Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic

Genes, Journal Year: 2023, Volume and Issue: 14(2), P. 407 - 407

Published: Feb. 4, 2023

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well resistance to monoclonal antibodies polyclonal sera, among other treatments. In order understand causes consequences observed SARS-CoV-2 diversity, a variety studies investigated evolution this virus humans. general, evolves with moderate rate evolution, 10

Language: Английский

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Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: June 25, 2022

Abstract Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, detection of recombination only feasible when genetically distinct viruses contemporaneously infect the same host. Here, we identify instance SARS-CoV-2 superinfection, whereby individual was infected with two viral variants: Alpha (B.1.1.7) Epsilon (B.1.429). This superinfection first noted genome sequence failed to exhibit classic S gene target failure behavior used track this variant. Full sequencing from four independent extracts reveals that variant alleles comprise around 75% genomes, whereas 20% sample. Further investigation presence numerous recombinant haplotypes spanning genome, specifically in spike, nucleocapsid, ORF 8 coding regions. These findings support potential for reshape genetic diversity.

Language: Английский

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SARS-CoV-2 and Emerging Variants: Unmasking Structure, Function, Infection, and Immune Escape Mechanisms

Frontiers in Cellular and Infection Microbiology, Journal Year: 2022, Volume and Issue: 12

Published: May 12, 2022

As of April 1, 2022, over 468 million COVID-19 cases and 6 deaths have been confirmed globally. Unlike the common coronavirus, SARS-CoV-2 has highly contagious attracted a high level concern worldwide. Through analysis structural, non-structural, accessory proteins, we can gain deeper understanding structure-function relationships, viral infection mechanisms, viable strategies for antiviral therapy. Angiotensin-converting enzyme 2 (ACE2) is first widely acknowledged receptor, but researches shown that there are additional co-receptors facilitate entry to infect humans. We performed an in-depth review published papers, searching or other auxiliary membrane proteins enhance infection, analyzing pertinent pathogenic mechanisms. The genome, especially spike gene, undergoes mutations at abnormally frequency during virus replication and/or when it transmitted from one individual another. summarized main mutant strains currently circulating global, elaborated structural feature increased infectivity immune evasion variants. Meanwhile, principal purpose update information on outbreak. Many countries novel findings early stage epidemic, accruing evidence rewritten timeline outbreak, triggering new thinking about origin spread COVID-19. It anticipated this provide further insights future research global epidemic prevention control.

Language: Английский

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The Deltacron conundrum: Its origin and potential health risks

Journal of Medical Virology, Journal Year: 2022, Volume and Issue: 94(11), P. 5096 - 5102

Published: July 11, 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), since its outbreak in December 2019, has been capable of continuing the pandemic by mutating itself into different variants. Mass vaccinations, antibiotic treatment therapy, herd immunity, and preventive measures have reduced disease's severity from emerging However, virus is undergoing recombination among current two variants: Delta Omicron, resulting a new variant, informally known as "Deltacron," which was controversial it might be product lab contamination between Omicron samples. proclamation proved wrong, experts are putting more effort better understanding variant's epidemiological characteristics to control potential outbreaks. This review discussed mutations novel variant prospective risk factors therapeutic options context this variant. study could used guide for implementing appropriate controls sudden

Language: Английский

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The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron

Viruses, Journal Year: 2022, Volume and Issue: 14(9), P. 2009 - 2009

Published: Sept. 10, 2022

In late December of 2019, high-throughput sequencing technologies enabled rapid identification SARS-CoV-2 as the etiological agent COVID-19, and global efforts are now a critical tool for monitoring ongoing spread evolution this virus. Here, we provide short retrospective analysis variants by analyzing subset (n = 97,437) all publicly available genomes ~11.9 million) that were randomly selected but equally distributed over course pandemic. We plot appearance new concern (VOCs) time show mutation rates in Omicron (BA.1) sub-lineages (BA.2–BA.5) significantly elevated compared to previously identified variants. Mutations primarily restricted spike nucleocapsid proteins, while 24 other viral proteins—including those involved replication—are generally conserved. Collectively, suggests genetic distinction arose from selective pressures on spike, fidelity replication variant has not been altered.

Language: Английский

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T‐cell responses to SARS‐CoV‐2 Omicron spike epitopes with mutations after the third booster dose of an inactivated vaccine

Journal of Medical Virology, Journal Year: 2022, Volume and Issue: 94(8), P. 3998 - 4004

Published: April 27, 2022

The rapidly spreading severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant contains more than 30 mutations that mediate escape from antibody responses elicited by prior infection or current vaccines. Fortunately, T-cell are highly conserved in most individuals, but the impacts of not clear. Here, we showed individuals who underwent booster vaccination with CoronaVac were largely protective against SARS-CoV-2 spike protein. To specifically estimate impact on vaccinated participants, 16 peptides derived protein ancestral virus strain used to stimulate peripheral blood mononuclear cells (PBMCs) volunteers. Compared administration two doses vaccine, substantially enhanced activation response both and epitopes, although enhancement was slightly weakened mutations. Then, these proteins separately PBMCs. Interestingly, compared peptides, only G339D N440K mutation detected significantly destabilize response. Although participants need be evaluated confirm this conclusion, our study nonetheless estimates variant.

Language: Английский

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The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: July 25, 2023

Over three years’ pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and subvariants have emerged successively, outcompeted earlier become predominant. The sequential emergence reflects the evolutionary process mutation-selection-adaption severe acute respiratory syndrome 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in spike protein causes altered viral antigenicity, transmissibility, pathogenicity SARS-CoV-2. Early pandemic, D614G mutation conferred virus with advantages over previous increased it also laid a conservative background for subsequent substantial mutations. role genomic recombination evolution SARS-CoV-2 raised increasing concern occurrence recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, XBB.1.16 late phase pandemic. Co-circulation different co-infection immunocompromised patients accelerate recombinants. Surveillance variations, particularly recombination, is essential to identify ongoing changes genome antigenic epitopes thus leads development new vaccine strategies interventions.

Language: Английский

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Deltacron: Apprehending a new phase of the COVID-19 pandemic

International Journal of Surgery, Journal Year: 2022, Volume and Issue: 102, P. 106654 - 106654

Published: May 8, 2022

Language: Английский

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A Vaccine Strategy Based on the Identification of an Annular Ganglioside Binding Motif in Monkeypox Virus Protein E8L

Viruses, Journal Year: 2022, Volume and Issue: 14(11), P. 2531 - 2531

Published: Nov. 16, 2022

The recent outbreak of Monkeypox virus requires the development a vaccine specifically directed against this as quickly possible. We propose here new strategy based on two-step analysis combining (i) search for binding domains viral proteins to gangliosides present in lipid rafts host cells, and (ii) B epitope predictions. Based previous studies HIV SARS-CoV-2 proteins, we show that cell surface-binding protein E8L possesses ganglioside-binding motif consisting several subsites forming ring structure. cluster GM1 mimicking raft domain is driven by both shape electrostatic surface potential complementarities. An induced-fit mechanism unmasks selected amino acid side chains without significantly affecting secondary structure protein. overlaps three linear epitopes are well exposed unbound faces membrane. This situation ideal generating neutralizing antibodies. thus suggest using these sequences derived from immunogens formulation (recombinant protein, synthetic peptides or genetically based) specific virus. raft/ganglioside-based could be used developing therapeutic responses future outbreaks, parallel existing solutions.

Language: Английский

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Differential Evasion of Delta and Omicron Immunity and Enhanced Fusogenicity of SARS-CoV-2 Omicron BA.4/5 and BA.2.12.1 Subvariants

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: May 17, 2022

Summary The rising case numbers of the SARS-CoV-2 Omicron BA.4, BA.5, and BA.2.12.1 subvariants has generated serious concern about course pandemic. Here we examine neutralization resistance, infectivity, processing, fusogenicity spike from BA.4/5 variants compared with other Delta. Critically, found that new were more resistant to by mRNA-vaccinated boosted health care worker sera Omicron-BA.1-wave patient than BA.1 BA.2 variants. Interestingly, Delta-wave neutralized efficiently against not only Delta but also contain substitutions at position L452, similar exhibited higher fusogenicity, increased dependent on L452 substitution. These results highlight key role L452R L452Q mutations in subvariants.

Language: Английский

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