A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies

Viruses, Journal Year: 2023, Volume and Issue: 15(1), P. 167 - 167

Published: Jan. 5, 2023

The COVID-19 pandemic has created significant concern for everyone. Recent data from many worldwide reports suggest that most infections are caused by the Omicron variant and its sub-lineages, dominating all previously emerged variants. numerous mutations in Omicron’s viral genome sub-lineages attribute it a larger amount of fitness, owing to alteration transmission pathophysiology virus. With rapid change structure, sub-variants, namely BA.1, BA.2, BA.3, BA.4, BA.5, dominate community with an ability escape neutralization efficiency induced prior vaccination or infections. Similarly, several recombinant sub-variants Omicron, XBB, XBD, XBF, etc., have emerged, which better understanding. This review mainly entails changes due having higher number mutations. binding affinity, cellular entry, disease severity, infection rates, importantly, immune evading potential them discussed this review. A comparative analysis Delta other variants evolved before gives readers in-depth understanding landscape infection. Furthermore, discusses range abilities possessed approved antiviral therapeutic molecules neutralizing antibodies functional against sub-variants. evolution is causing infections, but broader aspect their not been explored. Thus, scientific should adopt elucidative approach obtain clear idea about recently including variants, so effective vaccines drugs can be achieved. This, turn, will lead drop cases and, finally, end pandemic.

Language: Английский

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SARS-CoV-2 Vaccines, Vaccine Development Technologies, and Significant Efforts in Vaccine Development during the Pandemic: The Lessons Learned Might Help to Fight against the Next Pandemic

Vaccines, Journal Year: 2023, Volume and Issue: 11(3), P. 682 - 682

Published: March 17, 2023

We are currently approaching three years since the beginning of coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV-2 has caused extensive disruptions in everyday life, public health, and global economy. Thus far, vaccine worked better than expected against virus. During pandemic, we experienced several things, such as virus its pathogenesis, clinical manifestations, treatments; emerging variants; different vaccines; development processes. This review describes how each been developed approved with help modern technology. also discuss critical milestones during process. Several lessons were learned from countries two research, development, trials, vaccination. The process will to fight next

Language: Английский

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Changing epidemiology of COVID-19: potential future impact on vaccines and vaccination strategies

Expert Review of Vaccines, Journal Year: 2024, Volume and Issue: 23(1), P. 510 - 522

Published: April 24, 2024

COVID-19 was an unprecedented challenge worldwide; however, disease epidemiology has evolved, and no longer constitutes a public health emergency of international concern. Nonetheless, remains global threat uncertainties remain, including definition the end pandemic transition to endemicity, understanding true rates SARS-CoV-2 infection/transmission.

Language: Английский

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Exploring the structural and molecular interaction landscape of nirmatrelvir and Mpro complex: The study might assist in designing more potent antivirals targeting SARS-CoV-2 and other viruses

Journal of Infection and Public Health, Journal Year: 2023, Volume and Issue: 16(12), P. 1961 - 1970

Published: Sept. 30, 2023

Several therapeutics have been developed and approved against SARS-CoV-2 occasionally; nirmatrelvir is one of them. The drug target Mpro, therefore, it necessary to comprehend the structural molecular interaction Mpro-nirmatrelvir complex.Integrative bioinformatics, system biology, statistical models were used analyze macromolecular complex.Using two complexes, study illustrated interactive residues, H-bonds, interfaces. It informed six nine H-bond formations for first second complex, respectively. maximum bond length was observed as 3.33 Å. ligand binding pocket's surface area volume noted 303.485 Å2 295.456 Å3 complex 308.397 304.865 complex. proteome dynamics evaluated by analyzing complex's NMA mobility, eigenvalues, deformability, B-factor. Conversely, a model created assess therapeutic status nirmatrelvir.Our reveals landscape will guide researchers in designing more broad-spectrum antiviral molecules mimicking nirmatrelvir, which assist fighting other infectious viruses. also help prepare future epidemics or pandemics.

Language: Английский

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Molecular characterization of SARS-CoV-2 Omicron clade and clinical presentation in children

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: March 4, 2024

Abstract Since its emergence, SARS-CoV-2 Omicron clade has shown a marked degree of variability and different clinical presentation compared with previous clades. Here we demonstrate that at least four lineages circulated in children since December 2021, studied until November 2022: BA.1 (33.6%), BA.2 (40.6%), BA.5 (23.7%) BQ.1 (2.1%). At 70% infections concerned under 1 year, most them being infected (n = 201, 75.6%). Looking genetic variability, 69 SNPs were found to be significantly associated pairs, (phi < − 0.3 or > p-value 0.001). 16 involved 4 distinct clusters (bootstrap 0.75). One these (A23040G, A27259C, T23617G, T23620G) was also positively moderate/severe COVID-19 (AOR [95% CI] 2.49 [1.26–4.89] p-value: 0.008) together comorbidities 2.67 [1.36–5.24] 0.004). Overall, results highlight the extensive circulation children, mostly aged provide insights on viral diversification even considering low-abundant SNPs, finally suggesting potential contribution affecting disease severity.

Language: Английский

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Recent SARS-CoV-2 evolution trajectories indicate the emergence of Omicron’s several subvariants and the current rise of KP.3.1.1 and XEC

Virology, Journal Year: 2025, Volume and Issue: unknown, P. 110508 - 110508

Published: March 1, 2025

Language: Английский

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Can the RBD mutation R346X provide an additional fitness to the “variant soup,” including offspring of BQ and XBB of SARS-CoV-2 Omicron for the antibody resistance?

Molecular Therapy — Nucleic Acids, Journal Year: 2023, Volume and Issue: 32, P. 61 - 63

Published: March 15, 2023

The COVID-19 pandemic has resulted in nearly billions of infected cases and millions deaths. Monoclonal antibodies (mAbs), antiviral drugs, vaccines, several non-pharmaceutical interventions have been employed to control the virus's spread diminish disease's harms.1Liu C. Zhou Q. Li Y. Garner L.V. Watkins S.P. Carter L.J. Smoot J. Gregg A.C. Daniels A.D. Jervey S. Albaiu D. Research development on therapeutic agents vaccines for related human coronavirus diseases.ACS Cent. Sci. 2020; 6: 315-331Crossref PubMed Scopus (867) Google Scholar,2Saha R.P. Sharma A.R. Singh M.K. Samanta Bhakta Mandal Bhattacharya M. Lee S.S. Chakraborty Repurposing ongoing vaccine, new initiatives against COVID-19.Front. Pharmacol. 11: 1258Crossref (83) Scholar,3Chakraborty G. Saha Ongoing clinical trials fight pandemic.Immune Netw. 2021; 21: e5Crossref (16) Scholar,4Chakraborty Agoramoorthy drug repurposing provide very effective combinations: lessons learned from major studies.Front. 12: 704205Crossref (56) Scholar However, antibody escape or resistance is a significant concern severe acute respiratory syndrome 2 (SARS-CoV-2) variants, which reported time time.5Chakraborty A detailed overview immune escape, partial vaccine SARS-CoV-2 their emerging variants with mutations.Front. Immunol. 2022; 13: 801522Crossref (38) Scholar,6Mohapatra R.K. Tiwari R. Sarangi A.K. Islam M.R. Dhama K. Omicron (B.1.1.529) variant SARS-CoV-2: concerns, challenges, recent updates.J. Med. Virol. 94: 2336-2342Crossref (59) Scholar,7Chakraborty Emerging mutations role small molecule-based resistance.Curr. Opin. 62: 64-73Crossref (24) Spike subvariants are as cause resistance.8Wang Iketani Z. Liu L. Guo Huang Bowen Wang Yu et al.Alarming evasion properties rising BQ XBB subvariants.Cell. 2023; 186: 279-286.e8Abstract Full Text PDF (150) Scholar,9Chakraborty Mallik B. - heavily mutated variant: mapped location probable its an emphasis S-glycoprotein.Int. Biol. Macromol. 219: 980-997Crossref (13) Scholar,10Chakraborty comprehensive analysis mutational landscape newly comparison VOCs VOIs.GeroScience. 44: 2393-2425Crossref (6) continues higher infectivity triple-vaccinated persons, even though infections led many antibody-positive individuals.11Blom Havervall Marking U. Norin N.G. Bacchus P. Groenheit Bråve A. Thålin Klingström Infection rate asymptomatic healthcare workers, Sweden, June 2022.Emerg. Infect. Dis. 28: 2119-2121Crossref (5) discovered point mutation virus spike R346X, primarily R346T, located receptor-binding domain (RBD) region (Figure 1A). surge directly connected quick appearance R346T mutation, predominantly expressed subvariants. R346 position results improved immunological by neutralizing antibodies.12Cao Jian F. Xiao T. Song W. Yisimayi An al.Omicron escapes majority existing antibodies.Nature. 602: 657-663Crossref (832) comparative study using sera people who already received three doses mRNA patients BA.1 BA.2 highlighted property neutralization al. conducted VSV-based pseudovirus assays assess antigenic emerged subvariants, namely BA.5.9, BA.4.7, BA.4.6. They also used panel twenty-three mAbs confirm this assay. Compared BA.5, BA.4.6 were marginally but considerably more resistant than BA.5 breakthrough sera. Still, BA.4.7 BA.5.9 sublineages displayed similar binding ACE2 receptor compared subvariant offspring. Moreover, because presence R346X (T/S/I) increased certain class (Figures 1B–1D).13Wang Ho Yeh A.Y. Mohri H. Shah J.G. al.Resistance omicron neutralisation.Lancet 22: 1666-1668Abstract (22) At end 2022, novel transmissibility rates that descended BA.4/BA.5 rapidly created massive across globe. diverse geographic distribution possess few extra mutations, particularly glycoprotein. For instance, BA.2.75.2, descendant subvariant, contains F486S, D1199N initially India Singapore.14Kurhade Zou Xia Chang H.C. Ren Xie X. Shi P.Y. Low BQ.1.1 XBB.1 parental bivalent booster.Nat. 29: 344-347Crossref (99) Scholar,15Qu Evans J.P. Faraone J.N. Zheng Y.M. Carlin Anghelina Stevens Fernandez Jones Lozanski al.Enhanced BQ.1, BQ.1.1, BA.4.6, BF.7, BA.2.75.2.Cell Host Microbe. 31: 9-17.e3Abstract (65) Scholar,16Sheward D.J. Kim Fischbach Sato Muschiol Ehling R.A. Björkström N.K. Karlsson Hedestam G.B. Reddy S.T. Albert sublineage BA.2.75.2 exhibits extensive neutralising antibodies.Lancet 1538-1540Abstract (30) N658S found nations, including USA UK.17Oneal E. simple way modify behavior.Geriatr. Nurs. 1986; 7: 45Crossref (1) Scholar,18Hachmann N.P. Miller Collier A.R.Y. Barouch D.H. Neutralization BA.4.6.N. Engl. 387: 1904-1906Crossref started dominate circulating lineages numerous countries December 2022. It carries along K444T N460K substitutions, was BA.2.75.2.19Miller Hachmann Lasrado N. Mazurek C.R. Patio R.C. Powers O. Surve Theiler Korber Substantial XBB.1.N. 388: 662-664Crossref (36) linked vaccine-induced mAbs.15Qu Scholar,20Cao Chen Zhang al.Imprinted humoral immunity induces convergent RBD evolution.Nature. 614: 521-529PubMed multiple circulation may subject comparable selective pressure due imprinted preexisting immunity, according evolution observed protein.20Cao Scholar,21Park Y.J. Pinto Walls De Marco Benigni Zatta Silacci-Fregni Bassi Sprouse K.R. responses sublineages.Science. 378: 619-627Crossref (45) demonstrated rapid R346T-expressing identical RBD, suggesting next wave anticipated involve plethora share phenotype rather particular single sublineage.22Groenheit Galanis I. Sondén Sperk Movert Efimova Petersson Rapp Sahlén V. al.Rapid emergence expressing protein R346T.Lancet Reg. Health. Eur. 24: 100564Abstract (7) Numerous reports different global sources suggest all previously responsible most infections. Omicron's viral genome undergone changes, altered pathophysiology transmission given it level fitness.23Chatterjee Nag omicron: sub-variants, pathophysiology, characteristics, landscape, therapies.Viruses. 15: 167Crossref diversity current immunity-eluding mutant offspring generated byproduct combinations especially region. This intricacy makes challenging anticipate upcoming waves infection. In some instances, might result "double wave," where one variety engulfs population before being replaced another. Scientists refer "variant soup" "a swarm variants."24Callaway COVID 'variant soup' making winter surges hard predict.Nature. 611: 213-214Crossref (21) According Cao al., evident possesses protein.12Cao Generally, notable amino acid substitutions at R346K, R346I. Most sublineages, BJ.1, BR.3, BA.2.75.5, show strong predominance R346T. Arora sought determine impact concluded offers BA.4 potential.25Arora Nehlmeier Kempf Cossmann Schulz S.R. Dopfer-Jablonka Baier Tampe Moerer Dickel al.Lung cell entry, cell-cell fusion capacity, neutralisation sensitivity BA.2.75.Lancet 1537-1538Abstract Due protein, increasing, be capabilities.8Wang middle August first India, they swiftly Singapore other parts Asia. rose BQ.1 whereas BJ.1 BA.2.75, two BA.2, recombined produce XBB.1. These still evolving diversifying, complexity getting intricate. present dominant addition those identified 1B).8Wang containing potently escaped efficacy elicited monovalent boosting significantly variant. booster cohort cohort, titers noticeably lower earlier Wuhan strain.19Miller findings imply protection diseases caused depend CD8 T polymorphisms impair efficiency vaccines.26Wherry E.J. vaccines.Science. 377: 821-822Crossref elevation 2022 2021 following likely reflects administration larger prevalence infection cohort. Thus, suggested subsequent 1).19Miller incidence subvariants' descendants alarming scientific community enhanced antibodies. One notably additional fitness these R346X. predesigned therapeutics loosen if prevails variants. need design develop considering will capability combat coming days, essential. It, turn, potent weapon eradicate pandemic. authors data supporting available within article. declare no competing interests.

Language: Английский

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Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves

Microorganisms, Journal Year: 2023, Volume and Issue: 11(5), P. 1288 - 1288

Published: May 15, 2023

SARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified in nucleocapsid their possible association with patient characteristics. We analyzed 695 samples from patients confirmed COVID-19 Saudi Arabia between 1 April 2021, 30 2022. Nucleocapsid were through whole genome sequencing. 𝜒2 tests t assessed associations Logistic regression estimated risk of intensive care unit (ICU) admission or death. Of 60 identified, R203K was most common, followed by G204R, P13L, E31del, R32del, S33del. These associated reduced ICU admission. S33del also By contrast, D63G, R203M, D377Y increased Most detected SR-rich region, which low The C-tail central linker regions admission, whereas N-arm region risk. Consequently, N must be observed, as they exacerbate viral infection severity. Additional research is needed to validate mutations' clinical outcomes.

Language: Английский

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Physicochemical effects of emerging exchanges on the spike protein's RBM of the SARS-CoV-2 Omicron subvariants BA.1-BA.5 and its influence on the biological properties and attributes developed by these subvariants

Virology, Journal Year: 2023, Volume and Issue: 587, P. 109850 - 109850

Published: July 28, 2023

Language: Английский

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Stratification of COVID-19 Severity Using SeptiCyte RAPID, a Novel Host Immune Response Test

Viruses, Journal Year: 2023, Volume and Issue: 15(2), P. 419 - 419

Published: Feb. 2, 2023

SeptiCyte® RAPID is a gene expression assay measuring the relative levels of host response genes PLA2G7 and PLAC8, indicative dysregulated immune during sepsis. As severe forms COVID-19 may be considered viral sepsis, we evaluated SeptiCyte in series 94 patients admitted to Foch Hospital (Suresnes, France) with proven SARS-CoV-2 infection. EDTA blood was collected emergency department (ED) 67 cases, intensive care unit (ICU) 23 cases conventional units 4 cases. SeptiScore (0–15 scale) increased severity. Patients ICU had highest SeptiScores, producing values comparable 8 culture-confirmed bacterial Receiver operating characteristic (ROC) curve analysis an area under (AUC) 0.81 for discriminating requiring admission from who were immediately discharged or hospitalization units. SeptiScores extent lung injury. For 68 patients, chest computed tomography (CT) scan performed within 24 h diagnosis. >7 suggested injury ≥50% (AUC = 0.86). compared other biomarkers Critical + Severe ICU, versus Moderate Mild not ICU. The mean AUC superior that any individual biomarker combination thereof. In contrast C-reactive protein (CRP), correlation impacted by treatment anti-inflammatory agents. can useful tool identify ED, as well follow-up.

Language: Английский

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