CIENCE.ABQ2679_MDAR_REPRODUCIBILITY_CHECK LIST.PDF

Luo, S., Zhang, J., Kreutzberger, A. J. B., Eaton, A., Edwards, R. J., Jing, C., Dai, H.-Q., Sempowski, G. D., Cronin, K., Parks, R., Ye, A. Y., Mansouri, K., Barr, M., Pishesha, N., Williams, A. C., Francisco, L. V., Saminathan, A., Peng, H., Batra, H., Alt, F. W. (2022). Humanized antibody potently neutralizes all SARS-CoV-2 variants by a novel mechanism. bioRxiv , 2022.06.26.497634-2022.06.26.497634.

https://doi.org/10.1101/2022.06.26.497634 https://doi.org/10.1126/SCITRANSLMED.ABJ7125/SUPPL_F

Martinez, D. R., Schäfer, A., Gobeil, S., Li, D., De la Cruz, G., Parks, R., Lu, X., Barr, M., Stalls, V., Janowska, K., Beaudoin, E., Manne, K., Mansouri, K., Edwards, R. J., Cronin, K., Yount, B., Anasti, K., Montgomery, S. A., Tang, J., … Baric, R. S. (2022). A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice. Science TranslationalMedicine , 14(629), 7125–7125.

ILE/SCITRANSLMED.ABJ7125_DATA_FILE_S1.ZIP https://doi.org/10.1016/j.cell.2022.02.023

Milligan, J. C., Davis, C. W., Yu, X., Ilinykh, P. A., Huang, K., Halfmann, P. J., Cross, R. W., Borisevich, V., Agans, K. N., Geisbert, J. B., Chennareddy, C., Goff, A. J., Piper, A. E., Hui, S., Shaffer, K. C. L., Buck, T., Heinrich, M. L., Branco, L. M., Crozier, I., … Saphire, E. O. (2022). Asymmetric and nonstoichiometric glycoprotein recognition by two distinct antibodies results in broad protection against ebolaviruses. Cell , 185(6), 995-1007.e18.

MonoclonalAntibodies:TheOnceandFutureCureforCovid-19

Moreira, T. G., Matos, K. T. F., De Paula, G. S., Santana, T. M. M., Da Mata, R. G., Pansera, F. C., Cortina, A. S., Spinola, M. G., Keppeke, G. D., Jacob, J., Palejwala, V., Chen, K., Izzy, S., Healey, B. C., Rezende, R. M., Dedivitis, R. A., Shailubhai, K., & Weiner, H. L. (2021). Nasal Administration of Anti-CD3 Monoclonal Antibody (Foralumab) Reduces Lung https://doi.org/10.3389/FIMMU.2021.709861/BIBTEX https://doi.org/10.1101/2021.10.13.464254 https://doi.org/10.1038/s41467-023-36028-8 https://doi.org/10.1038/s41467-023-36028-8

Inflammation and Blood Inflammatory Biomarkers in Mild to Moderate COVID-19 Patients: A Pilot Study. Frontiers in Immunology , 12 , 3255–3255.

Park, Y.-J., Marco, A. D., Starr, T. N., Liu, Z., Pinto, D., Walls, A. C., Zatta, F., Zepeda, S. K., Bowen, J., Sprouse, K. S., Joshi, A., Giurdanella, M., Guarino, B., Noack, J., Abdelnabi, R., Foo, S.-Y. C., Lempp, F. A., Benigni, F., Snell, G., Veesler, D. (2021). Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry. bioRxiv , 2021.10.13.464254-2021.10.13.464254.

Parkinson, J., Hard, R., & Wang, W. (2023a). The RESP AI model accelerates the identification of tight-binding antibodies.

NatureCommunications202314:1 , 14(1), 1–18.

Parkinson, J., Hard, R., & Wang, W. (2023b). The RESP AI model accelerates the identification of tight-binding antibodies.

NatureCommunications202314:1 , 14(1), 1–18.

Pinto, D., Park, Y. J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., De Marco, A.,

Peter, A., Guarino, B., Spreafico, R., Cameroni, E., Case, J. B., Chen, R. E., Havenar-Daughton, C., Snell, G., Telenti, A., … Corti, D. (2020). Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature2020

583:7815 , 583(7815), 290–295. https://doi.org/10.1038/s41586020-2349-y https://doi.org/10.1084/JEM.20220638/213286

Planchais, C., Fernández, I., Bruel, T., de Melo, G. D., Prot, M., Beretta, M., Guardado-Calvo, P., Dufloo, J., Molinos-Albert, L. M., Backovic, M., Chiaravalli, J., Giraud, E., Vesin, B., Conquet, L., Grzelak, L., Planas, D., Staropoli, I., GuivelBenhassine, F., Hieu, T., … Fontanet, A. (2022). Potent human broadly SARS-CoV-2–neutralizing IgA and IgG antibodies effective against Omicron BA.1 and BA.2. Journalof ExperimentalMedicine , 219(7).

Prelog, M. (2006). Aging of the immune system: A risk factor for autoimmunity? AutoimmunityReviews , 5(2 SPEC. ISS.), 136–139. https://doi.org/10.1016/j.autrev.2005.09.008

Pushparaj, P., Nicoletto, A., Sheward, D. J., Das, H., Castro

Dopico, X., Perez Vidakovics, L., Hanke, L., Chernyshev, M., Narang, S., Kim, S., Fischbach, J., Ekström, S., McInerney, G., Hällberg, B. M., Murrell, B., Corcoran, M., & Karlsson https://doi.org/10.1016/j.immuni.2022.12.005

Hedestam, G. B. (2023). Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies. Immunity , 56(1), 193-206.e7.

Ricciardi, M. J., Rust, L. N., Pedreño-Lopez, N., Yusova, S., Biswas, S., Webb, G. M., Gonsales-Nieto, L., Voigt, T. B.,

MonoclonalAntibodies:TheOnceandFutureCureforCovid-19 https://doi.org/10.1101/2022.05.16.491863 https://doi.org/10.1038/s41586-020-2456-9 https://doi.org/10.1101/2021.12.18.21267628

Louw, J. J., Laurino, F. D., DiBello, J. R., Raué, H.-P., BarberAxthelm, A. M., Uttke, S., Raphael, L. M. S., Yrizarry-Medina, A., Rosen, B. C., Agnor, R., Gao, L., Burwitz, B. J. (2022). Therapeutic neutralizing monoclonal antibody administration protects against lethal Yellow Fever infection. bioRxiv , 2022.05.16.491863-2022.05.16.491863.

RidgebackBiotherapeuticsandMerckAnnouncePreliminary Findingsfroma Phase2aTrialofInvestigationalCOVID-19 TherapeuticMolnupiravir - Merck.com (n.d.).

Robbiani, D. F., Gaebler, C., Muecksch, F., Lorenzi, J. C. C., Wang, Z., Cho, A., Agudelo, M., Barnes, C. O., Gazumyan, A., Finkin, S., Hägglöf, T., Oliveira, T. Y., Viant, C., Hurley, A., Hoffmann, H. H., Millard, K. G., Kost, R. G., Cipolla, M., Gordon, K., … Nussenzweig, M. C. (2020). Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature2020584:7821 , 584(7821), 437–442.

Rockett, R. J., Basile, K., Maddocks, S., Fong, W., Agius, J. E., Mackinnon, J. J., Arnott, A., Chandra, S., Gall, M., Draper, J., Martinez, E., Sim, E. M., Lee, C., Ngo, C., Ramsperger, M., Ginn, A. N., Wang, Q., Fennell, M., Ko, D., … Sintchenko, V. (2021). RESISTANCE CONFERRING MUTATIONS IN SARS-CoV-2 DELTA FOLLOWING SOTROVIMAB INFUSION. medRxiv , 2021.12.18.212676282021.12.18.21267628.

Sauer, M. M., Tortorici, M. A., Park, Y.-J., Walls, A. C., Homad, L., Acton, O., Bowen, J., Wang, C., Xiong, X., Schueren, W. de van der, Quispe, J., Hoffstrom, B. G., Bosch, B.-J., McGuire, A. T., & Veesler, D. (2021). Structural basis for broad coronavirus neutralization. bioRxiv , 2020.12.29.4244822020.12.29.424482. https://doi.org/10.1101/2020.12.29.424482 https://doi.org/10.3389/FIMMU.2019.01296/BIBTEX https://doi.org/10.1038/s41586-022-05609-w https://doi.org/10.1016/J.CELL.2021.04.032

Saunders, K. O. (2019). Conceptual approaches to modulating antibody effector functions and circulation half-life. Frontiers inImmunology , 10(JUN), 1296–1296.

Schaefer-Babajew, D., Wang, Z., Muecksch, F., Cho, A., Loewe, M., Cipolla, M., Raspe, R., Johnson, B., Canis, M., DaSilva, J., Ramos, V., Turroja, M., Millard, K. G., Schmidt, F., Witte, L., Dizon, J., Shimeliovich, I., Yao, K. H., Oliveira, T. Y., … Nussenzweig, M. C. (2022). Antibody feedback regulates immune memory after SARS-CoV-2 mRNA vaccination.

Nature2022613:7945 , 613(7945), 735–742.

Scheid, J. F., Barnes, C. O., Eraslan, B., Hudak, A., Keeffe, J. R., Cosimi, L. A., Brown, E. M., Muecksch, F., Weisblum, Y., Zhang, S., Delorey, T., Woolley, A. E., Ghantous, F., Park, S. M., Phillips, D., Tusi, B., Huey-Tubman, K. E., Cohen, A. A., Gnanapragasam, P. N. P., … Xavier, R. J. (2021). B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell , 184(12), 3205–3205.

Starr, T. N., Czudnochowski, N., Zatta, F., Park, Y.-J., Liu, Z., Addetia, A., Pinto, D., Beltramello, M., Hernandez, P.,

Greaney, A. J., Marzi, R., Glass, W. G., Zhang, I., Dingens, A. S., Bowen, J. E., Wojcechowskyj, J. A., Marco, A. D., Rosen, L. E., Zhou, J., Snell, G. (2021). Antibodies to the SARS-CoV2 receptor-binding domain that maximize breadth and resistance to viral escape. bioRxiv , 2021.04.06.4387092021.04.06.438709. https://doi.org/10.1101/2021.04.06.438709 https://doi.org/10.1016/S2213-2600(22)00297-1 https://doi.org/10.1001/JAMANETWORKOPEN.2021.4920

UnderstandingRisk|CDC . (n.d.).

USCoronavirusvaccine tracker|USAFacts . (n.d.).

Vlaar, A. P. J., Witzenrath, M., van Paassen, P., Heunks, L. M. A., Mourvillier, B., de Bruin, S., Lim, E. H. T., Brouwer, M. C., Tuinman, P. R., Saraiva, J. F. K., Marx, G., Lobo, S. M., Boldo, R., Simon-Campos, J. A., Cornet, A. D., Grebenyuk, A., Engelbrecht, J. M., Mukansi, M., Jorens, P. G., Neukirchen, D. (2022). Anti-C5a antibody (vilobelimab) therapy for critically ill, invasively mechanically ventilated patients with COVID-19 (PANAMO): a multicentre, doubleblind, randomised, placebo-controlled, phase 3 trial. The LancetRespiratory Medicine , 10(12), 1137–1146.

Wallace, B. I., Kenney, B., Malani, P. N., Clauw, D. J., Nallamothu, B. K., & Waljee, A. K. (2021). Prevalence of Immunosuppressive Drug Use Among Commercially Insured US Adults, 2018-2019. JAMANetworkOpen , 4(5), e214920–e214920.

Wang, X., Chen, X., Tan, J., Yue, S., Zhou, R., Xu, Y., Lin, Y., Yang, Y., Zhou, Y., Deng, K., Chen, Z., Ye, L., & Zhu, Y. (2022). 35B5 antibody potently neutralizes SARS-CoV-2 https://doi.org/10.1016/J.CHOM.2022.03.035 https://doi.org/10.1101/2021.11.29.470356 https://doi.org/10.1126/SCIENCE.ABM5561/SUPPL_FILE/S CIENCE.ABM5561_MDAR_REPRODUCIBILITY_CHECK LIST.PDF https://doi.org/10.1101/2021.04.30.442182

Omicron by disrupting the N-glycan switch via a conserved spike epitope. CellHost &Microbe , 30(6), 887-895.e4.

Wang, X., Hu, A., Chen, X., Zhang, Y., Yu, F., Yue, S., Li, A., Zhang, J., Pan, Z., Yang, Y., Lin, Y., Gao, L., Zhou, J., Zhao, J., Li, F., Shi, Y., Huang, F., Yang, X., Peng, Y., … Ye, L. (2022). A potent human monoclonal antibody with panneutralizing activities directly dislocates S trimer of SARSCoV-2 through binding both up and down forms of RBD. bioRxiv , 2021.11.29.470356-2021.11.29.470356.

Wang, Z., Amaya, M., Addetia, A., Dang, H. V., Reggiano, G., Yan, L., Hickey, A. C., DiMaio, F., Broder, C. C., & Veesler, D. (2022). Architecture and antigenicity of the Nipah virus attachment glycoprotein. Science , 375(6587), 1373–1378.

Westendorf, K., Žentelis, S., Wang, L., Foster, D., Vaillancourt, P., Wiggin, M., Lovett, E., Lee, R. van der, Hendle, J., Pustilnik, A., Sauder, J. M., Kraft, L., Hwang, Y., Siegel, R. W., Chen, J., Heinz, B. A., Higgs, R. E., Kallewaard, N. L., Jepson, K., … Barnhart, B. C. (2022). LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants. bioRxiv , 2021.04.30.442182-2021.04.30.442182.

Woodruff, M. C., Ramonell, R. P., Lee, E.-H., & Sanz, I. (n.d.). Clinicallyidentifiableautoreactivity is common in severe https://doi.org/10.1101/2020.10.21.20216192 https://doi.org/10.1126/SCIENCE.ABC2241/SUPPL_FILE/A BC2241_WU_SM.PDF

SARS-CoV-2Infection .

Wu, Y., Wang, F., Shen, C., Peng, W., Li, D., Zhao, C., Li, Z., Li, S., Bi, Y., Yang, Y., Gong, Y., Xiao, H., Fan, Z., Tan, S., Wu, G., Tan, W., Lu, X., Fan, C., Wang, Q., … Liu, L. (2020). A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2. Science , 368(6496), 1274–1278.

Yamasoba, D., Kimura, I., Kosugi, Y., Uriu, K., Fujita, S., Ito, J., Sato, K., & Consortium, T. G. to P. J. (G2P-J. (2022). Neutralization sensitivity of Omicron BA.2.75 to therapeutic monoclonal antibodies. bioRxiv , 2022.07.14.5000412022.07.14.500041. https://doi.org/10.1101/2022.07.14.500041

Zalevsky, J., Chamberlain, A. K., Horton, H. M., Karki, S., Leung, I. W. L., Sproule, T. J., Lazar, G. A., Roopenian, D. C., & Desjarlais, J. R. (2010). Enhanced antibody half-life improves in vivo activity. NatureBiotechnology200928:2 , 28(2), 157–159. https://doi.org/10.1038/nbt.1601

Zhou, B., Zhou, R., Tang, B., Chan, J. F. W., Luo, M., Peng, Q., Yuan, S., Liu, H., Mok, B. W. Y., Chen, B., Wang, P., Poon, V. K. M., Chu, H., Chan, C. C. S., Tsang, J. O. L., Chan, C. C. Y., Au, K. K., Man, H. O., Lu, L., Chen, Z. (2022). A broadly neutralizing antibody protects Syrian hamsters against SARS-CoV-2 Omicron challenge. NatureCommunications 202213:1 , 13(1), 1–14. https://doi.org/10.1038/s41467-02231259-7