Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages DOI Creative Commons
Naveen Kumar, Rahul Kaushik, Ashutosh Singh

et al.

Viruses, Journal Year: 2022, Volume and Issue: 14(12), P. 2764 - 2764

Published: Dec. 12, 2022

The ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in the recent emergence a highly divergent variant concern (VOC) defined as Omicron or B.1.1.529. This VOC is particular because it potential to evade most therapeutic antibodies and undergone sustained genetic evolution, resulting five distinct sub-lineages. However, evolutionary dynamics initially identified BA.1 BA.2 sub-lineages remain poorly understood. Herein, we combined Bayesian phylogenetic analysis, mutational profiling, selection pressure analysis track virus's changes that drive early Omicron. Based on dataset chosen for improved temporal signals sampled globally between November 2021 January 2022, common ancestor (tMRCA) substitution rates were estimated be 18 September (95% highest posterior density (HPD), 4 August-22 October 2021) 1.435 × 10

Language: Английский

Omicron variant: Current insights and future directions DOI Creative Commons

Rashmi Rana,

Ravi Kant,

Rohit Singh Huirem

et al.

Microbiological Research, Journal Year: 2022, Volume and Issue: 265, P. 127204 - 127204

Published: Sept. 17, 2022

Language: Английский

Citations

69
SARS‐CoV‐2 and its variants of concern including Omicron: A never ending pandemic DOI Creative Commons
Ranjan K. Mohapatra, Satwik Kuppili, Tarun Kumar Suvvari

et al.

Chemical Biology & Drug Design, Journal Year: 2022, Volume and Issue: 99(5), P. 769 - 788

Published: Feb. 20, 2022

Abstract The ongoing COVID‐19 pandemic caused by SARS‐CoV‐2 is associated with high morbidity and mortality. This zoonotic virus has emerged in Wuhan of China December 2019 from bats pangolins probably continuing the human‐to‐human transmission globally since last two years. As there no efficient approved treatment, a number vaccines were developed at an unprecedented speed to counter pandemic. Moreover, vaccine hesitancy observed that may be another possible reason for this never ending In meantime, several variants mutations identified causing multiple waves globally. Now safety efficacy these are debatable recommended determine whether able interrupt variant concern (VOC). VOCs continue emerge appear more transmissible less sensitive virus‐specific immune responses. overview, we have highlighted various drugs used along their reported side effects. preliminary data novel VOC “Omicron” discussed existing animal models.

Language: Английский

Citations

58
Challenges of the Omicron (B.1.1.529) Variant and Its Lineages: A Global Perspective DOI
Ranjan K. Mohapatra,

Venkataramana Kandi,

Sarika Verma

et al.

ChemBioChem, Journal Year: 2022, Volume and Issue: 23(9)

Published: March 23, 2022

The SARS-CoV-2 virus has shown increased ability to mutate over the past two years, especially in regions of spike protein and receptor binding sites. Omicron (B.1.1.529) is fifth variant concern (VOC) after emergence Alpha, Beta, Gamma, Delta VOCs SARS-CoV-2. This new now circulated 128 countries according Global Initiative on Sharing All Influenza Data (GISAID), these have shared 650,657 genome sequences as 26 January, 2022. In this article, we highlight real challenges its different lineages.

Language: Английский

Citations

51
Virtual screening and molecular dynamics simulations provide insight into repurposing drugs against SARS-CoV-2 variants Spike protein/ACE2 interface DOI Creative Commons
Davide Pirolli, Benedetta Righino, Chiara Camponeschi

et al.

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Jan. 27, 2023

After over two years of living with Covid-19 and hundreds million cases worldwide there is still an unmet need to find proper treatments for the novel coronavirus, due also rapid mutation its genome. In this context, a drug repositioning study has been performed, using in silico tools targeting Delta Spike protein/ACE2 interface. To aim, it virtually screened library composed by 4388 approved drugs through deep learning-based QSAR model identify protein-protein interactions modulators molecular docking against receptor binding domain (RBD). Binding energies predicted complexes were calculated Molecular Mechanics/Generalized Born Surface Area from dynamics simulations. Four out top twenty ranking compounds showed stable modes on RBD evaluated their effectiveness Omicron. Among them antihistaminic drug, fexofenadine, revealed very low energy, complex, interesting RBD. Several found exhibit direct antiviral activity SARS-CoV-2 vitro, mechanisms action debated. This not only highlights potential our computational methodology screening variant-specific drugs, but represents further tool investigating properties selected drugs.

Language: Английский

Citations

40
The SARS‐CoV‐2 Omicron Variant and its Multiple Sub‐lineages: Transmissibility, Vaccine Development, Antiviral Drugs, Monoclonal Antibodies, and Strategies for Infection Control – a Review DOI
Ranjan K. Mohapatra, Sarika Verma,

Venkataramana Kandi

et al.

ChemistrySelect, Journal Year: 2023, Volume and Issue: 8(9)

Published: Feb. 28, 2023

Abstract The Omicron (B.1.1.529), fifth variant of concern (VOC) SARS‐CoV‐2, initially identified following a steep increase in COVID‐19 cases Southern Africa November 2021. It is highly‐mutated and more contagious as compared with the Delta variant, however less deadly. Due to its high transmission rate, it spreads dramatically, causing huge surges worldwide. causes “mild infection”, hospitalisations likely occur. However, this known show resistance neutralizing antibodies (nAbs) generated through vaccination and/or prior infection well monoclonal (mAbs) used treat patients. In many countries, booster doses vaccines have been recommended protective levels vaccinated individuals. Along implementation appropriate prevention control strategy measures, current efforts are also focussed on development better mAbs counter variant. This review highlights global health concerns challenges posed by present an update sub‐lineages.

Language: Английский

Citations

17
Self-assembled ferritin-based nanoparticles elicit a robust broad-spectrum protective immune response against SARS-CoV-2 variants DOI

Weiqi Wang,

Xianyong Meng, Huan Cui

et al.

International Journal of Biological Macromolecules, Journal Year: 2024, Volume and Issue: 264, P. 130820 - 130820

Published: March 12, 2024

Language: Английский

Citations

6
Sputnik V Effectiveness against Hospitalization with COVID-19 during Omicron Dominance DOI Creative Commons
А. С. Шкода, Vladimir А. Gushchin, Darya A. Ogarkova

et al.

Vaccines, Journal Year: 2022, Volume and Issue: 10(6), P. 938 - 938

Published: June 13, 2022

Mass vaccination campaigns against COVID-19 affected more than 90% of the population in most developed countries. The new epidemiologic wave has been ongoing since end 2021. It is caused by a virus variant B.1.1.529, also known as "Omicron" and its descendants. effectiveness major vaccines Omicron not known. purpose this study to evaluate efficacy Sputnik V vaccine. main goal assess protection hospitalization period dominance. We conducted our based on large clinical center Moscow (Russia) where 1112 patients were included. used case-population method perform calculations. data we obtained indicate that causes at least infections studied cohort. with was 85.9% (95% CI 83.0-88.0%) for those who received one dose. 87.6% 85.4-89.5%) 97.0% 95.9-97.8%) two or three doses. cases severe forms higher less ones. Thus, present indicates high protective case lineage.

Language: Английский

Citations

27
Computational studies on potential new anti-Covid-19 agents with a multi-target mode of action DOI Creative Commons
Ranjan K. Mohapatra, Mohammad Azam, Pranab Kishor Mohapatra

et al.

Journal of King Saud University - Science, Journal Year: 2022, Volume and Issue: 34(5), P. 102086 - 102086

Published: May 13, 2022

A compound that could inhibit multiple targets associated with SARS-CoV-2 infection would prove to be a drug of choice against the virus. Human receptor-ACE2, receptor binding domain (RBD) S-protein, Papain-like protein (PLpro), reverse transcriptase (RdRp) were chosen for in silico study. set previously synthesized compounds (1-5) docked into active sites targets. Based on docking score, ligand efficiency, free energy, and dissociation constants definite conformational position ligand, inhibitory potentials measured. The stability protein-ligand (P-L) complex was validated by using molecular dynamics simulations YASARA suit. Moreover, pharmacokinetic properties, FMO NBO analysis performed ranking potentiality as drug. geometry optimizations electronic structures investigated DFT. As per study, compound-5 has best affinity all four 1, 3 5 are less toxic can considered oral consumption.

Language: Английский

Citations

26
Need of booster vaccine doses to counteract the emergence of SARS-CoV-2 variants in the context of the Omicron variant and increasing COVID-19 cases: An update DOI Creative Commons
Ranjan K. Mohapatra, Nahed A. El‐Shall, Ruchi Tiwari

et al.

Human Vaccines & Immunotherapeutics, Journal Year: 2022, Volume and Issue: 18(5)

Published: May 20, 2022

The emergence of different variants SARS-CoV-2, including the Omicron (B.1.1.529) variant in November 2021, has resulted a continuous major health concern at global scale. Presently, spread very rapidly worldwide within short time period. As most mutated instilled serious uncertainties on effectiveness humoral adaptive immunity generated by COVID-19 vaccination or an active viral infection as well protection provided antibody-based immunotherapies. Amidst such high public concerns, need to carry out booster been emphasized. Current evidence reveals importance incorporating using several vaccine platforms, vector- and mRNA-based vaccines, other platforms that are under explorative investigations. Further research is being conducted assess durability against SARS-CoV-2 variants.

Language: Английский

Citations

24
Molecular dynamic analyses of the interaction of SARS-CoV-1 or 2 variants with various angiotensin-converting enzyme-2 species DOI
Abeer S. Aloufi, Amr Ahmed El–Arabey, Wafa Ali Eltayb

et al.

Journal of Biomolecular Structure and Dynamics, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 10

Published: Feb. 12, 2024

The transmembrane glycoprotein angiotensin-converting enzyme 2 (ACE2) is a key component of the renin-angiotensin system (RAS). It was shown to be receptor severe acute respiratory syndrome coronavirus in COVID-19 outbreak (SARS-COV-2). Furthermore, ACE2 aids transport amino acids across membrane. lost from membrane, resulting soluble (sACE2). We aim examine structural conformation alterations between SARS-CoV-1 or variants at various periods with sources, particularly area where it interacts viral protein and receptor. important study molecular dynamics ACE2/SARS-COV RBD when structure available on database. Here we analyzed crystal Human, Dog, Mus, Cat, Bat complex SARS-COV-1 SARS-COV-2. result shows, there variation type residues, number contact atoms hydrogen bonds during interaction interfaces. By using simulation, can measure RMSD, RMSF, SASA, Rg difference percentage α helix β strand. As bat & SARS-CoV-2 found have high amount strand compared another complex, while hACE2 has fewer amounts Our provides deep view which summary many works around ACE2/SARS-CoV interaction.

Language: Английский

Citations

4