Evolution of the SARS‐CoV‐2 omicron variants BA.1 to BA.5: Implications for immune escape and transmission

Reviews in Medical Virology, Год журнала: 2022, Номер 32(5)

Опубликована: Июль 20, 2022

Abstract The first dominant SARS‐CoV‐2 Omicron variant BA.1 harbours 35 mutations in its Spike protein from the original that emerged late 2019. Soon after discovery, rapidly to become worldwide and has since evolved into several variants. is of major public health concern owing high infectivity antibody evasion. This review article examines theories have been proposed on evolution including zoonotic spillage, infection immunocompromised individuals cryptic spread community without being diagnosed. Added complexity Omicron's are multiple reports recombination events occurring between co‐circulating variants with Delta other such as XE. Current literature suggests combination novel resulted having higher than Wuhan‐Hu‐1 variant. However, severity believed be less reduced syncytia formation lower multiplication human lung tissue. Perhaps most challenging studies indicate efficacy available vaccines against (8–127 times reduction) compared administration booster vaccine, however, compensates reduction improves by 12–35 fold. Concerningly though, broadly neutralising monoclonal antibodies, those approved FDA for therapeutic use previous variants, mostly ineffective exception Sotrovimab recent suggest BA.2 also resistant Sotrovimab. Currently two new BA.4 BA.5 emerging reported more transmissible immunity generated antibodies. As will likely continue emerge it important evolution, biological consequences mutations, existing well understood.

Язык: Английский

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Recombination in Coronaviruses, with a Focus on SARS-CoV-2

Viruses, Год журнала: 2022, Номер 14(6), С. 1239 - 1239

Опубликована: Июнь 7, 2022

Recombination is a common evolutionary tool for RNA viruses, and coronaviruses are no exception. We review here the evidence recombination in SARS-CoV-2 reconcile nomenclature recombinants, discuss their origin fitness, speculate how recombinants could make difference future of COVID-19 pandemics.

Язык: Английский

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Omicron variant (B.1.1.529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2?

Biomedicine & Pharmacotherapy, Год журнала: 2022, Номер 154, С. 113522 - 113522

Опубликована: Авг. 15, 2022

Since the start of COVID-19 pandemic, numerous variants SARS-CoV-2 have been reported worldwide. The advent concern (VOCs) raises severe concerns amid serious containment efforts against that include physical measures, pharmacological repurposing, immunization, and genomic/community surveillance. Omicron variant (B.1.1.529) has identified as a highly modified, contagious, crucial among five VOCs SARS-CoV-2. increased affinity spike protein (S-protein), host receptor, angiotensin converting enzyme-2 (ACE-2), due to higher number mutations in receptor-binding domain (RBD) S-protein proposed primary reason for decreased efficacy majorly available vaccines transmissible nature variant. Because its significant competitive advantage, sublineages swiftly surpassed other become dominant circulating lineages nations. prevalent strain United Kingdom South Africa. Furthermore, emergence recombinant through conjunction with or by mixing variant's sublineages/subvariants poses major threat humanity. This various issues hazards regarding sublineages, such an breakout susceptible populations fully vaccinated persons. As result, understanding features genetic implications this is crucial. Hence, we explained depth evolution analyzed repercussions on infectiousness, dissemination ability, viral entry mechanism, immune evasion. We also presented viewpoint feasible strategies precluding counteracting any future catastrophic spread omicron could result detrimental wave cases.

Язык: Английский

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Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

Med, Год журнала: 2022, Номер 3(12), С. 848 - 859.e4

Опубликована: Окт. 20, 2022

Язык: Английский

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Mutational signature dynamics indicate SARS-CoV-2’s evolutionary capacity is driven by host antiviral molecules

PLoS Computational Biology, Год журнала: 2024, Номер 20(1), С. e1011795 - e1011795

Опубликована: Янв. 25, 2024

The COVID-19 pandemic has been characterised by sequential variant-specific waves shaped viral, individual human and population factors. SARS-CoV-2 variants are defined their unique combinations of mutations there a clear adaptation to more efficient infection since the emergence this new coronavirus in late 2019. Here, we use machine learning models identify shared signatures, i.e., common underlying mutational processes link these subset that define concern (VOCs). First, examined global genomes associated metadata determine how viral properties public health measures have influenced magnitude waves, as measured number cases, different geographic locations using regression models. This analysis showed that, expected, both virus were with regional reported numbers impact varies geographically. We attribute intrinsic differences such vaccine coverage, testing sequencing capacity effectiveness government stringency. To assess evolutionary change, used non-negative matrix factorisation observed three distinct substitution patterns exposures from genomes. Signatures 1, 2 3 biased C→T, T→C/A→G G→T point mutations. hypothesise assignments signatures host antiviral molecules APOBEC, ADAR ROS respectively. observe shift amidst relative signature activity predominantly Signature 1 changes an increasingly high proportion consistent 2. could represent immune response interact indicates may continue generate variation future. Linkage detected VOC-defining amino acids substitutions majority SARS-CoV-2’s is likely be action rather than replication errors.

Язык: Английский

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Unique mutations in SARS-CoV-2 Omicron subvariants' non-spike proteins: Potential impacts on viral pathogenesis and host immune evasion

Microbial Pathogenesis, Год журнала: 2022, Номер 170, С. 105699 - 105699

Опубликована: Авг. 6, 2022

Язык: Английский

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RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication

Nucleic Acids Research, Год журнала: 2022, Номер 51(D1), С. D1388 - D1396

Опубликована: Авг. 24, 2022

Recent advances in epitranscriptomics have unveiled functional associations between RNA modifications (RMs) and multiple human diseases, but distinguishing the or disease-related single nucleotide variants (SNVs) from majority of 'silent' remains a major challenge. We previously developed RMDisease database for unveiling association genetic RMs concerning disease pathogenesis. In this work, we present v2.0, an updated with expanded coverage. Using deep learning models 873 819 experimentally validated RM sites, identified total 1 366 252 RM-associated that may affect (add remove site) 16 different types (m6A, m5C, m1A, m5U, Ψ, m6Am, m7G, A-to-I, ac4C, Am, Cm, Um, Gm, hm5C, D f5C) 20 organisms (human, mouse, rat, zebrafish, maize, fruit fly, yeast, fission Arabidopsis, rice, chicken, goat, sheep, pig, cow, rhesus monkey, tomato, chimpanzee, green monkey SARS-CoV-2). Among them, 14 749 disease- 2441 trait-associated function via perturbation epitranscriptomic markers. v2.0 should serve as useful resource studying drivers phenotypes lie within epitranscriptome layer circuitry, is freely accessible at: www.rnamd.org/rmdisease2.

Язык: Английский

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Omicron Variant of SARS-CoV-2: An Indian Perspective of Vaccination and Management

Vaccines, Год журнала: 2023, Номер 11(1), С. 160 - 160

Опубликована: Янв. 11, 2023

Omicron variants have highly influenced the entire globe. It has a high rate of transmissibility, which makes its management tedious. There are various subtypes omicron, namely BA.1, BA.2, BA.3, BA.4, and BA.5. Currently, one omicron subvariant BF.7 is also immersed in some parts India. Further studies required for better understanding new immersing SARS-CoV-2 omicron. They differ mutation spike proteins, alters their attachment to host receptor hence modifies virulence adaptability. Delta great disastrous influence on world, especially While overcoming it, another mutant catches pace. The Indian population affected by variants. diagnosis system against COVID-19. demanded forcemeat health care system, both qualitatively quantitively, cope with wave. alteration protein, major target vaccines, leads varied immunization subvariants. efficacy vaccines variant was questioned. Every vaccine had different shielding effect variant. hesitancy vaccination prevalent factor India that might contributed outbreak. prevalence monkeypox, tomato flu shared similarities distinct features when compared population. This review emphasizes changes brings it how outrage this dangerous

Язык: Английский

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

Genes, Год журнала: 2023, Номер 14(2), С. 407 - 407

Опубликована: Фев. 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

Язык: Английский

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Characterization of SARS-CoV-2 recombinants and emerging Omicron sublineages

International Journal of Medical Sciences, Год журнала: 2023, Номер 20(1), С. 151 - 162

Опубликована: Янв. 1, 2023

The SARS-CoV-2 Omicron is currently the predominant circulating variant in COVID-19 pandemic. dominating sublineages respond to host immune pressure and develop advantageous mutations or genetic recombination, which result variants that are more contagious better at escaping responses response previous infection vaccination. Meanwhile, multiple recombination events have been reported coinfection cases, majority of resulted from between co-circulating BA.1 (or BA.1.1) Delta BA.2. Here, we review knowledge characterization for population level, provide an update on occurrence newly sublineages, discuss effectiveness novel vaccines/therapeutic drugs against variant.

Язык: Английский

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