13. Geng Q, Shi K, Ye G, Zhang W, Aihara H, Li F. 2022. Structural basis for
human receptor recognition by SARS-CoV-2 omicron variant BA.1. J Virol
96:e0024922. https://doi.org/10.1128/jvi.00249-22.
14. Rogers TF, Zhao F, Huang D, Beutler N, Burns A, He WT, Limbo O, Smith C,
Song G, Woehl J, Yang L, Abbott RK, Callaghan S, Garcia E, Hurtado J, Parren
M, Peng L, Ramirez S, Ricketts J, Ricciardi MJ, Rawlings SA, Wu NC, Yuan M,
Smith DM, Nemazee D, Teijaro JR, Voss JE, Wilson IA, Andrabi R, Briney B,
Landais E, Sok D, Jardine JG, Burton DR. 2020. Isolation of potent SARS-CoV-2
neutralizing antibodies and protection from disease in a small animal model.
Science 369:956–963. https://doi.org/10.1126/science.abc7520.
15. Yamasoba D, Kimura I, Nasser H, Morioka Y, Nao N, Ito J, Uriu K, Tsuda M,
Zahradnik J, Shirakawa K, Suzuki R, Kishimoto M, Kosugi Y, Kobiyama K,
Hara T, Toyoda M, Tanaka YL, Butlertanaka EP, Shimizu R, Ito H, Wang L,
Oda Y, Orba Y, Sasaki M, Nagata K, Yoshimatsu K, Asakura H, Nagashima
M, Sadamasu K, Yoshimura K, Kuramochi J, Seki M, Fujiki R, Kaneda A,
Shimada T, Nakada TA, Sakao S, Suzuki T, Ueno T, Takaori-Kondo A, Ishii
KJ, Schreiber G, Sawa H, Saito A, Irie T, Tanaka S, Matsuno K, Fukuhara T,
Ikeda T, Sato K, Genotype to Phenotype Japan (G2P-Japan) Consortium.
2022. Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike.
Cell 185:2103–2115.e19. https://doi.org/10.1016/j.cell.2022.04.035.
16. Westendorf K, Žentelis S, Wang L, Foster D, Vaillancourt P, Wiggin M,
Lovett E, van der Lee R, Hendle J, Pustilnik A, Sauder JM, Kraft L, Hwang Y,
Siegel RW, Chen J, Heinz BA, Higgs RE, Kallewaard NL, Jepson K, Goya R,
Smith MA, Collins DW, Pellacani D, Xiang P, de Puyraimond V, Ricicova M,
Devorkin L, Pritchard C, O'Neill A, Dalal K, Panwar P, Dhupar H, Garces FA,
Cohen CA, Dye JM, Huie KE, Badger CV, Kobasa D, Audet J, Freitas JJ,
Hassanali S, Hughes I, Munoz L, Palma HC, Ramamurthy B, Cross RW,
Geisbert TW, Menachery V, Lokugamage K, Borisevich V, et al. 2022. LYCoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants. Cell
Rep 39:110812. https://doi.org/10.1016/j.celrep.2022.110812.
17. Cao Y, Yisimayi A, Jian F, Song W, Xiao T, Wang L, Du S, Wang J, Li Q, Chen
X, Yu Y, Wang P, Zhang Z, Liu P, An R, Hao X, Wang Y, Wang J, Feng R, Sun
H, Zhao L, Zhang W, Zhao D, Zheng J, Yu L, Li C, Zhang N, Wang R, Niu X,
Yang S, Song X, Chai Y, Hu Y, Shi Y, Zheng L, Li Z, Gu Q, Shao F, Huang W,
Jin R, Shen Z, Wang Y, Wang X, Xiao J, Xie XS. 2022. BA.2.12.1, BA.4 and
BA.5 escape antibodies elicited by Omicron infection. Nature 608:
593–602. https://doi.org/10.1038/s41586-022-04980-y.
18. Dong J, Zost SJ, Greaney AJ, Starr TN, Dingens AS, Chen EC, Chen RE, Case JB,
Sutton RE, Gilchuk P, Rodriguez J, Armstrong E, Gainza C, Nargi RS, Binshtein
E, Xie X, Zhang X, Shi PY, Logue J, Weston S, McGrath ME, Frieman MB, Brady
T, Tuffy KM, Bright H, Loo YM, McTamney PM, Esser MT, Carnahan RH,
Diamond MS, Bloom JD, Crowe JE. Jr, 2021. Genetic and structural basis for
SARS-CoV-2 variant neutralization by a two-antibody cocktail. Nat Microbiol
6:1233–1244. https://doi.org/10.1038/s41564-021-00972-2.
19. Yamasoba D, Kosugi Y, Kimura I, Fujita S, Uriu K, Ito J, Sato K, Genotype to
Phenotype Japan (G2P-Japan) Consortium. 2022. Neutralisation sensitivity of SARS-CoV-2 omicron subvariants to therapeutic monoclonal antibodies. Lancet Infectious Diseases 22:942–943. https://doi.org/10.1016/
S1473-3099(22)00365-6.
20. Kumar S, Patel A, Lai L, Chakravarthy C, Valanparambil R, Reddy ES,
Gottimukkala K, Davis-Gardner ME, Edara VV, Linderman S, Nayak K, Dixit
K, Sharma P, Bajpai P, Singh V, Frank F, Cheedarla N, Verkerke HP, Neish
AS, Roback JD, Mantus G, Goel PK, Rahi M, Davis CW, Wrammert J,
Godbole S, Henry AR, Douek DC, Suthar MS, Ahmed R, Ortlund E, Sharma
A, Murali-Krishna K, Chandele A. 2022. Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody. Sci Adv 8:eadd2032. https://doi.org/10.1126/
sciadv.add2032.
21. Iketani S, Liu L, Guo Y, Liu L, Chan JF-W, Huang Y, Wang M, Luo Y, Yu J, Chu
H, Chik KK-H, Yuen TT-T, Yin MT, Sobieszczyk ME, Huang Y, Yuen K-Y, Wang
HH, Sheng Z, Ho DD. 2022. Antibody evasion properties of SARS-CoV-2 Omicron sublineages. Nature 604:553–556. https://doi.org/10.1038/s41586-022
-04594-4.
22. Evans JP, Zeng C, Qu P, Faraone J, Zheng YM, Carlin C, Bednash JS, Zhou
T, Lozanski G, Mallampalli R, Saif LJ, Oltz EM, Mohler PJ, Xu K, Gumina RJ,
Liu SL. 2022. Neutralization of SARS-CoV-2 Omicron sub-lineages BA.1,
BA.1.1, and BA.2. Cell Host Microbe 30:1093–1102.e3. https://doi.org/10
.1016/j.chom.2022.04.014.
23. Wang Q, Iketani S, Li Z, Liu L, Guo Y, Huang Y, Bowen AD, Liu M, Wang M,
Yu J, Valdez R, Lauring AS, Sheng Z, Wang HH, Gordon A, Liu L, Ho DD.
2023. Alarming antibody evasion properties of rising SARS-CoV-2 BQ and
XBB subvariants. Cell 186:279–286.e8. https://doi.org/10.1016/j.cell.2022
.12.018.
June 2023 Volume 97 Issue 6
Journal of Virology
24. Ren Z, Nishimura M, Tjan LH, Furukawa K, Kurahashi Y, Sutandhio S, Aoki K,
Hasegawa N, Arii J, Uto K, Matsui K, Sato I, Saegusa J, Godai N, Takeshita K,
Yamamoto M, Nagashima T, Mori Y. 2022. Large-scale serosurveillance of COVID19 in Japan: acquisition of neutralizing antibodies for Delta but not for Omicron
and requirement of booster vaccination to overcome the Omicron's outbreak.
PLoS One 17:e0266270. https://doi.org/10.1371/journal.pone.0266270.
25. Niwa H, Yamamura K, Miyazaki J. 1991. Efficient selection for high-expression transfectants with a novel eukaryotic vector. Gene 108:193–199.
https://doi.org/10.1016/0378-1119(91)90434-D.
26. Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le
KC, Wrapp D, Lee AG, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV,
Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Lavinder JJ, Ippolito
GC, Maynard JA, Finkelstein IJ, McLellan JS. 2020. Structure-based design of
prefusion-stabilized SARS-CoV-2 spikes. Science 369:1501–1505. https://doi
.org/10.1126/science.abd0826.
27. Matsuyama S, Nao N, Shirato K, Kawase M, Saito S, Takayama I, Nagata N,
Sekizuka T, Katoh H, Kato F, Sakata M, Tahara M, Kutsuna S, Ohmagari N,
Kuroda M, Suzuki T, Kageyama T, Takeda M. 2020. Enhanced isolation of
SARS-CoV-2 by TMPRSS2-expressing cells. Proc Natl Acad Sci U S A 117:
7001–7003. https://doi.org/10.1073/pnas.2002589117.
28. Furukawa K, Tjan LH, Sutandhio S, Kurahashi Y, Iwata S, Tohma Y, Sano S,
Nakamura S, Nishimura M, Arii J, Kiriu T, Yamamoto M, Nagano T, Nishimura
Y, Mori Y. 2021. Cross-neutralizing activity against SARS-CoV-2 variants in
COVID-19 patients: comparison of 4 waves of the pandemic in Japan. Open
Forum Infect Dis 8:ofab430. https://doi.org/10.1093/ofid/ofab430.
29. Mastronarde DN. 2005. Automated electron microscope tomography using
robust prediction of specimen movements. J Struct Biol 152:36–51. https://
doi.org/10.1016/j.jsb.2005.07.007.
30. Yonekura K, Maki-Yonekura S, Naitow H, Hamaguchi T, Takaba K. 2021.
Machine learning-based real-time object locator/evaluator for cryo-EM
data collection. Commun Biol 4:1044. https://doi.org/10.1038/s42003-021
-02577-1.
31. Zivanov J, Nakane T, Forsberg BO, Kimanius D, Hagen WJ, Lindahl E,
Scheres SH. 2018. New tools for automated high-resolution cryo-EM
structure determination in RELION-3. Elife 7:e42166. https://doi.org/10
.7554/eLife.42166.
32. Rohou A, Grigorieff N. 2015. CTFFIND4: fast and accurate defocus estimation
from electron micrographs. J Struct Biol 192:216–221. https://doi.org/10.1016/
j.jsb.2015.08.008.
33. Wagner T, Merino F, Stabrin M, Moriya T, Antoni C, Apelbaum A, Hagel P,
Sitsel O, Raisch T, Prumbaum D, Quentin D, Roderer D, Tacke S, Siebolds
B, Schubert E, Shaikh TR, Lill P, Gatsogiannis C, Raunser S. 2019. SPHIREcrYOLO is a fast and accurate fully automated particle picker for cryo-EM.
Commun Biol 2:218. https://doi.org/10.1038/s42003-019-0437-z.
34. Yin W, Xu Y, Xu P, Cao X, Wu C, Gu C, He X, Wang X, Huang S, Yuan Q, Wu
K, Hu W, Huang Z, Liu J, Wang Z, Jia F, Xia K, Liu P, Wang X, Song B, Zheng
J, Jiang H, Cheng X, Jiang Y, Deng S-J, Xu HE. 2022. Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody. Science 375:
1048–1053. https://doi.org/10.1126/science.abn8863.
35. Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O,
Tunyasuvunakool K, Bates R, Zidek A, Potapenko A, Bridgland A, Meyer
C, Kohl SAA, Ballard AJ, Cowie A, Romera-Paredes B, Nikolov S, Jain R,
Adler J, Back T, Petersen S, Reiman D, Clancy E, Zielinski M, Steinegger
M, Pacholska M, Berghammer T, Bodenstein S, Silver D, Vinyals O,
Senior AW, Kavukcuoglu K, Kohli P, Hassabis D. 2021. Highly accurate
protein structure prediction with AlphaFold. Nature 596:583–589.
https://doi.org/10.1038/s41586-021-03819-2.
36. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng
EC, Ferrin TE. 2004. UCSF Chimera–a visualization system for exploratory
research and analysis. J Comput Chem 25:1605–1612. https://doi.org/10
.1002/jcc.20084.
37. Emsley P, Lohkamp B, Scott WG, Cowtan K. 2010. Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486–501. https://doi
.org/10.1107/S0907444910007493.
38. Liebschner D, Afonine PV, Baker ML, Bunkoczi G, Chen VB, Croll TI, Hintze B,
Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG,
Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell
DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD. 2019.
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D Struct Biol 75:
861–877. https://doi.org/10.1107/S2059798319011471.
39. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH,
Ferrin TE. 2021. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci 30:70–82. https://doi.org/10.1002/pro.3943.
10.1128/jvi.00286-23
16
Downloaded from https://journals.asm.org/journal/jvi on 09 August 2023 by 133.30.169.29.
Neutralizing Antibodies for Variants of SARS-CoV-2
...