SARS-CoV-2 variant biology: immune escape, transmission and fitness

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 18, 2023

In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited major step change its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates transmission relative previous variants and were termed 'variants concern' (VOCs). Designated Alpha, Beta, Gamma, Delta Omicron, VOCs emerged independently from one another, turn each rapidly became dominant, regionally or globally, outcompeting variants. The success VOC previously dominant variant was enabled by altered intrinsic functional properties virus and, various degrees, changes antigenicity conferring ability evade primed immune response. increased fitness associated with is result complex interplay biology context changing immunity due both vaccination prior infection. this Review, we summarize literature on transmissibility variants, role mutations at furin spike cleavage site non-spike proteins, potential importance recombination success, evolution T cells, innate population immunity. shows complicated relationship among antigenicity, virulence, which has unpredictable implications future trajectory disease burden COVID-19.

Language: Английский

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Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution

Nature, Journal Year: 2022, Volume and Issue: unknown

Published: Dec. 19, 2022

Abstract Continuous evolution of Omicron has led to a rapid and simultaneous emergence numerous variants that display growth advantages over BA.5 (ref. 1 ). Despite their divergent evolutionary courses, mutations on receptor-binding domain (RBD) converge several hotspots. The driving force destination such sudden convergent its effect humoral immunity remain unclear. Here we demonstrate these can cause evasion neutralizing antibody drugs convalescent plasma, including those from breakthrough infection, while maintaining sufficient ACE2-binding capability. BQ.1.1.10 (BQ.1.1 + Y144del), BA.4.6.3, XBB CH.1.1 are the most antibody-evasive strains tested. To delineate origin evolution, determined escape mutation profiles neutralization activity monoclonal antibodies isolated individuals who had BA.2 infections 2,3 . Owing immune imprinting, especially infection reduced diversity binding sites increased proportions non-neutralizing clones, which, in turn, focused pressure promoted RBD. Moreover, show RBD could be accurately inferred by deep mutational scanning 4,5 , trends BA.2.75 subvariants well foreseen through constructed pseudovirus mutants. These results suggest current herd vaccine boosters may not efficiently prevent variants.

Language: Английский

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Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations

Nature Methods, Journal Year: 2023, Volume and Issue: 20(4), P. 512 - 522

Published: Feb. 23, 2023

Language: Английский

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Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2

Cell Host & Microbe, Journal Year: 2022, Volume and Issue: 31(1), P. 9 - 17.e3

Published: Nov. 22, 2022

Language: Английский

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Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution

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

Published: Sept. 16, 2022

Abstract Continuous evolution of Omicron has led to a rapid and simultaneous emergence numerous variants that display growth advantages over BA. 5. Despite their divergent evolutionary courses, mutations on receptor-binding domain (RBD) converge several hotspots. The driving force destination such convergent its impact humoral immunity remain unclear. Here, we demonstrate these can cause striking evasion neutralizing antibody (NAb) drugs convalescent plasma, including those from BA.5 breakthrough infection, while maintaining sufficient ACE2 binding capability. BQ.1.1.10, BA.4.6.3, XBB, CH. 1.1 are the most antibody-evasive strain tested, even exceeding SARS-CoV-1 level. To delineate origin evolution, determined escape mutation profiles neutralization activity monoclonal antibodies (mAbs) isolated BA.2 breakthrough-infection convalescents. Importantly, due immune imprinting, especially infection caused significant reductions in epitope diversity NAbs increased proportion non-neutralizing mAbs, which turn concentrated pressure promoted evolution. Moreover, showed RBD could be accurately inferred by integrated deep mutational scanning (DMS) profiles, trends BA.2.75/BA.5 subvariants well-simulated through constructed pseudovirus mutants. Together, our results suggest current herd vaccine boosters may not provide good protection against infection. Broad-spectrum SARS-CoV-2 vaccines NAb development should highly prioritized, mutants help examine effectiveness advance.

Language: Английский

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A multinational Delphi consensus to end the COVID-19 public health threat

Nature, Journal Year: 2022, Volume and Issue: 611(7935), P. 332 - 345

Published: Nov. 3, 2022

Abstract Despite notable scientific and medical advances, broader political, socioeconomic behavioural factors continue to undercut the response COVID-19 pandemic 1,2 . Here we convened, as part of this Delphi study, a diverse, multidisciplinary panel 386 academic, health, non-governmental organization, government other experts in from 112 countries territories recommend specific actions end persistent global threat public health. The developed set 41 consensus statements 57 recommendations governments, health systems, industry key stakeholders across six domains: communication; systems; vaccination; prevention; treatment care; inequities. In wake nearly three years fragmented national responses, it is instructive note that highest-ranked call for adoption whole-of-society whole-of-government approaches 1 , while maintaining proven prevention measures using vaccines-plus approach 2 employs range financial support complement vaccination. Other with at least 99% combined agreement advise governments improve communication, rebuild trust engage communities 3 management responses. findings which have been further endorsed by 184 organizations globally, include points unanimous agreement, well >5% disagreement, provide social policy address inadequacies help bring an end.

Language: Английский

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Effectiveness of mRNA-1273 vaccination against SARS-CoV-2 omicron subvariants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Jan. 12, 2023

Studies have reported reduced natural SARS-CoV-2 infection- and vaccine-induced neutralization against omicron BA.4/BA.5 compared with earlier subvariants. This test-negative case-control study evaluates mRNA-1273 vaccine effectiveness (VE) infection hospitalization The includes 30,809 positive 92,427 negative individuals aged ≥18 years tested during 1/1/2022-6/30/2022. While 3-dose VE BA.1 is high wanes slowly, BA.2, BA.2.12.1, BA.4, BA.5 initially moderate to (61.0%-90.6% 14-30 days post third dose) rapidly. 4-dose BA.4 ranges between 64.3%-75.7%, low (30.8%) fourth dose, disappearing beyond 90 for all BA.1, 97.5%, 82.0%, 72.4%, respectively; 88.5%. Evaluation of the updated bivalent booster warranted.

Language: Английский

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Distinct Neutralizing Antibody Escape of SARS-CoV-2 Omicron Subvariants BQ.1, BQ.1.1, BA.4.6, BF.7 and BA.2.75.2

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

Published: Oct. 20, 2022

Abstract Continued evolution of SARS-CoV-2 has led to the emergence several new Omicron subvariants, including BQ.1, BQ. 1.1, BA.4.6, BF.7 and BA.2.75.2. Here we examine neutralization resistance these as well their ancestral BA.4/5, BA.2.75 D614G variants, against sera from 3-dose vaccinated health care workers, hospitalized BA.1-wave patients, BA.5-wave patients. We found enhanced in all especially BQ.1 BQ.1.1 subvariants driven by a key N460K mutation, lesser extent, R346T K444T mutations, BA.2.75.2 subvariant largely its F486S mutation. The also exhibited fusogenicity S processing dictated Interestingly, saw an enhancement mutation reduction D1199N processing, resulting minimal overall change. Molecular modelling revealed mechanisms receptor-binding non-receptor binding monoclonal antibody-mediated immune evasion R346T, K444T, mutations. Altogether, findings shed light on concerning newly emerging subvariants.

Language: Английский

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Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Dec. 6, 2023

Abstract Omicron BA.2.86 subvariant differs from BA.2 as well recently circulating variants by over 30 mutations in the spike protein alone. Here we report on isolation of live a diagnostic swab collected South Africa which tested for escape neutralizing antibodies and viral replication properties cell culture. We found that does not have significantly more relative to XBB.1.5 immunity elicited either XBB-family infection or residual sera African population. extensive ancestral virus with D614G substitution (B.1 lineage) when neutralized pre-Omicron vaccinated individuals BA.1 infected individuals. show similar dynamics VeroE6-TMPRSS2 H1299-ACE2 lines. also investigate relationship sequences. The closest sequences are samples Southern early 2022. Similarly, many basal were sampled Africa. This suggests potentially evolved this region, unobserved evolution led scale strains SARS-CoV-2.

Language: Английский

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SARS-CoV-2 Omicron variants: burden of disease, impact on vaccine effectiveness and need for variant-adapted vaccines

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

Published: May 23, 2023

The highly transmissible Omicron (B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in late 2021. Initial waves were primarily made up sub-lineages BA.1 and/or BA.2, BA.4, and BA.5 subsequently became dominant mid-2022, several descendants these have since emerged. infections generally caused less disease on average than those by earlier variants concern healthy adult populations, at least, part, due to increased population immunity. Nevertheless, healthcare systems many countries, particularly with low immunity, been overwhelmed unprecedented surges prevalence during waves. Pediatric admissions also higher compared previous concern. All exhibit partial escape from wild-type (Wuhan-Hu 1) spike-based vaccine-elicited neutralizing antibodies, more enhanced immuno-evasive properties emerging over time. Evaluating vaccine effectiveness (VE) against has become challenging a complex background varying coverage, platforms, prior infection rates, hybrid Original messenger RNA booster doses substantially improved VE or BA.2 symptomatic disease. However, protection waned, reductions months after administration. While original CD8 + CD4 T-cell responses cross-recognize sub-lineages, thereby retaining outcomes, variant-adapted vaccines are required expand the breadth B-cell improve durability protection. Variant-adapted rolled out 2022 increase overall antigenically aligned immune mechanisms.

Language: Английский

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