omicron, from letter ‘’όμικρον’’ in the Greek alphabet - as a variant of concern (B.1.1529 variant). Potentially this new variant is associated with high transmissibility leading to elevated infectivity and probably increased re-infection rates. Its impact on morbidity/mortality remains under investigation. In the current paper, analyzing and comparing the alterations of SARS-CoV-2 S RNA sequences in the defined variants (Alpha to Omicron), we observed some interesting findings regarding the S1-RBD/S2 mutation/deletion equilibrium that maybe affect and modify its activity.

Abbreviations

SARS-CoV-2
severe acute respiratory syndrome coronavirus-2
COVID-19
coronavirus disease 2019
ACE
angiotensin-converting enzyme
SARS
severe acute respiratory syndrome
MERS
Middle East respiratory syndrome
RBD
receptor-binding domain
S
spike
TMPRSS2
transmembrane serine protease 2
World Health Organization (WHO) CDC
Centers for Disease control
Monoclonal antibodies mAbs
monoclonal antibodies
LNP
lipid nanoparticles
m RNA
messenger RNA
NSP
non-structural proteins

Keywords

SARS-CoV-2
COVID-19
Variants
Mutations
RNA
Genome

Cited by (0)

1

Authors equally contributed.

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