A recombinant spike‐XBB.1.5 protein vaccine induces broad‐spectrum immune responses against XBB.1.5‐included Omicron variants of SARS‐CoV‐2 DOI Creative Commons
Cai He, Aqu Alu, Lei Hong

et al.

MedComm, Journal Year: 2023, Volume and Issue: 4(3)

Published: April 26, 2023

The XBB.1.5 subvariant has drawn great attention owing to its exceptionality in immune evasion and transmissibility. Therefore, it is essential develop a universally protective coronavirus disease 2019 vaccine against various strains of Omicron, especially XBB.1.5. In this study, we evaluated compared the responses induced by six different spike protein vaccines targeting ancestral or Omicron severe acute respiratory syndrome 2 (SARS-CoV-2) mice. We found that spike-wild-type immunization high titers neutralizing antibodies (NAbs) SARS-CoV-2. However, activity subvariants decreased sharply as number mutations receptor-binding domain (RBD) these viruses increased. Spike-BA.5, spike-BF.7, spike-BQ.1.1 strong NAbs BA.5, BF.7, BQ.1, BQ.1.1 but were poor protecting XBB XBB.1.5, which have more RBD mutations. sharp contrast, spike-XBB.1.5 vaccination can activate broadly other common Omicron. By performing correlation analysis, negatively correlated with subvariants. Vaccines effectively overcome resistance caused accumulation mutations, making most promising candidate universal variants.

Language: Английский

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants DOI Creative Commons
Tomokazu Tamura, Jumpei Ito,

Keiya Uriu

et al.

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

Published: May 16, 2023

In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that emerged through recombination of two cocirculating BA.2 lineages, BJ.1 BM.1.1.1 (a progeny BA.2.75), during summer 2022. XBB.1 variant most profoundly resistant to BA.2/5 breakthrough infection sera date more fusogenic than BA.2.75. The breakpoint located in receptor-binding domain spike, each region recombinant spike confers immune evasion increases fusogenicity. We further provide structural basis for interaction between human ACE2. Finally, intrinsic pathogenicity male hamsters comparable or even lower multiscale investigation provides evidence suggesting first observed increase its fitness rather substitutions.

Language: Английский

Citations

261
Enhanced transmissibility, infectivity, and immune resistance of the SARS-CoV-2 omicron XBB.1.5 variant DOI Open Access

Keiya Uriu,

Jumpei Ito, Jiří Zahradník

et al.

The Lancet Infectious Diseases, Journal Year: 2023, Volume and Issue: 23(3), P. 280 - 281

Published: Feb. 1, 2023

Language: Английский

Citations

123
The rapid rise of SARS‐CoV‐2 Omicron subvariants with immune evasion properties: XBB.1.5 and BQ.1.1 subvariants DOI Creative Commons
Danyi Ao, Xuemei He, Weiqi Hong

et al.

MedComm, Journal Year: 2023, Volume and Issue: 4(2)

Published: March 15, 2023

As the fifth variant of concern SARS-CoV-2 virus, Omicron (B.1.1.529) has quickly become dominant type among previous circulating variants worldwide. During wave, several subvariants have emerged, with some exhibiting greater infectivity and immune evasion, accounting for their fast spread across many countries. Recently, two subvariants, BQ.1 XBB lineages, including BQ.1.1, XBB.1, XBB.1.5, a global public health issue given ability to escape from therapeutic monoclonal antibodies herd immunity induced by prior coronavirus disease 2019 (COVID-19) vaccines, boosters, infection. In this respect, which been established harbor rare mutation F486P, demonstrates superior transmissibility compared other emerged as strain in This review provides comprehensive overview epidemiological features, spike mutations, evasion lineages. We expounded on mechanisms underlying mutations neutralizing vaccinated or convalescent COVID-19 individuals (mAbs) proposed strategies prevention against sublineages.

Language: Английский

Citations

108
SARS-CoV-2 BA.2.86 enters lung cells and evades neutralizing antibodies with high efficiency DOI Creative Commons
Lu Zhang,

Amy Kempf,

Inga Nehlmeier

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(3), P. 596 - 608.e17

Published: Jan. 8, 2024

Language: Английский

Citations

78
Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron Lineages — United States, January 2022–May 2023 DOI Open Access
C. Kevin,

Philip Shirk,

Anastasia S. Lambrou

et al.

MMWR Morbidity and Mortality Weekly Report, Journal Year: 2023, Volume and Issue: 72(24), P. 651 - 656

Published: June 15, 2023

CDC has used national genomic surveillance since December 2020 to monitor SARS-CoV-2 variants that have emerged throughout the COVID-19 pandemic, including Omicron variant. This report summarizes U.S. trends in variant proportions from during January 2022-May 2023. During this period, remained predominant, with various descendant lineages reaching predominance (>50% prevalence). first half of 2022, BA.1.1 reached by week ending 8, followed BA.2 (March 26), BA.2.12.1 (May 14), and BA.5 (July 2); each coincided surges cases. The latter 2022 was characterized circulation sublineages BA.2, BA.4, (e.g., BQ.1 BQ.1.1), some which independently acquired similar spike protein substitutions associated immune evasion. By end 2023, XBB.1.5 became predominant. As May 13, most common circulating were (61.5%), XBB.1.9.1 (10.0%), XBB.1.16 (9.4%); XBB.1.16.1 (2.4%), containing K478R substitution, XBB.2.3 (3.2%), P521S had fastest doubling times at point. Analytic methods for estimating been updated as availability sequencing specimens declined. continued evolution highlights importance emerging help guide vaccine development use therapeutics.

Language: Английский

Citations

69
Virological characteristics of the SARS-CoV-2 BA.2.86 variant DOI Creative Commons
Tomokazu Tamura,

Keita Mizuma,

Hesham Nasser

et al.

Cell Host & Microbe, Journal Year: 2024, Volume and Issue: 32(2), P. 170 - 180.e12

Published: Jan. 26, 2024

In late 2023, several SARS-CoV-2 XBB descendants, notably EG.5.1, were predominant worldwide. However, a distinct lineage, the BA.2.86 variant, also emerged. is phylogenetically from other Omicron sublineages, accumulating over 30 amino acid mutations in its spike protein. Here, we examined virological characteristics of variant. Our epidemic dynamics modeling suggested that relative reproduction number significantly higher than EG.5.1. Additionally, four clinically available antivirals effective against BA.2.86. Although fusogenicity similar to parental BA.2 spike, intrinsic pathogenicity hamsters was lower BA.2. Since growth kinetics are those both vitro and vivo, attenuated likely due decreased replication capacity. These findings uncover features BA.2.86, providing insights for control treatment.

Language: Английский

Citations

61
Antiviral efficacy of the SARS-CoV-2 XBB breakthrough infection sera against omicron subvariants including EG.5 DOI Open Access

Yu Kaku,

Yusuke Kosugi,

Keiya Uriu

et al.

The Lancet Infectious Diseases, Journal Year: 2023, Volume and Issue: 23(10), P. e395 - e396

Published: Sept. 11, 2023

Language: Английский

Citations

52
Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant DOI Creative Commons
Tomokazu Tamura, Takashi Irie, Sayaka Deguchi

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 8, 2024

Abstract Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence XBB.1.5, a new Variant Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring S486P spike (S) mutation, subsequent to acquisition nonsense mutation ORF8. Neutralization assays showed similar abilities immune escape between and XBB.1. We determine structural basis for interaction human ACE2 S protein showing overall structures proteins XBB.1.5. provide intrinsic pathogenicity hamsters. Importantly, we find ORF8 impairment MHC suppression. In vivo experiments using recombinant viruses reveal mutations are involved with reduced virulence Together, our study identifies two viral functions defined difference

Language: Английский

Citations

49
Evolution of enhanced innate immune suppression by SARS-CoV-2 Omicron subvariants DOI Creative Commons
Ann‐Kathrin Reuschl, Lucy Thorne, Matthew Whelan

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(2), P. 451 - 463

Published: Jan. 16, 2024

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) human adaptation resulted in distinct lineages with enhanced transmissibility called variants of concern (VOCs). Omicron is the first VOC to evolve globally dominant subvariants. Here we compared their replication cell lines and primary airway cultures measured host responses infection. We discovered that subvariants BA.4 BA.5 have improved suppression innate immunity when earlier BA.1 BA.2. Similarly, more recent (BA.2.75 XBB lineages) also triggered reduced immune activation. This correlated increased expression viral antagonists Orf6 nucleocapsid, reminiscent VOCs Alpha Delta. Increased levels suppressed infection by decreasing IRF3 STAT1 signalling transcription factor phosphorylation nuclear translocation. Our data suggest convergent evolution antagonist a common pathway link subvariant dominance evasion.

Language: Английский

Citations

44
Characteristics of the SARS-CoV-2 omicron HK.3 variant harbouring the FLip substitution DOI Creative Commons

Yusuke Kosugi,

Arnon Plianchaisuk, Olivia Putri

et al.

The Lancet Microbe, Journal Year: 2024, Volume and Issue: 5(4), P. e313 - e313

Published: Jan. 11, 2024

As of November, 2023, SARS-CoV-2 XBB variants, including EG.5.1 (XBB.1.9.2.5.1), the currently predominant lineage, have been circulating worldwide, according to Nextstrain datasets. The strain has a characteristic amino acid substitution in spike protein (S; S:F456L), which allows escape humoral immunity (appendix p 16).1Kaku Y Kosugi Uriu K et al.Antiviral efficacy breakthrough infection sera against omicron subvariants EG.5.Lancet Infect Dis. 2023; 23: e395-e396Summary Full Text PDF PubMed Google Scholar further evolved, and its descendant lineage harbouring S:L455F (ie, EG.5.1+S:L455F) variant emerged named HK.3 (XBB.1.9.2.5.1.1.3). was initially discovered east Asia is rapidly spreading worldwide. Notably, bearing both S:F456L substitutions, HK.3, are defined as FLip variants. These JG.3 (XBB.1.9.2.5.1.3.3), JF.1 (XBB.1.16.6.1), GK.3 (XBB.1.5.70.3) concurrently, suggesting that acquisition these two substitutions confers growth advantage human population.2Ito J Suzuki R al.Convergent evolution leading emergence BQ.1.1 variant.Nat Commun. 14: 2671Crossref Scopus (19) Scholar,3Bloom JD Neher RA Fitness effects mutations proteins.Virus Evol. 9vead055Crossref (2) We investigated virological properties representative estimated relative effective reproduction number (Re) on basis genome surveillance data obtained from 13 countries reporting substantial presence with Bayesian hierarchical multinomial logistic regression model pp 9–14, 16).4Yamasoba D Kimura I Nasser H al.Virological characteristics BA.2 spike.Cell. 2022; 185: 2103-2115.e19Summary (149) global mean Re for 1·29 times higher than XBB.1.5 1·12 EG.5.1, might soon become Oct 15, outcompeted such Australia, China, South Korea, Singapore 16). Next, identify whether enhanced infectivity contributes Re, we constructed lentivirus-based pseudoviruses carrying S proteins XBB.1.5, an derivative, XBB.1.5+L455F. Although significantly increased (identical similar difference effect between be attributed epistatic due structures EG.5.1. results suggest not owing caused by S:L455F. then performed neutralisation assay using serum samples (XBB.1.5 [n=20], XBB.1.9 [n=15], XBB.1.16 or [n=18]) address evades antiviral response induced 50% titre (NT50) all tested XBB.1.5+S:L455F lower observed parental NT50 (1·6 times, p=0·0003) Thus, partly immune evasion elicited XBB, ancestor. key mutation this evasion. JI received consulting fees honoraria lectures Takeda Pharmaceutical. KSat Moderna Japan Pharmaceutical Gilead Sciences, Japan, Shionogi & Co. All other authors declare no competing interests. YKo, AP, OP contributed equally. This work supported part Agency Medical Research Development (AMED) Strategic Center Biomedical Advanced Vaccine Preparedness Response (SCARDA) Initiative World-leading Centers UTOPIA (JP223fa627001, KSat), AMED SCARDA Programme R&D New Generation Modality Application (JP223fa727002, KSat); Emerging Re-emerging Infectious Diseases (JP22fk0108146, KSat; JP21fk0108494, G2P-Japan Consortium JP21fk0108425, JP21fk0108432, JP22fk0108511, JP22fk0108516, JP22fk0108506, HIV/AIDS (JP22fk0410039, JST PRESTO (JPMJPR22R1, JI); CREST (JPMJCR20H4, JSPS KAKENHI Grant-in-Aid Early-Career Scientists (23K14526, Core-to-Core Program (A. Networks) (JPJSCCA20190008, Fellow DC2 (22J11578, KU); DC1 (23KJ0710, YKo); Tokyo Biochemical Foundation (to Mitsubishi KSat). Members listed appendix (p 18). Download .pdf (.63 MB) Help pdf files Supplementary

Language: Английский

Citations

34