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Ryder R, Smith E, Borthwick D, Elder J, Panditrao M, Morales C, Wadford DA. Emergence of Recombinant SARS-CoV-2 Variants in California from 2020 to 2022. Viruses 2024; 16:1209. [PMID: 39205183 PMCID: PMC11359944 DOI: 10.3390/v16081209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024] Open
Abstract
The detection, characterization, and monitoring of SARS-CoV-2 recombinant variants constitute a challenge for public health authorities worldwide. Recombinant variants, composed of two or more SARS-CoV-2 lineages, often have unknown impacts on transmission, immune escape, and virulence in the early stages of emergence. We examined 4213 SARS-CoV-2 recombinant SARS-CoV-2 genomes collected between 2020 and 2022 in California to describe regional and statewide trends in prevalence. Many of these recombinant genomes, such as those belonging to the XZ lineage or novel recombinant lineages, likely originated within the state of California. We discuss the challenges and limitations surrounding Pango lineage assignments, the use of publicly available sequence data, and adequate sample sizes for epidemiologic analyses. Although these challenges will continue as SARS-CoV-2 sequencing volumes decrease globally, this study enhances our understanding of SARS-CoV-2 recombinant genomes to date while providing a foundation for future insights into emerging recombinant lineages.
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Affiliation(s)
- Rahil Ryder
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Emily Smith
- Theiagen Genomics, Highlands Ranch, CO 80129, USA;
| | - Deva Borthwick
- COVID Control Branch, Division of Communicable Disease Control, CDPH, Richmond, CA 94804, USA
| | - Jesse Elder
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Mayuri Panditrao
- COVID Control Branch, Division of Communicable Disease Control, CDPH, Richmond, CA 94804, USA
| | - Christina Morales
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Debra A. Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
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2
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Evans JP, Liu SL. Challenges and Prospects in Developing Future SARS-CoV-2 Vaccines: Overcoming Original Antigenic Sin and Inducing Broadly Neutralizing Antibodies. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1459-1467. [PMID: 37931210 DOI: 10.4049/jimmunol.2300315] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/27/2023] [Indexed: 11/08/2023]
Abstract
The impacts of the COVID-19 pandemic led to the development of several effective SARS-CoV-2 vaccines. However, waning vaccine efficacy as well as the antigenic drift of SARS-CoV-2 variants has diminished vaccine efficacy against SARS-CoV-2 infection and may threaten public health. Increasing interest has been given to the development of a next generation of SARS-CoV-2 vaccines with increased breadth and effectiveness against SARS-CoV-2 infection. In this Brief Review, we discuss recent work on the development of these next-generation vaccines and on the nature of the immune response to SARS-CoV-2. We examine recent work to develop pan-coronavirus vaccines as well as to develop mucosal vaccines. We further discuss challenges associated with the development of novel vaccines including the need to overcome "original antigenic sin" and highlight areas requiring further investigation. We place this work in the context of SARS-CoV-2 evolution to inform how the implementation of future vaccine platforms may impact human health.
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Affiliation(s)
- John P Evans
- Center for Retrovirus Research, The Ohio State University, Columbus, OH
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH
- Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH
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3
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Chrysostomou AC, Vrancken B, Haralambous C, Alexandrou M, Gregoriou I, Ioannides M, Ioannou C, Kalakouta O, Karagiannis C, Marcou M, Masia C, Mendris M, Papastergiou P, Patsalis PC, Pieridou D, Shammas C, Stylianou DC, Zinieri B, Lemey P, Network TCOMESSAR, Kostrikis LG. Unraveling the Dynamics of Omicron (BA.1, BA.2, and BA.5) Waves and Emergence of the Deltacton Variant: Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus (Oct 2021-Oct 2022). Viruses 2023; 15:1933. [PMID: 37766339 PMCID: PMC10535466 DOI: 10.3390/v15091933] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that impact both immune evasion and transmissibility. This ongoing process has led to successive waves of infections. This study offers a comprehensive assessment spanning genetic, phylogenetic, phylodynamic, and phylogeographic dimensions, focused on the trajectory of the SARS-CoV-2 epidemic in Cyprus. Based on a dataset comprising 4700 viral genomic sequences obtained from affected individuals between October 2021 and October 2022, our analysis is presented. Over this timeframe, a total of 167 distinct lineages and sublineages emerged, including variants such as Delta and Omicron (1, 2, and 5). Notably, during the fifth wave of infections, Omicron subvariants 1 and 2 gained prominence, followed by the ascendancy of Omicron 5 in the subsequent sixth wave. Additionally, during the fifth wave (December 2021-January 2022), a unique set of Delta sequences with genetic mutations associated with Omicron variant 1, dubbed "Deltacron", was identified. The emergence of this phenomenon initially evoked skepticism, characterized by concerns primarily centered around contamination or coinfection as plausible etiological contributors. These hypotheses were predominantly disseminated through unsubstantiated assertions within the realms of social and mass media, lacking concurrent scientific evidence to validate their claims. Nevertheless, the exhaustive molecular analyses presented in this study have demonstrated that such occurrences would likely lead to a frameshift mutation-a genetic aberration conspicuously absent in our provided sequences. This substantiates the accuracy of our initial assertion while refuting contamination or coinfection as potential etiologies. Comparable observations on a global scale dispelled doubt, eventually leading to the recognition of Delta-Omicron variants by the scientific community and their subsequent monitoring by the World Health Organization (WHO). As our investigation delved deeper into the intricate dynamics of the SARS-CoV-2 epidemic in Cyprus, a discernible pattern emerged, highlighting the major role of international connections in shaping the virus's local trajectory. Notably, the United States and the United Kingdom were the central conduits governing the entry and exit of the virus to and from Cyprus. Moreover, notable migratory routes included nations such as Greece, South Korea, France, Germany, Brazil, Spain, Australia, Denmark, Sweden, and Italy. These empirical findings underscore that the spread of SARS-CoV-2 within Cyprus was markedly influenced by the influx of new, highly transmissible variants, triggering successive waves of infection. This investigation elucidates the emergence of new waves of infection subsequent to the advent of highly contagious and transmissible viral variants, notably characterized by an abundance of mutations localized within the spike protein. Notably, this discovery decisively contradicts the hitherto hypothesis of seasonal fluctuations in the virus's epidemiological dynamics. This study emphasizes the importance of meticulously examining molecular genetics alongside virus migration patterns within a specific region. Past experiences also emphasize the substantial evolutionary potential of viruses such as SARS-CoV-2, underscoring the need for sustained vigilance. However, as the pandemic's dynamics continue to evolve, a balanced approach between caution and resilience becomes paramount. This ethos encourages an approach founded on informed prudence and self-preservation, guided by public health authorities, rather than enduring apprehension. Such an approach empowers societies to adapt and progress, fostering a poised confidence rooted in well-founded adaptation.
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Affiliation(s)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Christos Haralambous
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | - Maria Alexandrou
- Microbiology Department, Larnaca General Hospital, 6301 Larnaca, Cyprus
| | - Ioanna Gregoriou
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | | | - Costakis Ioannou
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus
| | - Olga Kalakouta
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | | | - Markella Marcou
- Department of Microbiology, Archbishop Makarios III Hospital, 2012 Nicosia, Cyprus
| | - Christina Masia
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus
| | - Michail Mendris
- Microbiology Department, Limassol General Hospital, 4131 Limassol, Cyprus
| | | | - Philippos C. Patsalis
- Medicover Genetics, 2409 Nicosia, Cyprus
- Medical School, University of Nicosia, 2417 Nicosia, Cyprus
| | - Despo Pieridou
- Microbiology Department, Nicosia General Hospital, 2029 Nicosia, Cyprus
| | - Christos Shammas
- S.C.I.N.A. Bioanalysis Sciomedical Centre Ltd., 4040 Limassol, Cyprus
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | - Barbara Zinieri
- Microbiology Department, Paphos General Hospital, Achepans, 8026 Paphos, Cyprus
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | | | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
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4
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Fang L, Xu J, Zhao Y, Fan J, Shen J, Liu W, Cao G. The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2. Front Microbiol 2023; 14:1228128. [PMID: 37560529 PMCID: PMC10409611 DOI: 10.3389/fmicb.2023.1228128] [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: 05/24/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Over three years' pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and novel subvariants have emerged successively, outcompeted earlier variants and become predominant. The sequential emergence of variants reflects the evolutionary process of mutation-selection-adaption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in the spike protein causes altered viral antigenicity, transmissibility, and pathogenicity of SARS-CoV-2. Early in the pandemic, D614G mutation conferred virus with advantages over previous variants and increased transmissibility, and it also laid a conservative background for subsequent substantial mutations. The role of genomic recombination in the evolution of SARS-CoV-2 raised increasing concern with the occurrence of novel recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, and XBB.1.16 in the late phase of pandemic. Co-circulation of different variants and co-infection in immunocompromised patients accelerate the emergence of recombinants. Surveillance for SARS-CoV-2 genomic variations, particularly spike protein mutation and recombination, is essential to identify ongoing changes in the viral genome and antigenic epitopes and thus leads to the development of new vaccine strategies and interventions.
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Affiliation(s)
- Letian Fang
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jie Xu
- Department of Foreign Languages, International Exchange Center for Military Medicine, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Junyan Fan
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jiaying Shen
- School of Medicine, Tongji University, Shanghai, China
| | - Wenbin Liu
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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5
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Wang ST, Li L, Zhang J, Li Y, Luo XF, Sun GQ. Quantitative evaluation of the role of Fangcang shelter hospitals in the control of Omicron transmission: A case study of the outbreak in Shanghai, China in 2022. One Health 2023; 16:100475. [PMID: 36593980 PMCID: PMC9803829 DOI: 10.1016/j.onehlt.2022.100475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/06/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Since Omicron began to spread in China, Shanghai has become one of the cities with more severe outbreaks. Under the comprehensive consideration of the vaccine coverage rate, the number of Fangcang shelter hospital beds and the number of designated hospital beds in Shanghai, this paper established a deterministic compartmental model and used the Nelder-Mead Simplex Direct Search Algorithm and chi-square values to estimate the model parameters. we calculate ℛ0 = 3.6429 when the number of beds in the Fangcang shelter hospital is relatively tight in the second stage and ℛ0 = 0.4974 in the fifth stage when there are enough beds in both Fangcang shelter hospital and designated hospital. Then we perform a sensitivity analysis on ℛ0 by using perturbation of fixed point estimation of model parameters in the fifth stage, and obtain three parameters that are more sensitive to ℛ0, which are transmission rate (β 1d ), proportion of the infectious (η) and the hospitalization rate of asymptomatic infected cases (δ 1). Through simulation, we obtain that if the hospitalization rate of asymptomatic infections δ 2 > 0.9373 or the transmission rate β 1b < 0.0467, the second stage of Omicron transmission in Shanghai can be well controlled. Finally, we find the measure that converting the National Convention and Exhibition Center (NECC) into a Fangcang shelter hospital has played an important role in curbing the epidemic. Whether this temporary Fangcang shelter hospital is not built or delayed, the cumulative number of confirmed cases will both exceed 100,000, and the cumulative asymptomatic infections will both exceed 1 million. In addition, for a city of 10 million people, we obtain that if a permanent Fangcang shelter hospital with 17,784 beds is built ahead of epidemic, there will be no shortage of beds during the outbreak of Omicron. Our findings enrich the content of the impact of Fangcang shelter hospital beds on the spread of Omicron and confirm the correct policy adopted by the Chinese government.
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Affiliation(s)
- Sheng-Tao Wang
- Complex Systems Research Center, Shanxi University, Taiyuan 030006, China
| | - Li Li
- School of Computer and Information Technology, Shanxi University, Shanxi, Taiyuan 030006, China
| | - Juan Zhang
- Complex Systems Research Center, Shanxi University, Taiyuan 030006, China
| | - Yong Li
- School of Information and Mathematics, Yangtze University, Jingzhou 434023, China
| | - Xiao-Feng Luo
- School of Mathematics, North University of China, Shanxi, Taiyuan 030051, China
| | - Gui-Quan Sun
- Complex Systems Research Center, Shanxi University, Taiyuan 030006, China
- School of Mathematics, North University of China, Shanxi, Taiyuan 030051, China
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6
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Wang ST, Wu YP, Li L, Li Y, Sun GQ. Forecast for peak infections in the second wave of the Omicron after the adjustment of zero-COVID policy in the mainland of China. Infect Dis Model 2023; 8:562-573. [PMID: 37305609 PMCID: PMC10251123 DOI: 10.1016/j.idm.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/17/2023] [Accepted: 05/28/2023] [Indexed: 06/13/2023] Open
Abstract
On December 7, 2022, the Chinese government optimized the current epidemic prevention and control policy, and no longer adopted the zero-COVID policy and mandatory quarantine measures. Based on the above policy changes, this paper establishes a compartment dynamics model considering age distribution, home isolation and vaccinations. Parameter estimation was performed using improved least squares and Nelder-Mead simplex algorithms combined with modified case data. Then, using the estimated parameter values to predict a second wave of the outbreak, the peak of severe cases will reach on 8 May 2023, the number of severe cases will reach 206,000. Next, it is proposed that with the extension of the effective time of antibodies obtained after infection, the peak of severe cases in the second wave of the epidemic will be delayed, and the final scale of the disease will be reduced. When the effectiveness of antibodies is 6 months, the severe cases of the second wave will peak on July 5, 2023, the number of severe cases is 194,000. Finally, the importance of vaccination rates is demonstrated, when the vaccination rate of susceptible people under 60 years old reaches 98%, and the vaccination rate of susceptible people over 60 years old reaches 96%, the peak of severe cases in the second wave of the epidemic will be reached on 13 July 2023, when the number of severe cases is 166,000.
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Affiliation(s)
- Sheng-Tao Wang
- Complex Systems Research Center, Shanxi University, Taiyuan, 030006, China
| | - Yong-Ping Wu
- College of Physical Science and Technology, Yangzhou University, Yangzhou, 225002, China
| | - Li Li
- School of Computer and Information Technology, Shanxi University, Shanxi, Taiyuan, 030006, China
| | - Yong Li
- School of Information and Mathematics, Yangtze University, Jingzhou, 434023, China
| | - Gui-Quan Sun
- Complex Systems Research Center, Shanxi University, Taiyuan, 030006, China
- School of Mathematics, North University of China, Shanxi, Taiyuan, 030051, China
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7
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Efficacy of the neutralizing antibodies after the booster dose on SARS-CoV-2 Omicron variant and a two-year longitudinal antibody study on Wild Type convalescents. Int Immunopharmacol 2023; 119:110151. [PMID: 37044040 PMCID: PMC10073579 DOI: 10.1016/j.intimp.2023.110151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/24/2023] [Accepted: 04/01/2023] [Indexed: 04/09/2023]
Abstract
Objectives Waning vaccine-induced immunity and emergence of new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants which may lead to immune escape, pose a major threat to the COVID-19 pandemic. Currently, enhanced efficacy of the neutralization antibodies (NAb) produced after the booster dose of vaccinations against the Omicron variant is the main focus of vaccine strategy research. In this study we have analyzed the potency of the NAbs and IgGs produced after the third vaccine dose in patients infected with Omicron variant and wild-type (WT) SARS-CoV-2. Methods We enrolled 75 patients with Omicron variant breakthrough infections, and 87 patients with WT infections. We recorded the clinical characteristics and vaccination information of all patients and measured the NAb and anti-S1 (spike protein)+N (nucleocapsid protein) IgG-binding antibodies against SARS-CoV-2 in serum samples of Omicron variant-infected patients at admission, and patients with WT COVID-19 infection from the time of admission and discharge, and one-year to two-years follow-ups. Results Our results demonstrated higher NAb levels, fewer clinical symptoms, and faster viral shedding in Omicron variant infected patients vaccinated with the booster dose. Hybrid immunity (natural infection plus vaccination) induces higher NAb levels than vaccine-only immunity. NAb and IgG levels decreased significantly at one-year follow-up in WT convalescents with natural infection. The NAb and IgG levels in booster-vaccinated COVID-19 patients were higher than those in two-dose-vaccinated patients. Conclusion Our results suggest that booster vaccinations are required to improve the level of protective NAbs. Moreover, our data provide important evidence for vaccination strategies based on existing vaccines.
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Chavda VP, Vuppu S, Mishra T, Balar P. The Emergence of Hybrid Variants of SARS-CoV-2: Towards Hybrid Immunity. Vaccines (Basel) 2023; 11:vaccines11040764. [PMID: 37112676 PMCID: PMC10144432 DOI: 10.3390/vaccines11040764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/19/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023] Open
Abstract
In this review work, the authors emphasize the discussion on different emerging variants of SARS-CoV-2 and vaccine effectiveness against them [...]
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Ren P, Hu Y, Peng L, Yang L, Suzuki K, Fang Z, Bai M, Zhou L, Feng Y, Zou Y, Xiong Y, Chen S. Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.08.09.503414. [PMID: 35982661 PMCID: PMC9387138 DOI: 10.1101/2022.08.09.503414] [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] [Indexed: 11/24/2022]
Abstract
The SARS-CoV-2 variant, Omicron (B.1.1.529), rapidly swept the world since its emergence. Compared with previous variants, Omicron has a high number of mutations, especially those in its spike glycoprotein that drastically dampen or abolish the efficacy of currently available vaccines and therapeutic antibodies. Several major sublineages of Omicron evolved, including BA.1, BA.1.1, BA.2, BA.2.12.1, BA.3, BA.4/5, and BA.2.75, which rapidly changing the global and regional landscape of the pandemic. Although vaccines are available, therapeutic antibodies remain critical for infected and especially hospitalized patients. To address this, we have designed and generated a panel of human/humanized therapeutic bispecific antibodies against Omicron and its sub-lineage variants, with activity spectrum against other lineages. Among these, the top clone CoV2-0213 has broadly potent activities against multiple SARS-CoV-2 ancestral and Omicron lineages, including BA.1, BA.1.1, BA.2, BA.2.12.1, BA.3, BA.4/5, and BA.2.75. We have solved the cryo-EM structure of the lead bi-specific antibody CoV-0213 and its major Fab arm MB.02. Three-dimensional structural analysis shows distinct epitope of antibody - spike receptor binding domain (RBD) interactions and reveals that both Fab fragments of CoV2-0213 can simultaneously target one single spike RBD or two adjacent ones in the same spike trimer, further corroborating its mechanism of action. CoV2-0213 represents a unique and potent broad-spectrum SARS-CoV-2 neutralizing bispecific antibody (nbsAb) against the currently circulating major Omicron variants (BA.1, BA.1.1, BA.2, BA.2.12.1, BA.2.75, BA.3, and BA.4/5). CoV2-0213 is primarily human and ready for translational testing as a countermeasure against the ever-evolving pathogen.
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Affiliation(s)
- Ping Ren
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lei Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Luojia Yang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kazushi Suzuki
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Zhenhao Fang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Meizhu Bai
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Liqun Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Yanzhi Feng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Yongji Zou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Correspondence: SC (), +1-203-737-3825 (office), +1-203-737-4952 (lab), YX (), +1 (203) 436-2609 (lab)
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
- Immunobiology Program, Yale University, New Haven, CT, USA
- Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
- Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA
- Correspondence: SC (), +1-203-737-3825 (office), +1-203-737-4952 (lab), YX (), +1 (203) 436-2609 (lab)
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10
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Zhao G, Zhang Z, Ding Y, Hou J, Liu Y, Zhang M, Sui C, Wang L, Xu X, Gao X, Kou Z. A DNA Vaccine Encoding the Full-Length Spike Protein of Beta Variant (B.1.351) Elicited Broader Cross-Reactive Immune Responses against Other SARS-CoV-2 Variants. Vaccines (Basel) 2023; 11:513. [PMID: 36992097 PMCID: PMC10054764 DOI: 10.3390/vaccines11030513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
The SARS-CoV-2 pandemic remains an ongoing threat to global health with emerging variants, especially the Omicron variant and its sub-lineages. Although large-scale vaccination worldwide has delivered outstanding achievements for COVID-19 prevention, a declining effectiveness to a different extent in emerging SARS-CoV-2 variants was observed in the vaccinated population. Vaccines eliciting broader spectrum neutralizing antibodies and cellular immune responses are urgently needed and important. To achieve this goal, rational vaccine design, including antigen modeling, screening and combination, vaccine pipelines, and delivery, are keys to developing a next-generation COVID-19 vaccine. In this study, we designed several DNA constructs based on codon-optimized spike coding regions of several SARS-CoV-2 variants and analyzed their cross-reactive antibodies, including neutralizing antibodies, and cellular immune responses against several VOCs in C57BL/6 mice. The results revealed that different SARS-CoV-2 VOCs induced different cross-reactivity; pBeta, a DNA vaccine encoding the spike protein of the Beta variant, elicited broader cross-reactive neutralizing antibodies against other variants including the Omicron variants BA.1 and BA.4/5. This result demonstrates that the spike antigen from the Beta variant potentially serves as one of the antigens for multivalent vaccine design and development against variants of SARS-CoV-2.
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Affiliation(s)
- Gan Zhao
- Advaccine Biopharmaceutics (Suzhou) Co., Ltd., Suzhou 215000, China
| | | | | | | | | | | | | | | | | | | | - Zhihua Kou
- Advaccine Biopharmaceutics (Suzhou) Co., Ltd., Suzhou 215000, China
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11
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Duerr R, Zhou H, Tada T, Dimartino D, Marier C, Zappile P, Wang G, Plitnick J, Griesemer SB, Girardin R, Machowski J, Bialosuknia S, Lasek-Nesselquist E, Hong SL, Baele G, Dittmann M, Ortigoza MB, Prasad PJ, McDonough K, Landau NR, St George K, Heguy A. Delta-Omicron recombinant escapes therapeutic antibody neutralization. iScience 2023; 26:106075. [PMID: 36844451 PMCID: PMC9937133 DOI: 10.1016/j.isci.2023.106075] [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: 10/11/2022] [Revised: 12/29/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
The emergence of recombinant viruses is a threat to public health, as recombination may integrate variant-specific features that together result in escape from treatment or immunity. The selective advantages of recombinant SARS-CoV-2 isolates over their parental lineages remain unknown. We identified a Delta-Omicron (AY.45-BA.1) recombinant in an immunosuppressed transplant recipient treated with monoclonal antibody Sotrovimab. The single recombination breakpoint is located in the spike N-terminal domain adjacent to the Sotrovimab binding site. While Delta and BA.1 are sensitive to Sotrovimab neutralization, the Delta-Omicron recombinant is highly resistant. To our knowledge, this is the first described instance of recombination between circulating SARS-CoV-2 variants as a functional mechanism of resistance to treatment and immune escape.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
- Vaccine Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Dacia Dimartino
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY 10016, USA
| | - Christian Marier
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY 10016, USA
| | - Paul Zappile
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY 10016, USA
| | - Guiqing Wang
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jonathan Plitnick
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Sara B Griesemer
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Roxanne Girardin
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Jessica Machowski
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Sean Bialosuknia
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Erica Lasek-Nesselquist
- Bioinformatics Core, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
- Biomedical Sciences Department, School of Public Health, University at Albany, SUNY, Albany, NY 12144, USA
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Meike Dittmann
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Mila B Ortigoza
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Prithiv J Prasad
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kathleen McDonough
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Biomedical Sciences Department, School of Public Health, University at Albany, SUNY, Albany, NY 12144, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kirsten St George
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Biomedical Sciences Department, School of Public Health, University at Albany, SUNY, Albany, NY 12144, USA
| | - Adriana Heguy
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
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12
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Park JK, Bhandari S. Literature review on COVID-19 vaccine efficacy in the immunocompromised population, and possible implications to future vaccination in kidney transplant patients. Front Med (Lausanne) 2023; 10:1103699. [PMID: 36817787 PMCID: PMC9931721 DOI: 10.3389/fmed.2023.1103699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Since the emergence of the virulent coronavirus in 2019, efforts to tackle the coronavirus-disease-2019 (COVID-19) pandemic have been made globally. The development of the coronavirus disease (COVID) vaccine was a significant breakthrough in ways to tackle the virus. Various research studies have been conducted to identify how the virus works and ways to manage COVID, including the efficacy of the vaccines. However, there is limited data on how these measures work for the immunocompromised, despite the grave impact of these virulent strains in this population. Specifically, this review aims to focus on kidney transplant recipients (KTRs). Studies have suggested that there is significantly lower vaccine response in some immunocompromised groups despite additional booster doses, and hence warrants an augmented or alternative protection against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for these patients. This suggests a need for alternative or more tailored approach in providing adequate protection against the COVID-19 in these cohorts. Some suggested ways include withholding immunosuppressants before and/or after vaccination, increasing the vaccine doses or reducing intervals and providing a mixture of monoclonal antibody (mAb) or antiviral therapy. However, the appropriate degree of alteration and augmentation, as well as its safety and effectiveness remains to be determined. Furthermore, continuous emergence of more virulent strains, such as the Omicron and its sub-lineages or the Deltacron, emphasises the need for ongoing research to assess the effectiveness of the current treatment against these new variants. Overall, active interest and appropriate updates to COVID-19 guidelines is necessary.
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Affiliation(s)
- Joo Kyung Park
- Department of Renal Medicine, Hull University Teaching Hospitals NHS Trust, Kingston upon Hull, United Kingdom,Joo Kyung Park, ; orcid.org/0000-0002-7034-4998
| | - Sunil Bhandari
- Department of Renal Medicine, Hull University Teaching Hospitals NHS Trust, Kingston upon Hull, United Kingdom,Hull York Medical School, Kingston upon Hull, United Kingdom,*Correspondence: Sunil Bhandari, ; orcid.org/0000-0002-0996-9622
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13
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Chavda VP, Balar P, Vaghela D, Solanki HK, Vaishnav A, Hala V, Vora L. Omicron Variant of SARS-CoV-2: An Indian Perspective of Vaccination and Management. Vaccines (Basel) 2023; 11:160. [PMID: 36680006 PMCID: PMC9860853 DOI: 10.3390/vaccines11010160] [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: 12/10/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Omicron variants have highly influenced the entire globe. It has a high rate of transmissibility, which makes its management tedious. There are various subtypes of omicron, namely BA.1, BA.2, BA.3, BA.4, and BA.5. Currently, one omicron subvariant BF.7 is also immersed in some parts of India. Further studies are required for a better understanding of the new immersing SARS-CoV-2 subvariant of the omicron. They differ in the mutation of the spike proteins, which alters their attachment to the host receptor and hence modifies their virulence and adaptability. Delta variants have a great disastrous influence on the entire world, especially in India. While overcoming it, another mutant catches the pace. The Indian population is highly affected by omicron variants. It alters the entire management and diagnosis system against COVID-19. It demanded forcemeat in the health care system, both qualitatively and quantitively, to cope with the omicron wave. The alteration in spike protein, which is the major target of vaccines, leads to varied immunization against the subvariants. The efficacy of vaccines against the new variant was questioned. Every vaccine had a different shielding effect on the new variant. The hesitancy of vaccination was a prevalent factor in India that might have contributed to its outbreak. The prevalence of omicron, monkeypox, and tomato flu shared some similarities and distinct features when compared to their influence on the Indian population. This review emphasizes the changes omicron brings with it and how the Indian health care system outrage this dangerous variant.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Pankti Balar
- Pharmacy Section, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Dixa Vaghela
- Pharmacy Section, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Hetvi K. Solanki
- Pharmacy Section, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Akta Vaishnav
- Pharmacy Section, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Vivek Hala
- Pharmacy Section, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Lalitkumar Vora
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
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14
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Najeeb N, Murukan AB, Renjitha A, Jayaram M, Jabbar AA, Haridasan H, Prijikumar A, Baiju S, Nixon AA, Krishnan PA, Rodriguez S, Kumar S, Polipalli SK, Singh KK, Nair BG, Ghate SD, Rao RSP, Kishor PBK, Aloor A, Suravajhala R, Chaubey G, Suravajhala P. Inferring Recombination Events in SARS-CoV-2 Variants In Silico. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:253-270. [PMID: 37378772 DOI: 10.1007/978-3-031-28012-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Over the last 34 months, at least 10 severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) distinct variants have evolved. Among these, some were more infectious while others were not. These variants may serve as candidates for identification of the signature sequences linked to infectivity and viral transgressions. Based on our previous hijacking and transgression hypothesis, we aimed to investigate whether SARS-CoV-2 sequences associated with infectivity and trespassing of long noncoding RNAs (lncRNAs) provide a possible recombination mechanism to drive the formation of new variants. This work involved a sequence and structure-based approach to screen SARS-CoV-2 variants in silico, taking into account effects of glycosylation and links to known lncRNAs. Taken together, the findings suggest that transgressions involving lncRNAs may be linked with changes in SARS-CoV-2-host interactions driven by glycosylation events.
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Affiliation(s)
- Nihal Najeeb
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Aparna B Murukan
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Anagha Renjitha
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Malavika Jayaram
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Ayisha A Jabbar
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Haripriya Haridasan
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Akshara Prijikumar
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Sneha Baiju
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Adrial Ann Nixon
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | | | - Sunu Rodriguez
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Somesh Kumar
- Genome Sequencing Lab, Lok Nayak Hospital, Delhi, India
| | | | - Keshav K Singh
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Birmingham, AL, USA
| | - Bipin G Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Sudeep D Ghate
- Center for Bioinformatics, NITTE University, Mangaluru, India
| | | | | | - Arya Aloor
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Renuka Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India.
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15
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The SARS-CoV-2 Delta-Omicron Recombinant Lineage (XD) Exhibits Immune-Escape Properties Similar to the Omicron (BA.1) Variant. Int J Mol Sci 2022; 23:ijms232214057. [PMID: 36430535 PMCID: PMC9696394 DOI: 10.3390/ijms232214057] [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: 10/24/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Recently, a recombinant SARS-CoV-2 lineage, XD, emerged that harbors a spike gene that is largely derived from the Omicron variant BA.1 in the genetic background of the Delta variant. This finding raised concerns that the recombinant virus might exhibit altered biological properties as compared to the parental viruses and might pose an elevated threat to human health. Here, using pseudotyped particles, we show that ACE2 binding and cell tropism of XD mimics that of BA.1. Further, XD and BA.1 displayed comparable sensitivity to neutralization by antibodies induced upon vaccination with BNT162b2/Comirnaty (BNT) or BNT vaccination followed by breakthrough infection. Our findings reveal important biological commonalities between XD and Omicron BA.1 host cell entry and its inhibition by antibodies.
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16
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Chavda VP, Yao Q, Vora LK, Apostolopoulos V, Patel CA, Bezbaruah R, Patel AB, Chen ZS. Fast-track development of vaccines for SARS-CoV-2: The shots that saved the world. Front Immunol 2022; 13:961198. [PMID: 36263030 PMCID: PMC9574046 DOI: 10.3389/fimmu.2022.961198] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
In December 2019, an outbreak emerged of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which leads to coronavirus disease 2019 (COVID-19). The World Health Organisation announced the outbreak a global health emergency on 30 January 2020 and by 11 March 2020 it was declared a pandemic. The spread and severity of the outbreak took a heavy toll and overburdening of the global health system, particularly since there were no available drugs against SARS-CoV-2. With an immediate worldwide effort, communication, and sharing of data, large amounts of funding, researchers and pharmaceutical companies immediately fast-tracked vaccine development in order to prevent severe disease, hospitalizations and death. A number of vaccines were quickly approved for emergency use, and worldwide vaccination rollouts were immediately put in place. However, due to several individuals being hesitant to vaccinations and many poorer countries not having access to vaccines, multiple SARS-CoV-2 variants quickly emerged that were distinct from the original variant. Uncertainties related to the effectiveness of the various vaccines against the new variants as well as vaccine specific-side effects have remained a concern. Despite these uncertainties, fast-track vaccine approval, manufacturing at large scale, and the effective distribution of COVID-19 vaccines remain the topmost priorities around the world. Unprecedented efforts made by vaccine developers/researchers as well as healthcare staff, played a major role in distributing vaccine shots that provided protection and/or reduced disease severity, and deaths, even with the delta and omicron variants. Fortunately, even for those who become infected, vaccination appears to protect against major disease, hospitalisation, and fatality from COVID-19. Herein, we analyse ongoing vaccination studies and vaccine platforms that have saved many deaths from the pandemic.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, LM College of Pharmacy, Ahmedabad, Gujarat, India
| | - Qian Yao
- Graduate School, University of St. La Salle, Bacolod City, Philippines
| | | | | | - Chirag A. Patel
- Department of Pharmacology, LM College of Pharmacy, Ahmedabad, Gujarat, India
| | - Rajashri Bezbaruah
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Aayushi B. Patel
- Pharmacy Section, LM. College of Pharmacy, Ahmedabad, Gujarat, India
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Science, College of Pharmacy and Health Sciences, St. John’s University, New York, NY, United States
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17
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Duan LJ, Jiang WG, Wang ZY, Yao L, Zhu KL, Meng QC, Wang BS, Li LB, Wang GL, Ma MJ. Neutralizing immunity against SARS-CoV-2 Omicron BA.1 by infection and vaccination. iScience 2022; 25:104886. [PMID: 35966041 PMCID: PMC9359924 DOI: 10.1016/j.isci.2022.104886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/16/2022] [Accepted: 08/01/2022] [Indexed: 12/03/2022] Open
Abstract
The emergence of the SARS-CoV-2 Omicron BA.1 (B.1.1.529) variant has raised questions regarding resistance to neutralizing antibodies elicited by natural infection or immunization. We examined the neutralization activity of sera collected from previously SARS-CoV-2-infected individuals and SARS-CoV-2 naive individuals who received BBIBP-CorV or CoronaVac to BA.1 and the earlier variants Alpha, Beta, and Delta. Both sera from convalescent patients over three months after infection and two-dose BBIBP-CorV or CoronaVac vaccine recipients barely inhibited BA.1, less effectively neutralized Beta and Delta, and moderately neutralized Alpha. However, administering a single dose of BBIBP-CorV or CoronaVac in previously infected individuals or a third dose booster vaccination of BBIBP-CorV or CoronaVac in previously vaccinated individuals enhances neutralizing activity against BA.1 and other variants, albeit with a lower antibody titer for BA.1. Our data suggest that a booster vaccination is important to broaden neutralizing antibody responses against the variants. Limited duration of antibody response against BA.1 in convalescent individuals Infection before BBIBP-CorV or CoronaVac vaccination boosts neutralization Two doses of BBIBP-CorV or CoronaVac elicit limited neutralizing activity against VOCs Neutralization breadth for BA.1 is boosted by a third dose of BBIBP-CorV or CoronaVac
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Affiliation(s)
- Li-Jun Duan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wen-Guo Jiang
- Jining Center for Disease Control and Prevention, Jining, China
| | - Zhuang-Ye Wang
- Dezhou Center for Disease Control and Prevention, Dezhou, China
| | - Lin Yao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ka-Li Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Qing-Chuan Meng
- Ningjin County Community Health Service Center, Dezhou, China
| | - Bao-Shan Wang
- Decheng District Center for Disease Control and Prevention, Dezhou, China
| | - Li-Bo Li
- Jining Center for Disease Control and Prevention, Jining, China
| | - Guo-Lin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Mai-Juan Ma
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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18
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Li X, Pan Y, Yin Q, Wang Z, Shan S, Zhang L, Yu J, Qu Y, Sun L, Gui F, Lu J, Jing Z, Wu W, Huang T, Shi X, Li J, Li X, Li D, Wang S, Yang M, Zhang L, Duan K, Liang M, Yang X, Wang X. Structural basis of a two-antibody cocktail exhibiting highly potent and broadly neutralizing activities against SARS-CoV-2 variants including diverse Omicron sublineages. Cell Discov 2022; 8:87. [PMID: 36075908 PMCID: PMC9453709 DOI: 10.1038/s41421-022-00449-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/23/2022] [Indexed: 11/19/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs), especially the latest Omicron, have exhibited severe antibody evasion. Broadly neutralizing antibodies with high potency against Omicron are urgently needed for understanding the working mechanisms and developing therapeutic agents. In this study, we characterized the previously reported F61, which was isolated from convalescent patients infected with prototype SARS-CoV-2, as a broadly neutralizing antibody against all VOCs including Omicron BA.1, BA.1.1, BA.2, BA.3 and BA.4 sublineages by utilizing antigen binding and cell infection assays. We also identified and characterized another broadly neutralizing antibody D2 with epitope distinct from that of F61. More importantly, we showed that a combination of F61 with D2 exhibited synergy in neutralization and protecting mice from SARS-CoV-2 Delta and Omicron BA.1 variants. Cryo-Electron Microscopy (Cryo-EM) structures of the spike-F61 and spike-D2 binary complexes revealed the distinct epitopes of F61 and D2 at atomic level and the structural basis for neutralization. Cryo-EM structure of the Omicron-spike-F61-D2 ternary complex provides further structural insights into the synergy between F61 and D2. These results collectively indicated F61 and F61-D2 cocktail as promising therapeutic antibodies for combating SARS-CoV-2 variants including diverse Omicron sublineages.
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Affiliation(s)
- Xiaoman Li
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yongbing Pan
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Qiangling Yin
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zejun Wang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Sisi Shan
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Laixing Zhang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuanyuan Qu
- Institution of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Lina Sun
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fang Gui
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Jia Lu
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Zhaofei Jing
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Wei Wu
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tao Huang
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuanling Shi
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Jiandong Li
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinguo Li
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Dexin Li
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Wuhan, Hubei, China
| | - Shiwen Wang
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Wuhan, Hubei, China
| | - Maojun Yang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Linqi Zhang
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Kai Duan
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Mifang Liang
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
- CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Wuhan, Hubei, China.
| | - Xiaoming Yang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
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19
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Connelly GG, Kirkland OO, Bohannon S, Lim DC, Wilson RM, Richards EJ, Tay DM, Jee H, Hellinger RD, Hoang NK, Hao L, Chhabra A, Martin-Alonso C, Tan EK, Koehler AN, Yaffe MB, London WB, Lee PY, Krammer F, Bohannon RC, Bhatia SN, Sikes HD, Li H. Direct capture of neutralized RBD enables rapid point-of-care assessment of SARS-CoV-2 neutralizing antibody titer. CELL REPORTS METHODS 2022; 2:100273. [PMID: 35942328 PMCID: PMC9350670 DOI: 10.1016/j.crmeth.2022.100273] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/13/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
Neutralizing antibody (NAb) titer is a key biomarker of protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but point-of-care methods for assessing NAb titer are not widely available. Here, we present a lateral flow assay that captures SARS-CoV-2 receptor-binding domain (RBD) that has been neutralized from binding angiotensin-converting enzyme 2 (ACE2). Quantification of neutralized RBD in this assay correlates with NAb titer from vaccinated and convalescent patients. This methodology demonstrated superior performance in assessing NAb titer compared with either measurement of total anti-spike immunoglobulin G titer or quantification of the absolute reduction in binding between ACE2 and RBD. Our testing platform has the potential for mass deployment to aid in determining at population scale the degree of protective immunity individuals may have following SARS-CoV-2 vaccination or infection and can enable simple at-home assessment of NAb titer.
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Affiliation(s)
- Guinevere G. Connelly
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Orville O. Kirkland
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Daniel C. Lim
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert M. Wilson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward J. Richards
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Dragonfly Therapeutics, Waltham, MA 02451, USA
| | - Dousabel M. Tay
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hyuk Jee
- Division of Rheumatology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Riley D. Hellinger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ngoc K. Hoang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Liang Hao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arnav Chhabra
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Satellite Bio, Cambridge, MA 02139, USA
| | - Carmen Martin-Alonso
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward K.W. Tan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Angela N. Koehler
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael B. Yaffe
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wendy B. London
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Pui Y. Lee
- Division of Rheumatology, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Florian Krammer
- Department of Microbiology, and Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, and Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Wyss Institute at Harvard, Boston, MA 02115, USA
| | - Hadley D. Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hojun Li
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
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20
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Duerr R, Zhou H, Tada T, Dimartino D, Marier C, Zappile P, Wang G, Plitnick J, Griesemer SB, Girardin R, Machowski J, Bialosuknia S, Lasek-Nesselquist E, Hong SL, Baele G, Dittmann M, Ortigoza MB, Prasad PJ, McDonough K, Landau NR, George KS, Heguy A. Delta-Omicron recombinant escapes therapeutic antibody neutralization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.04.06.487325. [PMID: 35411351 PMCID: PMC8996620 DOI: 10.1101/2022.04.06.487325] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Background The emergence of recombinant viruses is a threat to public health. Recombination of viral variants may combine variant-specific features that together catalyze viral escape from treatment or immunity. The selective advantages of recombinant SARS-CoV-2 isolates over their parental lineages remain unknown. Methods Multi-method amplicon and metagenomic sequencing of a clinical swab and the in vitro grown virus allowed for high-confidence detection of a novel recombinant variant. Mutational, phylogeographic, and structural analyses determined features of the recombinant genome and spike protein. Neutralization assays using infectious as well as pseudotyped viruses and point mutants thereof defined the recombinant's sensitivity to a panel of monoclonal antibodies and sera from vaccinated and/or convalescent individuals. Results A novel Delta-Omicron SARS-CoV-2 recombinant was identified in an unvaccinated, immunosuppressed kidney transplant recipient treated with monoclonal antibody Sotrovimab. The recombination breakpoint is located in the spike N-terminal domain, adjacent to the Sotrovimab quaternary binding site, and results in a 5'-Delta AY.45 and a 3'-Omicron BA.1 mosaic spike protein. Delta and BA.1 are sensitive to Sotrovimab neutralization, whereas the Delta-Omicron recombinant is highly resistant to Sotrovimab, both with and without the RBD resistance mutation E340D. Conclusions Recombination between circulating SARS-CoV-2 variants can functionally contribute to immune escape. It is critical to validate phenotypes of mosaic viruses and monitor immunosuppressed COVID-19 patients treated with monoclonal antibodies for the selection of recombinant and immune escape variants. (Funded by NYU, the National Institutes of Health, and others).
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21
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Abdelhamid AG, Faraone JN, Evans JP, Liu SL, Yousef AE. SARS-CoV-2 and Emerging Foodborne Pathogens: Intriguing Commonalities and Obvious Differences. Pathogens 2022; 11:837. [PMID: 36014958 PMCID: PMC9415055 DOI: 10.3390/pathogens11080837] [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: 06/30/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) has resulted in tremendous human and economic losses around the globe. The pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus that is closely related to SARS-CoV and other human and animal coronaviruses. Although foodborne diseases are rarely of pandemic proportions, some of the causative agents emerge in a manner remarkably similar to what was observed recently with SARS-CoV-2. For example, Shiga toxin-producing Escherichia coli (STEC), the most common cause of hemolytic uremic syndrome, shares evolution, pathogenesis, and immune evasion similarities with SARS-CoV-2. Both agents evolved over time in animal hosts, and during infection, they bind to specific receptors on the host cell's membrane and develop host adaptation mechanisms. Mechanisms such as point mutations and gene loss/genetic acquisition are the main driving forces for the evolution of SARS-CoV-2 and STEC. Both pathogens affect multiple body organs, and the resulting diseases are not completely cured with non-vaccine therapeutics. However, SARS-CoV-2 and STEC obviously differ in the nature of the infectious agent (i.e., virus vs. bacterium), disease epidemiological details (e.g., transmission vehicle and symptoms onset time), and disease severity. SARS-CoV-2 triggered a global pandemic while STEC led to limited, but sometimes serious, disease outbreaks. The current review compares several key aspects of these two pathogenic agents, including the underlying mechanisms of emergence, the driving forces for evolution, pathogenic mechanisms, and the host immune responses. We ask what can be learned from the emergence of both infectious agents in order to alleviate future outbreaks or pandemics.
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Affiliation(s)
- Ahmed G. Abdelhamid
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA;
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Julia N. Faraone
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA; (J.N.F.); (J.P.E.)
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA;
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - John P. Evans
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA; (J.N.F.); (J.P.E.)
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA;
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA;
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Ahmed E. Yousef
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA;
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
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22
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Qu P, Faraone JN, Evans JP, Zheng YM, Carlin C, Lozanski G, Saif LJ, Oltz EM, Gumina RJ, Liu SL. Durability of the Neutralizing Antibody Response to mRNA Booster Vaccination Against SARS-CoV-2 BA.2.12.1 and BA.4/5 Variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.07.21.501010. [PMID: 35898337 PMCID: PMC9327628 DOI: 10.1101/2022.07.21.501010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The recent emergence of the SARS-CoV-2 BA.4/5 and BA.2.12.1 variants has led to rising COVID-19 case numbers and concerns over the continued efficacy of mRNA booster vaccination. Here we examine the durability of neutralizing antibody (nAb) responses against these SARS-CoV-2 Omicron subvariants in a cohort of health care workers 1-40 weeks after mRNA booster dose administration. Neutralizing antibody titers fell by ~1.5-fold 4-6 months and by ~2.5-fold 7-9 months after booster dose, with average nAb titers falling by 11-15% every 30 days, far more stable than two dose induced immunity. Notably, nAb titers from booster recipients against SARS-CoV-2 BA.1, BA.2.12.1, and BA.4/5 variants were ~4.7-, 7.6-, and 13.4-fold lower than against the ancestral D614G spike. However, the rate of waning of booster dose immunity was comparable across variants. Importantly, individuals reporting prior infection with SARS-CoV-2 exhibited significantly higher nAb titers compared to those without breakthrough infection. Collectively, these results highlight the broad and stable neutralizing antibody response induced by mRNA booster dose administration, implicating a significant role of virus evolution to evade nAb specificity, versus waning humoral immunity, in increasing rates of breakthrough infection.
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Affiliation(s)
- Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Julia N. Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - John P. Evans
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Gerard Lozanski
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Linda J. Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
- Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M. Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Richard J. Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
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23
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Ijaz MK, Nims RW, McKinney J. Emerging SARS-CoV-2 Mutational Variants of Concern Should Not Vary in Susceptibility to Microbicidal Actives. Life (Basel) 2022; 12:987. [PMID: 35888077 PMCID: PMC9323193 DOI: 10.3390/life12070987] [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: 06/01/2022] [Revised: 06/20/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is evolving, with emergence of mutational variants due to the error-prone replication process of RNA viruses, in general. More recently, the Delta and Omicron variants (including sub-variants BA.1-5) predominate globally, and a Delta-Omicron recombinant termed Deltacron has emerged. The emergence of variants of concern (VOC) demonstrating immune evasion and potentially greater transmissibility and virulence naturally raises concern in both the infection control communities and the public at large, as to the continued suitability of interventions intended to mitigate the risk of viral dissemination and acquisition of the associated disease COVID-19. We evaluated the virucidal efficacy of targeted surface hygiene products (an ethanol/quaternary ammonium compound (QAC)-containing disinfectant spray, a QAC disinfectant wipe, a lactic acid disinfectant wipe, and a citric acid disinfectant wipe) through both theoretical arguments and empirical testing using international standard methodologies (ASTM E1053-20 hard surface test and EN14476:2013+A2:2019 suspension test) in the presence of soil loads simulating patients' bodily secretions/excretions containing shed virus. The results demonstrate, as expected, complete infectious viral inactivation (≥3.0 to ≥4.7 log10 reduction in infectious virus titer after as little as 15 s contact time at room temperature) by these surface hygiene agents of the original SARS-CoV-2 isolate and its Beta and Delta VOC. Through appropriate practices of targeted surface hygiene, it is expected that irrespective of the SARS-CoV-2 VOC encountered as the current pandemic unfolds (and, for that matter, any emerging and/or re-emerging enveloped virus), the chain of infection from virus-contaminated fomites to the hand and mucous membranes of a susceptible person may be disrupted.
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Affiliation(s)
- M. Khalid Ijaz
- Global Research and Development for Lysol and Dettol, Reckitt Benckiser LLC, One Phillips Drive, Montvale, NJ 07645, USA;
| | | | - Julie McKinney
- Global Research and Development for Lysol and Dettol, Reckitt Benckiser LLC, One Phillips Drive, Montvale, NJ 07645, USA;
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