Shark nanobodies with potent SARS-CoV-2 neutralizing activity and broad sarbecovirus reactivity

Wei-Hung Chen; Agnes Hajduczki; Elizabeth J Martinez; Hongjun Bai; Hanover Matz; Thomas M Hill; Eric Lewitus; William C Chang; Layla Dawit; Caroline E Peterson; Phyllis A Rees; Adelola B Ajayi; Emily S Golub; Isabella Swafford; Vincent Dussupt; Sapna David; Sandra V Mayer; Sandrine Soman; Caitlin Kuklis; Courtney Corbitt; Jocelyn King; Misook Choe; Rajeshwer S Sankhala; Paul V Thomas; Michelle Zemil; Lindsay Wieczorek; Tricia Hart; Debora Duso; Larry Kummer; Lianying Yan; Spencer L Sterling; Eric D Laing; Christopher C Broder; Jazmean K Williams; Edgar Davidson; Benjamin J Doranz; Shelly J Krebs; Victoria R Polonis; Dominic Paquin-Proulx; Morgane Rolland; William W Reiley; Gregory D Gromowski; Kayvon Modjarrad; Helen Dooley; M Gordon Joyce

doi:10.1038/s41467-023-36106-x

Shark nanobodies with potent SARS-CoV-2 neutralizing activity and broad sarbecovirus reactivity

Nat Commun. 2023 Feb 3;14(1):580. doi: 10.1038/s41467-023-36106-x.

Authors

Wei-Hung Chen^#^{1

2}, Agnes Hajduczki^#^{1

2}, Elizabeth J Martinez^{1

2}, Hongjun Bai^{1

2

3}, Hanover Matz^{4

5}, Thomas M Hill^{4

5}, Eric Lewitus^{1

2

3}, William C Chang^{1

2}, Layla Dawit^{1

2}, Caroline E Peterson^{1

2}, Phyllis A Rees^{1

2}, Adelola B Ajayi^{1

2}, Emily S Golub^{1

2}, Isabella Swafford^{1

2

3}, Vincent Dussupt^{1

2

3}, Sapna David^{1

2}, Sandra V Mayer^{2

6}, Sandrine Soman⁶, Caitlin Kuklis⁶, Courtney Corbitt^{1

2

6}, Jocelyn King^{1

2

6}, Misook Choe^{1

2}, Rajeshwer S Sankhala^{1

2}, Paul V Thomas^{1

2}, Michelle Zemil³, Lindsay Wieczorek^{2

3}, Tricia Hart⁷, Debora Duso⁷, Larry Kummer⁷, Lianying Yan⁸, Spencer L Sterling⁸, Eric D Laing⁸, Christopher C Broder⁸, Jazmean K Williams⁹, Edgar Davidson⁹, Benjamin J Doranz⁹, Shelly J Krebs^{1

2

3}, Victoria R Polonis³, Dominic Paquin-Proulx^{1

2

3}, Morgane Rolland^{1

2

3}, William W Reiley⁷, Gregory D Gromowski⁶, Kayvon Modjarrad¹, Helen Dooley^{10

11}, M Gordon Joyce^{12

13}

Affiliations

¹ Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
² Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
³ U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
⁴ Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
⁵ Institute of Marine and Environmental Technology, Baltimore, MD, USA.
⁶ Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
⁷ Trudeau Institute, Saranac Lake, NY, USA.
⁸ Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA.
⁹ Integral Molecular, Philadelphia, PA, USA.
¹⁰ Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA. hdooley@som.umaryland.edu.
¹¹ Institute of Marine and Environmental Technology, Baltimore, MD, USA. hdooley@som.umaryland.edu.
¹² Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA. gjoyce@eidresearch.org.
¹³ Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA. gjoyce@eidresearch.org.

^# Contributed equally.

Abstract

Despite rapid and ongoing vaccine and therapeutic development, SARS-CoV-2 continues to evolve and evade, presenting a need for next-generation diverse therapeutic modalities. Here we show that nurse sharks immunized with SARS-CoV-2 recombinant receptor binding domain (RBD), RBD-ferritin (RFN), or spike protein ferritin nanoparticle (SpFN) immunogens elicit a set of new antigen receptor antibody (IgNAR) molecules that target two non-overlapping conserved epitopes on the spike RBD. Representative shark antibody variable NAR-Fc chimeras (ShAbs) targeting either of the two epitopes mediate cell-effector functions, with high affinity to all SARS-CoV-2 viral variants of concern, including the divergent Omicron strains. The ShAbs potently cross-neutralize SARS-CoV-2 WA-1, Alpha, Beta, Delta, Omicron BA.1 and BA.5, and SARS-CoV-1 pseudoviruses, and confer protection against SARS-CoV-2 challenge in the K18-hACE2 transgenic mouse model. Structural definition of the RBD-ShAb01-ShAb02 complex enabled design and production of multi-specific nanobodies with enhanced neutralization capacity, and picomolar affinity to divergent sarbecovirus clade 1a, 1b and 2 RBD molecules. These shark nanobodies represent potent immunotherapeutics both for current use, and future sarbecovirus pandemic preparation.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Antibodies, Neutralizing
Antibodies, Viral
COVID-19* / prevention & control
Epitopes
Ferritins / genetics
Immunoglobulin Fc Fragments
Mice
Mice, Transgenic
SARS-CoV-2 / genetics
Severe acute respiratory syndrome-related coronavirus*
Sharks
Single-Domain Antibodies*
Spike Glycoprotein, Coronavirus / genetics

Substances

Antibodies, Neutralizing
Antibodies, Viral
Epitopes
Ferritins
Immunoglobulin Fc Fragments
Single-Domain Antibodies
Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2

Supplementary concepts

SARS-CoV-2 variants

Abstract

Publication types

MeSH terms

Substances

Supplementary concepts

Grants and funding