26 oktober 2022: Bron: NRC en Science Direct

De NRC schreef een uitstekend artikel over deze studie (abstract onderaan dit artikel): 

Imprinted antibody responses against SARS-CoV-2 Omicron sublineage


Hier het artikel in de NRC:

Brede afweer na Omikron-infectie

Coronavaccinatie 

Een doorbraakinfectie na een volledige vaccinatie roept een sterke afweer op. Dat is ook goed nieuws voor het combinatievaccin.

Bij volledig gevaccineerde mensen die daarbovenop een infectie met de Omikron subvariant BA.1 kregen, ontstaan breed werkende antistoffen tegen zowel het oorspronkelijke coronavirus uit Wuhan als tegen allerlei subvarianten van Omikron, waaronder BA.4/5. Die laatste is nu in Nederland dominant. De antistoffen neutraliseren die subvariant BA.4/5 wel iets minder goed dan andere subvarianten, zoals BA.1 en BA.2, maar ze kunnen hem wel onschadelijk maken. Dat schrijft een groep internationale onderzoekers in een publicatie die vorige week in het wetenschappelijke tijdschrift Science verscheen. De vinding is goed nieuws: het bevestigt de verwachting dat de nieuwe vaccins tegen Omikron BA.1 ook beschermen tegen nieuwe subvarianten.

Een grote zorg van wetenschappers is dat het afweersysteem te rigide wordt. Kan het immuunsysteem, eenmaal getraind door een infectie met het originele virus uit Wuhan, of door een vaccinatieserie tegen dat oorspronkelijke virus, het afweergeschut nog wel omvormen tegen andere varianten? Die zorg groeit met de opkomst van een ‘variantensoep’; de talrijke subvarianten van Omikron die nu de corona-infecties veroorzaken en die aan de afweer weten te ontsnappen (Denemarken telde er recent zo’n 120).

De studie in Science laat zien dat het de eerste infectie of vaccinatie inderdaad een diepe stempel heeft gedrukt op het immuunsysteem.>>>>>>>>lees verder

Imprinted antibody responses against SARS-CoV-2 Omicron sublineages

SCIENCE
20 Oct 2022
First Release

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations and represent an antigenic shift resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters elicit plasma neutralizing activity against Omicron BA.1, BA.2, BA.2.12.1 and BA.4/5 and that breakthrough infections, but not vaccination-only, induce neutralizing activity in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1, BA.2, and BA.4/5 receptor-binding domains whereas Omicron primary infections elicit B cells of narrow specificity up to 6 months post infection. Although most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant neutralizing antibody, that is a strong candidate for clinical development.
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron at the end of 2021 caused worldwide COVID-19 case surges. The Omicron BA.1 and BA.1.1 lineages swept the world followed by the BA.2 lineage (1). Although BA.1 and BA.2 share a large number of spike (S) mutations, they are each characterized by unique sets of amino acid changes, which are associated with different antigenic properties (24). The BA.2.12.1 sublineage emerged in the United States, peaking at the beginning of June and is characterized by the presence of the S1 L452Q receptor-binding domain (RBD) and S704L S2 subunit mutations in addition to the BA.2-defining mutations (4). The BA.2.75 sublineage is spreading in multiple countries and carries unique mutations (added to the BA.2 background) in the N-terminal domain (NTD), along with D339H, G446S and N460K mutations and the R493Q reversion in the RBD (5). The BA.3 S glycoprotein comprises a combination of mutations found in BA.1 S and BA.2 S (6), whereas BA.4 S and BA.5 S are identical to each other and comprise a deletion of residues 69-70, the L452R and F486V substitutions along with the R493Q reversion compared to BA.2 S (7). We characterized the emergence of Omicron (BA.1) as a major antigenic shift due to the unprecedented magnitude of immune evasion associated with this variant of concern (3812). Mutations in the BA.1 S glycoprotein NTD and RBD, which are the main targets of neutralizing antibodies (381318), explain the markedly reduced plasma neutralizing activity of previously infected or vaccinated subjects, especially those that have not received booster doses, and the escape from most monoclonal antibodies (mAbs) used in the clinic. As a result, an increasing number of reinfections or breakthrough infections are occurring (1922), even though these cases tend to be milder than infections of immunologically naive individuals.


Acknowledgments

We thank Abigail E. Powell and Nadine Czudnochowski for assistance with protein production.
Funding: This study was supported by the National Institute of Allergy and Infectious Diseases (DP1AI158186 and HHSN272201700059C to D.V.), a Pew Biomedical Scholars Award (D.V.), an Investigators in the Pathogenesis of Infectious Disease Awards from the Burroughs Wellcome Fund (D.V.), Fast Grants (D.V.), the University of Washington Arnold and Mabel Beckman cryoEM center and the National Institute of Health grant S10OD032290 (to D.V.). S.P.J.W. supported be NIH grant AI163019. D.V. is an Investigator of the Howard Hughes Medical Institute. O.G. is funded by the Swiss Kidney Foundation.
Author contributions: A.C.W., A.L., D.P., D.C., M.S.P. and D.V. designed the experiments; A.C.W., A.D.M., D.P., C.S., W.R., K.R.S. F.Z., H.V.D., M.G., G.Sc. and F.A.L. isolated mAb and performed binding, neutralization assays, biolayer interferometry and surface plasmon resonance binding measurements; A.R., J.Z., N.F., M.M.R., J.N. performed neutralization assays using authentic virus. H.K. confirmed the Spike mutations of authentic virus by Sanger sequencing. A.D.M. and D.P. performed ACE2 binding inhibition and S1 shedding assays; B.G. and M.A.S. evaluated effector functions; C.S.F., J.B. and L.P performed memory B cell repertoire analysis. O.G., A.C. and P.F. contributed to the recruitment of donors and collection of plasma samples. J.d.I., L.S. and A.T. performed bioinformatic and epidemiology analyses. Z.L. and S.P.J.W. performed mutant selection and fitness assays; R.A., J.J., F.B., P.M., J.N., G.D.d.M., L.K. and H.B. performed hamster model experiments and data analysis; Y.J.P. carried out cryoEM specimen preparation, data collection and processing. Y.J.P. and D.V. built and refined the atomic models. J.E.B., C.S. purified recombinant glycoproteins. A.L., D.P., Y.J.P., A.D.M., Z.L., D.P., D.C., M.S.P. and D.V. analyzed the data; A.C.W., D.P., D.C., M.S.P. and D.V. wrote the manuscript with input from all authors; F.B., G.S., J.N., S.P.J.W., H.W.V, M.S.P., D.C., and D.V. supervised the project.
Competing interests: D.P., Ad.M., F.Z., M.G., C.S.F., J.B., C.S., H.V.D., K.H., W.R., M.A.S., G.Sc., B.G., F.B., J.d.I., A.R., J.Z., N.F., H.K., M.M.R, J.N., F.A.L., G.S., L.P., A.T., H.W.V., A.L., M.S.P. and D.C. are employees of Vir Biotechnology Inc. and may hold shares in Vir Biotechnology Inc. L.A.P. is a former employee and shareholder in Regeneron Pharmaceuticals. Regeneron provided no funding for this work. H.W.V. is a founder and holds shares in PierianDx and Casma Therapeutics. Neither company provided resources. D.C. is currently listed as an inventor on multiple patent applications, which disclose the subject matter described in this manuscript. The Veesler laboratory has received a sponsored research agreement from Vir Biotechnology Inc. S.P.J.W. has licensing agreements with Vir Biotechnology and Merck and is a consultant for Thylacine Bio. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Data and materials availability: The cryoEM map and coordinates have been deposited to the Electron Microscopy Databank and Protein Data Bank with accession numbers listed in table S5. Materials generated in this study will be made available on request, but may require a completed materials transfer agreement signed with Vir Biotechnology Inc. or the University of Washington.
License information: This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author-accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.

Supplementary Materials

This PDF file includes:

Materials and Methods
Figs. S1 to S18
Tables S1 to S9
References (95126)

Other Supplementary Material for this manuscript includes the following:

MDAR Reproducibility Checklist
Data S1

References and Notes

1
R. Viana, S. Moyo, D. G. Amoako, H. Tegally, C. Scheepers, C. L. Althaus, U. J. Anyaneji, P. A. Bester, M. F. Boni, M. Chand, W. T. Choga, R. Colquhoun, M. Davids, K. Deforche, D. Doolabh, L. du Plessis, S. Engelbrecht, J. Everatt, J. Giandhari, M. Giovanetti, D. Hardie, V. Hill, N.-Y. Hsiao, A. Iranzadeh, A. Ismail, C. Joseph, R. Joseph, L. Koopile, S. L. Kosakovsky Pond, M. U. G. Kraemer, L. Kuate-Lere, O. Laguda-Akingba, O. Lesetedi-Mafoko, R. J. Lessells, S. Lockman, A. G. Lucaci, A. Maharaj, B. Mahlangu, T. Maponga, K. Mahlakwane, Z. Makatini, G. Marais, D. Maruapula, K. Masupu, M. Matshaba, S. Mayaphi, N. Mbhele, M. B. Mbulawa, A. Mendes, K. Mlisana, A. Mnguni, T. Mohale, M. Moir, K. Moruisi, M. Mosepele, G. Motsatsi, M. S. Motswaledi, T. Mphoyakgosi, N. Msomi, P. N. Mwangi, Y. Naidoo, N. Ntuli, M. Nyaga, L. Olubayo, S. Pillay, B. Radibe, Y. Ramphal, U. Ramphal, J. E. San, L. Scott, R. Shapiro, L. Singh, P. Smith-Lawrence, W. Stevens, A. Strydom, K. Subramoney, N. Tebeila, D. Tshiabuila, J. Tsui, S. van Wyk, S. Weaver, C. K. Wibmer, E. Wilkinson, N. Wolter, A. E. Zarebski, B. Zuze, D. Goedhals, W. Preiser, F. Treurnicht, M. Venter, C. Williamson, O. G. Pybus, J. Bhiman, A. Glass, D. P. Martin, A. Rambaut, S. Gaseitsiwe, A. von Gottberg, T. de Oliveira, Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature603, 679–686 (2022).
2
J. Yu, A.-R. Y. Collier, M. Rowe, F. Mardas, J. D. Ventura, H. Wan, J. Miller, O. Powers, B. Chung, M. Siamatu, N. P. Hachmann, N. Surve, F. Nampanya, A. Chandrashekar, D. H. Barouch, Comparable neutralization of the SARS-CoV-2 Omicron BA.1 and BA.2 variants. medRxiv 2022.02.06.22270533 (2022); .
3
E. Cameroni, J. E. Bowen, L. E. Rosen, C. Saliba, S. K. Zepeda, K. Culap, D. Pinto, L. A. VanBlargan, A. De Marco, J. di Iulio, F. Zatta, H. Kaiser, J. Noack, N. Farhat, N. Czudnochowski, C. Havenar-Daughton, K. R. Sprouse, J. R. Dillen, A. E. Powell, A. Chen, C. Maher, L. Yin, D. Sun, L. Soriaga, J. Bassi, C. Silacci-Fregni, C. Gustafsson, N. M. Franko, J. Logue, N. T. Iqbal, I. Mazzitelli, J. Geffner, R. Grifantini, H. Chu, A. Gori, A. Riva, O. Giannini, A. Ceschi, P. Ferrari, P. E. Cippà, A. Franzetti-Pellanda, C. Garzoni, P. J. Halfmann, Y. Kawaoka, C. Hebner, L. A. Purcell, L. Piccoli, M. S. Pizzuto, A. C. Walls, M. S. Diamond, A. Telenti, H. W. Virgin, A. Lanzavecchia, G. Snell, D. Veesler, D. Corti, Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift. Nature602, 664–670 (2022).
4
J. E. Bowen, A. Addetia, H. V. Dang, C. Stewart, J. T. Brown, W. K. Sharkey, K. R. Sprouse, A. C. Walls, I. G. Mazzitelli, J. K. Logue, N. M. Franko, N. Czudnochowski, A. E. Powell, E. DellotaJr., K. Ahmed, A. S. Ansari, E. Cameroni, A. Gori, A. Bandera, C. M. Posavad, J. M. Dan, Z. Zhang, D. Weiskopf, A. Sette, S. Crotty, N. T. Iqbal, D. Corti, J. Geffner, G. Snell, R. Grifantini, H. Y. Chu, D. Veesler, Omicron spike function and neutralizing activity elicited by a comprehensive panel of vaccines. Science377, 890–894 (2022).
5
C.-W. Tan, B.-L. Lim, B. E. Young, A. Y.-Y. Yeoh, C.-F. Yung, W.-C. Yap, T. Althaus, W.-N. Chia, F. Zhu, D. C. Lye, L.-F. Wang, Comparative neutralisation profile of SARS-CoV-2 omicron subvariants BA.2.75 and BA.5. Lancet MicrobeS2666-5247(22)00220-8 (2022).
6
P. A. Desingu, K. Nagarajan, K. Dhama, Emergence of Omicron third lineage BA.3 and its importance. J. Med. Virol.94, 1808–1810 (2022).
7
H. Tegally, M. Moir, J. Everatt, M. Giovanetti, C. Scheepers, E. Wilkinson, K. Subramoney, S. Moyo, D. G. Amoako, C. Baxter, C. L. Althaus, U. J. Anyaneji, D. Kekana, R. Viana, J. Giandhari, R. J. Lessells, T. Maponga, D. Maruapula, W. Choga, M. Matshaba, S. Mayaphi, N. Mbhele, M. B. Mbulawa, N. Msomi, Y. Naidoo, S. Pillay, T. J. Sanko, J. E. San, L. Scott, L. Singh, N. A. Magini, P. Smith-Lawrence, W. Stevens, G. Dor, D. Tshiabuila, N. Wolter, W. Preiser, F. K. Treurnicht, M. Venter, M. Davids, G. Chiloane, A. Mendes, C. McIntyre, A. O’Toole, C. Ruis, T. P. Peacock, C. Roemer, C. Williamson, O. G. Pybus, J. Bhiman, A. Glass, D. P. Martin, A. Rambaut, S. Gaseitsiwe, A. von Gottberg, T. de Oliveira, NGS-SA consortium, Continued emergence and evolution of Omicron in South Africa: New BA.4 and BA.5 lineages. medRxiv 2022.05.01.22274406 (2022); .
8
L. Liu, S. Iketani, Y. Guo, J. F.-W. Chan, M. Wang, L. Liu, Y. Luo, H. Chu, Y. Huang, M. S. Nair, J. Yu, K. K.-H. Chik, T. T.-T. Yuen, C. Yoon, K. K.-W. To, H. Chen, M. T. Yin, M. E. Sobieszczyk, Y. Huang, H. H. Wang, Z. Sheng, K.-Y. Yuen, D. D. Ho, Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2. Nature602, 676–681 (2022).
9
D. Planas, N. Saunders, P. Maes, F. Guivel-Benhassine, C. Planchais, J. Buchrieser, W. H. Bolland, F. Porrot, I. Staropoli, F. Lemoine, H. Péré, D. Veyer, J. Puech, J. Rodary, G. Baele, S. Dellicour, J. Raymenants, S. Gorissen, C. Geenen, B. Vanmechelen, T. Wawina-Bokalanga, J. Martí-Carreras, L. Cuypers, A. Sève, L. Hocqueloux, T. Prazuck, F. A. Rey, E. Simon-Loriere, T. Bruel, H. Mouquet, E. André, O. Schwartz, Considerable escape of SARS-CoV-2 Omicron to antibody neutralization. Nature602, 671–675 (2022).
10
M. Hoffmann, N. Krüger, S. Schulz, A. Cossmann, C. Rocha, A. Kempf, I. Nehlmeier, L. Graichen, A.-S. Moldenhauer, M. S. Winkler, M. Lier, A. Dopfer-Jablonka, H.-M. Jäck, G. M. N. Behrens, S. Pöhlmann, The Omicron variant is highly resistant against antibody-mediated neutralization – implications for control of the COVID-19 pandemic. bioRxiv 472286 (2021); .
11
W. F. Garcia-Beltran, K. J. St. Denis, A. Hoelzemer, E. C. Lam, A. D. Nitido, M. L. Sheehan, C. Berrios, O. Ofoman, C. C. Chang, B. M. Hauser, J. Feldman, A. L. Roederer, D. J. Gregory, M. C. Poznansky, A. G. Schmidt, A. J. Iafrate, V. Naranbhai, A. B. Balazs, mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant. Cell185, 457–466.e4 (2022).
12
H. Gruell, K. Vanshylla, M. Korenkov, P. Tober-Lau, M. Zehner, F. Münn, H. Janicki, M. Augustin, P. Schommers, L. E. Sander, F. Kurth, C. Kreer, F. Klein, Delineating antibody escape from Omicron variants. bioRxiv 487257 (2022); .
13
L. Piccoli, Y. J. Park, M. A. Tortorici, N. Czudnochowski, A. C. Walls, M. Beltramello, C. Silacci-Fregni, D. Pinto, L. E. Rosen, J. E. Bowen, O. J. Acton, S. Jaconi, B. Guarino, A. Minola, F. Zatta, N. Sprugasci, J. Bassi, A. Peter, A. De Marco, J. C. Nix, F. Mele, S. Jovic, B. F. Rodriguez, S. V. Gupta, F. Jin, G. Piumatti, G. Lo Presti, A. F. Pellanda, M. Biggiogero, M. Tarkowski, M. S. Pizzuto, E. Cameroni, C. Havenar-Daughton, M. Smithey, D. Hong, V. Lepori, E. Albanese, A. Ceschi, E. Bernasconi, L. Elzi, P. Ferrari, C. Garzoni, A. Riva, G. Snell, F. Sallusto, K. Fink, H. W. Virgin, A. Lanzavecchia, D. Corti, D. Veesler, Mapping neutralizing and immunodominant sites on the SARS-CoV-2 Spike receptor-binding domain by structure-guided high-resolution serology. Cell183, 1024–1042.e21 (2020).
14
J. E. Bowen, A. C. Walls, A. Joshi, K. R. Sprouse, C. Stewart, M. Alejandra Tortorici, N. M. Franko, J. K. Logue, I. G. Mazzitelli, S. W. Tiles, K. Ahmed, A. Shariq, G. Snell, N. T. Iqbal, J. Geffner, A. Bandera, A. Gori, R. Grifantini, H. Y. Chu, W. C. Van Voorhis, D. Corti, D. Veesler, SARS-CoV-2 spike conformation determines plasma neutralizing activity. bioRxiv 473391 (2021); .
15
L. Stamatatos, J. Czartoski, Y.-H. Wan, L. J. Homad, V. Rubin, H. Glantz, M. Neradilek, E. Seydoux, M. F. Jennewein, A. J. MacCamy, J. Feng, G. Mize, S. C. De Rosa, A. Finzi, M. P. Lemos, K. W. Cohen, Z. Moodie, M. J. McElrath, A. T. McGuire, mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection. Science372, eabg9175 (2021).
16
A. J. Greaney, A. N. Loes, L. E. Gentles, K. H. D. Crawford, T. N. Starr, K. D. Malone, H. Y. Chu, J. D. Bloom, Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection. Sci. Transl. Med.13, eabi9915 (2021).
17
M. McCallum, A. De Marco, F. A. Lempp, M. A. Tortorici, D. Pinto, A. C. Walls, M. Beltramello, A. Chen, Z. Liu, F. Zatta, S. Zepeda, J. di Iulio, J. E. Bowen, M. Montiel-Ruiz, J. Zhou, L. E. Rosen, S. Bianchi, B. Guarino, C. S. Fregni, R. Abdelnabi, S. C. Foo, P. W. Rothlauf, L.-M. Bloyet, F. Benigni, E. Cameroni, J. Neyts, A. Riva, G. Snell, A. Telenti, S. P. J. Whelan, H. W. Virgin, D. Corti, M. S. Pizzuto, D. Veesler, N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell184, 2332–2347.e16 (2021).
18
M. McCallum, N. Czudnochowski, L. E. Rosen, S. K. Zepeda, J. E. Bowen, A. C. Walls, K. Hauser, A. Joshi, C. Stewart, J. R. Dillen, A. E. Powell, T. I. Croll, J. Nix, H. W. Virgin, D. Corti, G. Snell, D. Veesler, Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement. Science375, 864–868 (2022).
19
A. C. Walls, K. R. Sprouse, J. E. Bowen, A. Joshi, N. Franko, M. J. Navarro, C. Stewart, E. Cameroni, M. McCallum, E. A. Goecker, E. J. Degli-Angeli, J. Logue, A. Greninger, D. Corti, H. Y. Chu, D. Veesler, SARS-CoV-2 breakthrough infections elicit potent, broad, and durable neutralizing antibody responses. Cell185, 872–880.e3 (2022).
20
A. Y. Collier, C. M. Brown, K. A. McMahan, J. Yu, J. Liu, C. Jacob-Dolan, A. Chandrashekar, D. Tierney, J. L. Ansel, M. Rowe, D. Sellers, K. Ahmad, R. Aguayo, T. Anioke, S. Gardner, M. Siamatu, L. Bermudez-Rivera, M. R. Hacker, L. C. Madoff, D. H. Barouch, Characterization of immune responses in fully vaccinated individuals after breakthrough infection with the SARS-CoV-2 delta variant. Sci. Transl. Med.14, eabn6150 (2022).
21
T. A. Bates, S. K. McBride, B. Winders, D. Schoen, L. Trautmann, M. E. Curlin, F. G. Tafesse, Antibody response and variant cross-neutralization after SARS-CoV-2 breakthrough infection. JAMA327, 179–181 (2022).
22
P. Mlcochova, S. Kemp, M. S. Dhar, G. Papa, B. Meng, S. Mishra, C. Whittaker, T. Mellan, I. Ferreira, R. Datir, D. A. Collier, S. Singh, R. Pandey, R. Marwal, M. Datta, S. Sengupta, K. Ponnusamy, V. S. Radhakrishnan, A. Abdullahi, N. Goonawardne, J. Brown, O. Charles, P. Chattopadhyay, P. Devi, D. Caputo, T. Peacock, C. Wattal, N. Goel, R. Vaishya, M. Agarwal, H. Lee, W. S. Barcla, S. Bhatt, S. Flaxman, L. James, P. Rakshit, A. Agrawal, The Indian SARS-CoV-2 Genomics Consortium (INSACOG), CITIID-NIHR BioResource COVID-19 Collaboration, A. Mavousian, R. K. Gupta, SARS-CoV-2 B.1.617.2 Delta variant emergence and vaccine breakthrough. Research Square (2021); .
23
M. McCallum, A. C. Walls, K. R. Sprouse, J. E. Bowen, L. E. Rosen, H. V. Dang, A. De Marco, N. Franko, S. W. Tilles, J. Logue, M. C. Miranda, M. Ahlrichs, L. Carter, G. Snell, M. S. Pizzuto, H. Y. Chu, W. C. Van Voorhis, D. Corti, D. Veesler, Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants. Science374, 1621–1626 (2021).
24
R. Suzuki, D. Yamasoba, I. Kimura, L. Wang, M. Kishimoto, J. Ito, Y. Morioka, N. Nao, H. Nasser, K. Uriu, Y. Kosugi, M. Tsuda, Y. Orba, M. Sasaki, R. Shimizu, R. Kawabata, K. Yoshimatsu, H. Asakura, M. Nagashima, K. Sadamasu, K. Yoshimura, Genotype to Phenotype Japan (G2P-Japan) Consortium, H. Sawa, T. Ikeda, T. Irie, K. Matsuno, S. Tanaka, T. Fukuhara, K. Sato, Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant. Nature603, 700–705 (2022).
25
P. Mlcochova, S. A. Kemp, M. S. Dhar, G. Papa, B. Meng, I. A. T. M. Ferreira, R. Datir, D. A. Collier, A. Albecka, S. Singh, R. Pandey, J. Brown, J. Zhou, N. Goonawardane, S. Mishra, C. Whittaker, T. Mellan, R. Marwal, M. Datta, S. Sengupta, K. Ponnusamy, V. S. Radhakrishnan, A. Abdullahi, O. Charles, P. Chattopadhyay, P. Devi, D. Caputo, T. Peacock, C. Wattal, N. Goel, A. Satwik, R. Vaishya, M. Agarwal, A. Mavousian, J. H. Lee, J. Bassi, C. Silacci-Fegni, C. Saliba, D. Pinto, T. Irie, I. Yoshida, W. L. Hamilton, K. Sato, S. Bhatt, S. Flaxman, L. C. James, D. Corti, L. Piccoli, W. S. Barclay, P. Rakshit, A. Agrawal, R. K. Gupta; Indian SARS-CoV-2 Genomics Consortium (INSACOG); Genotype to Phenotype Japan (G2P-Japan) Consortium; CITIID-NIHR BioResource COVID-19 Collaboration, SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature599, 114–119 (2021).
26
S. Crotty, Hybrid immunity. Science372, 1392–1393 (2021).
27
T. N. Starr, N. Czudnochowski, Z. Liu, F. Zatta, Y.-J. Park, A. Addetia, D. Pinto, M. Beltramello, P. Hernandez, A. J. Greaney, R. Marzi, W. G. Glass, I. Zhang, A. S. Dingens, J. E. Bowen, M. A. Tortorici, A. C. Walls, J. A. Wojcechowskyj, A. De Marco, L. E. Rosen, J. Zhou, M. Montiel-Ruiz, H. Kaiser, J. R. Dillen, H. Tucker, J. Bassi, C. Silacci-Fregni, M. P. Housley, J. di Iulio, G. Lombardo, M. Agostini, N. Sprugasci, K. Culap, S. Jaconi, M. Meury, E. DellotaJr., R. Abdelnabi, S. C. Foo, E. Cameroni, S. Stumpf, T. I. Croll, J. C. Nix, C. Havenar-Daughton, L. Piccoli, F. Benigni, J. Neyts, A. Telenti, F. A. Lempp, M. S. Pizzuto, J. D. Chodera, C. M. Hebner, H. W. Virgin, S. P. J. Whelan, D. Veesler, D. Corti, J. D. Bloom, G. Snell, SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Nature597, 97–102 (2021).
28
C.-W. Tan, W.-N. Chia, B. E. Young, F. Zhu, B.-L. Lim, W.-R. Sia, T.-L. Thein, M. I.-C. Chen, Y.-S. Leo, D. C. Lye, L.-F. Wang, Pan-sarbecovirus neutralizing antibodies in BNT162b2-immunized SARS-CoV-1 survivors. N. Engl. J. Med.385, 1401–1406 (2021).
29
D. Pinna, D. Corti, D. Jarrossay, F. Sallusto, A. Lanzavecchia, Clonal dissection of the human memory B-cell repertoire following infection and vaccination. Eur. J. Immunol.39, 1260–1270 (2009).
30
K. Khan, F. Karim, Y. Ganga, M. Bernstein, Z. Jule, K. Reedoy, S. Cele, G. Lustig, D. Amoako, N. Wolter, N. Samsunder, A. Sivro, J. E. San, J. Giandhari, H. Tegally, S. Pillay, Y. Naidoo, M. Mazibuko, Y. Miya, N. Ngcobo, N. Manickchund, N. Magula, Q. A. Karim, A. von Gottberg, S. S. Abdool Karim, W. Hanekom, B. I. Gosnell, R. J. Lessells, T. de Oliveira, M.-Y. S. Moosa, A. Sigal, COMMIT-KZN Team, Omicron sub-lineages BA.4/BA.5 escape BA.1 infection elicited neutralizing immunity (2022), doi:.
31
A. Muik, B. G. Lui, M. Bacher, A.-K. Wallisch, A. Toker, A. Finlayson, K. Krüger, O. Ozhelvaci, K. Grikscheit, S. Hoehl, S. Ciesek, Ö. Türeci, U. Sahin, B. A. Omicron, 2 breakthrough infection enhances cross-neutralization of BA.2.12.1 and BA.4/BA.5. bioRxiv 502461 (2022); .
32
C. W. Tan, W. N. Chia, X. Qin, P. Liu, M. I. C. Chen, C. Tiu, Z. Hu, V. C.-W. Chen, B. E. Young, W. R. Sia, Y.-J. Tan, R. Foo, Y. Yi, D. C. Lye, D. E. Anderson, L.-F. Wang, A SARS-CoV-2 surrogate virus neutralization test based on antibody-mediated blockage of ACE2-spike protein-protein interaction. Nat. Biotechnol.38, 1073–1078 (2020).
33
M. A. Tortorici, M. Beltramello, F. A. Lempp, D. Pinto, H. V. Dang, L. E. Rosen, M. McCallum, J. Bowen, A. Minola, S. Jaconi, F. Zatta, A. De Marco, B. Guarino, S. Bianchi, E. J. Lauron, H. Tucker, J. Zhou, A. Peter, C. Havenar-Daughton, J. A. Wojcechowskyj, J. B. Case, R. E. Chen, H. Kaiser, M. Montiel-Ruiz, M. Meury, N. Czudnochowski, R. Spreafico, J. Dillen, C. Ng, N. Sprugasci, K. Culap, F. Benigni, R. Abdelnabi, S. C. Foo, M. A. Schmid, E. Cameroni, A. Riva, A. Gabrieli, M. Galli, M. S. Pizzuto, J. Neyts, M. S. Diamond, H. W. Virgin, G. Snell, D. Corti, K. Fink, D. Veesler, Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms. Science370, 950–957 (2020).
34
M. A. Tortorici, N. Czudnochowski, T. N. Starr, R. Marzi, A. C. Walls, F. Zatta, J. E. Bowen, S. Jaconi, J. Di Iulio, Z. Wang, A. De Marco, S. K. Zepeda, D. Pinto, Z. Liu, M. Beltramello, I. Bartha, M. P. Housley, F. A. Lempp, L. E. Rosen, E. DellotaJr., H. Kaiser, M. Montiel-Ruiz, J. Zhou, A. Addetia, B. Guarino, K. Culap, N. Sprugasci, C. Saliba, E. Vetti, I. Giacchetto-Sasselli, C. S. Fregni, R. Abdelnabi, S. C. Foo, C. Havenar-Daughton, M. A. Schmid, F. Benigni, E. Cameroni, J. Neyts, A. Telenti, H. W. Virgin, S. P. J. Whelan, G. Snell, J. D. Bloom, D. Corti, D. Veesler, M. S. Pizzuto, Broad sarbecovirus neutralization by a human monoclonal antibody. Nature597, 103–108 (2021).
35
L. Azzi, D. Dalla Gasperina, G. Veronesi, M. Shallak, G. Ietto, D. Iovino, A. Baj, F. Gianfagna, V. Maurino, D. Focosi, F. Maggi, M. M. Ferrario, F. Dentali, G. Carcano, A. Tagliabue, L. S. Maffioli, R. S. Accolla, G. Forlani, Mucosal immune response in BNT162b2 COVID-19 vaccine recipients. EBioMedicine75, 103788 (2022).
36
J. Tang, C. Zeng, T. M. Cox, C. Li, Y. M. Son, I. S. Cheon, Y. Wu, S. Behl, J. J. Taylor, R. Chakraborty, A. J. Johnson, D. N. Schiavo, J. P. Utz, J. S. Reisenauer, D. E. Midthun, J. J. Mullon, E. S. Edell, M. G. Alameh, L. Borish, W. G. Teague, M. H. Kaplan, D. Weissman, R. Kern, H. Hu, R. Vassallo, S.-L. Liu, J. Sun, Respiratory mucosal immunity against SARS-CoV-2 following mRNA vaccination. Sci. Immunol.•••, eadd4853 (2022).
37
D. Planas, I. Staropoli, F. Porot, F. Guivel-Benhassine, L. Handala, M. Prot, W.-H. Bolland, J. Puech, H. Péré, D. Veyer, A. Sève, E. Simon-Lorière, T. Bruel, T. Prazuck, K. Stefic, L. Hocqueloux, O. Schwartz, Duration of BA.5 neutralization in sera and nasal swabs from SARS-CoV-2 vaccinated individuals, with or without Omicron breakthrough infection. medRxiv 2022.07.22.22277885 (2022); .
38
J. M. E. Lim, A. T. Tan, N. Le Bert, S. K. Hang, J. G. H. Low, A. Bertoletti, SARS-CoV-2 breakthrough infection in vaccinees induces virus-specific nasal-resident CD8+ and CD4+ T cells of broad specificity. J. Exp. Med.219, e20220780 (2022).
39
J. Dong, S. J. Zost, A. J. Greaney, T. N. Starr, A. S. Dingens, E. C. Chen, R. E. Chen, J. B. Case, R. E. Sutton, P. Gilchuk, J. Rodriguez, E. Armstrong, C. Gainza, R. S. Nargi, E. Binshtein, X. Xie, X. Zhang, P.-Y. Shi, J. Logue, S. Weston, M. E. McGrath, M. B. Frieman, T. Brady, K. M. Tuffy, H. Bright, Y.-M. Loo, P. M. McTamney, M. T. Esser, R. H. Carnahan, M. S. Diamond, J. D. Bloom, J. E. CroweJr., Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail. Nat. Microbiol.6, 1233–1244 (2021).
40
Y.-J. Park, A. De Marco, T. N. Starr, Z. Liu, D. Pinto, A. C. Walls, F. Zatta, S. K. Zepeda, J. E. Bowen, K. R. Sprouse, A. Joshi, M. Giurdanella, B. Guarino, J. Noack, R. Abdelnabi, S. C. Foo, L. E. Rosen, F. A. Lempp, F. Benigni, G. Snell, J. Neyts, S. P. J. Whelan, H. W. Virgin, J. D. Bloom, D. Corti, M. S. Pizzuto, D. Veesler, Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry. Science375, 449–454 (2022).
41
D. Pinto, Y.-J. Park, M. Beltramello, A. C. Walls, M. A. Tortorici, S. Bianchi, S. Jaconi, K. Culap, F. Zatta, A. De Marco, A. Peter, B. Guarino, R. Spreafico, E. Cameroni, J. B. Case, R. E. Chen, C. Havenar-Daughton, G. Snell, A. Telenti, H. W. Virgin, A. Lanzavecchia, M. S. Diamond, K. Fink, D. Veesler, D. Corti, Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature583, 290–295 (2020).
42
E. Cameroni, C. Saliba, J. E. Bowen, L. E. Rosen, K. Culap, D. Pinto, A. De Marco, S. K. Zepeda, J. di Iulio, F. Zatta, H. Kaiser, J. Noack, N. Farhat, N. Czudnochowski, C. Havenar-Daughton, K. R. Sprouse, J. R. Dillen, A. E. Powell, A. Chen, C. Maher, L. Yin, D. Sun, L. Soriaga, C. Gustafsson, N. M. Franko, J. Logue, N. T. Iqbal, I. Mazzitelli, J. Geffner, R. Grifantini, H. Chu, A. Gori, A. Riva, O. Giannini, A. Ceschi, P. Ferrari, A. Franzetti-Pellanda, C. Garzoni, C. Hebner, L. A. Purcell, L. Piccoli, M. S. Pizzuto, A. C. Walls, A. Telenti, H. W. Virgin, A. Lanzavecchia, D. Veesler, G. Snell, D. Corti, Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift. bioRxiv 472269 (2021); .
43
A. L. Cathcart, C. Havenar-Daughton, F. A. Lempp, D. Ma, M. Schmid, M. L. Agostini, B. Guarino, J. Di iulio, L. Rosen, H. Tucker, J. Dillen, S. Subramanian, B. Sloan, S. Bianchi, J. Wojcechowskyj, J. Zhou, H. Kaiser, A. Chase, M. Montiel-Ruiz, N. Czudnochowski, E. Cameroni, S. Ledoux, C. Colas, L. Soriaga, A. Telenti, S. Hwang, G. Snell, H. W. Virgin, D. Corti, C. M. Hebner, The dual function monoclonal antibodies VIR-7831 and VIR-7832 demonstrate potent in vitro and in vivo activity against SARS-CoV-2. bioRxiv 434607 (2021); .
44
J. B. Case, S. Mackin, J. M. Errico, Z. Chong, E. A. Madden, B. Whitener, B. Guarino, M. A. Schmid, K. Rosenthal, K. Ren, H. V. Dang, G. Snell, A. Jung, L. Droit, S. A. Handley, P. J. Halfmann, Y. Kawaoka, J. E. CroweJr., D. H. Fremont, H. W. Virgin, Y.-M. Loo, M. T. Esser, L. A. Purcell, D. Corti, M. S. Diamond, Resilience of S309 and AZD7442 monoclonal antibody treatments against infection by SARS-CoV-2 Omicron lineage strains. Nat. Commun.13, 3824 (2022).
45
V. Stalls, J. Lindenberger, S. M.-C. Gobeil, R. Henderson, R. Parks, M. Barr, M. Deyton, M. Martin, K. Janowska, X. Huang, A. May, M. Speakman, E. Beaudoin, B. Kraft, X. Lu, R. J. Edwards, A. Eaton, D. C. Montefiori, W. B. Williams, K. O. Saunders, K. Wiehe, B. F. Haynes, P. Acharya, Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike. Cell Rep.39, 111009 (2022).
46
A. C. Walls, Y. J. Park, M. A. Tortorici, A. Wall, A. T. McGuire, D. Veesler, Structure, function, and antigenicity of the SARS-CoV-2 Spike glycoprotein. Cell181, 281–292.e6 (2020).
47
A. C. Walls, X. Xiong, Y. J. Park, M. A. Tortorici, J. Snijder, J. Quispe, E. Cameroni, R. Gopal, M. Dai, A. Lanzavecchia, M. Zambon, F. A. Rey, D. Corti, D. Veesler, Unexpected receptor functional mimicry elucidates activation of coronavirus fusion. Cell176, 1026–1039.e15 (2019).
48
K. Westendorf, S. Žentelis, L. Wang, D. Foster, P. Vaillancourt, M. Wiggin, E. Lovett, R. van der Lee, J. Hendle, A. Pustilnik, J. M. Sauder, L. Kraft, Y. Hwang, R. W. Siegel, J. Chen, B. A. Heinz, R. E. Higgs, N. L. Kallewaard, K. Jepson, R. Goya, M. A. Smith, D. W. Collins, D. Pellacani, P. Xiang, V. de Puyraimond, M. Ricicova, L. Devorkin, C. Pritchard, A. O’Neill, K. Dalal, P. Panwar, H. Dhupar, F. A. Garces, C. A. Cohen, J. M. Dye, K. E. Huie, C. V. Badger, D. Kobasa, J. Audet, J. J. Freitas, S. Hassanali, I. Hughes, L. Munoz, H. C. Palma, B. Ramamurthy, R. W. Cross, T. W. Geisbert, V. Menacherry, K. Lokugamage, V. Borisevich, I. Lanz, L. Anderson, P. Sipahimalani, K. S. Corbett, E. S. Yang, Y. Zhang, W. Shi, T. Zhou, M. Choe, J. Misasi, P. D. Kwong, N. J. Sullivan, B. S. Graham, T. L. Fernandez, C. L. Hansen, E. Falconer, J. R. Mascola, B. E. Jones, B. C. Barnhart, LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants. bioRxiv 442182 (2022); .
49
K. Westendorf, S. Žentelis, L. Wang, D. Foster, P. Vaillancourt, M. Wiggin, E. Lovett, R. van der Lee, J. Hendle, A. Pustilnik, J. M. Sauder, L. Kraft, Y. Hwang, R. W. Siegel, J. Chen, B. A. Heinz, R. E. Higgs, N. L. Kallewaard, K. Jepson, R. Goya, M. A. Smith, D. W. Collins, D. Pellacani, P. Xiang, V. de Puyraimond, M. Ricicova, L. Devorkin, C. Pritchard, A. O’Neill, K. Dalal, P. Panwar, H. Dhupar, F. A. Garces, C. A. Cohen, J. M. Dye, K. E. Huie, C. V. Badger, D. Kobasa, J. Audet, J. J. Freitas, S. Hassanali, I. Hughes, L. Munoz, H. C. Palma, B. Ramamurthy, R. W. Cross, T. W. Geisbert, V. Menachery, K. Lokugamage, V. Borisevich, I. Lanz, L. Anderson, P. Sipahimalani, K. S. Corbett, E. S. Yang, Y. Zhang, W. Shi, T. Zhou, M. Choe, J. Misasi, P. D. Kwong, N. J. Sullivan, B. S. Graham, T. L. Fernandez, C. L. Hansen, E. Falconer, J. R. Mascola, B. E. Jones, B. C. Barnhart, LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants. Cell Rep.39, 110812 (2022).
50
J. B. Case, P. W. Rothlauf, R. E. Chen, Z. Liu, H. Zhao, A. S. Kim, L. M. Bloyet, Q. Zeng, S. Tahan, L. Droit, M. X. G. Ilagan, M. A. Tartell, G. Amarasinghe, J. P. Henderson, S. Miersch, M. Ustav, S. Sidhu, H. W. Virgin, D. Wang, S. Ding, D. Corti, E. S. Theel, D. H. Fremont, M. S. Diamond, S. P. J. Whelan, Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2. Cell Host Microbe28, 475–485.e5 (2020).
51
A. Schäfer, F. Muecksch, J. C. C. Lorenzi, S. R. Leist, M. Cipolla, S. Bournazos, F. Schmidt, R. M. Maison, A. Gazumyan, D. R. Martinez, R. S. Baric, D. F. Robbiani, T. Hatziioannou, J. V. Ravetch, P. D. Bieniasz, R. A. Bowen, M. C. Nussenzweig, T. P. Sheahan, Antibody potency, effector function, and combinations in protection and therapy for SARS-CoV-2 infection in vivo. J. Exp. Med.218, e20201993 (2021).
52
J. B. Case, S. Mackin, J. Errico, Z. Chong, E. A. Madden, B. Guarino, M. A. Schmid, K. Rosenthal, K. Ren, A. Jung, L. Droit, S. A. Handley, P. J. Halfmann, Y. Kawaoka, J. E. Crowe Jr., D. H. Fremont, H. W. Virgin, Y.-M. Loo, M. T. Esser, L. A. Purcell, D. Corti, M. S. Diamond, Resilience of S309 and AZD7442 monoclonal antibody treatments against infection by SARS-CoV-2 Omicron lineage strains. bioRxiv 484787 (2022); .
53
T. Francis, On the doctrine of original antigenic sin. Proc. Am. Philos. Soc.104, 572–578 (1960).
54
D. Corti, J. Voss, S. J. Gamblin, G. Codoni, A. Macagno, D. Jarrossay, S. G. Vachieri, D. Pinna, A. Minola, F. Vanzetta, C. Silacci, B. M. Fernandez-Rodriguez, G. Agatic, S. Bianchi, I. Giacchetto-Sasselli, L. Calder, F. Sallusto, P. Collins, L. F. Haire, N. Temperton, J. P. Langedijk, J. J. Skehel, A. Lanzavecchia, A neutralizing antibody selected from plasma cells that binds to group 1 and group 2 influenza A hemagglutinins. Science333, 850–856 (2011).
55
J. Wrammert, D. Koutsonanos, G.-M. Li, S. Edupuganti, J. Sui, M. Morrissey, M. McCausland, I. Skountzou, M. Hornig, W. I. Lipkin, A. Mehta, B. Razavi, C. Del Rio, N.-Y. Zheng, J.-H. Lee, M. Huang, Z. Ali, K. Kaur, S. Andrews, R. R. Amara, Y. Wang, S. R. Das, C. D. O’Donnell, J. W. Yewdell, K. Subbarao, W. A. Marasco, M. J. Mulligan, R. Compans, R. Ahmed, P. C. Wilson, Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection. J. Exp. Med.208, 181–193 (2011).
56
C. S.-F. Cheung, A. Fruehwirth, P. C. G. Paparoditis, C.-H. Shen, M. Foglierini, M. G. Joyce, K. Leung, L. Piccoli, R. Rawi, C. Silacci-Fregni, Y. Tsybovsky, R. Verardi, L. Wang, S. Wang, E. S. Yang, B. Zhang, Y. Zhang, G.-Y. Chuang, D. Corti, J. R. Mascola, L. Shapiro, P. D. Kwong, A. Lanzavecchia, T. Zhou, Identification and structure of a multidonor class of head-directed influenza-neutralizing antibodies reveal the mechanism for its recurrent elicitation. Cell Rep.32, 108088 (2020).
57
K. M. Gostic, M. Ambrose, M. Worobey, J. O. Lloyd-Smith, Potent protection against H5N1 and H7N9 influenza via childhood hemagglutinin imprinting. Science354, 722–726 (2016).
58
J. Quandt, A. Muik, N. Salisch, B. G. Lui, S. Lutz, K. Krüger, A.-K. Wallisch, P. Adams-Quack, M. Bacher, A. Finlayson, O. Ozhelvaci, I. Vogler, K. Grikscheit, S. Hoehl, U. Goetsch, S. Ciesek, Ö. Türeci, U. Sahin, Omicron BA.1 breakthrough infection drives cross-variant neutralization and memory B cell formation against conserved epitopes. Sci. Immunol.7, eabq2427 (2022).
59
M. Gagne, J. I. Moliva, K. E. Foulds, S. F. Andrew, B. J. Flynn, A. P. Werner, D. A. Wagner, I.-T. Teng, B. C. Lin, C. Moore, N. Jean-Baptiste, R. Carroll, S. L. Foster, M. Patel, M. Ellis, V.-V. Edara, N. V. Maldonado, M. Minai, L. McCormick, C. C. Honeycutt, B. M. Nagata, K. W. Bock, C. N. M. Dulan, J. Cordon, D. R. Flebbe, J. M. Todd, E. McCarthy, L. Pessaint, A. Van Ry, B. Narvaez, D. Valentin, A. Cook, A. Dodson, K. Steingrebe, S. T. Nurmukhambetova, S. Godbole, A. R. Henry, F. Laboune, J. Roberts-Torres, C. G. Lorang, S. Amin, J. Trost, M. Naisan, M. Basappa, J. Willis, L. Wang, W. Shi, N. A. Doria-Rose, Y. Zhang, E. S. Yang, K. Leung, S. O’Dell, S. D. Schmidt, A. S. Olia, C. Liu, D. R. Harris, G.-Y. Chuang, G. Stewart-Jones, I. Renzi, Y.-T. Lai, A. Malinowski, K. Wu, J. R. Mascola, A. Carfi, P. D. Kwong, D. K. Edwards, M. G. Lewis, H. Andersen, K. S. Corbett, M. C. Nason, A. B. McDermott, M. S. Suthar, I. N. Moore, M. Roederer, N. J. Sullivan, D. C. Douek, R. A. Seder, mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits similar B cell expansion, neutralizing responses, and protection from Omicron. Cell185, 1556–1571.e18 (2022).
60
K. S. Corbett, M. Gagne, D. A. Wagner, S. O’ Connell, S. R. Narpala, D. R. Flebbe, S. F. Andrew, R. L. Davis, B. Flynn, T. S. Johnston, C. D. Stringham, L. Lai, D. Valentin, A. Van Ry, Z. Flinchbaugh, A. P. Werner, J. I. Moliva, M. Sriparna, S. O’Dell, S. D. Schmidt, C. Tucker, A. Choi, M. Koch, K. W. Bock, M. Minai, B. M. Nagata, G. S. Alvarado, A. R. Henry, F. Laboune, C. A. Schramm, Y. Zhang, E. S. Yang, L. Wang, M. Choe, S. Boyoglu-Barnum, S. Wei, E. Lamb, S. T. Nurmukhambetova, S. J. Provost, M. M. Donaldson, J. Marquez, J. M. Todd, A. Cook, A. Dodson, A. Pekosz, E. Boritz, A. Ploquin, N. Doria-Rose, L. Pessaint, H. Andersen, K. E. Foulds, J. Misasi, K. Wu, A. Carfi, M. C. Nason, J. Mascola, I. N. Moore, D. K. Edwards, M. G. Lewis, M. S. Suthar, M. Roederer, A. McDermott, D. C. Douek, N. J. Sullivan, B. S. Graham, R. A. Seder, Protection against SARS-CoV-2 Beta variant in mRNA-1273 vaccine-boosted nonhuman primates. Science374, 1343–1353 (2021).
61
P. S. Arunachalam, Y. Feng, U. Ashraf, M. Hu, A. C. Walls, V. V. Edara, V. I. Zarnitsyna, P. P. Aye, N. Golden, M. C. Miranda, K. W. M. Green, B. M. Threeton, N. J. Maness, B. J. Beddingfield, R. P. Bohm, S. E. Scheuermann, K. Goff, J. Dufour, K. Russell-Lodrigue, E. Kepl, B. Fiala, S. Wrenn, R. Ravichandran, D. Ellis, L. Carter, K. Rogers, L. M. Shirreff, D. E. Ferrell, N. R. Deb Adhikary, J. Fontenot, H. L. Hammond, M. Frieman, A. Grifoni, A. Sette, D. T. O’Hagan, R. Van Der Most, R. Rappuoli, F. Villinger, H. Kleanthous, J. Rappaport, M. S. Suthar, D. Veesler, T. T. Wang, N. P. King, B. Pulendran, Durable protection against the SARS-CoV-2 Omicron variant is induced by an adjuvanted subunit vaccine. Sci. Transl. Med.14, eabq4130 (2022).
62
E. K. Accorsi, A. Britton, K. E. Fleming-Dutra, Z. R. Smith, N. Shang, G. Derado, J. Miller, S. J. Schrag, J. R. Verani, Association between 3 doses of mRNA COVID-19 vaccine and symptomatic infection caused by the SARS-CoV-2 Omicron and Delta variants. JAMA327, 639–651 (2022).
63
H. F. Tseng, B. K. Ackerson, Y. Luo, L. S. Sy, C. A. Talarico, Y. Tian, K. J. Bruxvoort, J. E. Tubert, A. Florea, J. H. Ku, G. S. Lee, S. K. Choi, H. S. Takhar, M. Aragones, L. Qian, Effectiveness of mRNA-1273 against SARS-CoV-2 Omicron and Delta variants. Nat. Med.28, 1063–1071 (2022).
64
R. Pajon, N. A. Doria-Rose, X. Shen, S. D. Schmidt, S. O’Dell, C. McDanal, W. Feng, J. Tong, A. Eaton, M. Maglinao, H. Tang, K. E. Manning, V.-V. Edara, L. Lai, M. Ellis, K. M. Moore, K. Floyd, S. L. Foster, C. M. Posavad, R. L. Atmar, K. E. Lyke, T. Zhou, L. Wang, Y. Zhang, M. R. Gaudinski, W. P. Black, I. Gordon, M. Guech, J. E. Ledgerwood, J. N. Misasi, A. Widge, N. J. Sullivan, P. C. Roberts, J. H. Beigel, B. Korber, L. R. Baden, H. El Sahly, S. Chalkias, H. Zhou, J. Feng, B. Girard, R. Das, A. Aunins, D. K. Edwards, M. S. Suthar, J. R. Mascola, D. C. Montefiori, SARS-CoV-2 omicron variant neutralization after mRNA-1273 booster vaccination. N. Engl. J. Med.386, 1088–1091 (2022).
65
J. E. Bowen, K. R. Sprouse, A. C. Walls, I. G. Mazzitelli, J. K. Logue, N. M. Franko, K. Ahmed, A. Shariq, E. Cameroni, A. Gori, A. Bori, C. M. Posavad, J. M. Dan, Z. Zhang, D. Weiskopf, A. Sette, S. Crotty, N. T. Iqbal, D. Corti, J. Geffner, R. Grifantini, H. Y. Chu, D. Veesler, Omicron BA.1 and BA.2 neutralizing activity elicited by a comprehensive panel of human vaccines. bioRxiv 484542 (2022); .
66
A. Rössler, L. Knabl, D. von Laer, J. Kimpel, Neutralization profile after recovery from SARS-CoV-2 omicron infection. N. Engl. J. Med.386, 1764–1766 (2022).
67
I.-J. Lee, C.-P. Sun, P.-Y. Wu, Y.-H. Lan, I.-H. Wang, W.-C. Liu, S.-C. Tseng, S.-I. Tsung, Y.-C. Chou, M. Kumari, Y.-W. Chang, H.-F. Chen, Y.-S. Lin, T.-Y. Chen, C.-W. Chiu, C.-H. Hsieh, C.-Y. Chuang, C.-C. Lin, C.-M. Cheng, H.-T. Lin, W.-Y. Chen, P.-C. Chiang, C.-C. Lee, J. C. Liao, H.-C. Wu, M.-H. Tao, Omicron-specific mRNA vaccine induced potent neutralizing antibody against Omicron but not other SARS-CoV-2 variants. bioRxiv 478406 (2022); .
68
S. I. Richardson, V. S. Madzorera, H. Spencer, N. P. Manamela, M. A. van der Mescht, B. E. Lambson, B. Oosthuysen, F. Ayres, Z. Makhado, T. Moyo-Gwete, N. Mzindle, T. Motlou, A. Strydom, A. Mendes, H. Tegally, Z. de Beer, T. Roma de Villiers, A. Bodenstein, G. van den Berg, M. Venter, T. de Oliviera, V. Ueckermann, T. M. Rossouw, M. T. Boswell, P. L. Moore, SARS-CoV-2 Omicron triggers cross-reactive neutralization and Fc effector functions in previously vaccinated, but not unvaccinated, individuals. Cell Host Microbe30, 880–886.e4 (2022).
69
K. Stiasny, I. Medits, D. Springer, M. Graninger, J. Camp, E. Höltl, S. Aberle, M. Traugott, W. Hoepler, J. Deutsch, O. Lammel, C. Borsodi, A. Zoufaly, L. Weseslindtner, J. Aberle, E. Puchhammer, Human primary Omicron BA.1 and BA.2 infections result in sub-lineage-specific neutralization. Research Square (2022); .
70
A. C. Walls, M. C. Miranda, A. Schäfer, M. N. Pham, A. Greaney, P. S. Arunachalam, M.-J. Navarro, M. A. Tortorici, K. Rogers, M. A. O’Connor, L. Shirreff, D. E. Ferrell, J. Bowen, N. Brunette, E. Kepl, S. K. Zepeda, T. Starr, C.-L. Hsieh, B. Fiala, S. Wrenn, D. Pettie, C. Sydeman, K. R. Sprouse, M. Johnson, A. Blackstone, R. Ravichandran, C. Ogohara, L. Carter, S. W. Tilles, R. Rappuoli, S. R. Leist, D. R. Martinez, M. Clark, R. Tisch, D. T. O’Hagan, R. Van Der Most, W. C. Van Voorhis, D. Corti, J. S. McLellan, H. Kleanthous, T. P. Sheahan, K. D. Smith, D. H. Fuller, F. Villinger, J. Bloom, B. Pulendran, R. S. Baric, N. P. King, D. Veesler, Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. Cell184, 5432–5447.e16 (2021).
71
A. A. Cohen, P. N. P. Gnanapragasam, Y. E. Lee, P. R. Hoffman, S. Ou, L. M. Kakutani, J. R. Keeffe, H.-J. Wu, M. Howarth, A. P. West, C. O. Barnes, M. C. Nussenzweig, P. J. Bjorkman, Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice. Science371, 735–741 (2021).
72
S. Chalkias, F. Eder, B. Essink, S. Khetan, B. Nestorova, J. Feng, X. Chen, Y. Chang, H. Zhou, D. Montefiori, D. K. Edwards, B. Girard, R. Pajon, B. Leav, S. R. Walsh, L. R. Baden, J. M. Miller, R. Das, Safety, immunogenicity and antibody persistence of a bivalent Beta-containing booster vaccine. Research Square (2022); .
73
S. S. M. Cheng, C. K. P. Mok, J. K. C. Li, S. S. Ng, B. H. S. Lam, T. Jeevan, A. Kandeil, A. Pekosz, K. C. K. Chan, L. C. H. Tsang, F. W. Ko, C. Chen, K. Yiu, L. L. H. Luk, K. K. P. Chan, R. J. Webby, L. L. M. Poon, D. S. C. Hui, M. Peiris, Plaque-neutralizing antibody to BA.2.12.1, BA.4 and BA.5 in individuals with three doses of BioNTech or CoronaVac vaccines, natural infection and breakthrough infection. J. Clin. Virol.156, 105273 (2022).
74
W. B. Alsoussi, S. K. Malladi, J. Q. Zhou, Z. Liu, B. Ying, W. Kim, A. J. Schmitz, T. Lei, S. C. Horvath, A. J. Sturtz, K. M. McIntire, B. Evavold, F. Han, S. M. Scheaffer, I. F. Fox, L. Parra-Rodriguez, R. Nachbagauer, B. Nestorova, S. Chalkias, C. W. Farnsworth, M. K. Klebert, I. Pusic, B. S. Strnad, W. D. Middleton, S. A. Teefey, S. P. J. Whelan, M. S. Diamond, R. Paris, J. A. O’Halloran, R. M. Presti, J. S. Turner, A. H. Ellebedy, SARS-CoV-2 Omicron boosting induces de novo B cell response in humans. bioRxiv 509040 (2022); .
75
C. Gaebler, Z. Wang, J. C. C. Lorenzi, F. Muecksch, S. Finkin, M. Tokuyama, A. Cho, M. Jankovic, D. Schaefer-Babajew, T. Y. Oliveira, M. Cipolla, C. Viant, C. O. Barnes, Y. Bram, G. Breton, T. Hägglöf, P. Mendoza, A. Hurley, M. Turroja, K. Gordon, K. G. Millard, V. Ramos, F. Schmidt, Y. Weisblum, D. Jha, M. Tankelevich, G. Martinez-Delgado, J. Yee, R. Patel, J. Dizon, C. Unson-O’Brien, I. Shimeliovich, D. F. Robbiani, Z. Zhao, A. Gazumyan, R. E. Schwartz, T. Hatziioannou, P. J. Bjorkman, S. Mehandru, P. D. Bieniasz, M. Caskey, M. C. Nussenzweig, Evolution of antibody immunity to SARS-CoV-2. Nature591, 639–644 (2021).
76
Z. Wang, F. Muecksch, D. Schaefer-Babajew, S. Finkin, C. Viant, C. Gaebler, H.-H. Hoffmann, C. O. Barnes, M. Cipolla, V. Ramos, T. Y. Oliveira, A. Cho, F. Schmidt, J. Da Silva, E. Bednarski, L. Aguado, J. Yee, M. Daga, M. Turroja, K. G. Millard, M. Jankovic, A. Gazumyan, Z. Zhao, C. M. Rice, P. D. Bieniasz, M. Caskey, T. Hatziioannou, M. C. Nussenzweig, Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection. Nature595, 426–431 (2021).
77
D. Pinto, M. M. Sauer, N. Czudnochowski, J. S. Low, M. A. Tortorici, M. P. Housley, J. Noack, A. C. Walls, J. E. Bowen, B. Guarino, L. E. Rosen, J. di Iulio, J. Jerak, H. Kaiser, S. Islam, S. Jaconi, N. Sprugasci, K. Culap, R. Abdelnabi, C. Foo, L. Coelmont, I. Bartha, S. Bianchi, C. Silacci-Fregni, J. Bassi, R. Marzi, E. Vetti, A. Cassotta, A. Ceschi, P. Ferrari, P. E. Cippà, O. Giannini, S. Ceruti, C. Garzoni, A. Riva, F. Benigni, E. Cameroni, L. Piccoli, M. S. Pizzuto, M. Smithey, D. Hong, A. Telenti, F. A. Lempp, J. Neyts, C. Havenar-Daughton, A. Lanzavecchia, F. Sallusto, G. Snell, H. W. Virgin, M. Beltramello, D. Corti, D. Veesler, Broad betacoronavirus neutralization by a stem helix-specific human antibody. Science373, 1109–1116 (2021).
78
J. S. Low, J. Jerak, M. A. Tortorici, M. McCallum, D. Pinto, A. Cassotta, M. Foglierini, F. Mele, R. Abdelnabi, B. Weynand, J. Noack, M. Montiel-Ruiz, S. Bianchi, F. Benigni, N. Sprugasci, A. Joshi, J. E. Bowen, A. C. Walls, D. Jarrossay, D. Morone, P. Paparoditis, C. Garzoni, P. Ferrari, A. Ceschi, J. Neyts, L. A. Purcell, G. Snell, D. Corti, A. Lanzavecchia, D. Veesler, F. Sallusto, ACE2 engagement exposes the fusion peptide to pan-coronavirus neutralizing antibodies. bioRxiv 486377 (2022); .
79
R. Marzi, J. Bassi, C. Silacci-Fregni, I. Bartha, F. Muoio, K. Culap, N. Sprugasci, G. Lombardo, C. Saliba, E. Cameroni, A. Cassotta, J. S. Low, A. C. Walls, M. McCallum, M. A. Tortorici, J. E. Bowen, E. A. Dellota, J. R. Dillen, N. Czudnochowski, L. Pertusini, T. Terrot, V. Lepori, M. Tarkowski, A. Riva, M. Biggiogero, A. F. Pellanda, C. Garzoni, P. Ferrari, A. Ceschi, O. Giannini, C. Havenar-Daughton, A. Telenti, A. Arvin, H. W. Virgin, F. Sallusto, D. Veesler, A. Lanzavecchia, D. Corti, L. Piccoli, Maturation of SARS-CoV-2 Spike-specific memory B cells drives resilience to viral escape. bioRxiv 509852 (2022); .
80
S. Chalkias, C. Harper, K. Vrbicky, S. R. Walsh, B. Essink, A. Brosz, N. McGhee, J. E. Tomassini, X. Chen, Y. Chang, A. Sutherland, D. C. Montefiori, B. Girard, D. K. Edwards, J. Feng, H. Zhou, L. R. Baden, J. M. Miller, R. Das, A bivalent omicron-containing booster vaccine against covid-19. N. Engl. J. Med.387, 1279–1291 (2022).
81
S. M. Scheaffer, D. Lee, B. Whitener, B. Ying, K. Wu, H. Jani, P. Martin, N. J. Amato, L. E. Avena, D. M. Berrueta, S. D. Schmidt, S. O’Dell, A. Nasir, G.-Y. Chuang, G. Stewart-Jones, R. A. Koup, N. A. Doria-Rose, A. Carfi, S. M. Elbashir, L. B. Thackray, D. K. Edwards, M. S. Diamond, Bivalent SARS-CoV-2 mRNA vaccines increase breadth of neutralization and protect against the BA.5 Omicron variant. bioRxiv 507614 (2022); .
82
A. Muik, B. G. Lui, M. Bacher, A.-K. Wallisch, A. Toker, C. I. C. Couto, A. Güler, V. Mampilli, G. J. Schmitt, J. Mottl, T. Ziegenhals, S. Fesser, J. Reinholz, F. Wernig, K.-G. Schraut, H. Hefesha, H. Cai, Q. Yang, K. C. Walzer, J. Grosser, S. Strauss, A. Finlayson, K. Krüger, O. Ozhelvaci, K. Grikscheit, N. Kohmer, S. Ciesek, K. A. Swanson, A. B. Vogel, Ö. Türeci, U. Sahin, Exposure to BA.4/BA.5 Spike glycoprotein drives pan-Omicron neutralization in vaccine-experienced humans and mice. bioRxiv 508818 (2022); .
83
A. A. Cohen, N. van Doremalen, A. J. Greaney, H. Andersen, A. Sharma, T. N. Starr, J. R. Keeffe, C. Fan, J. E. Schulz, P. N. P. Gnanapragasam, L. M. Kakutani, A. P. West, G. Saturday, Y. E. Lee, H. Gao, C. A. Jette, M. G. Lewis, T. K. Tan, A. R. Townsend, J. D. Bloom, V. J. Munster, P. J. Bjorkman, Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models. bioRxiv 485875 (2022); .
84
D. R. Martinez, A. Schäfer, S. R. Leist, G. De la Cruz, A. West, E. N. Atochina-Vasserman, L. C. Lindesmith, N. Pardi, R. Parks, M. Barr, D. Li, B. Yount, K. O. Saunders, D. Weissman, B. F. Haynes, S. A. Montgomery, R. S. Baric, Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice. Science373, 991–998 (2021).
85
D. Li, D. R. Martinez, A. Schäfer, H. Chen, M. Barr, L. L. Sutherland, E. Lee, R. Parks, D. Mielke, W. Edwards, A. Newman, K. W. Bock, M. Minai, B. M. Nagata, M. Gagne, D. Douek, C. T. DeMarco, T. N. Denny, T. H. Oguin, A. Brown, W. Rountree, Y. Wang, K. Mansouri, R. J. Edwards, G. Ferrari, G. D. Sempowski, A. Eaton, J. Tang, D. W. Cain, S. Santra, N. Pardi, D. Weissman, M. Tomai, C. Fox, I. N. Moore, H. Andersen, M. G. Lewis, H. Golding, S. Khurana, R. Seder, R. S. Baric, D. C. Montefiori, K. O. Saunders, B. F. Haynes, Breadth of SARS-CoV-2 neutralization and protection induced by a nanoparticle vaccine. bioRxiv 477915 (2022); .
86
L.-F. Wang, C. W. Tan, W. N. Chia, F. Zhu, B. Young, N. Chantasrisawad, S.-H. Hwa, A. Y.-Y. Yeoh, B. L. Lim, W. C. Yap, S. K. Pada, S. Y. Tan, W. Jantarabenjakul, S. Chen, J. Zhang, Y. Y. Mah, V. Chen, M. Chen, S. Wacharapluesadee, COMMIT-KZN Team, O. Putcharoen, D. Lye, Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. Research Square (2022); .
87
D. R. Martinez, A. Schäfer, S. Gobeil, D. Li, G. De la Cruz, R. Parks, X. Lu, M. Barr, V. Stalls, K. Janowska, E. Beaudoin, K. Manne, K. Mansouri, R. J. Edwards, K. Cronin, B. Yount, K. Anasti, S. A. Montgomery, J. Tang, H. Golding, S. Shen, T. Zhou, P. D. Kwong, B. S. Graham, J. R. Mascola, D. C. Montefiori, S. M. Alam, G. Sempowski, G. D. Sempowski, S. Khurana, K. Wiehe, K. O. Saunders, P. Acharya, B. F. Haynes, R. S. Baric, A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice. Sci. Transl. Med.14, eabj7125 (2022).
88
C. G. Rappazzo, L. V. Tse, C. I. Kaku, D. Wrapp, M. Sakharkar, D. Huang, L. M. Deveau, T. J. Yockachonis, A. S. Herbert, M. B. Battles, C. M. O’Brien, M. E. Brown, J. C. Geoghegan, J. Belk, L. Peng, L. Yang, Y. Hou, T. D. Scobey, D. R. Burton, D. Nemazee, J. M. Dye, J. E. Voss, B. M. Gunn, J. S. McLellan, R. S. Baric, L. E. Gralinski, L. M. Walker, Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody. Science371, 823–829 (2021).
89
T. Mao, B. Israelow, A. Suberi, L. Zhou, M. Reschke, M. A. Peña-Hernández, H. Dong, R. J. Homer, W. M. Saltzman, A. Iwasaki, Unadjuvanted intranasal spike vaccine booster elicits robust protective mucosal immunity against sarbecoviruses. bioRxiv 477597 (2022); .
90
J. E. Oh, E. Song, M. Moriyama, P. Wong, S. Zhang, R. Jiang, S. Strohmeier, S. H. Kleinstein, F. Krammer, A. Iwasaki, Intranasal priming induces local lung-resident B cell populations that secrete protective mucosal antiviral IgA. Sci. Immunol.6, eabj5129 (2021).
91
S. N. Langel, S. Johnson, C. I. Martinez, S. N. Tedjakusuma, N. Peinovich, E. G. Dora, P. J. Kuehl, H. Irshad, E. G. Barrett, A. D. Werts, S. N. Tucker, Adenovirus type 5 SARS-CoV-2 vaccines delivered orally or intranasally reduced disease severity and transmission in a hamster model. Sci. Transl. Med.14, eabn6868 (2022).
92
A. O. Hassan, F. Feldmann, H. Zhao, D. T. Curiel, A. Okumura, T.-L. Tang-Huau, J. B. Case, K. Meade-White, J. Callison, R. E. Chen, J. Lovaglio, P. W. Hanley, D. P. Scott, D. H. Fremont, H. Feldmann, M. S. Diamond, A single intranasal dose of chimpanzee adenovirus-vectored vaccine protects against SARS-CoV-2 infection in rhesus macaques. Cell Rep. Med.2, 100230 (2021).
93
F. A. Lempp, L. B. Soriaga, M. Montiel-Ruiz, F. Benigni, J. Noack, Y.-J. Park, S. Bianchi, A. C. Walls, J. E. Bowen, J. Zhou, H. Kaiser, A. Joshi, M. Agostini, M. Meury, E. DellotaJr., S. Jaconi, E. Cameroni, J. Martinez-Picado, J. Vergara-Alert, N. Izquierdo-Useros, H. W. Virgin, A. Lanzavecchia, D. Veesler, L. A. Purcell, A. Telenti, D. Corti, Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies. Nature598, 342–347 (2021).
94
J. Lan, J. Ge, J. Yu, S. Shan, H. Zhou, S. Fan, Q. Zhang, X. Shi, Q. Wang, L. Zhang, X. Wang, Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature581, 215–220 (2020).
95
D. J. McCulloch, A. E. Kim, N. C. Wilcox, J. K. Logue, A. L. Greninger, J. A. Englund, H. Y. Chu, Comparison of unsupervised home self-collected midnasal swabs with clinician-collected nasopharyngeal swabs for detection of SARS-CoV-2 infection. JAMA Netw. Open3, e2016382 (2020).
96
A. A. Weil, K. G. Luiten, A. M. Casto, J. C. Bennett, J. O’Hanlon, P. D. Han, L. S. Gamboa, E. McDermot, M. Truong, G. S. Gottlieb, Z. Acker, C. R. Wolf, A. Magedson, E. J. Chow, N. K. Lo, L. C. Pothan, D. McDonald, T. C. Wright, K. M. McCaffrey, M. D. Figgins, J. A. Englund, M. Boeckh, C. M. Lockwood, D. A. Nickerson, J. Shendure, T. Bedford, J. P. Hughes, L. M. Starita, H. Y. Chu, Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus. Nat. Commun.13, 5240 (2022).
97
E. Olmedillas, C. J. Mann, W. Peng, Y. T. Wang, R. D. Avalos, Structure-based design of a highly stable, covalently-linked SARS-CoV-2 spike trimer with improved structural properties and immunogenicity. bioRxiv 441046 (2021); .
98
K. H. D. Crawford, R. Eguia, A. S. Dingens, A. N. Loes, K. D. Malone, C. R. Wolf, H. Y. Chu, M. A. Tortorici, D. Veesler, M. Murphy, D. Pettie, N. P. King, A. B. Balazs, J. D. Bloom, Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays. Viruses12, 513 (2020).
99
C. Suloway, J. Pulokas, D. Fellmann, A. Cheng, F. Guerra, J. Quispe, S. Stagg, C. S. Potter, B. Carragher, Automated molecular microscopy: The new Leginon system. J. Struct. Biol.151, 41–60 (2005).
100
D. Tegunov, P. Cramer, Real-time cryo-electron microscopy data preprocessing with Warp. Nat. Methods16, 1146–1152 (2019).
101
A. Punjani, J. L. Rubinstein, D. J. Fleet, M. A. Brubaker, cryoSPARC: Algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods14, 290–296 (2017).
102
J. Zivanov, T. Nakane, B. O. Forsberg, D. Kimanius, W. J. Hagen, E. Lindahl, S. H. Scheres, New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife7, e42166 (2018).
103
A. Punjani, H. Zhang, D. J. Fleet, Non-uniform refinement: Adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods17, 1214–1221 (2020).
104
J. Zivanov, T. Nakane, S. H. W. Scheres, A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis. IUCrJ6, 5–17 (2019).
105
S. Chen, G. McMullan, A. R. Faruqi, G. N. Murshudov, J. M. Short, S. H. Scheres, R. Henderson, High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy135, 24–35 (2013).
106
P. B. Rosenthal, R. Henderson, Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol.333, 721–745 (2003).
107
E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, T. E. Ferrin, UCSF Chimera—A visualization system for exploratory research and analysis. J. Comput. Chem.25, 1605–1612 (2004).
108
P. Emsley, B. Lohkamp, W. G. Scott, K. Cowtan, Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr.66, 486–501 (2010).
109
B. Frenz, S. Rämisch, A. J. Borst, A. C. Walls, J. Adolf-Bryfogle, W. R. Schief, D. Veesler, F. DiMaio, Automatically Fixing Errors in Glycoprotein Structures with Rosetta. Structure27, 134–139.e3 (2019).
110
R. Y. Wang, Y. Song, B. A. Barad, Y. Cheng, J. S. Fraser, F. DiMaio, Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife5, e17219 (2016).
111
G. Dias De Melo, F. Lazarini, S. Levallois, C. Hautefort, V. Michel, F. Larrous, B. Verillaud, C. Aparicio, S. Wagner, G. Gheusi, L. Kergoat, E. Kornobis, T. Cokelaer, R. Hervochon, Y. Madec, E. Roze, D. Salmon, H. Bourhy, M. Lecuit, P.-M. Lledo, COVID-19-associated olfactory dysfunction reveals SARS-CoV-2 neuroinvasion and persistence in the olfactory system. bioRxiv 388819 (2020); .
112
R. Boudewijns, H. J. Thibaut, S. J. F. Kaptein, R. Li, V. Vergote, L. Seldeslachts, J. Van Weyenbergh, C. De Keyzer, L. Bervoets, S. Sharma, L. Liesenborghs, J. Ma, S. Jansen, D. Van Looveren, T. Vercruysse, X. Wang, D. Jochmans, E. Martens, K. Roose, D. De Vlieger, B. Schepens, T. Van Buyten, S. Jacobs, Y. Liu, J. Martí-Carreras, B. Vanmechelen, T. Wawina-Bokalanga, L. Delang, J. Rocha-Pereira, L. Coelmont, W. Chiu, P. Leyssen, E. Heylen, D. Schols, L. Wang, L. Close, J. Matthijnssens, M. Van Ranst, V. Compernolle, G. Schramm, K. Van Laere, X. Saelens, N. Callewaert, G. Opdenakker, P. Maes, B. Weynand, C. Cawthorne, G. Vande Velde, Z. Wang, J. Neyts, K. Dallmeier, STAT2 signaling restricts viral dissemination but drives severe pneumonia in SARS-CoV-2 infected hamsters. Nat. Commun.11, 5838 (2020).
113
L. Sanchez-Felipe, T. Vercruysse, S. Sharma, J. Ma, V. Lemmens, D. Van Looveren, M. P. Arkalagud Javarappa, R. Boudewijns, B. Malengier-Devlies, L. Liesenborghs, S. J. F. Kaptein, C. De Keyzer, L. Bervoets, S. Debaveye, M. Rasulova, L. Seldeslachts, L.-H. Li, S. Jansen, M. B. Yakass, B. E. Verstrepen, K. P. Böszörményi, G. Kiemenyi-Kayere, N. van Driel, O. Quaye, X. Zhang, S. Ter Horst, N. Mishra, W. Deboutte, J. Matthijnssens, L. Coelmont, C. Vandermeulen, E. Heylen, V. Vergote, D. Schols, Z. Wang, W. Bogers, T. Kuiken, E. Verschoor, C. Cawthorne, K. Van Laere, G. Opdenakker, G. Vande Velde, B. Weynand, D. E. Teuwen, P. Matthys, J. Neyts, H. Jan Thibaut, K. Dallmeier, A single-dose live-attenuated YF17D-vectored SARS-CoV-2 vaccine candidate. Nature590, 320–325 (2021).
114
S. J. F. Kaptein, S. Jacobs, L. Langendries, L. Seldeslachts, S. Ter Horst, L. Liesenborghs, B. Hens, V. Vergote, E. Heylen, K. Barthelemy, E. Maas, C. De Keyzer, L. Bervoets, J. Rymenants, T. Van Buyten, X. Zhang, R. Abdelnabi, J. Pang, R. Williams, H. J. Thibaut, K. Dallmeier, R. Boudewijns, J. Wouters, P. Augustijns, N. Verougstraete, C. Cawthorne, J. Breuer, C. Solas, B. Weynand, P. Annaert, I. Spriet, G. Vande Velde, J. Neyts, J. Rocha-Pereira, L. Delang, Favipiravir at high doses has potent antiviral activity in SARS-CoV-2-infected hamsters, whereas hydroxychloroquine lacks activity. Proc. Natl. Acad. Sci. U.S.A.117, 26955–26965 (2020).
115
V. M. Corman, O. Landt, M. Kaiser, R. Molenkamp, A. Meijer, D. K. Chu, T. Bleicker, S. Brünink, J. Schneider, M. L. Schmidt, D. G. Mulders, B. L. Haagmans, B. van der Veer, S. van den Brink, L. Wijsman, G. Goderski, J.-L. Romette, J. Ellis, M. Zambon, M. Peiris, H. Goossens, C. Reusken, M. P. Koopmans, C. Drosten, Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill.25, 2000045 (2020).
116
B. D. Lindenbach, Measuring HCV infectivity produced in cell culture and in vivo. Methods Mol. Biol.510, 329–336 (2009).
117
L. J. Reed, H. Muench, A simple method of estimating fifty per cent endpoints12. Am. J. Epidemiol.27, 493–497 (1938).
118
T. N. Starr, A. J. Greaney, W. W. Hannon, A. N. Loes, K. Hauser, J. R. Dillen, E. Ferri, A. G. Farrell, B. Dadonaite, M. McCallum, K. A. Matreyek, D. Corti, D. Veesler, G. Snell, J. D. Bloom, Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution. bioRxiv 481899 (2022); .
119
E. C. Thomson, L. E. Rosen, J. G. Shepherd, R. Spreafico, A. da Silva Filipe, J. A. Wojcechowskyj, C. Davis, L. Piccoli, D. J. Pascall, J. Dillen, S. Lytras, N. Czudnochowski, R. Shah, M. Meury, N. Jesudason, A. De Marco, K. Li, J. Bassi, A. O’Toole, D. Pinto, R. M. Colquhoun, K. Culap, B. Jackson, F. Zatta, A. Rambaut, S. Jaconi, V. B. Sreenu, J. Nix, I. Zhang, R. F. Jarrett, W. G. Glass, M. Beltramello, K. Nomikou, M. Pizzuto, L. Tong, E. Cameroni, T. I. Croll, N. Johnson, J. Di Iulio, A. Wickenhagen, A. Ceschi, A. M. Harbison, D. Mair, P. Ferrari, K. Smollett, F. Sallusto, S. Carmichael, C. Garzoni, J. Nichols, M. Galli, J. Hughes, A. Riva, A. Ho, M. Schiuma, M. G. Semple, P. J. M. Openshaw, E. Fadda, J. K. Baillie, J. D. Chodera, S. J. Rihn, S. J. Lycett, H. W. Virgin, A. Telenti, D. Corti, D. L. Robertson, G. Snell; ISARIC4C Investigators; COVID-19 Genomics UK (COG-UK) Consortium, Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell184, 1171–1187.e20 (2021).
120
T. I. Croll, ISOLDE: A physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D Struct. Biol.74, 519–530 (2018).
121
J. A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K. E. Hauser, C. Simmerling, Ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. J. Chem. Theory Comput.11, 3696–3713 (2015).
122
K. N. Kirschner, A. B. Yongye, S. M. Tschampel, J. González-Outeiriño, C. R. Daniels, B. L. Foley, R. J. Woods, GLYCAM06: A generalizable biomolecular force field. Carbohydrates. J. Comput. Chem.29, 622–655 (2008).
123
W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, M. L. Klein, Comparison of simple potential functions for simulating liquid water. J. Chem. Phys.79, 926–935 (1983).
124
I. S. Joung, T. E. Cheatham3rd, Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J. Phys. Chem. B112, 9020–9041 (2008).
125
D. R. Roe, T. E. Cheatham3rd, Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data. J. Comput. Chem.39, 2110–2117 (2018).
126
W. Humphrey, A. Dalke, K. Schulten, VMD: Visual molecular dynamics. J. Mol. Graph.14, 33–38, 27–28 (1996).

Plaats een reactie ...

Reageer op "Natuurlijke besmetting met coronavirus (Omikron) na vaccinatie geeft uitstekende bescherming, al zijn er twijfels over bescherming door mRNA vaccins tegen nieuwe varianten van Omikron."


Gerelateerde artikelen
 

Gerelateerde artikelen

Covid-19 infectie kan het >> Mediterrane dieet als dagelijks >> Er stierven in Japan beduidend >> Dr. Sabine Hazan mocht eindelijk >> Booster vaccinaties lijken >> Maurice de Hond geeft commentaar >> Opsluiting van kwetsbare mensen >> mRNA vaccinatie tegen coronavirus >> Vitamine-C infusen met hoge >> Hydroxychloroquine plus azithromycine >>