Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations

Vincent Dussupt; Rajeshwer S. Sankhala; Letzibeth Mendez-Rivera; Samantha M. Townsley; Fabian Schmidt; Lindsay Wieczorek; Kerri G. Lal; Gina C. Donofrio; Ursula Tran; Nathaniel D. Jackson; Weam I. Zaky; Michelle Zemil; Sarah R. Tritsch; Wei Hung Chen; Elizabeth J. Martinez; Aslaa Ahmed; Misook Choe; William C. Chang; Agnes Hajduczki; Ningbo Jian; Caroline E. Peterson; Phyllis A. Rees; Magdalena Rutkowska; Bonnie M. Slike; Christopher N. Selverian; Isabella Swafford; I. Ting Teng; Paul V. Thomas; Tongqing Zhou; Clayton J. Smith; Jeffrey R. Currier; Peter D. Kwong; Morgane Rolland; Edgar Davidson; Benjamin J. Doranz; Christopher N. Mores; Theodora Hatziioannou; William W. Reiley; Paul D. Bieniasz; Dominic Paquin-Proulx; Gregory D. Gromowski; Victoria R. Polonis; Nelson L. Michael; Kayvon Modjarrad; M. Gordon Joyce; Shelly J. Krebs

doi:10.1038/s41590-021-01068-z

Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations

Vincent Dussupt, Rajeshwer S. Sankhala, Letzibeth Mendez-Rivera, Samantha M. Townsley, Fabian Schmidt, Lindsay Wieczorek, Kerri G. Lal, Gina C. Donofrio, Ursula Tran, Nathaniel D. Jackson, Weam I. Zaky, Michelle Zemil, Sarah R. Tritsch, Wei Hung Chen, Elizabeth J. Martinez, Aslaa Ahmed, Misook Choe, William C. Chang, Agnes Hajduczki, Ningbo JianCaroline E. Peterson, Phyllis A. Rees, Magdalena Rutkowska, Bonnie M. Slike, Christopher N. Selverian, Isabella Swafford, I. Ting Teng, Paul V. Thomas, Tongqing Zhou, Clayton J. Smith, Jeffrey R. Currier, Peter D. Kwong, Morgane Rolland, Edgar Davidson, Benjamin J. Doranz, Christopher N. Mores, Theodora Hatziioannou, William W. Reiley, Paul D. Bieniasz, Dominic Paquin-Proulx, Gregory D. Gromowski, Victoria R. Polonis, Nelson L. Michael, Kayvon Modjarrad, M. Gordon Joyce^*, Shelly J. Krebs^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

Abstract

Prevention of viral escape and increased coverage against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern require therapeutic monoclonal antibodies (mAbs) targeting multiple sites of vulnerability on the coronavirus spike glycoprotein. Here we identify several potent neutralizing antibodies directed against either the N-terminal domain (NTD) or the receptor-binding domain (RBD) of the spike protein. Administered in combinations, these mAbs provided low-dose protection against SARS-CoV-2 infection in the K18-human angiotensin-converting enzyme 2 mouse model, using both neutralization and Fc effector antibody functions. The RBD mAb WRAIR-2125, which targets residue F486 through a unique heavy-chain and light-chain pairing, demonstrated potent neutralizing activity against all major SARS-CoV-2 variants of concern. In combination with NTD and other RBD mAbs, WRAIR-2125 also prevented viral escape. These data demonstrate that NTD/RBD mAb combinations confer potent protection, likely leveraging complementary mechanisms of viral inactivation and clearance.

Original language	English
Pages (from-to)	1503-1514
Number of pages	12
Journal	Nature Immunology
Volume	22
Issue number	12
DOIs	https://doi.org/10.1038/s41590-021-01068-z
State	Published - Dec 2021
Externally published	Yes

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Dussupt, V., Sankhala, R. S., Mendez-Rivera, L., Townsley, S. M., Schmidt, F., Wieczorek, L., Lal, K. G., Donofrio, G. C., Tran, U., Jackson, N. D., Zaky, W. I., Zemil, M., Tritsch, S. R., Chen, W. H., Martinez, E. J., Ahmed, A., Choe, M., Chang, W. C., Hajduczki, A., ... Krebs, S. J. (2021). Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations. Nature Immunology, 22(12), 1503-1514. https://doi.org/10.1038/s41590-021-01068-z

@article{edf7837cbaad49da85865a0357a24441,

title = "Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations",

abstract = "Prevention of viral escape and increased coverage against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern require therapeutic monoclonal antibodies (mAbs) targeting multiple sites of vulnerability on the coronavirus spike glycoprotein. Here we identify several potent neutralizing antibodies directed against either the N-terminal domain (NTD) or the receptor-binding domain (RBD) of the spike protein. Administered in combinations, these mAbs provided low-dose protection against SARS-CoV-2 infection in the K18-human angiotensin-converting enzyme 2 mouse model, using both neutralization and Fc effector antibody functions. The RBD mAb WRAIR-2125, which targets residue F486 through a unique heavy-chain and light-chain pairing, demonstrated potent neutralizing activity against all major SARS-CoV-2 variants of concern. In combination with NTD and other RBD mAbs, WRAIR-2125 also prevented viral escape. These data demonstrate that NTD/RBD mAb combinations confer potent protection, likely leveraging complementary mechanisms of viral inactivation and clearance.",

author = "Vincent Dussupt and Sankhala, {Rajeshwer S.} and Letzibeth Mendez-Rivera and Townsley, {Samantha M.} and Fabian Schmidt and Lindsay Wieczorek and Lal, {Kerri G.} and Donofrio, {Gina C.} and Ursula Tran and Jackson, {Nathaniel D.} and Zaky, {Weam I.} and Michelle Zemil and Tritsch, {Sarah R.} and Chen, {Wei Hung} and Martinez, {Elizabeth J.} and Aslaa Ahmed and Misook Choe and Chang, {William C.} and Agnes Hajduczki and Ningbo Jian and Peterson, {Caroline E.} and Rees, {Phyllis A.} and Magdalena Rutkowska and Slike, {Bonnie M.} and Selverian, {Christopher N.} and Isabella Swafford and Teng, {I. Ting} and Thomas, {Paul V.} and Tongqing Zhou and Smith, {Clayton J.} and Currier, {Jeffrey R.} and Kwong, {Peter D.} and Morgane Rolland and Edgar Davidson and Doranz, {Benjamin J.} and Mores, {Christopher N.} and Theodora Hatziioannou and Reiley, {William W.} and Bieniasz, {Paul D.} and Dominic Paquin-Proulx and Gromowski, {Gregory D.} and Polonis, {Victoria R.} and Michael, {Nelson L.} and Kayvon Modjarrad and Joyce, {M. Gordon} and Krebs, {Shelly J.}",

note = "Funding Information: (pSV) were produced by co-transfection of HEK293T/17 cells with a pcDNA3.1 encoding SARS-CoV-2 S protein and an HIV-1 NL4-3 luciferase reporter plasmid (pNL4-3.Luc.R-E-, National Institutes of Health (NIH) AIDS Reagent Program). The S expression plasmid sequence was derived from the Wuhan Hu-1 strain (GenBank, NC_045512), which is also identical to the IL1/2020 and WA1/2020 strains. The S expression plasmid sequence was also codon optimized and modified to remove the last 18 amino acids of the cytoplasmic tail to improve S incorporation into the pseudovirions and thereby enhance infectivity. S expression plasmids for current SARS-CoV-2 VOCs and VOIs were similarly codon optimized, modified and included the following mutations: B.1.1.7 or Alpha, (69-70del, Tyr144del, p.Asn501Tyr, p.Ala570Asp, p.Asp614Gly, p.Pro681His, p.Thr718Ile, p.Ser982Ala and p.Asp1118His), B.1.351 or Beta, (p.Leu18Phe, p.Asp80Ala, p.Asp215Gly, 241-243del, p.Lys417Asn, p.Glu484Lys, p.Asn501Tyr, p.Asp614Gly, p.Ala701Val and p.Glu1195Gln), B.1.617.2 or Delta, (p.Thr19Arg, p.Gly142Asp, del156-157, p.Arg158Gly, p.Leu452Arg, p.Thr478Lys, p.Asp614Gly, p.Pro681Arg and p.Asp950Asn), P.1 or Gamma (p.Leu18Phe, p.Thr20Asn, p.Pro26Ser, p.Asp138Tyr, p.Arg190Ser, p.Lys417Thr, p.Glu484Lys, p.Asn501Tyr, p.Asp614Gly, p.His655Tyr and p.Thr1027Ile) and B.1.427/429 (p.Ser13Ile, p.Trp152Cys, p.Leu452R and p.Asp614Gly). An Asp614Gly variant was also made from the Wuhan Hu-1 construct using the Q5 site-directed mutagenesis kit (NEB). In addition, a codon-optimized S expression plasmid encoding SARS-CoV-1 (Sino 1-11; GenBank, AY485277) was generated that incorporated a 28 amino acid C-terminal deletion to improve infectivity52. Virions pseudotyped with the VSV G protein were used as control. Infectivity and neutralization titers were determined using ACE2-expressing HEK293 target cells (Integral Molecular) in a semiautomated assay format using robotic liquid handling (Biomek NXp Beckman Coulter), as previously described18. Neutralization dose–response curves were fitted by nonlinear regression using the LabKey server, and the final titers are reported as the reciprocal of the dilution of plasma necessary to achieve 50% neutralization (50% inhibitory dose (ID50) or IC50) and 80% neutralization (80% inhibitory dose (ID80) or 80% inhibitory concentration (IC80)). Assay equivalency was verified by participation in the SARS-CoV-2 Neutralizing Assay Concordance Survey run by the Virology Quality Assurance Program and External Quality Assurance Program Oversite Laboratory at the Duke Human Vaccine Institute, sponsored through programs supported by the NIAID, Division of AIDS. Funding Information: We thank S. Vasan, P. Scott, S. Daye, J. Headley, and M. Amare for programmatic, administrative and regulatory support and planning within the Henry M. Jackson Foundation for the Advancement of Military Medicine (HJF) and WRAIR. We sincerely thank the participants and staff of protocols EID029 and RV229H. The coding sequence for the SARS-CoV-2 stabilized trimer (S-2P) was a generous gift from J. McLellan, University of Texas at Austin. We also thank M. Creegan, and the MHRP FlowCore facility for help with FACS sorting, and E. Kavusak, S. Molnar, J. Heller, C. Kuklis, S. Soman, C. Kannadka, T. Lang, D. Duso, L. Kummer, S. Muncil, K. Lanzer, T. Cookenham, F. Szaba, M. Rao, D. Bolton and J. K. Williams for technical support within HJF/WRAIR. This work was primarily funded by the US Department of Defense, Defense Health Agency, through the CARES Act. Funding was executed through a cooperative agreement (W81XWH-18-2-0040) between the Medical Research and Development Command of the Army Futures Command in the US Department of the Army and the HJF. Additional support was provided by the Intramural Research Program of the Vaccine Research Center, NIAID and the NIH and by NIH grants R01AI50111 (to P.D.B.) and R01AI78788 (to T.H.) as well as NIH contract HHSN 75N93019C00073 (to B.J.D). The X-ray crystallographic work is based upon research conducted at the Northeastern Collaborative Access Team beamlines, funded by the NIH NIGMS (P30 GM124165). The Eiger 16M detector on 24-ID-E is funded by an NIH-ORIP HEI grant (S10OD021527). This research used resources of the Advanced Photon Source, a US Department of Energy Office of Science User Facility under contract no. DE-AC02-06CH11357. EM data were collected at the Cryo-EM Facility of the National Cancer Institute. This research was supported by the National Cancer Institute Cryo-EM Facility at FNLCR under contract HSSN261200800001E (to C.J.S.). Material has been reviewed by the WRAIR. The opinions or assertions contained herein are the private views of the authors, and are not to be construed as official, or as reflecting true views of the Department of the Army or the Department of Defense. Publisher Copyright: {\textcopyright} 2021, The Author(s).",

year = "2021",

month = dec,

doi = "10.1038/s41590-021-01068-z",

language = "English",

volume = "22",

pages = "1503--1514",

journal = "Nature Immunology",

issn = "1529-2908",

number = "12",

}

Dussupt, V, Sankhala, RS, Mendez-Rivera, L, Townsley, SM, Schmidt, F, Wieczorek, L, Lal, KG, Donofrio, GC, Tran, U, Jackson, ND, Zaky, WI, Zemil, M, Tritsch, SR, Chen, WH, Martinez, EJ, Ahmed, A, Choe, M, Chang, WC, Hajduczki, A, Jian, N, Peterson, CE, Rees, PA, Rutkowska, M, Slike, BM, Selverian, CN, Swafford, I, Teng, IT, Thomas, PV, Zhou, T, Smith, CJ, Currier, JR, Kwong, PD, Rolland, M, Davidson, E, Doranz, BJ, Mores, CN, Hatziioannou, T, Reiley, WW, Bieniasz, PD, Paquin-Proulx, D, Gromowski, GD, Polonis, VR, Michael, NL, Modjarrad, K, Joyce, MG & Krebs, SJ 2021, 'Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations', Nature Immunology, vol. 22, no. 12, pp. 1503-1514. https://doi.org/10.1038/s41590-021-01068-z

TY - JOUR

T1 - Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations

AU - Dussupt, Vincent

AU - Sankhala, Rajeshwer S.

AU - Mendez-Rivera, Letzibeth

AU - Townsley, Samantha M.

AU - Schmidt, Fabian

AU - Wieczorek, Lindsay

AU - Lal, Kerri G.

AU - Donofrio, Gina C.

AU - Tran, Ursula

AU - Jackson, Nathaniel D.

AU - Zaky, Weam I.

AU - Zemil, Michelle

AU - Tritsch, Sarah R.

AU - Chen, Wei Hung

AU - Martinez, Elizabeth J.

AU - Ahmed, Aslaa

AU - Choe, Misook

AU - Chang, William C.

AU - Hajduczki, Agnes

AU - Jian, Ningbo

AU - Peterson, Caroline E.

AU - Rees, Phyllis A.

AU - Rutkowska, Magdalena

AU - Slike, Bonnie M.

AU - Selverian, Christopher N.

AU - Swafford, Isabella

AU - Teng, I. Ting

AU - Thomas, Paul V.

AU - Zhou, Tongqing

AU - Smith, Clayton J.

AU - Currier, Jeffrey R.

AU - Kwong, Peter D.

AU - Rolland, Morgane

AU - Davidson, Edgar

AU - Doranz, Benjamin J.

AU - Mores, Christopher N.

AU - Hatziioannou, Theodora

AU - Reiley, William W.

AU - Bieniasz, Paul D.

AU - Paquin-Proulx, Dominic

AU - Gromowski, Gregory D.

AU - Polonis, Victoria R.

AU - Michael, Nelson L.

AU - Modjarrad, Kayvon

AU - Joyce, M. Gordon

AU - Krebs, Shelly J.

N1 - Funding Information: (pSV) were produced by co-transfection of HEK293T/17 cells with a pcDNA3.1 encoding SARS-CoV-2 S protein and an HIV-1 NL4-3 luciferase reporter plasmid (pNL4-3.Luc.R-E-, National Institutes of Health (NIH) AIDS Reagent Program). The S expression plasmid sequence was derived from the Wuhan Hu-1 strain (GenBank, NC_045512), which is also identical to the IL1/2020 and WA1/2020 strains. The S expression plasmid sequence was also codon optimized and modified to remove the last 18 amino acids of the cytoplasmic tail to improve S incorporation into the pseudovirions and thereby enhance infectivity. S expression plasmids for current SARS-CoV-2 VOCs and VOIs were similarly codon optimized, modified and included the following mutations: B.1.1.7 or Alpha, (69-70del, Tyr144del, p.Asn501Tyr, p.Ala570Asp, p.Asp614Gly, p.Pro681His, p.Thr718Ile, p.Ser982Ala and p.Asp1118His), B.1.351 or Beta, (p.Leu18Phe, p.Asp80Ala, p.Asp215Gly, 241-243del, p.Lys417Asn, p.Glu484Lys, p.Asn501Tyr, p.Asp614Gly, p.Ala701Val and p.Glu1195Gln), B.1.617.2 or Delta, (p.Thr19Arg, p.Gly142Asp, del156-157, p.Arg158Gly, p.Leu452Arg, p.Thr478Lys, p.Asp614Gly, p.Pro681Arg and p.Asp950Asn), P.1 or Gamma (p.Leu18Phe, p.Thr20Asn, p.Pro26Ser, p.Asp138Tyr, p.Arg190Ser, p.Lys417Thr, p.Glu484Lys, p.Asn501Tyr, p.Asp614Gly, p.His655Tyr and p.Thr1027Ile) and B.1.427/429 (p.Ser13Ile, p.Trp152Cys, p.Leu452R and p.Asp614Gly). An Asp614Gly variant was also made from the Wuhan Hu-1 construct using the Q5 site-directed mutagenesis kit (NEB). In addition, a codon-optimized S expression plasmid encoding SARS-CoV-1 (Sino 1-11; GenBank, AY485277) was generated that incorporated a 28 amino acid C-terminal deletion to improve infectivity52. Virions pseudotyped with the VSV G protein were used as control. Infectivity and neutralization titers were determined using ACE2-expressing HEK293 target cells (Integral Molecular) in a semiautomated assay format using robotic liquid handling (Biomek NXp Beckman Coulter), as previously described18. Neutralization dose–response curves were fitted by nonlinear regression using the LabKey server, and the final titers are reported as the reciprocal of the dilution of plasma necessary to achieve 50% neutralization (50% inhibitory dose (ID50) or IC50) and 80% neutralization (80% inhibitory dose (ID80) or 80% inhibitory concentration (IC80)). Assay equivalency was verified by participation in the SARS-CoV-2 Neutralizing Assay Concordance Survey run by the Virology Quality Assurance Program and External Quality Assurance Program Oversite Laboratory at the Duke Human Vaccine Institute, sponsored through programs supported by the NIAID, Division of AIDS. Funding Information: We thank S. Vasan, P. Scott, S. Daye, J. Headley, and M. Amare for programmatic, administrative and regulatory support and planning within the Henry M. Jackson Foundation for the Advancement of Military Medicine (HJF) and WRAIR. We sincerely thank the participants and staff of protocols EID029 and RV229H. The coding sequence for the SARS-CoV-2 stabilized trimer (S-2P) was a generous gift from J. McLellan, University of Texas at Austin. We also thank M. Creegan, and the MHRP FlowCore facility for help with FACS sorting, and E. Kavusak, S. Molnar, J. Heller, C. Kuklis, S. Soman, C. Kannadka, T. Lang, D. Duso, L. Kummer, S. Muncil, K. Lanzer, T. Cookenham, F. Szaba, M. Rao, D. Bolton and J. K. Williams for technical support within HJF/WRAIR. This work was primarily funded by the US Department of Defense, Defense Health Agency, through the CARES Act. Funding was executed through a cooperative agreement (W81XWH-18-2-0040) between the Medical Research and Development Command of the Army Futures Command in the US Department of the Army and the HJF. Additional support was provided by the Intramural Research Program of the Vaccine Research Center, NIAID and the NIH and by NIH grants R01AI50111 (to P.D.B.) and R01AI78788 (to T.H.) as well as NIH contract HHSN 75N93019C00073 (to B.J.D). The X-ray crystallographic work is based upon research conducted at the Northeastern Collaborative Access Team beamlines, funded by the NIH NIGMS (P30 GM124165). The Eiger 16M detector on 24-ID-E is funded by an NIH-ORIP HEI grant (S10OD021527). This research used resources of the Advanced Photon Source, a US Department of Energy Office of Science User Facility under contract no. DE-AC02-06CH11357. EM data were collected at the Cryo-EM Facility of the National Cancer Institute. This research was supported by the National Cancer Institute Cryo-EM Facility at FNLCR under contract HSSN261200800001E (to C.J.S.). Material has been reviewed by the WRAIR. The opinions or assertions contained herein are the private views of the authors, and are not to be construed as official, or as reflecting true views of the Department of the Army or the Department of Defense. Publisher Copyright: © 2021, The Author(s).

PY - 2021/12

Y1 - 2021/12

N2 - Prevention of viral escape and increased coverage against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern require therapeutic monoclonal antibodies (mAbs) targeting multiple sites of vulnerability on the coronavirus spike glycoprotein. Here we identify several potent neutralizing antibodies directed against either the N-terminal domain (NTD) or the receptor-binding domain (RBD) of the spike protein. Administered in combinations, these mAbs provided low-dose protection against SARS-CoV-2 infection in the K18-human angiotensin-converting enzyme 2 mouse model, using both neutralization and Fc effector antibody functions. The RBD mAb WRAIR-2125, which targets residue F486 through a unique heavy-chain and light-chain pairing, demonstrated potent neutralizing activity against all major SARS-CoV-2 variants of concern. In combination with NTD and other RBD mAbs, WRAIR-2125 also prevented viral escape. These data demonstrate that NTD/RBD mAb combinations confer potent protection, likely leveraging complementary mechanisms of viral inactivation and clearance.

AB - Prevention of viral escape and increased coverage against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern require therapeutic monoclonal antibodies (mAbs) targeting multiple sites of vulnerability on the coronavirus spike glycoprotein. Here we identify several potent neutralizing antibodies directed against either the N-terminal domain (NTD) or the receptor-binding domain (RBD) of the spike protein. Administered in combinations, these mAbs provided low-dose protection against SARS-CoV-2 infection in the K18-human angiotensin-converting enzyme 2 mouse model, using both neutralization and Fc effector antibody functions. The RBD mAb WRAIR-2125, which targets residue F486 through a unique heavy-chain and light-chain pairing, demonstrated potent neutralizing activity against all major SARS-CoV-2 variants of concern. In combination with NTD and other RBD mAbs, WRAIR-2125 also prevented viral escape. These data demonstrate that NTD/RBD mAb combinations confer potent protection, likely leveraging complementary mechanisms of viral inactivation and clearance.

UR - http://www.scopus.com/inward/record.url?scp=85118323133&partnerID=8YFLogxK

U2 - 10.1038/s41590-021-01068-z

DO - 10.1038/s41590-021-01068-z

M3 - Article

C2 - 34716452

AN - SCOPUS:85118323133

SN - 1529-2908

VL - 22

SP - 1503

EP - 1514

JO - Nature Immunology

JF - Nature Immunology

IS - 12

ER -

Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations

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