Superimmunity by pan-sarbecovirus nanobodies

Yufei Xiang, Wei Huang, Hejun Liu, Zhe Sang, Sham Nambulli, Jérôme Tubiana, Kevin L. Williams, W. Paul Duprex, Dina Schneidman-Duhovny, Ian A. Wilson, Derek J. Taylor, Yi Shi*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Vaccine boosters and infection can facilitate the development of SARS-CoV-2 antibodies with improved potency and breadth. Here, we observe superimmunity in a camelid extensively immunized with the SARS-CoV-2 receptor-binding domain (RBD). We rapidly isolate a large repertoire of specific ultra-high-affinity nanobodies that bind strongly to all known sarbecovirus clades using integrative proteomics. These pan-sarbecovirus nanobodies (psNbs) are highly effective against SARS-CoV and SARS-CoV-2 variants, including Omicron, with the best median neutralization potency at single-digit nanograms per milliliter. A highly potent, inhalable, and bispecific psNb (PiN-31) is also developed. Structural determinations of 13 psNbs with the SARS-CoV-2 spike or RBD reveal five epitope classes, providing insights into the mechanisms and evolution of their broad activities. The highly evolved psNbs target small, flat, and flexible epitopes that contain over 75% of conserved RBD surface residues. Their potencies are strongly and negatively correlated with the distance of the epitopes from the receptor binding sites.

Original languageAmerican English
Article number111004
JournalCell Reports
Volume39
Issue number13
DOIs
StatePublished - 28 Jun 2022

Bibliographical note

Funding Information:
We thank P.J. Bjorkman (Caltech) for sharing plasmids bearing sarbecovirus RBDs, the UPMC Genome Center for Illumina MiSeq, and Yong Joon Kim for proofreading the manuscript. We thank Wenli Yu, Henry Tien, Xueyong Zhu, Meng Yuan, and Robyn L. Stanfield, from the Wilson lab, for help with insect cell culture, crystal screening, and X-ray data collection. This work was supported by NIH grants R35GM137905 (Y.S.), R01GM133841 (D.J.T.), RM1 GM142002 (D.S.), R01AI163011 (Y.S. D.S. and P.W.D.), RM1GM142002 (D.J.T.), R01CA240993 (D.J.T.), and R01 CA240993 (D.S.); and the Bill and Melinda Gates Foundation INV-004923 (I.A.W.). A portion of this research was supported by NIH grant U24GM129547 and performed at the PNCC at Oregon Health & Science University and accessed through the Environmental Molecular Sciences Laboratory (grid.436923.9), a US Department of Energy Office of Science User Facility sponsored by the Office of Biological and Environmental Research, ISF 1466/18, and the Israeli Ministry of Science and Technology (D.S.), the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, and from the Human Frontier Science Program (cross-disciplinary postdoctoral fellowship LT001058/2019-C) (J.T.). This research used resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility, operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357. Extraordinary facility operations were supported in part by the DOE Office of Science through the National Virtual Biotechnology Laboratory, a consortium of DOE national laboratories focused on the response to COVID-19, with funding provided by the Coronavirus CARES Act. Y.S. conceived the study. Y.X. identified and characterized Nbs. Z.S. developed scripts and analyzed structures. W.H. and D.J.T. solved cryo-EM structures. H.L. and I.A.W. determined and analyzed X-ray crystallographic structures. J.T. and D.S. analyzed viral antigenicity. S.N. and P.W.D. performed the PRNT assay. Y.S. and Y.X. drafted the manuscript with substantial input from I.A.W. W.H. Z.S. D.S. H.L. and D.J.T. All authors reviewed the manuscript. We thank D.S. Reed (University of Pittsburgh) and N.A. Crossland (Boston University) for technical assistance. Y.S. and Y.X. are co-inventors on a provisional patent filed by the University of Pittsburgh covering the Nbs herein described.

Funding Information:
We thank P.J. Bjorkman (Caltech) for sharing plasmids bearing sarbecovirus RBDs, the UPMC Genome Center for Illumina MiSeq, and Yong Joon Kim for proofreading the manuscript. We thank Wenli Yu, Henry Tien, Xueyong Zhu, Meng Yuan, and Robyn L. Stanfield, from the Wilson lab, for help with insect cell culture, crystal screening, and X-ray data collection. This work was supported by NIH grants R35GM137905 (Y.S.), R01GM133841 (D.J.T.), RM1 GM142002 (D.S.), R01AI163011 (Y.S., D.S., and P.W.D.), RM1GM142002 (D.J.T.), R01CA240993 (D.J.T.), and R01 CA240993 (D.S.); and the Bill and Melinda Gates Foundation INV-004923 (I.A.W.). A portion of this research was supported by NIH grant U24GM129547 and performed at the PNCC at Oregon Health & Science University and accessed through the Environmental Molecular Sciences Laboratory ( grid.436923.9 ), a US Department of Energy Office of Science User Facility sponsored by the Office of Biological and Environmental Research, ISF 1466/18 , and the Israeli Ministry of Science and Technology (D.S.), the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, and from the Human Frontier Science Program (cross-disciplinary postdoctoral fellowship LT001058/2019-C) (J.T.). This research used resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility, operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357. Extraordinary facility operations were supported in part by the DOE Office of Science through the National Virtual Biotechnology Laboratory, a consortium of DOE national laboratories focused on the response to COVID-19, with funding provided by the Coronavirus CARES Act .

Publisher Copyright:
© 2022 The Author(s)

Keywords

  • CP: Immunology
  • SARS-CoV-2
  • VH antibody
  • broadly neutralizing nanobody
  • inhalable bispecific nanobody PiN-31
  • pan-sarbecovirus neutralization
  • super immunity

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