Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants.
Animals
Antibodies, Neutralizing
/ chemistry
CRISPR-Cas Systems
Camelids, New World
/ genetics
Female
Gene Editing
Humans
Male
Mice
Mice, Inbred C57BL
Models, Molecular
Mutation
Neutralization Tests
SARS-CoV-2
/ chemistry
Single-Domain Antibodies
/ chemistry
Somatic Hypermutation, Immunoglobulin
/ genetics
Spike Glycoprotein, Coronavirus
/ chemistry
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
07 2021
07 2021
Historique:
received:
04
03
2021
accepted:
27
05
2021
pubmed:
8
6
2021
medline:
10
7
2021
entrez:
7
6
2021
Statut:
ppublish
Résumé
Since the start of the COVID-19 pandemic, SARS-CoV-2 has caused millions of deaths worldwide. Although a number of vaccines have been deployed, the continual evolution of the receptor-binding domain (RBD) of the virus has challenged their efficacy. In particular, the emerging variants B.1.1.7, B.1.351 and P.1 (first detected in the UK, South Africa and Brazil, respectively) have compromised the efficacy of sera from patients who have recovered from COVID-19 and immunotherapies that have received emergency use authorization
Identifiants
pubmed: 34098567
doi: 10.1038/s41586-021-03676-z
pii: 10.1038/s41586-021-03676-z
pmc: PMC8260353
doi:
Substances chimiques
Antibodies, Neutralizing
0
Single-Domain Antibodies
0
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
278-282Subventions
Organisme : CCR NIH HHS
ID : HHSN261200800001C
Pays : United States
Organisme : NCI NIH HHS
ID : HHSN261200800001E
Pays : United States
Commentaires et corrections
Type : UpdateOf
Type : CommentIn
Références
Wang, Z. et al. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. Nature 592, 616–622 (2021).
doi: 10.1038/s41586-021-03324-6
pubmed: 33567448
pmcid: 8503938
Wang, P. et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature 593, 130–135 (2021).
doi: 10.1038/s41586-021-03398-2
pubmed: 33684923
Wu, K. et al. mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants. Preprint at https://doi.org/10.1101/2021.01.25.427948 (2021).
Muyldermans, S. Nanobodies: natural single-domain antibodies. Annu. Rev. Biochem. 82, 775–797 (2013).
doi: 10.1146/annurev-biochem-063011-092449
pubmed: 23495938
Muyldermans, S. Applications of nanobodies. Annu. Rev. Anim. Biosci. 9, 401–421 (2021).
doi: 10.1146/annurev-animal-021419-083831
pubmed: 33233943
Scully, M. et al. Caplacizumab treatment for acquired thrombotic thrombocytopenic purpura. N. Engl. J. Med. 380, 335–346 (2019).
doi: 10.1056/NEJMoa1806311
pubmed: 30625070
Hussen, J. & Schuberth, H. J. Recent advances in camel immunology. Front. Immunol. 11, 614150 (2021).
doi: 10.3389/fimmu.2020.614150
pubmed: 33569060
pmcid: 7868527
Kong, R. et al. Antibody lineages with vaccine-induced antigen-binding hotspots develop broad HIV neutralization. Cell 178, 567–584 (2019).
doi: 10.1016/j.cell.2019.06.030
pubmed: 31348886
pmcid: 6755680
Pham, P., Bransteitter, R., Petruska, J. & Goodman, M. F. Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature 424, 103–107 (2003).
doi: 10.1038/nature01760
pubmed: 12819663
Hsieh, C. L. et al. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 369, 1501–1505 (2020).
doi: 10.1126/science.abd0826
pubmed: 32703906
Robbiani, D. F. et al. Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature 584, 437–442 (2020).
doi: 10.1038/s41586-020-2456-9
pubmed: 32555388
pmcid: 7442695
Schoof, M. et al. An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Science 370, 1473–1479 (2020).
pubmed: 33154106
pmcid: 7857409
Xiang, Y. et al. Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2. Science 370, 1479–1484 (2020).
pubmed: 33154108
pmcid: 7857400
Saelens, X. & Schepens, B. Single-domain antibodies make a difference. Science 371, 681–682 (2021).
doi: 10.1126/science.abg2294
pubmed: 33574203
Kupferschmidt, K. Fast-spreading U.K. virus variant raises alarms. Science 371, 9–10 (2021).
doi: 10.1126/science.371.6524.9
pubmed: 33384355
Faria, N. R. et al. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. Preprint at https://doi.org/10.1101/2021.02.26.21252554 (2021).
Schmidt, F. et al. Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses. J. Exp. Med. 217, e20201181 (2020).
doi: 10.1084/jem.20201181
pubmed: 32692348
pmcid: 7372514
Benton, D. J. et al. Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion. Nature 588, 327–330 (2020).
doi: 10.1038/s41586-020-2772-0
pubmed: 32942285
pmcid: 7116727
Lan, J. et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581, 215–220 (2020).
doi: 10.1038/s41586-020-2180-5
pubmed: 32225176
Zhou, T. et al. Cryo-EM structures of SARS-CoV-2 spike without and with ACE2 reveal a pH-dependent switch to mediate endosomal positioning of receptor-binding domains. Cell Host Microbe 28, 867–879 (2020).
doi: 10.1016/j.chom.2020.11.004
pubmed: 33271067
pmcid: 7670890
Wrapp, D. et al. Structural basis for potent neutralization of betacoronaviruses by single-domain camelid antibodies. Cell 181, 1004–1015 (2020).
doi: 10.1016/j.cell.2020.04.031
pubmed: 32375025
pmcid: 7199733
Koenig, P. A. et al. Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape. Science 371, eabe6230 (2021).
doi: 10.1126/science.abe6230
pubmed: 33436526
pmcid: 7932109
Janssens, R. et al. Generation of heavy-chain-only antibodies in mice. Proc. Natl Acad. Sci. USA 103, 15130–15135 (2006).
doi: 10.1073/pnas.0601108103
pubmed: 17015837
pmcid: 1586177
Han, L., Masani, S. & Yu, K. Overlapping activation-induced cytidine deaminase hotspot motifs in Ig class-switch recombination. Proc. Natl Acad. Sci. USA 108, 11584–11589 (2011).
doi: 10.1073/pnas.1018726108
pubmed: 21709240
pmcid: 3136278
Achour, I. et al. Tetrameric and homodimeric camelid IgGs originate from the same IgH locus. J. Immunol. 181, 2001–2009 (2008).
doi: 10.4049/jimmunol.181.3.2001
pubmed: 18641337
The Bactrian Camels Genome Sequencing and Analysis Consortium. Genome sequences of wild and domestic bactrian camels. Nat. Commun. 3, 1202 (2012).
doi: 10.1038/ncomms2192
Wu, H. et al. Camelid genomes reveal evolution and adaptation to desert environments. Nat. Commun. 5, 5188 (2014).
doi: 10.1038/ncomms6188
pubmed: 25333821
Pardon, E. et al. A general protocol for the generation of nanobodies for structural biology. Nat. Protocols 9, 674–693 (2014).
doi: 10.1038/nprot.2014.039
pubmed: 24577359
Gaspar, J. M. NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors. BMC Bioinformatics 19, 536 (2018).
doi: 10.1186/s12859-018-2579-2
pubmed: 30572828
pmcid: 6302405
Zhang, X. et al. pTrimmer: an efficient tool to trim primers of multiplex deep sequencing data. BMC Bioinformatics 20, 236 (2019).
doi: 10.1186/s12859-019-2854-x
pubmed: 31077131
pmcid: 6511130
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
doi: 10.1093/bioinformatics/bty560
pubmed: 30423086
pmcid: 6129281
Ye, J., Ma, N., Madden, T. L. & Ostell, J. M. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 41, W34–W40 (2013).
doi: 10.1093/nar/gkt382
pubmed: 23671333
pmcid: 3692102
Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
doi: 10.1093/bioinformatics/btr507
pubmed: 21903629
pmcid: 3198573
Dunbar, J. & Deane, C. M. ANARCI: antigen receptor numbering and receptor classification. Bioinformatics 32, 298–300 (2016).
pubmed: 26424857
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
doi: 10.1093/bioinformatics/btl158
pubmed: 16731699
Chuang, G. Y. et al. Structure-based design of a soluble prefusion-closed HIV-1 env trimer with reduced CD4 affinity and improved immunogenicity. J. Virol. 91, e02268-16 (2017).
doi: 10.1128/JVI.02268-16
pubmed: 28275193
pmcid: 5411596
Amanat, F. et al. A serological assay to detect SARS-CoV-2 seroconversion in humans. Nat. Med. 26, 1033–1036 (2020).
doi: 10.1038/s41591-020-0913-5
pubmed: 32398876
pmcid: 8183627
Stadlbauer, D. et al. SARS-CoV-2 seroconversion in humans: a detailed protocol for a serological assay, antigen production, and test setup. Curr. Protoc. Microbiol. 57, e100 (2020).
doi: 10.1002/cpmc.100
pubmed: 32302069
pmcid: 7235504
Zhou, T. et al. Structure-based design with tag-based purification and in-process biotinylation enable streamlined development of SARS-CoV-2 spike molecular probes. Cell Rep. 33, 108322 (2020).
Weisblum, Y. et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. eLife 9, e61312 (2020).
doi: 10.7554/eLife.61312
pubmed: 33112236
pmcid: 7723407
Muecksch, F. et al. Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies. Preprint at https://doi.org/10.1101/2021.03.07.434227 (2021).
Liu, L. et al. Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature 584, 450–456 (2020).
doi: 10.1038/s41586-020-2571-7
pubmed: 32698192
Wang, P. et al. SARS-CoV-2 neutralizing antibody responses are more robust in patients with severe disease. Emerg. Microbes Infect. 9, 2091–2093 (2020).
doi: 10.1080/22221751.2020.1823890
pubmed: 32930052
pmcid: 7534308
Leem, J., Dunbar, J., Georges, G., Shi, J. & Deane, C. M. ABodyBuilder: automated antibody structure prediction with data-driven accuracy estimation. MAbs 8, 1259–1268 (2016).
doi: 10.1080/19420862.2016.1205773
pubmed: 27392298
pmcid: 5058620