Virological characteristics of the SARS-CoV-2 XBB.1.5 variant

Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the F486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determined the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. The intrinsic pathogenicity of XBB.1.5 in hamsters is lower than that of XBB.1. Importantly, we found that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC expression. In vivo experiments using recombinant viruses revealed that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, these data suggest that the mutations in ORF8 and S could enhance spreading of XBB.1.5 in humans.

[1]  A. Farina,et al.  ACE2 mimetic antibody potently neutralizes all SARS-CoV-2 variants and fully protects in XBB.1.5 challenged monkeys , 2023, bioRxiv.

[2]  Y. Kawaoka,et al.  Transmission and re-infection of Omicron variant XBB.1.5 in hamsters , 2023, EBioMedicine.

[3]  J. Zahradník,et al.  Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants , 2023, Nature communications.

[4]  M. Diamond,et al.  A bivalent ChAd nasal vaccine protects against SARS-CoV-2 BQ.1.1 and XBB.1.5 infection and disease in mice and hamsters , 2023, bioRxiv.

[5]  Rui Qiao,et al.  Neutralization of SARS-CoV-2 BQ.1.1 and XBB.1.5 by Breakthrough Infection Sera from Previous and Current Waves in China , 2023, bioRxiv.

[6]  T. Maruyama,et al.  Rapid engineering of SARS-CoV-2 therapeutic antibodies to increase breadth of neutralization including XBB.1.5 and BQ.1.1 , 2023, bioRxiv.

[7]  Bette Korber,et al.  Waning Immunity Against XBB.1.5 Following Bivalent mRNA Boosters , 2023, bioRxiv.

[8]  P. Offit Bivalent Covid-19 Vaccines - A Cautionary Tale. , 2023, The New England journal of medicine.

[9]  J. Zahradník,et al.  Enhanced transmissibility, infectivity, and immune resistance of the SARS-CoV-2 omicron XBB.1.5 variant , 2023, bioRxiv.

[10]  J. Zahradník,et al.  Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant , 2022, bioRxiv.

[11]  H. Date,et al.  SARS-CoV-2 disrupts respiratory vascular barriers by suppressing Claudin-5 expression , 2022, Science advances.

[12]  J. Zahradník,et al.  Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5 , 2022, Cell.

[13]  J. Zahradník,et al.  Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 , 2022, bioRxiv.

[14]  Y. Ohba,et al.  Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5 , 2022, bioRxiv.

[15]  K. Ohmura,et al.  SARS-CoV-2 ORF8 is a viral cytokine regulating immune responses , 2022, bioRxiv.

[16]  Takeshi Noda,et al.  Cell response analysis in SARS-CoV-2 infected bronchial organoids , 2022, Communications Biology.

[17]  A. Kaneda,et al.  Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant , 2022, Nature.

[18]  Frances E. Muldoon,et al.  Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity , 2022, Nature.

[19]  S. Maurer-Stroh,et al.  GISAID’s Role in Pandemic Response , 2021, China CDC weekly.

[20]  Y. Kawaoka,et al.  Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation , 2021, Nature.

[21]  A. Kaneda,et al.  Neutralization of the SARS-CoV-2 Mu Variant by Convalescent and Vaccine Serum , 2021, The New England journal of medicine.

[22]  S. Scheres,et al.  New tools for automated cryo-EM single-particle analysis in RELION-4.0 , 2021, bioRxiv.

[23]  Ravindra K. Gupta,et al.  SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion , 2021, The Journal of infectious diseases.

[24]  J. Zahradník,et al.  SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity , 2021, Cell Host & Microbe.

[25]  J. Liu,et al.  The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating MHC-Ι , 2021, Proceedings of the National Academy of Sciences.

[26]  S. Kishigami,et al.  SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity , 2021, Nature Communications.

[27]  W. Kamitani,et al.  Establishment of a reverse genetics system for SARS-CoV-2 using circular polymerase extension reaction , 2020, bioRxiv.

[28]  G. Ippolito,et al.  Structure-based design of prefusion-stabilized SARS-CoV-2 spikes , 2020, Science.

[29]  Niema Moshiri,et al.  ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes , 2020, bioRxiv.

[30]  Fumihiro Kato,et al.  Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells , 2020, Proceedings of the National Academy of Sciences.

[31]  Guangchuang Yu,et al.  Using ggtree to Visualize Data on Tree‐Like Structures , 2020, Current protocols in bioinformatics.

[32]  Olga Chernomor,et al.  IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era , 2019, bioRxiv.

[33]  Emmanuel Paradis,et al.  ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R , 2018, Bioinform..

[34]  Conrad C. Huang,et al.  UCSF ChimeraX: Meeting modern challenges in visualization and analysis , 2018, Protein science : a publication of the Protein Society.

[35]  Yutaka Suzuki,et al.  Long-term expansion of alveolar stem cells derived from human iPS cells in organoids , 2017, Nature Methods.

[36]  Thomas K. F. Wong,et al.  ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates , 2017, Nature Methods.

[37]  David J. Fleet,et al.  cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination , 2017, Nature Methods.

[38]  S. Muro,et al.  Directed Induction of Functional Multi-ciliated Cells in Proximal Airway Epithelial Spheroids from Human Pluripotent Stem Cells , 2015, Stem cell reports.

[39]  N. Grigorieff,et al.  CTFFIND4: Fast and accurate defocus estimation from electron micrographs , 2015, bioRxiv.

[40]  S. Ogawa,et al.  Generation of Alveolar Epithelial Spheroids via Isolated Progenitor Cells from Human Pluripotent Stem Cells , 2014, Stem cell reports.

[41]  Steven P. Millard,et al.  EnvStats: An R Package for Environmental Statistics , 2013 .

[42]  N. Kondo,et al.  Monitoring Viral‐Mediated Membrane Fusion Using Fluorescent Reporter Methods , 2011, Current protocols in cell biology.

[43]  Y. Yanagi,et al.  Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM , 2011, Nature Structural &Molecular Biology.

[44]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[45]  H. Niwa,et al.  Efficient selection for high-expression transfectants with a novel eukaryotic vector. , 1991, Gene.

[46]  Christopher J. Williams,et al.  MolProbity: More and better reference data for improved all‐atom structure validation , 2018, Protein science : a publication of the Protein Society.

[47]  B. Berger,et al.  Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. , 2018, Annual International Conference on Research in Computational Molecular Biology.

[48]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .