The evolution of SARS-CoV-2

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 21(6), P. 361 - 379

Published: April 5, 2023

Language: Английский

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Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants

Cell, Journal Year: 2022, Volume and Issue: 186(2), P. 279 - 286.e8

Published: Dec. 14, 2022

The BQ and XBB subvariants of SARS-CoV-2 Omicron are now rapidly expanding, possibly due to altered antibody evasion properties deriving from their additional spike mutations. Here, we report that neutralization BQ.1, BQ.1.1, XBB, XBB.1 by sera vaccinees infected persons was markedly impaired, including individuals boosted with a WA1/BA.5 bivalent mRNA vaccine. Titers against were lower 13- 81-fold 66- 155-fold, respectively, far beyond what had been observed date. Monoclonal antibodies capable neutralizing the original variant largely inactive these new subvariants, responsible individual mutations identified. These found have similar ACE2-binding affinities as predecessors. Together, our findings indicate present serious threats current COVID-19 vaccines, render all authorized antibodies, may gained dominance in population because advantage evading antibodies.

Language: Английский

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Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum

Cell, Journal Year: 2022, Volume and Issue: 185(14), P. 2422 - 2433.e13

Published: June 9, 2022

The Omicron lineage of SARS-CoV-2, which was first described in November 2021, spread rapidly to become globally dominant and has split into a number sublineages. BA.1 dominated the initial wave but been replaced by BA.2 many countries. Recent sequencing from South Africa's Gauteng region uncovered two new sublineages, BA.4 BA.5, are taking over locally, driving wave. BA.5 contain identical spike sequences, although closely related BA.2, they further mutations receptor-binding domain their spikes. Here, we study neutralization BA.4/5 using range vaccine naturally immune serum panels monoclonal antibodies. shows reduced individuals vaccinated with triple doses AstraZeneca or Pfizer compared BA.2. Furthermore, breakthrough infections, there are, likewise, significant reductions BA.4/5, raising possibility repeat infections.

Language: Английский

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Fast evolution of SARS-CoV-2 BA.2.86 to JN.1 under heavy immune pressure

The Lancet Infectious Diseases, Journal Year: 2023, Volume and Issue: 24(2), P. e70 - e72

Published: Dec. 15, 2023

The SARS-CoV-2 saltation variant BA.2.86, which was quickly designated as a under monitoring after its emergence, has garnered global attention. Although BA.2.86 did not show substantial humoral immune escape and growth advantage compared with current dominant variants, such EG.5.1 HK.3, it showed remarkably high ACE2 binding affinity.1Yang S Yu Y Jian F et al.Antigenicity infectivity characterisation of BA.2.86.Lancet Infect Dis. 2023; 23: e457-e459Summary Full Text PDF PubMed Scopus (36) Google Scholar, 2Wannigama DL Amarasiri M Phattharapornjaroen P al.Tracing the new in community through wastewater surveillance Bangkok, Thailand.Lancet e464-e466Summary (11) 3Wang Q Guo Liu L receptor affinity spike.Nature. (published online Oct 23.)https://doi.org/10.1038/s41586-023-06750-wGoogle 4Uriu K Ito J Kosugi al.Transmissibility, infectivity, evasion variant.Lancet e460-e461Summary (29) 5Sheward DJ Yang Westerberg al.Sensitivity to prevailing neutralising antibody responses.Lancet e462-e463Summary (22) Scholar This increased affinity, coupled distinct antigenicity, could enable accumulate immune-evasive mutations during low-level populational transmission, akin previous evolution from BA.2.75 CH.1.1 XBB.6Cao Song W Wang al.Characterization enhanced Omicron BA.2.75.Cell Host Microbe. 2022; 30: 1527-1539Summary (74) 7Cao al.Imprinted immunity induces convergent RBD domain evolution.Nature. 614: 521-529PubMed 8Yue C al.ACE2 transmissibility XBB.1.5.Lancet 278-280Summary (108) 9Wang Li Z al.Evolving sublineage SARS-CoV-2.iScience. 26108254 Summary (3) With just one additional mutation (L455S) predecessor JN.1 rapidly became predominant France (figure A; appendix 1 p 12), surpassing both so-called FLip (L455F+F456L) strains. A thorough investigation into capability JN.1, particularly given few mutations, is imperative.FigureJN.1 shows profound decreased affinityShow full caption(A) Sequence percentages prevalent variants since August, 2023, including BA.2·86 (the original subvariants, except JN.1), HV.1, FLip+A475V, HK.3. advantages relative HK.3 past two months these strains are denoted legend within parentheses. Data collected covSPECTRUM. (B) 50% titer (NT50) convalescent plasma against measured individuals who received three CoronaVac doses had breakthrough infection BA.5 or BF.7 followed by XBB reinfection (n=54). Labels for geometric mean titers (GMT) located above each group, fold changes statistical significances indicated GMT labels. Below dashed line labels specifying numbers negative samples related limit detection (NT50=20). Two-tailed Wilcoxon signed-rank tests paired were used. *p<0·05, **p<0·01, ***p<0·001, ****p<0·0001. (C) human (angiotensin-converting enzyme 2) affinities (XBB.1.5+L455F+F456L), HV.1 (XBB.1.5+L452R+F456L), EG.5 (XBB.1.5+F456L), JD.1.1 (XBB.1.5+L455F+F456L+A475V), (BA.2.86+L455S) determined surface plasmon resonance sensorgrams. KD values (nM) displayed bars, all replicates represented points. (D) Class Nabs resistance pseudovirus XBB.1.5, EG.5, JD.1.1, IC50 (n=8). when D614G other labelled. (μg per mL) approved candidate monoclonal drugs targeting spike assessed pseudovirus. IC50=50% inhibitory concentration; KD=equilibrium dissociation constant; NAbs=neutralising antibodies; nM=nanomolarView Large Image Figure ViewerDownload Hi-res image Download (PPT) (A) nM=nanomolar We first study using pseudovirus-based neutralisation assays recovering infection. These individuals, having inactivated vaccines, subsequently contracted (XBB subvariants S486P substitution) infections. Our included cohorts, 27 participants post-vaccination infections another patients reinfected (appendix 2). significantly B). finding evidenced 2·1-fold decrease among post-BA.5 1·1-fold NT50 B; 13). Additionally, JN.1's surpassed that competitive (EG.5+L452R) (FLip+A475V). also lower their parental acquiring L452R A475V respectively, explaining advantages. As L455 on interface between 14),10Nutalai R Zhou D Tuekprakhon al.Potent cross-reactive antibodies following vaccinees.Cell. 185 (31.e18): 2116Summary (76) L455S change JN.1. By resonance, we found notable reduction domain, indicating capabilities come at expense reduced C). carried (XBB.1.5+FLip+A475V) resulted enhancing (XBB.1.5+FLip). However, affect affinity. Considering predominantly epitope antibodies, earlier research, our further examined response eight XBB.1·5-neutralising class antibodies.7Cao Pseudovirus addition ability evade D). effectively compensated BA.2.86's susceptibility this group Similarly, FLip+A475V (JD.1.1) (HK.3), offering insights trend variants. In terms therapeutic SA55 retained efficacy E). Together, findings suggest greatly compensation weakness antibodies. summary, inheriting antigenic diversity acquisition L455S, achieved extensive across 1, 2, 3 antibodies,1Yang higher resistant like JD.1·1, binding. evolutionary pattern, similar transition XBB,2Wannigama highlights importance closely BA.2.75, despite unremarkable capabilities. Such survive transmit low levels difference would allow them target populations have potential highly cost publication been corrected. corrected version appeared thelancet.com/infection January 3, 2024 YC inventor provisional patent applications BD series includes BD55–5514 (SA55). founder Singlomics Biopharmaceuticals. All authors declare no competing interests. .pdf (3.2 MB) Help pdf files Supplementary .xls (.02 xls 2 Correction Lancet Dis published Dec 15. https://doi.org/10.1016/S1473-3099(23)00744-2Yang S, Y, Xu al. Fast heavy pressure. https://doi.org/10.1016/S1473-3099(23)00744-2—In Correspondence, author's name should printed Yunlong Cao. corresponding email address read [email protected]. corrections made Jan 2024. Full-Text

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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Omicron BA.1 breakthrough infection drives cross-variant neutralization and memory B cell formation against conserved epitopes

Science Immunology, Journal Year: 2022, Volume and Issue: 7(75)

Published: June 2, 2022

Omicron is the evolutionarily most distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VOC) to date. We report that BA.1 breakthrough infection in BNT162b2-vaccinated individuals resulted strong neutralizing activity against BA.1, BA.2, and previous SARS-CoV-2 VOCs but not sublineages BA.4 BA.5. induced a robust recall response, primarily expanding memory B (B

Language: Английский

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Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75

Cell Host & Microbe, Journal Year: 2022, Volume and Issue: 30(11), P. 1527 - 1539.e5

Published: Oct. 4, 2022

Recently emerged SARS-CoV-2 Omicron subvariant, BA.2.75, displayed a growth advantage over circulating BA.2.38, BA.2.76, and BA.5 in India. However, the underlying mechanisms for enhanced infectivity, especially compared with BA.5, remain unclear. Here, we show that BA.2.75 exhibits substantially higher affinity host receptor angiotensin-converting enzyme 2 (ACE2) than other variants. Structural analyses of spike shows its decreased thermostability increased frequency binding domain (RBD) "up" conformation under acidic conditions, suggesting low-pH-endosomal cell entry. Relative to BA.4/BA.5, reduced evasion humoral immunity from BA.1/BA.2 breakthrough-infection convalescent plasma but greater Delta plasma. also weaker neutralization against mainly due BA.2.75's distinct neutralizing antibody (NAb) escape pattern. Antibody therapeutics Evusheld Bebtelovimab effective BA.2.75. These results suggest may prevail after receptor-binding capability could support further immune-evasive mutations.

Language: Английский

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Antigenicity and receptor affinity of SARS-CoV-2 BA.2.86 spike

Nature, Journal Year: 2023, Volume and Issue: 624(7992), P. 639 - 644

Published: Oct. 23, 2023

Language: Английский

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The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity

Journal of Medical Virology, Journal Year: 2022, Volume and Issue: 95(1)

Published: Sept. 13, 2022

As of November 2021, several SARS-CoV-2 variants appeared and became dominant epidemic strains in many countries, including five concern (VOCs) Alpha, Beta, Gamma, Delta, Omicron defined by the World Health Organization during COVID-19 pandemic. August 2022, is classified into main lineages, BA.1, BA.2, BA.3, BA.4, BA.5 some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) (https://www.gisaid.org/). Compared to previous VOCs (Alpha, Delta), all lineages have most highly mutations spike protein, with 50 accumulated throughout genome. Early data indicated that BA.2 sublineage had higher infectivity more immune escape than early wild-type (WT) strain, VOCs, BA.1. Recently, global surveillance suggest a transmissibility BA.4/BA.5 BA.1.1 becoming strain countries globally.

Language: Английский

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What Omicron’s BA.4 and BA.5 variants mean for the pandemic

Nature, Journal Year: 2022, Volume and Issue: 606(7916), P. 848 - 849

Published: June 23, 2022

Language: Английский

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