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Astakhova EA, Morozov AA, Byazrova MG, Sukhova MM, Mikhailov AA, Minnegalieva AR, Gorchakov AA, Filatov AV. Antigenic Cartography Indicates That the Omicron BA.1 and BA.4/BA.5 Variants Remain Antigenically Distant to Ancestral SARS-CoV-2 after Sputnik V Vaccination Followed by Homologous (Sputnik V) or Heterologous (Comirnaty) Revaccination. Int J Mol Sci 2023; 24:10493. [PMID: 37445671 PMCID: PMC10341525 DOI: 10.3390/ijms241310493] [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: 05/16/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
The rapid emergence of evasive SARS-CoV-2 variants is an ongoing challenge for COVID-19 vaccinology. Traditional virus neutralization tests provide detailed datasets of neutralization titers against the viral variants. Such datasets are difficult to interpret and do not immediately inform of the sufficiency of the breadth of the antibody response. Some of these issues could be tackled using the antigenic cartography approach. In this study, we created antigenic maps using neutralization titers of sera from donors who received the Sputnik V booster vaccine after primary Sputnik V vaccination and compared them with the antigenic maps based on serum neutralization titers of Comirnaty-boosted donors. A traditional analysis of neutralization titers against the WT (wild-type), Alpha, Beta, Delta, Omicron BA.1, and BA.4/BA.5 variants showed a significant booster humoral response after both homologous (Sputnik V) and heterologous (Comirnaty) revaccinations against all of the studied viral variants. However, despite this, a more in-depth analysis using antigenic cartography revealed that Omicron variants remain antigenically distant from the WT, which is indicative of the formation of insufficient levels of cross-neutralizing antibodies. The implications of these findings may be significant when developing a new vaccine regimen.
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Affiliation(s)
- Ekaterina A. Astakhova
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522 Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexey A. Morozov
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522 Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria G. Byazrova
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522 Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Ministry of Science and Higher Education of Russia, RUDN University, 117198 Moscow, Russia
| | - Maria M. Sukhova
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522 Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Artem A. Mikhailov
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522 Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Aygul R. Minnegalieva
- Laboratory of Synthetic and Evolutionary Biology, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
| | - Andrey A. Gorchakov
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexander V. Filatov
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522 Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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Zhao LP, Lybrand TP, Gilbert PB, Payne TH, Pyo CW, Geraghty DE, Jerome KR. Rapidly identifying new coronavirus mutations of potential concern in the Omicron variant using an unsupervised learning strategy. Sci Rep 2022; 12:19089. [PMID: 36352021 PMCID: PMC9645309 DOI: 10.1038/s41598-022-23342-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022] Open
Abstract
Extensive mutations in the Omicron spike protein appear to accelerate the transmission of SARS-CoV-2, and rapid infections increase the odds that additional mutants will emerge. To build an investigative framework, we have applied an unsupervised machine learning approach to 4296 Omicron viral genomes collected and deposited to GISAID as of December 14, 2021, and have identified a core haplotype of 28 polymutants (A67V, T95I, G339D, R346K, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, K796Y, N856K, Q954H, N69K, L981F) in the spike protein and a separate core haplotype of 17 polymutants in non-spike genes: (K38, A1892) in nsp3, T492 in nsp4, (P132, V247, T280, S284) in 3C-like proteinase, I189 in nsp6, P323 in RNA-dependent RNA polymerase, I42 in Exonuclease, T9 in envelope protein, (D3, Q19, A63) in membrane glycoprotein, and (P13, R203, G204) in nucleocapsid phosphoprotein. Using these core haplotypes as reference, we have identified four newly emerging polymutants (R346, A701, I1081, N1192) in the spike protein (p value = 9.37*10-4, 1.0*10-15, 4.76*10-7 and 1.56*10-4, respectively), and five additional polymutants in non-spike genes (D343G in nucleocapsid phosphoprotein, V1069I in nsp3, V94A in nsp4, F694Y in the RNA-dependent RNA polymerase and L106L/F of ORF3a) that exhibit significant increasing trajectories (all p values < 1.0*10-15). In the absence of relevant clinical data for these newly emerging mutations, it is important to monitor them closely. Two emerging mutations may be of particular concern: the N1192S mutation in spike protein locates in an extremely highly conserved region of all human coronaviruses that is integral to the viral fusion process, and the F694Y mutation in the RNA polymerase may induce conformational changes that could impact remdesivir binding.
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Affiliation(s)
- Lue Ping Zhao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Terry P Lybrand
- Quintepa Computing LLC, Nashville, TN, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Thomas H Payne
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Lusvarghi S, Pollett SD, Neerukonda SN, Wang W, Wang R, Vassell R, Epsi NJ, Fries AC, Agan BK, Lindholm DA, Colombo CJ, Mody R, Ewers EC, Lalani T, Ganesan A, Goguet E, Hollis-Perry M, Coggins SA, Simons MP, Katzelnick LC, Wang G, Tribble DR, Bentley L, Eakin AE, Broder CC, Erlandson KJ, Laing ED, Burgess TH, Mitre E, Weiss CD. SARS-CoV-2 Omicron neutralization by therapeutic antibodies, convalescent sera, and post-mRNA vaccine booster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.22.473880. [PMID: 34981057 PMCID: PMC8722594 DOI: 10.1101/2021.12.22.473880] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The rapid spread of the highly contagious Omicron variant of SARS-CoV-2 along with its high number of mutations in the spike gene has raised alarm about the effectiveness of current medical countermeasures. To address this concern, we measured neutralizing antibodies against Omicron in three important settings: (1) post-vaccination sera after two and three immunizations with the Pfizer/BNT162b2 vaccine, (2) convalescent sera from unvaccinated individuals infected by different variants, and (3) clinical-stage therapeutic antibodies. Using a pseudovirus neutralization assay, we found that titers against Omicron were low or undetectable after two immunizations and in most convalescent sera. A booster vaccination significantly increased titers against Omicron to levels comparable to those seen against the ancestral (D614G) variant after two immunizations. Neither age nor sex were associated with differences in post-vaccination antibody responses. Only three of 24 therapeutic antibodies tested retained their full potency against Omicron and high-level resistance was seen against fifteen. These findings underscore the potential benefit of booster mRNA vaccines for protection against Omicron and the need for additional therapeutic antibodies that are more robust to highly mutated variants. ONE SENTENCE SUMMARY Third dose of Pfizer/BioNTech COVID-19 vaccine significantly boosts neutralizing antibodies to the Omicron variant compared to a second dose, while neutralization of Omicron by convalescent sera, two-dose vaccine-elicited sera, or therapeutic antibodies is variable and often low.
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Affiliation(s)
- Sabrina Lusvarghi
- Division of Viral Products, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Simon D Pollett
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Sabari Nath Neerukonda
- Division of Viral Products, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Wei Wang
- Division of Viral Products, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Richard Wang
- Division of Viral Products, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Russell Vassell
- Division of Viral Products, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Nusrat J Epsi
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Anthony C Fries
- U.S. Air Force School of Aerospace Medicine, Wright-Patterson, OH, USA
| | - Brian K Agan
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - David A Lindholm
- Brooke Army Medical Center, Joint Base San Antonio-Fort Sam Houston, TX, USA
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Christopher J Colombo
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Madigan Army Medical Center, Joint Base Lewis McChord, WA, USA
| | - Rupal Mody
- William Beaumont Army Medical Center, El Paso, TX, USA
| | - Evan C Ewers
- Fort Belvoir Community Hospital, Fort Belvoir, VA, USA
| | - Tahaniyat Lalani
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
- Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - Anuradha Ganesan
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Emilie Goguet
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Monique Hollis-Perry
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, USA
| | - Si'Ana A Coggins
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Mark P Simons
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Leah C Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Gregory Wang
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, USA
- General Dynamics Information Technology, Falls Church, VA, USA
| | - David R Tribble
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Lisa Bentley
- Office of the Assistance Secretary for Preparedness and Response, U.S. Department of Human Health and Services, Washington D.C., USA
| | - Ann E Eakin
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, Maryland, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Karl J Erlandson
- Influenza and Emerging Infectious Diseases Division, Biomedical Advanced Research and Development Authority, U.S. Department of Health and Human Services, Washington, D.C., USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Timothy H Burgess
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Carol D Weiss
- Division of Viral Products, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
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