1
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Chan CWF, Wang B, Nan L, Huang X, Mao T, Chu HY, Luo C, Chu H, Choi GCG, Shum HC, Wong ASL. High-throughput screening of genetic and cellular drivers of syncytium formation induced by the spike protein of SARS-CoV-2. Nat Biomed Eng 2024; 8:291-309. [PMID: 37996617 DOI: 10.1038/s41551-023-01140-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 10/18/2023] [Indexed: 11/25/2023]
Abstract
Mapping mutations and discovering cellular determinants that cause the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to induce infected cells to form syncytia would facilitate the development of strategies for blocking the formation of such cell-cell fusion. Here we describe high-throughput screening methods based on droplet microfluidics and the size-exclusion selection of syncytia, coupled with large-scale mutagenesis and genome-wide knockout screening via clustered regularly interspaced short palindromic repeats (CRISPR), for the large-scale identification of determinants of cell-cell fusion. We used the methods to perform deep mutational scans in spike-presenting cells to pinpoint mutable syncytium-enhancing substitutions in two regions of the spike protein (the fusion peptide proximal region and the furin-cleavage site). We also used a genome-wide CRISPR screen in cells expressing the receptor angiotensin-converting enzyme 2 to identify inhibitors of clathrin-mediated endocytosis that impede syncytium formation, which we validated in hamsters infected with SARS-CoV-2. Finding genetic and cellular determinants of the formation of syncytia may reveal insights into the physiological and pathological consequences of cell-cell fusion.
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Affiliation(s)
- Charles W F Chan
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Bei Wang
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Lang Nan
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Xiner Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tianjiao Mao
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Hoi Yee Chu
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Cuiting Luo
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People's Republic of China.
| | - Gigi C G Choi
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
| | - Alan S L Wong
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
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2
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Cheedarla N, Verkerke HP, Potlapalli S, McLendon KB, Patel A, Frank F, O’Sick WH, Cheedarla S, Baugh TJ, Damhorst GL, Wu H, Graciaa D, Hudaib F, Alter DN, Bryksin J, Ortlund EA, Guarner J, Auld S, Shah S, Lam W, Mattoon D, Johnson JM, Wilson DH, Dhodapkar MV, Stowell SR, Neish AS, Roback JD. Rapid, high throughput, automated detection of SARS-CoV-2 neutralizing antibodies against Wuhan-WT, delta and omicron BA1, BA2 spike trimers. iScience 2023; 26:108256. [PMID: 37965140 PMCID: PMC10641509 DOI: 10.1016/j.isci.2023.108256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/17/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Traditional cellular and live-virus methods for detection of SARS-CoV-2 neutralizing antibodies (nAbs) are labor- and time-intensive, and thus not suited for routine use in the clinical lab to predict vaccine efficacy and natural immune protection. Here, we report the development and validation of a rapid, high throughput method for measuring SARS-CoV-2 nAbs against native-like trimeric spike proteins. This assay uses a blockade of human angiotensin converting enzyme 2 (hACE-2) binding (BoAb) approach in an automated digital immunoassay on the Quanterix HD-X platform. BoAb assays using Wuhan-WT (vaccine strain), delta (B.1.167.2), omicron BA1 and BA2 variant viral strains showed strong correlation with cell-based pseudovirus neutralization activity (PNA) and live-virus neutralization activity. Importantly, we were able to detect similar patterns of delta and omicron variant resistance to neutralization in samples with paired vaccine strain and delta variant BoAb measurements. Finally, we screened clinical samples from patients with or without evidence of SARS-CoV-2 exposure by a single-dilution screening version of our assays, finding significant nAb activity only in exposed individuals. Importantly, this completely automated assay can be performed in 4 h to measure neutralizing antibody titers for 16 samples over 8 serial dilutions or, 128 samples at a single dilution with replicates. In principle, these assays offer a rapid, robust, and scalable alternative to time-, skill-, and cost-intensive standard methods for measuring SARS-CoV-2 nAb levels.
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Affiliation(s)
- Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P. Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Sindhu Potlapalli
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kaleb Benjamin McLendon
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - William Henry O’Sick
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Suneethamma Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Tyler Jon Baugh
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gregory L. Damhorst
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Huixia Wu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Daniel Graciaa
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Fuad Hudaib
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David N. Alter
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Janetta Bryksin
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric A. Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeanette Guarner
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sara Auld
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Sarita Shah
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA 30322, USA
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Wilbur Lam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Dawn Mattoon
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Joseph M. Johnson
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - David H. Wilson
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Madhav V. Dhodapkar
- Department of Hematology/Medical Oncology, Emory University, Atlanta, GA, USA
| | - Sean R. Stowell
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
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3
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Stoddard CI, Sung K, Yaffe ZA, Weight H, Beaudoin-Bussières G, Galloway J, Gantt S, Adhiambo J, Begnel ER, Ojee E, Slyker J, Wamalwa D, Kinuthia J, Finzi A, Matsen FA, Lehman DA, Overbaugh J. Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers. Nat Commun 2023; 14:4864. [PMID: 37567924 PMCID: PMC10421871 DOI: 10.1038/s41467-023-40554-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Infant antibody responses to viral infection can differ from those in adults. However, data on the specificity and function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in infants, and direct comparisons between infants and adults are limited. Here, we characterize antibody binding and functionality against Wuhan-Hu-1 (B lineage) strain SARS-CoV-2 in convalescent plasma from 36 postpartum women and 14 of their infants infected with SARS-CoV-2 from a vaccine-naïve prospective cohort in Nairobi, Kenya. We find significantly higher antibody titers against SARS-CoV-2 Spike, receptor binding domain and N-terminal domain, and Spike-expressing cell-surface staining levels in infants versus mothers. Plasma antibodies from mothers and infants bind to similar regions of the Spike S2 subunit, including the fusion peptide (FP) and stem helix-heptad repeat 2. However, infants display higher antibody levels and more consistent antibody escape pathways in the FP region compared to mothers. Finally, infants have significantly higher levels of antibody-dependent cellular cytotoxicity (ADCC), though, surprisingly, Spike pseudovirus neutralization titers between infants and mothers are similar. These results suggest infants develop distinct SARS-CoV-2 binding and functional antibody activities and reveal age-related differences in humoral immunity to SARS-CoV-2 infection that could be relevant to protection and COVID-19 disease outcomes.
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Affiliation(s)
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Zak A Yaffe
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Haidyn Weight
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Jared Galloway
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Soren Gantt
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
- Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montreal, QC, Canada
| | - Judith Adhiambo
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Emily R Begnel
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Ednah Ojee
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Jennifer Slyker
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Dalton Wamalwa
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - John Kinuthia
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Andrés Finzi
- Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Frederick A Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Dara A Lehman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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4
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Yamamoto S, Yamayoshi S, Ito M, Sakai-Tagawa Y, Nakachi I, Baba R, Kamimoto S, Ogura T, Hagiwara S, Kato H, Nakajima H, Uwamino Y, Yagi K, Sugaya N, Nagai H, Saito M, Adachi E, Koga M, Tsutsumi T, Duong C, Okuda M, Murakami J, Furusawa Y, Ujie M, Iwatsuki-Horimoto K, Yotsuyanagi H, Kawaoka Y. Differences among epitopes recognized by neutralizing antibodies induced by SARS-CoV-2 infection or COVID-19 vaccination. iScience 2023; 26:107208. [PMID: 37448563 PMCID: PMC10290734 DOI: 10.1016/j.isci.2023.107208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/21/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
SARS-CoV-2 has gradually acquired amino acid substitutions in its S protein that reduce the potency of neutralizing antibodies, leading to decreased vaccine efficacy. Here, we attempted to obtain mutant viruses by passaging SARS-CoV-2 in the presence of plasma samples from convalescent patients or vaccinees to determine which amino acid substitutions affect the antigenicity of SARS-CoV-2. Several amino acid substitutions in the S2 region, as well as the N-terminal domain (NTD) and receptor-binding domain (RBD), affected the neutralization potency of plasma samples collected from vaccinees, indicating that amino acid substitutions in the S2 region as well as those in the NTD and RBD affect neutralization by vaccine-induced antibodies. Furthermore, the neutralizing potency of vaccinee plasma samples against mutant viruses we obtained or circulating viruses differed among individuals. These findings suggest that genetic backgrounds of vaccinees influence the recognition of neutralizing epitopes.
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Affiliation(s)
- Shinya Yamamoto
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
| | - Mutsumi Ito
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yuko Sakai-Tagawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Ichiro Nakachi
- Pulmonary Division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Rie Baba
- Pulmonary Division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Shigenobu Kamimoto
- Pulmonary Division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Takayuki Ogura
- Department of Emergency and Intensive Care, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Shigehiro Hagiwara
- Department of Clinical Laboratory, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Hideaki Kato
- Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Hideaki Nakajima
- Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Yoshifumi Uwamino
- Department of Laboratory Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kazuma Yagi
- Department of Pulmonary Medicine, Keiyu Hospital, Kanagawa 220-8521, Japan
| | - Norio Sugaya
- Department of Pediatrics, Keiyu Hospital, Kanagawa 220-8521, Japan
| | - Hiroyuki Nagai
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Makoto Saito
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Eisuke Adachi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Calvin Duong
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Moe Okuda
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Jurika Murakami
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yuri Furusawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Michiko Ujie
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | | | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
- The University of Tokyo, Pandemic Preparedness, Infection and Advanced Research Center, Tokyo 108-8639, Japan
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5
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Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CI, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J. Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection. Proc Natl Acad Sci U S A 2023; 120:e2220948120. [PMID: 37253011 PMCID: PMC10265947 DOI: 10.1073/pnas.2220948120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs through BA.4/BA.5 in both pseudovirus-based and authentic virus assays. Three mAbs also retain potency to recently circulating VOCs XBB.1.5 and BQ.1.1 and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor-binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are unique in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.
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Affiliation(s)
- Jamie Guenthoer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Michelle Lilly
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Tyler N. Starr
- Department of Biochemistry, University of Utah, Salt Lake City, UT84112
| | | | - Klaus N. Lovendahl
- Department of Medicinal Chemistry, University of Washington, Seattle, WA98195
| | - Jacob T. Croft
- Department of Medicinal Chemistry, University of Washington, Seattle, WA98195
| | | | - Vrasha Chohan
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QCH2X 0A9, Canada
| | - Felicitas Ruiz
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Mackenzie S. Kopp
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QCH2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QCH2X 0A9, Canada
| | - Jesse D. Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- HHMI, Seattle, WA98195
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA98195
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA98195
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
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6
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Lee J, Hadfield J, Black A, Sibley TR, Neher RA, Bedford T, Huddleston J. Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition. FRONTIERS IN BIOINFORMATICS 2023; 3:1069487. [PMID: 37035035 PMCID: PMC10073671 DOI: 10.3389/fbinf.2023.1069487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
Seasonal influenza vaccines must be updated regularly to account for mutations that allow influenza viruses to escape our existing immunity. A successful vaccine should represent the genetic diversity of recently circulating viruses and induce antibodies that effectively prevent infection by those recent viruses. Thus, linking the genetic composition of circulating viruses and the serological experimental results measuring antibody efficacy is crucial to the vaccine design decision. Historically, genetic and serological data have been presented separately in the form of static visualizations of phylogenetic trees and tabular serological results to identify vaccine candidates. To simplify this decision-making process, we have created an interactive tool for visualizing serological data that has been integrated into Nextstrain's real-time phylogenetic visualization framework, Auspice. We show how the combined interactive visualizations may be used by decision makers to explore the relationships between complex data sets for both prospective vaccine virus selection and retrospectively exploring the performance of vaccine viruses.
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Affiliation(s)
- Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Allison Black
- Chan Zuckerberg Initiative, San Francisco, CA, United States
| | - Thomas R. Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Richard A. Neher
- Biozentrum, Universität Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Howard Hughes Medical Institute, Seattle, WA, United States
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
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7
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Stoddard CI, Sung K, Yaffe ZA, Weight H, Beaudoin-Bussières G, Galloway J, Gantt S, Adhiambo J, Begnel ER, Ojee E, Slyker J, Wamalwa D, Kinuthia J, Finzi A, Matsen FA, Lehman DA, Overbaugh J. Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527330. [PMID: 36798400 PMCID: PMC9934573 DOI: 10.1101/2023.02.06.527330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Infant antibody responses to viral infection can differ from those in adults. However, data on the specificity and function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in infants, and direct comparisons between infants and adults are limited. We characterized antibody binding and functionality in convalescent plasma from postpartum women and their infants infected with SARS-CoV-2 from a vaccine-naïve prospective cohort in Nairobi, Kenya. Antibody titers against SARS-CoV-2 Spike, receptor binding domain and N-terminal domain, and Spike-expressing cell-surface staining levels were significantly higher in infants than in mothers. Plasma antibodies from mothers and infants bound to similar regions of the Spike S2 subunit, including the fusion peptide (FP) and stem helix-heptad repeat 2. However, infants displayed higher antibody levels and more consistent antibody escape pathways in the FP region compared to mothers. Finally, infants had significantly higher levels of antibody-dependent cellular cytotoxicity (ADCC), though, surprisingly, neutralization titers between infants and mothers were similar. These results suggest infants develop distinct SARS-CoV-2 binding and functional antibody repertoires and reveal age-related differences in humoral immunity to SARS-CoV-2 infection that could be relevant to protection and COVID-19 disease outcomes.
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Affiliation(s)
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Center
| | - Zak A Yaffe
- Human Biology Division, Fred Hutchinson Cancer Center
- Medical Scientist Training Program, University of Washington
| | - Haidyn Weight
- Human Biology Division, Fred Hutchinson Cancer Center
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Université de Montréal
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal
| | - Jared Galloway
- Public Health Sciences Division, Fred Hutchinson Cancer Center
| | - Soren Gantt
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal
- Centre de Recherche du CHU Sainte-Justine, Université de Montréal
| | - Judith Adhiambo
- Department of Pediatrics and Child Health, University of Nairobi
| | | | - Ednah Ojee
- Department of Pediatrics and Child Health, University of Nairobi
| | | | - Dalton Wamalwa
- Department of Pediatrics and Child Health, University of Nairobi
| | - John Kinuthia
- Department of Global Health, University of Washington
- Department of Research and Programs, Kenyatta National Hospital
| | - Andrés Finzi
- Centre de Recherche du CHUM, Université de Montréal
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal
| | - Frederick A Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Center
- Howard Hughes Medical Institute
| | - Dara A Lehman
- Human Biology Division, Fred Hutchinson Cancer Center
- Department of Global Health, University of Washington
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center
- Public Health Sciences Division, Fred Hutchinson Cancer Center
- Lead contact
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8
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Stanevich OV, Alekseeva EI, Sergeeva M, Fadeev AV, Komissarova KS, Ivanova AA, Simakova TS, Vasilyev KA, Shurygina AP, Stukova MA, Safina KR, Nabieva ER, Garushyants SK, Klink GV, Bakin EA, Zabutova JV, Kholodnaia AN, Lukina OV, Skorokhod IA, Ryabchikova VV, Medvedeva NV, Lioznov DA, Danilenko DM, Chudakov DM, Komissarov AB, Bazykin GA. SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19. Nat Commun 2023; 14:149. [PMID: 36627290 PMCID: PMC9831376 DOI: 10.1038/s41467-022-34033-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 10/11/2022] [Indexed: 01/11/2023] Open
Abstract
Evolution of SARS-CoV-2 in immunocompromised hosts may result in novel variants with changed properties. While escape from humoral immunity certainly contributes to intra-host evolution, escape from cellular immunity is poorly understood. Here, we report a case of long-term COVID-19 in an immunocompromised patient with non-Hodgkin's lymphoma who received treatment with rituximab and lacked neutralizing antibodies. Over the 318 days of the disease, the SARS-CoV-2 genome gained a total of 40 changes, 34 of which were present by the end of the study period. Among the acquired mutations, 12 reduced or prevented the binding of known immunogenic SARS-CoV-2 HLA class I antigens. By experimentally assessing the effect of a subset of the escape mutations, we show that they resulted in a loss of as much as ~1% of effector CD8 T cell response. Our results indicate that CD8 T cell escape represents a major underappreciated contributor to SARS-CoV-2 evolution in humans.
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Affiliation(s)
| | | | - Maria Sergeeva
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | - Artem V Fadeev
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | | | - Anna A Ivanova
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | | | - Kirill A Vasilyev
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | | | - Marina A Stukova
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | - Ksenia R Safina
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia
| | - Elena R Nabieva
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Sofya K Garushyants
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Galya V Klink
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Evgeny A Bakin
- First Pavlov State Medical University, Saint-Petersburg, Russia.,Bioinformatics Institute, Saint Petersburg, Russia
| | | | - Anastasia N Kholodnaia
- First Pavlov State Medical University, Saint-Petersburg, Russia.,City Hospital 31, Saint-Petersburg, Russia
| | - Olga V Lukina
- First Pavlov State Medical University, Saint-Petersburg, Russia
| | | | | | | | - Dmitry A Lioznov
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia.,First Pavlov State Medical University, Saint-Petersburg, Russia
| | - Daria M Danilenko
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | - Dmitriy M Chudakov
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia. .,A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.
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9
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Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CI, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J. Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.15.520606. [PMID: 36561191 PMCID: PMC9774213 DOI: 10.1101/2022.12.15.520606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs, including recently circulating BA.4/BA.5, in both pseudovirus-based and live virus assays, and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are novel in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.
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10
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Iketani S, Hong SJ, Sheng J, Bahari F, Culbertson B, Atanaki FF, Aditham AK, Kratz AF, Luck MI, Tian R, Goff SP, Montazeri H, Sabo Y, Ho DD, Chavez A. Functional map of SARS-CoV-2 3CL protease reveals tolerant and immutable sites. Cell Host Microbe 2022; 30:1354-1362.e6. [PMID: 36029764 PMCID: PMC9365866 DOI: 10.1016/j.chom.2022.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/20/2022] [Accepted: 08/05/2022] [Indexed: 01/03/2023]
Abstract
The SARS-CoV-2 3CL protease (3CLpro) is an attractive therapeutic target, as it is essential to the virus and highly conserved among coronaviruses. However, our current understanding of its tolerance to mutations is limited. Here, we develop a yeast-based deep mutational scanning approach to systematically profile the activity of all possible single mutants of the 3CLpro and validate a subset of our results within authentic viruses. We reveal that the 3CLpro is highly malleable and is capable of tolerating mutations throughout the protein. Yet, we also identify specific residues that appear immutable, suggesting that these may be targets for future 3CLpro inhibitors. Finally, we utilize our screening as a basis to identify E166V as a resistance-conferring mutation against the clinically used 3CLpro inhibitor, nirmatrelvir. Collectively, the functional map presented herein may serve as a guide to better understand the biological properties of the 3CLpro and for drug development against coronaviruses.
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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Seo Jung Hong
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jenny Sheng
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Farideh Bahari
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Bruce Culbertson
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, USA
| | - Fereshteh Fallah Atanaki
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Arjun K Aditham
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alexander F Kratz
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Maria I Luck
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Ruxiao Tian
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Stephen P Goff
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Hesam Montazeri
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Yosef Sabo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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11
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Wang T, Xu J, Wang B, Wang Y, Zhao W, Xiang B, Xue Y, Yuan Q, Wang Y. Receptor-binding domain-anchored peptides block binding of severe acute respiratory syndrome coronavirus 2 spike proteins with cell surface angiotensin-converting enzyme 2. Front Microbiol 2022; 13:910343. [PMID: 36177466 PMCID: PMC9513850 DOI: 10.3389/fmicb.2022.910343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022] Open
Abstract
Background The COVID-19 pandemic has killed over 6 million people worldwide. Despite the accumulation of knowledge about the causative pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the pathogenesis of this disease, cures remain to be discovered. We searched for certain peptides that might interfere with spike protein (S protein)-angiotensin-converting enzyme 2 (ACE2) interactions. Methods Phage display (PhD)-12 peptide library was screened against recombinant spike trimer (S-trimer) or receptor-binding domain (S-RBD) proteins. The resulting enriched peptide sequences were obtained, and their potential binding sites on S-trimer and S-RBD 3D structure models were searched. Synthetic peptides corresponding to these and other reference sequences were tested for their efficacy in blocking the binding of S-trimer protein onto recombinant ACE2 proteins or ACE2-overexpressing cells. Results After three rounds of phage selections, two peptide sequences (C2, DHAQRYGAGHSG; C6, HWKAVNWLKPWT) were enriched by S-RBD, but only C2 was present in S-trimer selected phages. When the 3D structures of static monomeric S-RBD (6M17) and S-trimer (6ZGE, 6ZGG, 7CAI, and 7CAK, each with different status of S-RBDs in the three monomer S proteins) were scanned for potential binding sites of C2 and C6 peptides, C6 opt to bind the saddle of S-RBD in both 6M17 and erected S-RBD in S-trimers, but C2 failed to cluster there in the S-trimers. In the competitive S-trimer-ACE2-binding experiments, synthetic C2 and C6 peptides inhibited S-trimer binding onto 293T-ACE2hR cells at high concentrations (50 μM) but not at lower concentrations (10 μM and below), neither for the settings of S-trimer binding onto recombinant ACE2 proteins. Conclusion Using PhD methodology, two peptides were generated bearing potentials to interfere with S protein-ACE2 interaction, which might be further exploited to produce peptidomimetics that block the attachment of SARS-CoV-2 virus onto host cells, hence diminishing the pathogenesis of COVID-19.
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Affiliation(s)
- Ting Wang
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jie Xu
- Central Laboratory, Xiang’an Hospital of Xiamen University, Xiang’an University Medical Center, Xiamen University, Xiamen, Fujian, China
- Eye Institute of Xiamen University, Medical College, Xiamen University, Xiamen, Fujian, China
| | - Beibei Wang
- Center for Advanced Materials Research, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong, China
| | - Yulian Wang
- Eye Institute of Xiamen University, Medical College, Xiamen University, Xiamen, Fujian, China
| | - Wei Zhao
- Eye Institute of Xiamen University, Medical College, Xiamen University, Xiamen, Fujian, China
| | - Bin Xiang
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yuhua Xue
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Quan Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Yiqiang Wang
- Central Laboratory, Xiang’an Hospital of Xiamen University, Xiang’an University Medical Center, Xiamen University, Xiamen, Fujian, China
- Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
- *Correspondence: Yiqiang Wang,
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12
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Wang Q, Iketani S, Li Z, Guo Y, Yeh AY, Liu M, Yu J, Sheng Z, Huang Y, Liu L, Ho DD. Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75. Cell Host Microbe 2022; 30:1512-1517.e4. [PMID: 36108630 PMCID: PMC9444898 DOI: 10.1016/j.chom.2022.09.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 01/02/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariant BA.2.75 emerged recently and appears to be spreading. It has nine mutations in spike compared with the currently circulating BA.2, raising concerns that it may further evade vaccine-elicited and therapeutic antibodies. We found BA.2.75 to be moderately more neutralization resistant to sera from vaccinated/boosted individuals than BA.2 (1.8-fold), similar to BA.2.12.1 (1.1-fold), but more neutralization sensitive than BA.4/5 (0.6-fold). Relative to BA.2, BA.2.75 showed heightened resistance to class 1 and class 3 monoclonal antibodies targeting the spike-receptor-binding domain while gaining sensitivity to class 2 antibodies. Resistance was largely conferred by G446S and R460K mutations. BA.2.75 was slightly resistant (3.7-fold) to bebtelovimab, a therapeutic antibody with potent activity against all Omicron subvariants. BA.2.75 also exhibited a higher binding affinity to host receptor ACE2 than other Omicron subvariants. BA.2.75 provides further insight into SARS-CoV-2 evolution as it gains transmissibility while incrementally evading antibody neutralization.
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Affiliation(s)
- Qian Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zhiteng Li
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Andre Yanchen Yeh
- School of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Michael Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
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13
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Considering epitopes conservity in targeting SARS-CoV-2 mutations in variants: a novel immunoinformatics approach to vaccine design. Sci Rep 2022; 12:14017. [PMID: 35982065 PMCID: PMC9386201 DOI: 10.1038/s41598-022-18152-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/05/2022] [Indexed: 11/08/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has gained mutations at an alarming rate in the past years. Developing mutations can increase the virus's pathogenicity and virulence; reduce the efficacy of vaccines, antibodies neutralization, and even challenge adaptive immunity. So, it is essential to identify conserved epitopes (with fewer mutations) in different variants with appropriate antigenicity to target the variants by an appropriate vaccine design. Yet as, 3369 SARS-CoV-2 genomes were collected from global initiative on sharing avian flu data. Then, mutations in the immunodominant regions (IDRs), immune epitope database (IEDB) epitopes, and also predicted epitopes were calculated. In the following, epitopes conservity score against the total number of events (mutations) and the number of mutated sites in each epitope was weighted by Shannon entropy and then calculated by the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS). Based on the TOPSIS conservity score and antigenicity score, the epitopes were plotted. The result demonstrates that almost all epitopes and IDRs with various lengths have gained different numbers of mutations in dissimilar sites. Herein, our two-step calculation for conservity recommends only 8 IDRs, 14 IEDB epitopes, and 10 predicted epitopes among all epitopes. The selected ones have higher conservity and higher immunogenicity. This method is an open-source multi-criteria decision-making platform, which provides a scientific approach to selecting epitopes with appropriate conservity and immunogenicity; against ever-changing viruses.
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14
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Abstract
The continuous emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) urges better understanding of the functional motifs in the spike (S) protein and their tolerance to mutations. Here, we focused on the S2′ motif, which, during virus entry, requires cleavage by a host cell protease to release the fusion peptide. Though belonging to an immunogenic region, the SARS-CoV-2 S2′ motif (811-KPSKR-815) has shown hardly any variation, with its three basic (K/R) residues being >99.99% conserved thus far. By creating a series of mutant pseudoviruses bearing the spikes of Wuhan-Hu-1, its G614 mutant or the Delta and Omicron variants, we show that residue K814 (preceding the scissile R815) is dispensable for TMPRSS2 yet favored by the alternative TMPRSS13 protease. Activation by TMPRSS13 was drastically reduced when the SARS-CoV-2 S2′ motif was swapped with that of the low pathogenic 229E coronavirus (685-RVAGR-689), and also, the reverse effect was seen. This swap had no impact on recognition by TMPRSS2. In the Middle East respiratory syndrome coronavirus (MERS-CoV) spike, introducing a dibasic scissile motif was easily accepted by TMPRSS13 but less so by TMPRSS2, confirming that TMPRSS13 favors a sequence rich in K/R residues. Pseudovirus entry experiments in Calu-3 cells confirmed that the S2′ mutations have minor impact on TMPRSS2. Our findings are the first to demonstrate which S2′ residues are important for SARS-CoV-2 spike activation by these two airway proteases, with TMPRSS2 being more tolerant to variation than TMPRSS13. This preemptive insight will help to estimate the impact of S2′ motif changes as they appear in new SARS-CoV-2 variants.
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15
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Ng KW, Faulkner N, Finsterbusch K, Wu M, Harvey R, Hussain S, Greco M, Liu Y, Kjaer S, Swanton C, Gandhi S, Beale R, Gamblin SJ, Cherepanov P, McCauley J, Daniels R, Howell M, Arase H, Wack A, Bauer DLV, Kassiotis G. SARS-CoV-2 S2-targeted vaccination elicits broadly neutralizing antibodies. Sci Transl Med 2022; 14:eabn3715. [PMID: 35895836 DOI: 10.1126/scitranslmed.abn3715] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Several variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged during the current coronavirus disease 2019 (COVID-19) pandemic. Although antibody cross-reactivity with the spike glycoproteins (S) of diverse coronaviruses, including endemic common cold coronaviruses (HCoVs), has been documented, it remains unclear whether such antibody responses, typically targeting the conserved S2 subunit, contribute to protection when induced by infection or through vaccination. Using a mouse model, we found that prior HCoV-OC43 S-targeted immunity primes neutralizing antibody responses to otherwise subimmunogenic SARS-CoV-2 S exposure and promotes S2-targeting antibody responses. Moreover, vaccination with SARS-CoV-2 S2 elicited antibodies in mice that neutralized diverse animal and human alphacoronaviruses and betacoronaviruses in vitro and provided a degree of protection against SARS-CoV-2 challenge in vivo. Last, in mice with a history of SARS-CoV-2 Wuhan-based S vaccination, further S2 vaccination induced broader neutralizing antibody response than booster Wuhan S vaccination, suggesting that it may prevent repertoire focusing caused by repeated homologous vaccination. These data establish the protective value of an S2-targeting vaccine and support the notion that S2 vaccination may better prepare the immune system to respond to the changing nature of the S1 subunit in SARS-CoV-2 variants of concern, as well as to future coronavirus zoonoses.
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Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Katja Finsterbusch
- Immunoregulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mary Wu
- High Throughput Screening STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Maria Greco
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Yafei Liu
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan
| | - Svend Kjaer
- Structural Biology STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Sonia Gandhi
- Neurodegradation Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Cherepanov
- Chromatin structure and mobile DNA Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rodney Daniels
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
| | - Andreas Wack
- Immunoregulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David L V Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Infectious Disease, St Mary's Hospital, Imperial College London, London W2 1PG, UK
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16
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Iketani S, Hong SJ, Sheng J, Bahari F, Culbertson B, Atanaki FF, Aditham AK, Kratz AF, Luck MI, Tian R, Goff SP, Montazeri H, Sabo Y, Ho DD, Chavez A. The Functional Landscape of SARS-CoV-2 3CL Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.23.497404. [PMID: 35860222 PMCID: PMC9298129 DOI: 10.1101/2022.06.23.497404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) as the etiologic agent of COVID-19 (coronavirus disease 2019) has drastically altered life globally. Numerous efforts have been placed on the development of therapeutics to treat SARS-CoV-2 infection. One particular target is the 3CL protease (3CL pro ), which holds promise as it is essential to the virus and highly conserved among coronaviruses, suggesting that it may be possible to find broad inhibitors that treat not just SARS-CoV-2 but other coronavirus infections as well. While the 3CL protease has been studied by many groups for SARS-CoV-2 and other coronaviruses, our understanding of its tolerance to mutations is limited, knowledge which is particularly important as 3CL protease inhibitors become utilized clinically. Here, we develop a yeast-based deep mutational scanning approach to systematically profile the activity of all possible single mutants of the SARS-CoV-2 3CL pro , and validate our results both in yeast and in authentic viruses. We reveal that the 3CL pro is highly malleable and is capable of tolerating mutations throughout the protein, including within the substrate binding pocket. Yet, we also identify specific residues that appear immutable for function of the protease, suggesting that these interactions may be novel targets for the design of future 3CL pro inhibitors. Finally, we utilize our screening results as a basis to identify E166V as a resistance-conferring mutation against the therapeutic 3CL pro inhibitor, nirmatrelvir, in clinical use. Collectively, the functional map presented herein may serve as a guide for further understanding of the biological properties of the 3CL protease and for drug development for current and future coronavirus pandemics.
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17
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Yang Y, Zhou D, Zhang X, Shi Y, Han J, Zhou L, Wu L, Ma M, Li J, Peng S, Xu Z, Zhu W. D3AI-CoV: a deep learning platform for predicting drug targets and for virtual screening against COVID-19. Brief Bioinform 2022; 23:6571526. [PMID: 35443040 PMCID: PMC9310271 DOI: 10.1093/bib/bbac147] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/13/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022] Open
Abstract
Target prediction and virtual screening are two powerful tools of computer-aided drug design. Target identification is of great significance for hit discovery, lead optimization, drug repurposing and elucidation of the mechanism. Virtual screening can improve the hit rate of drug screening to shorten the cycle of drug discovery and development. Therefore, target prediction and virtual screening are of great importance for developing highly effective drugs against COVID-19. Here we present D3AI-CoV, a platform for target prediction and virtual screening for the discovery of anti-COVID-19 drugs. The platform is composed of three newly developed deep learning-based models i.e., MultiDTI, MPNNs-CNN and MPNNs-CNN-R models. To compare the predictive performance of D3AI-CoV with other methods, an external test set, named Test-78, was prepared, which consists of 39 newly published independent active compounds and 39 inactive compounds from DrugBank. For target prediction, the areas under the receiver operating characteristic curves (AUCs) of MultiDTI and MPNNs-CNN models are 0.93 and 0.91, respectively, whereas the AUCs of the other reported approaches range from 0.51 to 0.74. For virtual screening, the hit rate of D3AI-CoV is also better than other methods. D3AI-CoV is available for free as a web application at http://www.d3pharma.com/D3Targets-2019-nCoV/D3AI-CoV/index.php, which can serve as a rapid online tool for predicting potential targets for active compounds and for identifying active molecules against a specific target protein for COVID-19 treatment.
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Affiliation(s)
- Yanqing Yang
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Deshan Zhou
- Department of Computer Science, Hunan University, Changsha, 410082, China
| | - Xinben Zhang
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yulong Shi
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jiaxin Han
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210046, China
| | - Liping Zhou
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Leyun Wu
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Minfei Ma
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jintian Li
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shaoliang Peng
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
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18
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Willcox AC, Sung K, Garrett ME, Galloway JG, Erasmus JH, Logue JK, Hawman DW, Chu HY, Hasenkrug KJ, Fuller DH, Matsen IV FA, Overbaugh J. Detailed analysis of antibody responses to SARS-CoV-2 vaccination and infection in macaques. PLoS Pathog 2022; 18:e1010155. [PMID: 35404959 PMCID: PMC9022802 DOI: 10.1371/journal.ppat.1010155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/21/2022] [Accepted: 03/21/2022] [Indexed: 02/02/2023] Open
Abstract
Macaques are a commonly used model for studying immunity to human viruses, including for studies of SARS-CoV-2 infection and vaccination. However, it is unknown whether macaque antibody responses resemble the response in humans. To answer this question, we employed a phage-based deep mutational scanning approach (Phage-DMS) to compare which linear epitopes are targeted on the SARS-CoV-2 Spike protein in convalescent humans, convalescent (re-infected) rhesus macaques, mRNA-vaccinated humans, and repRNA-vaccinated pigtail macaques. We also used Phage-DMS to determine antibody escape pathways within each epitope, enabling a granular comparison of antibody binding specificities at the locus level. Overall, we identified some common epitope targets in both macaques and humans, including in the fusion peptide (FP) and stem helix-heptad repeat 2 (SH-H) regions. Differences between groups included a response to epitopes in the N-terminal domain (NTD) and C-terminal domain (CTD) in vaccinated humans but not vaccinated macaques, as well as recognition of a CTD epitope and epitopes flanking the FP in convalescent macaques but not convalescent humans. There was also considerable variability in the escape pathways among individuals within each group. Sera from convalescent macaques showed the least variability in escape overall and converged on a common response with vaccinated humans in the SH-H epitope region, suggesting highly similar antibodies were elicited. Collectively, these findings suggest that the antibody response to SARS-CoV-2 in macaques shares many features with humans, but with substantial differences in the recognition of certain epitopes and considerable individual variability in antibody escape profiles, suggesting a diverse repertoire of antibodies that can respond to major epitopes in both humans and macaques. Differences in macaque species and exposure type may also contribute to these findings.
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Affiliation(s)
- Alexandra C. Willcox
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Meghan E. Garrett
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
| | - Jared G. Galloway
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jesse H. Erasmus
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- HDT Bio, Seattle, Washington, United States of America
| | - Jennifer K. Logue
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - David W. Hawman
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Kim J. Hasenkrug
- Laboratory of Persistent Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Deborah H. Fuller
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Infectious Diseases and Translational Medicine, Washington National Primate Research Center, Seattle, Washington, United States of America
- Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, United States of America
| | - Frederick A. Matsen IV
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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19
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Cheedarla N, Verkerke HP, Potlapalli S, McLendon KB, Patel A, Frank F, Damhorst GL, Wu H, O’Sick WH, Graciaa D, Hudaib F, Alter DN, Bryksin J, Ortlund EA, Guarner J, Auld S, Shah S, Lam W, Mattoon D, Johnson JM, Wilson DH, Dhodapkar MV, Stowell SR, Neish AS, Roback JD. Rapid, high throughput, automated detection of SARS-CoV-2 neutralizing antibodies against native-like vaccine and delta variant spike trimers. RESEARCH SQUARE 2022:rs.3.rs-1322411. [PMID: 35194599 PMCID: PMC8863158 DOI: 10.21203/rs.3.rs-1322411/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Traditional cellular and live-virus methods for detection of SARS-CoV-2 neutralizing antibodies (nAbs) are labor- and time-intensive, and thus not suited for routine use in the clinical lab to predict vaccine efficacy and natural immune protection. Here, we report the development and validation of a rapid, high throughput method for measuring SARS-CoV-2 nAbs against native-like trimeric spike proteins. This assay uses a blockade of hACE-2 binding (BoAb) approach in an automated digital immunoassay on the Quanterix HD-X platform. BoAb assays using vaccine and delta variant viral strains showed strong correlation with cell-based pseudovirus and live-virus neutralization activity. Importantly, we were able to detect similar patterns of delta variant resistance to neutralization in samples with paired vaccine and delta variant BoAb measurements. Finally, we screened clinical samples from patients with or without evidence of SARS-CoV-2 exposure by a single-dilution screening version of our assays, finding significant nAb activity only in exposed individuals. In principle, these assays offer a rapid, robust, and scalable alternative to time-, skill-, and cost-intensive standard methods for measuring SARS-CoV-2 nAb levels.
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Affiliation(s)
- Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- These authors contributed equally as a first authors
| | - Hans P. Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
- These authors contributed equally as a first authors
| | - Sindhu Potlapalli
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kaleb Benjamin McLendon
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gregory L. Damhorst
- Department of Medicine, Division of infectious diseases, Emory University, Atlanta, GA 30322, USA
| | - Huixia Wu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - William Henry O’Sick
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Daniel Graciaa
- Department of Medicine, Division of infectious diseases, Emory University, Atlanta, GA 30322, USA
| | - Fuad Hudaib
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David N Alter
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeannette Bryksin
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric A. Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeanette Guarner
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sara Auld
- Department of Medicine, Division of infectious diseases, Emory University, Atlanta, GA 30322, USA
| | - Sarita Shah
- Department of Medicine, Division of infectious diseases, Emory University, Atlanta, GA 30322, USA
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Wilbur Lam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Dawn Mattoon
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821
| | - Joseph M Johnson
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821
| | - David H Wilson
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821
| | | | - Sean R. Stowell
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
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20
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Gentles LE, Kehoe L, Crawford KH, Lacombe K, Dickerson J, Wolf C, Yuan J, Schuler S, Watson JT, Nyanseor S, Briggs-Hagen M, Saydah S, Midgley CM, Pringle K, Chu H, Bloom JD, Englund JA. Dynamics of infection-elicited SARS-CoV-2 antibodies in children over time. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.01.14.22269235. [PMID: 35118481 PMCID: PMC8811949 DOI: 10.1101/2022.01.14.22269235] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection elicits an antibody response that targets several viral proteins including spike (S) and nucleocapsid (N); S is the major target of neutralizing antibodies. Here, we assess levels of anti-N binding antibodies and anti-S neutralizing antibodies in unvaccinated children compared with unvaccinated older adults following infection. Specifically, we examine neutralization and anti-N binding by sera collected up to 52 weeks following SARS-CoV-2 infection in children and compare these to a cohort of adults, including older adults, most of whom had mild infections that did not require hospitalization. Neutralizing antibody titers were lower in children than adults early after infection, but by 6 months titers were similar between age groups. The neutralizing activity of the children's sera decreased modestly from one to six months; a pattern that was not significantly different from that observed in adults. However, infection of children induced much lower levels of anti-N antibodies than in adults, and levels of these anti-N antibodies decreased more rapidly in children than in adults, including older adults. These results highlight age-related differences in the antibody responses to SARS-CoV-2 proteins and, as vaccines for children are introduced, may provide comparator data for the longevity of infection-elicited and vaccination-induced neutralizing antibody responses.
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Affiliation(s)
- Lauren E. Gentles
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Leanne Kehoe
- Division of Infectious Disease, Seattle Children’s Hospital, Seattle, Washington, USA
| | - Katharine H.D. Crawford
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
| | - Kirsten Lacombe
- Division of Infectious Disease, Seattle Children’s Hospital, Seattle, Washington, USA
| | - Jane Dickerson
- Division of Infectious Disease, Seattle Children’s Hospital, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Caitlin Wolf
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Joanna Yuan
- Division of Infectious Disease, Seattle Children’s Hospital, Seattle, Washington, USA
| | - Susanna Schuler
- Division of Infectious Disease, Seattle Children’s Hospital, Seattle, Washington, USA
| | - John T. Watson
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sankan Nyanseor
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melissa Briggs-Hagen
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sharon Saydah
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Claire M. Midgley
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kimberly Pringle
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Helen Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Jesse D. Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, Washington, USA
| | - Janet A. Englund
- Division of Infectious Disease, Seattle Children’s Hospital, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
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21
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Garrett ME, Galloway JG, Wolf C, Logue JK, Franko N, Chu HY, Matsen FA, Overbaugh JM. Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection. eLife 2022; 11:73490. [PMID: 35072628 PMCID: PMC8887901 DOI: 10.7554/elife.73490] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Control of the COVID-19 pandemic will rely on SARS-CoV-2 vaccine-elicited antibodies to protect against emerging and future variants; an understanding of the unique features of the humoral responses to infection and vaccination, including different vaccine platforms, is needed to achieve this goal. Methods: The epitopes and pathways of escape for Spike-specific antibodies in individuals with diverse infection and vaccination history were profiled using Phage-DMS. Principal component analysis was performed to identify regions of antibody binding along the Spike protein that differentiate the samples from one another. Within these epitope regions, we determined potential sites of escape by comparing antibody binding of peptides containing wild-type residues versus peptides containing a mutant residue. Results: Individuals with mild infection had antibodies that bound to epitopes in the S2 subunit within the fusion peptide and heptad-repeat regions, whereas vaccinated individuals had antibodies that additionally bound to epitopes in the N- and C-terminal domains of the S1 subunit, a pattern that was also observed in individuals with severe disease due to infection. Epitope binding appeared to change over time after vaccination, but other covariates such as mRNA vaccine dose, mRNA vaccine type, and age did not affect antibody binding to these epitopes. Vaccination induced a relatively uniform escape profile across individuals for some epitopes, whereas there was much more variation in escape pathways in mildly infected individuals. In the case of antibodies targeting the fusion peptide region, which was a common response to both infection and vaccination, the escape profile after infection was not altered by subsequent vaccination. Conclusions: The finding that SARS-CoV-2 mRNA vaccination resulted in binding to additional epitopes beyond what was seen after infection suggests that protection could vary depending on the route of exposure to Spike antigen. The relatively conserved escape pathways to vaccine-induced antibodies relative to infection-induced antibodies suggests that if escape variants emerge they may be readily selected for across vaccinated individuals. Given that the majority of people will be first exposed to Spike via vaccination and not infection, this work has implications for predicting the selection of immune escape variants at a population level. Funding: This work was supported by NIH grants AI138709 (PI JMO) and AI146028 (PI FAM). JMO received support as the Endowed Chair for Graduate Education (FHCRC). The research of FAM was supported in part by a Faculty Scholar grant from the Howard Hughes Medical Institute and the Simons Foundation. Scientific Computing Infrastructure at Fred Hutch was funded by ORIP grant S10OD028685. When SARS-CoV-2 – the virus that causes COVID-19 – infects our bodies, our immune system reacts by producing small molecules called antibodies that stick to a part of the virus called the spike protein. Vaccines are thought to work by triggering the production of similar antibodies without causing disease. Some of the most effective antibodies against SARS-CoV-2 bind a specific area of the spike protein called the ‘receptor binding domain’ or RBD. When SARS-CoV-2 evolves it creates a challenge for our immune system: mutations, which are changes in the virus’s genetic code, can alter the shape of its spike protein, meaning that existing antibodies may no longer bind to it as effectively. This lowers the protection offered by past infection or vaccination, which makes it harder to tackle the pandemic. As it stands, it is not clear which mutations to the virus’s genetic code can affect antibody binding, especially to portions outside the RBD. To complicate things further, the antibodies people produce in response to mild infection, severe infection, and vaccination, while somewhat overlapping, exhibit some differences. Studying these differences could help minimize emergence of mutations that allow the virus to ‘escape’ the antibody response. A phage display library is a laboratory technique in which phages (viruses that infect bacteria) are used as a ‘repository’ for DNA fragments that code for a specific protein. The phages can then produce the protein (or fragments of it), and if the protein fragments bind to a target, it can be easily detected. Garrett, Galloway et al. exploited this technique to study how different portions of the SARS-CoV-2 spike protein were bound by antibodies. They made a phage library in which each phage encoded a portion of the spike protein with different mutations, and then exposed the different versions of the protein to antibodies from people who had experienced prior infection, vaccination, or both. The experiment showed that antibodies produced during severe infection or after vaccination bound to similar parts of the spike protein, while antibodies from people who had experienced mild infection targeted fewer areas. Garrett, Galloway et al. also found that mutations that affected the binding of antibodies produced after vaccination were more consistent than mutations that interfered with antibodies produced during infection. While these results show which mutations are most likely to help the virus escape existing antibodies, this does not mean that the virus will necessarily evolve in that direction. Indeed, some of the mutations may be impossible for the virus to acquire because they interfere with the virus’s ability to spread. Further studies could focus on revealing which of the mutations detected by Garrett, Galloway et al. are most likely to occur, to guide vaccine development in that direction. To help with this, Garrett, Galloway et al. have made the data accessible to other scientists and the public using a web tool.
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Affiliation(s)
- Meghan E Garrett
- Division of Human Biology, Fred Hutchinson Cancer Research Center
| | - Jared G Galloway
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center
| | - Caitlin Wolf
- Department of Medicine, University of Washington
| | | | | | - Helen Y Chu
- Department of Medicine, University of Washington
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22
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Lina B. [The different phases of molecular and antigenic evolution of SARS-CoV-2 viruses during the 20 months following its emergence]. BULLETIN DE L'ACADEMIE NATIONALE DE MEDECINE 2022; 206:87-99. [PMID: 34866635 PMCID: PMC8629187 DOI: 10.1016/j.banm.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/04/2021] [Indexed: 01/04/2023]
Abstract
From its emergence in December 2019 and until the end of the fourth pandemic wave in October 2021, SARS-CoV-2 circulation has been associated with significant molecular evolutions of the virus. These were linked to mutations that have led to new virus linages with replication advantages as a result of increased transmission, or partial immune escape in the context of progressively increasing global immunisation. The pandemic context with large scale epidemics massive outbreaks observed in highly populated areas has favoured this emergence of "variants". During the 20 months period, at least three evolutionary phases have been observed, leading to the situation observed in October 2021. For the first time, an unprecedented worldwide surveillance effort has been conducted to monitor the circulation of the emerging virus, with rapid data sharing. This molecular surveillance system has provided an accurate description of the circulating viruses, and their evolution. The implementation of these tools and skills able to provide SARS-CoV-2 molecular epidemiological data has upgraded the global capacity for surveillance worldwide, and may allow us to be better prepared for a future pandemic episode.
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Affiliation(s)
- B. Lina
- Laboratoire de virologie des HCL, institut des agents infectieux (IAI), CNR des virus à transmission respiratoire (dont la grippe), groupement hospitalier Nord, hôpital de la Croix Rousse, 103, grande rue de la Croix Rousse, 69317 Lyon cedex 04, France,Inserm U1111, laboratoire Virpath, CNRS UMR 5308, ENS de Lyon, UCBL, centre international de recherche en infectiologie (CIRI), université de Lyon, 7–11, rue Guillaume-Paradin, 69372 Lyon cedex 08, France
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23
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Focosi D, Maggi F, Franchini M, McConnell S, Casadevall A. Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. Int J Mol Sci 2021; 23:29. [PMID: 35008446 PMCID: PMC8744556 DOI: 10.3390/ijms23010029] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 12/31/2022] Open
Abstract
The accelerated SARS-CoV-2 evolution under selective pressure by massive deployment of neutralizing antibody-based therapeutics is a concern with potentially severe implications for public health. We review here reports of documented immune escape after treatment with monoclonal antibodies and COVID-19-convalescent plasma (CCP). While the former is mainly associated with specific single amino acid mutations at residues within the receptor-binding domain (e.g., E484K/Q, Q493R, and S494P), a few cases of immune evasion after CCP were associated with recurrent deletions within the N-terminal domain of the spike protein (e.g., ΔHV69-70, ΔLGVY141-144 and ΔAL243-244). The continuous genomic monitoring of non-responders is needed to better understand immune escape frequencies and the fitness of emerging variants.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy;
- Laboratory of Microbiology, Azienda Socio Sanitaria Territoriale Sette Laghi, 21100 Varese, Italy
| | - Massimo Franchini
- Division of Transfusion Medicine, Carlo Poma Hospital, 46100 Mantua, Italy;
| | - Scott McConnell
- Department of Medicine, Johns Hopkins School of Public Health, Baltimore, MD 21218, USA; (S.M.); (A.C.)
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
| | - Arturo Casadevall
- Department of Medicine, Johns Hopkins School of Public Health, Baltimore, MD 21218, USA; (S.M.); (A.C.)
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
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24
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Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Herlands L, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP. Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape. eLife 2021; 10:73027. [PMID: 34874007 PMCID: PMC8651292 DOI: 10.7554/elife.73027] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/07/2021] [Indexed: 02/06/2023] Open
Abstract
The emergence of SARS-CoV-2 variants threatens current vaccines and therapeutic antibodies and urgently demands powerful new therapeutics that can resist viral escape. We therefore generated a large nanobody repertoire to saturate the distinct and highly conserved available epitope space of SARS-CoV-2 spike, including the S1 receptor binding domain, N-terminal domain, and the S2 subunit, to identify new nanobody binding sites that may reflect novel mechanisms of viral neutralization. Structural mapping and functional assays show that indeed these highly stable monovalent nanobodies potently inhibit SARS-CoV-2 infection, display numerous neutralization mechanisms, are effective against emerging variants of concern, and are resistant to mutational escape. Rational combinations of these nanobodies that bind to distinct sites within and between spike subunits exhibit extraordinary synergy and suggest multiple tailored therapeutic and prophylactic strategies.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Natalia E Ketaren
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Erica Y Jacobs
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States.,Department of Chemistry, St. John's University, Queens, United States
| | - Jean Paul Olivier
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Tanmoy Sanyal
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Magdalena Rutkowska
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, United States
| | - Elizabeth R Vanderwall
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, United States
| | - Nicholas Dambrauskas
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Vladimir Vigdorovich
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, United States
| | - Jacob B Jiler
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | | | | | - D Noah Sather
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States.,Department of Pediatrics, University of Washington, Seattle, United States
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, United States.,Department of Pediatrics, University of Washington, Seattle, United States.,Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, United States
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States.,Department of Pediatrics, University of Washington, Seattle, United States.,Department of Biochemistry, University of Washington, Seattle, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
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25
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Willcox AC, Sung K, Garrett ME, Galloway JG, O’Connor MA, Erasmus JH, Logue JK, Hawman DW, Chu HY, Hasenkrug KJ, Fuller DH, Matsen FA, Overbaugh J. Macaque-human differences in SARS-CoV-2 Spike antibody response elicited by vaccination or infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.01.470697. [PMID: 34909774 PMCID: PMC8669841 DOI: 10.1101/2021.12.01.470697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Macaques are a commonly used model for studying immunity to human viruses, including for studies of SARS-CoV-2 infection and vaccination. However, it is unknown whether macaque antibody responses recapitulate, and thus appropriately model, the response in humans. To answer this question, we employed a phage-based deep mutational scanning approach (Phage-DMS) to compare which linear epitopes are targeted on the SARS-CoV-2 Spike protein in humans and macaques following either vaccination or infection. We also used Phage-DMS to determine antibody escape pathways within each epitope, enabling a granular comparison of antibody binding specificities at the locus level. Overall, we identified some common epitope targets in both macaques and humans, including in the fusion peptide (FP) and stem helix-heptad repeat 2 (SH-H) regions. Differences between groups included a response to epitopes in the N-terminal domain (NTD) and C-terminal domain (CTD) in vaccinated humans but not vaccinated macaques, as well as recognition of a CTD epitope and epitopes flanking the FP in convalescent macaques but not convalescent humans. There was also considerable variability in the escape pathways among individuals within each group. Sera from convalescent macaques showed the least variability in escape overall and converged on a common response with vaccinated humans in the SH-H epitope region, suggesting highly similar antibodies were elicited. Collectively, these findings suggest that the antibody response to SARS-CoV-2 in macaques shares many features with humans, but with substantial differences in the recognition of certain epitopes and considerable individual variability in antibody escape profiles, suggesting a diverse repertoire of antibodies that can respond to major epitopes in both humans and macaques.
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Affiliation(s)
- Alexandra C. Willcox
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Meghan E. Garrett
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Jared G. Galloway
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Megan A. O’Connor
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Infectious Diseases and Translational Medicine, Washington National Primate Research Center, Seattle, WA, USA
| | - Jesse H. Erasmus
- Department of Microbiology, University of Washington, Seattle, WA, USA
- HDT Bio, Seattle, WA, USA
| | | | - David W. Hawman
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kim J. Hasenkrug
- Laboratory of Persistent Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Deborah H. Fuller
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Infectious Diseases and Translational Medicine, Washington National Primate Research Center, Seattle, WA, USA
- Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, USA
| | - Frederick A. Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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26
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Lou F, Li M, Pang Z, Jiang L, Guan L, Tian L, Hu J, Fan J, Fan H. Understanding the Secret of SARS-CoV-2 Variants of Concern/Interest and Immune Escape. Front Immunol 2021; 12:744242. [PMID: 34804024 PMCID: PMC8602852 DOI: 10.3389/fimmu.2021.744242] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
The global pandemic of the coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), places a heavy burden on global public health. Four SARS-CoV-2 variants of concern including B.1.1.7, B.1.351, B.1.617.2, and P.1, and two variants of interest including C.37 and B.1.621 have been reported to have potential immune escape, and one or more mutations endow them with worrisome epidemiologic, immunologic, or pathogenic characteristics. This review introduces the latest research progress on SARS-CoV-2 variants of interest and concern, key mutation sites, and their effects on virus infectivity, mortality, and immune escape. Moreover, we compared the effects of various clinical SARS-CoV-2 vaccines and convalescent sera on epidemic variants, and evaluated the neutralizing capability of several antibodies on epidemic variants. In the end, SARS-CoV-2 evolution strategies in different transmission stages, the impact of different vaccination strategies on SARS-CoV-2 immune escape, antibody therapy strategies and COVID-19 epidemic control prospects are discussed. This review will provide a systematic and comprehensive understanding of the secret of SARS-CoV-2 variants of interest/concern and immune escape.
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Affiliation(s)
- Fuxing Lou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zehan Pang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lin Jiang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lin Guan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lili Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jiaming Hu
- Tandon School of Engineering, New York University, New York, NY, United States
| | - Junfen Fan
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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27
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Focosi D, Maggi F. Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. Rev Med Virol 2021; 31:e2231. [PMID: 33724631 PMCID: PMC8250244 DOI: 10.1002/rmv.2231] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/29/2021] [Accepted: 02/15/2021] [Indexed: 12/15/2022]
Abstract
The Spike protein is the target of both antibody-based therapeutics (convalescent plasma, polyclonal serum, monoclonal antibodies) and vaccines. Mutations in Spike could affect efficacy of those treatments. Hence, monitoring of mutations is necessary to forecast and readapt the inventory of therapeutics. Different phylogenetic nomenclatures have been used for the currently circulating SARS-CoV-2 clades. The Spike protein has different hotspots of mutation and deletion, the most dangerous for immune escape being the ones within the receptor binding domain (RBD), such as K417N/T, N439K, L452R, Y453F, S477N, E484K, and N501Y. Convergent evolution has led to different combinations of mutations among different clades. In this review we focus on the main variants of concern, that is, the so-called UK (B.1.1.7), South African (B.1.351) and Brazilian (P.1) strains.
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MESH Headings
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/metabolism
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/metabolism
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/chemistry
- Antibodies, Viral/metabolism
- Antibodies, Viral/therapeutic use
- Brazil/epidemiology
- COVID-19/epidemiology
- COVID-19/immunology
- COVID-19/therapy
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- Gene Expression
- Humans
- Immune Evasion
- Immunization, Passive/methods
- Mutation
- Phylogeny
- Protein Binding
- Risk Assessment
- SARS-CoV-2/classification
- SARS-CoV-2/drug effects
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- South Africa/epidemiology
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- United Kingdom/epidemiology
- COVID-19 Serotherapy
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Affiliation(s)
- Daniele Focosi
- North‐Western Tuscany Blood BankPisa University HospitalPisaItaly
| | - Fabrizio Maggi
- Department of Medicine and SurgeryUniversity of InsubriaVareseItaly
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28
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Garrett ME, Galloway JG, Wolf C, Logue JK, Franko N, Chu HY, Matsen FA, Overbaugh J. Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein after infection and/or vaccination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34642694 PMCID: PMC8509098 DOI: 10.1101/2021.10.05.463210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background: Control of the COVID-19 pandemic will rely on SARS-CoV-2 vaccine-elicited antibodies to protect against emerging and future variants; an understanding of the unique features of the humoral responses to infection and vaccination, including different vaccine platforms, is needed to achieve this goal. Methods: The epitopes and pathways of escape for Spike-specific antibodies in individuals with diverse infection and vaccination history were profiled using Phage-DMS. Principal component analysis was performed to identify regions of antibody binding along the Spike protein that differentiate the samples from one another. Within these epitope regions we determined potential escape mutations by comparing antibody binding of peptides containing wildtype residues versus peptides containing a mutant residue. Results: Individuals with mild infection had antibodies that bound to epitopes in the S2 subunit within the fusion peptide and heptad-repeat regions, whereas vaccinated individuals had antibodies that additionally bound to epitopes in the N- and C-terminal domains of the S1 subunit, a pattern that was also observed in individuals with severe disease due to infection. Epitope binding appeared to change over time after vaccination, but other covariates such as mRNA vaccine dose, mRNA vaccine type, and age did not affect antibody binding to these epitopes. Vaccination induced a relatively uniform escape profile across individuals for some epitopes, whereas there was much more variation in escape pathways in in mildly infected individuals. In the case of antibodies targeting the fusion peptide region, which was a common response to both infection and vaccination, the escape profile after infection was not altered by subsequent vaccination. Conclusions: The finding that SARS-CoV-2 mRNA vaccination resulted in binding to additional epitopes beyond what was seen after infection suggests protection could vary depending on the route of exposure to Spike antigen. The relatively conserved escape pathways to vaccine-induced antibodies relative to infection-induced antibodies suggests that if escape variants emerge, they may be readily selected for across vaccinated individuals. Given that the majority of people will be first exposed to Spike via vaccination and not infection, this work has implications for predicting the selection of immune escape variants at a population level.
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29
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Carnell GW, Ciazynska KA, Wells DA, Xiong X, Aguinam ET, McLaughlin SH, Mallery D, Ebrahimi S, Ceron-Gutierrez L, Asbach B, Einhauser S, Wagner R, James LC, Doffinger R, Heeney JL, Briggs JAG. SARS-CoV-2 Spike Protein Stabilized in the Closed State Induces Potent Neutralizing Responses. J Virol 2021; 95:e0020321. [PMID: 33963055 PMCID: PMC8274612 DOI: 10.1128/jvi.00203-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
The majority of SARS-CoV-2 vaccines in use or advanced development are based on the viral spike protein (S) as their immunogen. S is present on virions as prefusion trimers in which the receptor binding domain (RBD) is stochastically open or closed. Neutralizing antibodies have been described against both open and closed conformations. The long-term success of vaccination strategies depends upon inducing antibodies that provide long-lasting broad immunity against evolving SARS-CoV-2 strains. Here, we have assessed the results of immunization in a mouse model using an S protein trimer stabilized in the closed state to prevent full exposure of the receptor binding site and therefore interaction with the receptor. We compared this with other modified S protein constructs, including representatives used in current vaccines. We found that all trimeric S proteins induced a T cell response and long-lived, strongly neutralizing antibody responses against 2019 SARS-CoV-2 and variants of concern P.1 and B.1.351. Notably, the protein binding properties of sera induced by the closed spike differed from those induced by standard S protein constructs. Closed S proteins induced more potent neutralizing responses than expected based on the degree to which they inhibit interactions between the RBD and ACE2. These observations suggest that closed spikes recruit different, but equally potent, immune responses than open spikes and that this is likely to include neutralizing antibodies against conformational epitopes present in the closed conformation. We suggest that closed spikes, together with their improved stability and storage properties, may be a valuable component of refined, next-generation vaccines. IMPORTANCE Vaccines in use against SARS-CoV-2 induce immune responses against the spike protein. There is intense interest in whether the antibody response induced by vaccines will be robust against new variants, as well as in next-generation vaccines for use in previously infected or immunized individuals. We assessed the use as an immunogen of a spike protein engineered to be conformationally stabilized in the closed state where the receptor binding site is occluded. Despite occlusion of the receptor binding site, the spike induces potently neutralizing sera against multiple SARS-CoV-2 variants. Antibodies are raised against a different pattern of epitopes to those induced by other spike constructs, preferring conformational epitopes present in the closed conformation. Closed spikes, or mRNA vaccines based on their sequence, can be a valuable component of next-generation vaccines.
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Affiliation(s)
- George W. Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - David A. Wells
- DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - Xiaoli Xiong
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ernest T. Aguinam
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Donna Mallery
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Soraya Ebrahimi
- Department of Clinical Biochemistry and Immunology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Lourdes Ceron-Gutierrez
- Department of Clinical Biochemistry and Immunology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Benedikt Asbach
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Sebastian Einhauser
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Leo C. James
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Jonathan L. Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - John A. G. Briggs
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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30
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Duerr R, Crosse KM, Valero-Jimenez AM, Dittmann M. SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise. Microorganisms 2021; 9:1389. [PMID: 34198973 PMCID: PMC8307803 DOI: 10.3390/microorganisms9071389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 and HIV are zoonotic viruses that rapidly reached pandemic scale, causing global losses and fear. The COVID-19 and AIDS pandemics ignited massive efforts worldwide to develop antiviral strategies and characterize viral architectures, biological and immunological properties, and clinical outcomes. Although both viruses have a comparable appearance as enveloped viruses with positive-stranded RNA and envelope spikes mediating cellular entry, the entry process, downstream biological and immunological pathways, clinical outcomes, and disease courses are strikingly different. This review provides a systemic comparison of both viruses' structural and functional characteristics, delineating their distinct strategies for efficient spread.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA; (K.M.C.); (A.M.V.-J.); (M.D.)
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31
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Ng KW, Faulkner N, Wrobel AG, Gamblin SJ, Kassiotis G. Heterologous humoral immunity to human and zoonotic coronaviruses: Aiming for the achilles heel. Semin Immunol 2021; 55:101507. [PMID: 34716096 PMCID: PMC8542444 DOI: 10.1016/j.smim.2021.101507] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 02/04/2023]
Abstract
Coronaviruses are evolutionarily successful RNA viruses, common to multiple avian, amphibian and mammalian hosts. Despite their ubiquity and potential impact, knowledge of host immunity to coronaviruses remains incomplete, partly owing to the lack of overt pathogenicity of endemic human coronaviruses (HCoVs), which typically cause common colds. However, the need for deeper understanding became pressing with the zoonotic introduction of three novel coronaviruses in the past two decades, causing severe acute respiratory syndromes in humans, and the unfolding pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This renewed interest not only triggered the discovery of two of the four HCoVs, but also uncovered substantial cellular and humoral cross-reactivity with shared or related coronaviral antigens. Here, we review the evidence for cross-reactive B cell memory elicited by HCoVs and its potential impact on the puzzlingly variable outcome of SARS-CoV-2 infection. The available data indicate targeting of highly conserved regions primarily in the S2 subunits of the spike glycoproteins of HCoVs and SARS-CoV-2 by cross-reactive B cells and antibodies. Rare monoclonal antibodies reactive with conserved S2 epitopes and with potent virus neutralising activity have been cloned, underscoring the potential functional relevance of cross-reactivity. We discuss B cell and antibody cross-reactivity in the broader context of heterologous humoral immunity to coronaviruses, as well as the limits of protective immune memory against homologous re-infection. Given the bidirectional nature of cross-reactivity, the unprecedented current vaccination campaign against SARS-CoV-2 is expected to impact HCoVs, as well as future zoonotic coronaviruses attempting to cross the species barrier. However, emerging SARS-CoV-2 variants with resistance to neutralisation by vaccine-induced antibodies highlight a need for targeting more constrained, less mutable parts of the spike. The delineation of such cross-reactive areas, which humoral immunity can be trained to attack, may offer the key to permanently shifting the balance of our interaction with current and future coronaviruses in our favour.
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Affiliation(s)
- Kevin W. Ng
- Retroviral Immunology Laboratory, London, NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology Laboratory, London, NW1 1AT, UK,National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK
| | - Antoni G. Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Steve J. Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, London, NW1 1AT, UK,Department of Infectious Disease, St Mary's Hospital, Imperial College London, London W2 1PG, UK,Corresponding author at: Retroviral Immunology Laboratory, London, NW1 1AT, UK
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32
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Rochman N, Wolf YI, Koonin EV. Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics. F1000Res 2021; 10:315. [PMID: 34504684 PMCID: PMC8406440 DOI: 10.12688/f1000research.52341.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
Background: The start of 2021 was marked by the initiation of a global vaccination campaign against the novel coronavirus SARS-CoV-2. Formulating an optimal distribution strategy under social and economic constraints is challenging. Optimal distribution is additionally constrained by the potential emergence of vaccine resistance. Analogous to chronic low-dose antibiotic exposure, recently inoculated individuals who are not yet immune play an outsized role in the emergence of resistance. Classical epidemiological modelling is well suited to explore how the behavior of the inoculated population impacts the total number of infections over the entirety of an epidemic. Methods: A deterministic model of epidemic evolution is analyzed, with seven compartments defined by their relationship to the emergence of vaccine-resistant mutants and representing three susceptible populations, three infected populations, and one recovered population. This minimally computationally intensive design enables simulation of epidemics across a broad parameter space. The results are used to identify conditions minimizing the cumulative number of infections. Results: When an escape variant is only modestly less infectious than the originating strain within a naïve population, the cumulative number of infections does not monotonically decrease with the rate of vaccine distribution. Analysis of the model also demonstrates that inoculated individuals play a major role in the mitigation or exacerbation of vaccine-resistant outbreaks. Modulating the rate of host-host contact for the inoculated population by less than an order of magnitude can alter the cumulative number of infections by more than 20%. Conclusions: Mathematical modeling shows that limiting post-vaccination contacts can perceptibly affect the course of an epidemic. The consideration of limitations on post-vaccination contacts remains relevant for the entire duration of any vaccination campaign including the current status of SARS-CoV-2 vaccination.
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Affiliation(s)
- Nash Rochman
- National Center for Biotechnology Information, NIH, Bethesda, MD, 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, NIH, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, NIH, Bethesda, MD, 20894, USA
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33
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Rochman N, Wolf YI, Koonin EV. Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics. F1000Res 2021; 10:315. [PMID: 34504684 PMCID: PMC8406440 DOI: 10.12688/f1000research.52341.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 07/20/2023] Open
Abstract
Background: The start of 2021 was marked by the initiation of a global vaccination campaign against the novel coronavirus SARS-CoV-2. Formulating an optimal distribution strategy under social and economic constraints is challenging. Optimal distribution is additionally constrained by the potential emergence of vaccine resistance. Analogous to chronic low-dose antibiotic exposure, recently inoculated individuals who are not yet immune play an outsized role in the emergence of resistance. Classical epidemiological modelling is well suited to explore how the behavior of the inoculated population impacts the total number of infections over the entirety of an epidemic. Methods: A deterministic model of epidemic evolution is analyzed, with seven compartments defined by their relationship to the emergence of vaccine-resistant mutants and representing three susceptible populations, three infected populations, and one recovered population. This minimally computationally intensive design enables simulation of epidemics across a broad parameter space. The results are used to identify conditions minimizing the cumulative number of infections. Results: When an escape variant is only modestly less infectious than the originating strain within a naïve population, there exists an optimal rate of vaccine distribution. Exceeding this rate increases the cumulative number of infections due to vaccine escape. Analysis of the model also demonstrates that inoculated individuals play a major role in the mitigation or exacerbation of vaccine-resistant outbreaks. Modulating the rate of host-host contact for the inoculated population by less than an order of magnitude can alter the cumulative number of infections by more than 20%. Conclusions: Mathematical modeling shows that optimization of the vaccination rate and limiting post-vaccination contacts can perceptibly affect the course of an epidemic. The consideration of limitations on post-vaccination contacts remains relevant for the entire duration of any vaccination campaign including the current status of SARS-CoV-2 vaccination.
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Affiliation(s)
- Nash Rochman
- National Center for Biotechnology Information, NIH, Bethesda, MD, 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, NIH, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, NIH, Bethesda, MD, 20894, USA
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