1
|
Marano JM, Weger-Lucarelli J. Preexisting inter-serotype immunity drives antigenic evolution of dengue virus serotype 2. Virology 2024; 590:109951. [PMID: 38096749 PMCID: PMC10855010 DOI: 10.1016/j.virol.2023.109951] [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: 09/19/2023] [Revised: 11/10/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024]
Abstract
Dengue virus (DENV) infects roughly 400 million people annually, causing febrile and hemorrhagic disease. While preexisting inter-serotype immunity (PISI) provides transient protection, it may drive severe disease over time. PISI's impact on virus evolution, however, is less understood. Retrospective epidemiological analyses suggest that PISI may drive DENV evolution. Using in vitro directed evolution, we explored how DENV2 evolves in the presence of DENV3/4 convalescent serum. Two post-passaging mutations (E-I6M and E-N203D) were then studied for fitness effects in mammalian and insect hosts and immune escape. E-I6M resisted neutralization, altered fitness in mammalian cell culture models, and had no effect in Aedes albopictus mosquitoes. E-N203D showed no change in neutralization sensitivity, reduced fitness in a DENV-naïve epithelial model, and no effects in the other models. These results align with surveillance data, where E-I6M emerged and disappeared, while E-203D and E-203 N cocirculate, thus suggesting that PISI can drive DENV evolution.
Collapse
Affiliation(s)
- Jeffrey M Marano
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, United States; Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States.
| |
Collapse
|
2
|
Paulino-Ramírez R, López P, Mueses S, Cuevas P, Jabier M, Rivera-Amill V. Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085503. [PMID: 37107785 PMCID: PMC10138544 DOI: 10.3390/ijerph20085503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 05/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from samples collected between March 2020 and mid-February 2022 in the Dominican Republic were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Phylogenetic relationships and evolution rates were analyzed using the maximum likelihood method and the Bayesian Markov chain Monte Carlo (MCMC) approach. The genotyping details (lineages) were obtained using the Pangolin web application. In addition, the web tools Coronapp, and Genome Detective Viral Tools, among others, were used to monitor epidemiological characteristics. Our results show that the most frequent non-synonymous mutation over the study period was D614G. Of the 1149 samples, 870 (75.74%) were classified into 8 relevant variants according to Pangolin/Scorpio. The first Variants Being Monitored (VBM) were detected in December 2020. Meanwhile, in 2021, the variants of concern Delta and Omicron were identified. The mean mutation rate was estimated to be 1.5523 × 10-3 (95% HPD: 1.2358 × 10-3, 1.8635 × 10-3) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. A better understanding of viral evolution and genomic surveillance data will help to inform strategies to mitigate the impact on public health.
Collapse
Affiliation(s)
- Robert Paulino-Ramírez
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
- Correspondence:
| | - Pablo López
- RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA (V.R.-A.)
| | - Sayira Mueses
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
| | - Paula Cuevas
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
| | - Maridania Jabier
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
- Servicio Nacional de Salud (SNS), Ministry of Health, Santo Domingo 10201, Dominican Republic
| | - Vanessa Rivera-Amill
- RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA (V.R.-A.)
- Basic Sciences Department, School of Medicine, Ponce Health Sciences University, Ponce, PR 00716-2348, USA
| |
Collapse
|
3
|
Chang CC, Algaissi A, Lai CC, Chang CK, Lin JS, Wang YS, Chang BH, Chang YC, Chen WT, Fan YQ, Peng BH, Chao CY, Tzeng SR, Liang PH, Sung WC, Hu AYC, Chang SC, Chang MF. Subunit vaccines with a saponin-based adjuvant boost humoral and cellular immunity to MERS coronavirus. Vaccine 2023; 41:3337-3346. [PMID: 37085450 PMCID: PMC10083212 DOI: 10.1016/j.vaccine.2023.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) outbreaks have constituted a public health issue with drastic mortality higher than 34%, necessitating the development of an effective vaccine. During MERS-CoV infection, the trimeric spike protein on the viral envelope is primarily responsible for attachment to host cellular receptor, dipeptidyl peptidase 4 (DPP4). With the goal of generating a protein-based prophylactic, we designed a subunit vaccine comprising the recombinant S1 protein with a trimerization motif (S1-Fd) and examined its immunogenicity and protective immune responses in combination with various adjuvants. We found that sera from immunized wild-type and human DPP4 transgenic mice contained S1-specific antibodies that can neutralize MERS-CoV infection in susceptible cells. Vaccination with S1-Fd protein in combination with a saponin-based QS-21 adjuvant provided long-term humoral as well as cellular immunity in mice. Our findings highlight the significance of the trimeric S1 protein in the development of MERS-CoV vaccines and offer a suitable adjuvant, QS-21, to induce robust and prolonged memory T cell response.
Collapse
Affiliation(s)
- Chi-Chieh Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Abdullah Algaissi
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555, USA; Center for Biodefense and Emerging Disease, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chia-Chun Lai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan; College of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chun-Kai Chang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100025, Taiwan
| | - Jr-Shiuan Lin
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yi-Shiang Wang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Bo-Hau Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yu-Chiuan Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Wei-Ting Chen
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Yong-Qing Fan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Bi-Hung Peng
- Department of Neurosciences, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chih-Yu Chao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Shiou-Ru Tzeng
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Pi-Hui Liang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100025, Taiwan
| | - Wang-Chou Sung
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Alan Yung-Chih Hu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Shin C Chang
- Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Ming-Fu Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.
| |
Collapse
|
4
|
Marano JM, Weger-Lucarelli J. Replication in the presence of dengue convalescent serum impacts Zika virus neutralization sensitivity and fitness. Front Cell Infect Microbiol 2023; 13:1130749. [PMID: 36968111 PMCID: PMC10034770 DOI: 10.3389/fcimb.2023.1130749] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
IntroductionFlaviviruses like dengue virus (DENV) and Zika virus (ZIKV) are mosquito-borne viruses that cause febrile, hemorrhagic, and neurological diseases in humans, resulting in 400 million infections annually. Due to their co-circulation in many parts of the world, flaviviruses must replicate in the presence of pre-existing adaptive immune responses targeted at serologically closely related pathogens, which can provide protection or enhance disease. However, the impact of pre-existing cross-reactive immunity as a driver of flavivirus evolution, and subsequently the implications on the emergence of immune escape variants, is poorly understood. Therefore, we investigated how replication in the presence of convalescent dengue serum drives ZIKV evolution.MethodsWe used an in vitro directed evolution system, passaging ZIKV in the presence of serum from humans previously infected with DENV (anti-DENV) or serum from DENV-naïve patients (control serum). Following five passages in the presence of serum, we performed next-generation sequencing to identify mutations that arose during passaging. We studied two non-synonymous mutations found in the anti-DENV passaged population (E-V355I and NS1-T139A) by generating individual ZIKV mutants and assessing fitness in mammalian cells and live mosquitoes, as well as their sensitivity to antibody neutralization.Results and discussionBoth viruses had increased fitness in Vero cells with and without the addition of anti-DENV serum and in human lung epithelial and monocyte cells. In Aedes aegypti mosquitoes—using blood meals with and without anti-DENV serum—the mutant viruses had significantly reduced fitness compared to wild-type ZIKV. These results align with the trade-off hypothesis of constrained mosquito-borne virus evolution. Notably, only the NS1-T139A mutation escaped neutralization, while E-V335I demonstrated enhanced neutralization sensitivity to neutralization by anti-DENV serum, indicating that neutralization escape is not necessary for viruses passaged under cross-reactive immune pressures. Future studies are needed to assess cross-reactive immune selection in humans and relevant animal models or with different flaviviruses.
Collapse
Affiliation(s)
- Jeffrey M. Marano
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, United States
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
- *Correspondence: James Weger-Lucarelli,
| |
Collapse
|
5
|
Kane Y, Wong G, Gao GF. Animal Models, Zoonotic Reservoirs, and Cross-Species Transmission of Emerging Human-Infecting Coronaviruses. Annu Rev Anim Biosci 2023; 11:1-31. [PMID: 36790890 DOI: 10.1146/annurev-animal-020420-025011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Over the past three decades, coronavirus (CoV) diseases have impacted humans more than any other emerging infectious disease. The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19 (coronavirus disease 2019), has resulted in huge economic disruptions and loss of human lives. The SARS-CoV-2 genome was found to mutate more rapidly due to sustained transmission in humans and potentially animals, resulting in variants of concern (VOCs) that threaten global human health. However, the primary difficulties are filling in the current knowledge gaps in terms of the origin and modalities of emergence for these viruses. Because many CoVs threatening human health are suspected to have a zoonotic origin, identifying the animal hosts implicated in the spillover or spillback events would be beneficial for current pandemic management and to prevent future outbreaks. In this review, wesummarize the animal models, zoonotic reservoirs, and cross-species transmission of the emerging human CoVs. Finally, we comment on potential sources of SARS-CoV-2 Omicron VOCs and the new SARS-CoV-2 recombinants currently under investigation.
Collapse
Affiliation(s)
- Yakhouba Kane
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China; , .,University of Chinese Academy of Sciences, Beijing, China
| | - Gary Wong
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China; ,
| | - George F Gao
- University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; .,Chinese Center for Disease Control and Prevention, Beijing, China
| |
Collapse
|
6
|
In silico analysis of SARS-CoV-2 spike protein N501Y and N501T mutation effects on human ACE2 binding. J Mol Graph Model 2022; 116:108260. [PMID: 35809511 PMCID: PMC9247859 DOI: 10.1016/j.jmgm.2022.108260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 05/05/2022] [Accepted: 06/21/2022] [Indexed: 12/14/2022]
Abstract
The SARS-CoV-2 is an RNA-based virus and the most vital step of its survival is the attachment to hACE2 through its spike protein. Although SARS-CoV-2 has the ability to maintain high accurate replication and it can be accepted as a low mutation risked virus, it already showed more than nine thousand mutations in spike protein, of which 44 mutations are located within a 3.2 Å interacting distance from the hACE2 receptor. Mutations on spike protein, N501Y and N501T raised serious concerns for higher transmissibility and resistance towards current vaccines. In the current study, the mutational outcomes of N501Y and N501T on the hACE2-SARS CoV-2 spike protein complexation were analyzed by employing all-atom classic molecular dynamics (MD) simulations. These simulations revealed that both N501Y and N501T mutations increased the binding strength of spike protein to the host hACE2, predicted by binding free energy analysis via MM/GBSA rescoring scheme. This study highlights the importance of energy-based analysis for identifying mutational outcomes and will shed light on handling long-term and effective treatment strategies including repurposing anti-viral drugs, anti-SARS-CoV-2 antibodies, vaccines, and antisense based-therapies.
Collapse
|
7
|
Fan Y, Sun Z, Conrad F, Wen W, Zhao L, Lou J, Zhou Y, Farr-Jones S, Marks JD. Multicolor fluorescence activated cell sorting to generate humanized monoclonal antibody binding seven subtypes of BoNT/F. PLoS One 2022; 17:e0273512. [PMID: 36048906 PMCID: PMC9436041 DOI: 10.1371/journal.pone.0273512] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022] Open
Abstract
Generating specific monoclonal antibodies (mAbs) that neutralize multiple antigen variants is challenging. Here, we present a strategy to generate mAbs that bind seven subtypes of botulinum neurotoxin serotype F (BoNT/F) that differ from each other in amino acid sequence by up to 36%. Previously, we identified 28H4, a mouse mAb with poor cross-reactivity to BoNT/F1, F3, F4, and F6 and with no detectable binding to BoNT/F2, F5, or F7. Using multicolor labeling of the different BoNT/F subtypes and fluorescence-activated cell sorting (FACS) of yeast displayed single-chain Fv (scFv) mutant libraries, 28H4 was evolved to a humanized mAb hu6F15.4 that bound each of seven BoNT/F subtypes with high affinity (KD 5.81 pM to 659.78 pM). In contrast, using single antigen FACS sorting, affinity was increased to the subtype used for sorting but with a decrease in affinity for other subtypes. None of the mAb variants showed any binding to other BoNT serotypes or to HEK293 or CHO cell lysates by flow cytometry, thus demonstrating stringent BoNT/F specificity. Multicolor FACS-mediated antibody library screening is thus proposed as a general method to generate multi-specific antibodies to protein subtypes such as toxins or species variants.
Collapse
Affiliation(s)
- Yongfeng Fan
- Zuckerberg San Francisco General Hospital and Trauma Center, Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, United States of America
| | - Zhengda Sun
- Zuckerberg San Francisco General Hospital and Trauma Center, Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, United States of America
| | - Fraser Conrad
- Zuckerberg San Francisco General Hospital and Trauma Center, Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, United States of America
| | - Weihua Wen
- Zuckerberg San Francisco General Hospital and Trauma Center, Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, United States of America
| | - Lequn Zhao
- Zuckerberg San Francisco General Hospital and Trauma Center, Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, United States of America
| | - Jianlong Lou
- Zuckerberg San Francisco General Hospital and Trauma Center, Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, United States of America
| | - Yu Zhou
- Zuckerberg San Francisco General Hospital and Trauma Center, Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, United States of America
| | - Shauna Farr-Jones
- Zuckerberg San Francisco General Hospital and Trauma Center, Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, United States of America
| | - James D. Marks
- Zuckerberg San Francisco General Hospital and Trauma Center, Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, United States of America
| |
Collapse
|
8
|
Poustforoosh A, Hashemipour H, Tüzün B, Azadpour M, Faramarz S, Pardakhty A, Mehrabani M, Nematollahi MH. The Impact of D614G Mutation of SARS-COV-2 on the Efficacy of Anti-viral Drugs: A Comparative Molecular Docking and Molecular Dynamics Study. Curr Microbiol 2022; 79:241. [PMID: 35792936 PMCID: PMC9258457 DOI: 10.1007/s00284-022-02921-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 06/01/2022] [Indexed: 02/07/2023]
Abstract
D614G is one of the most reported mutations in the spike protein of SARS-COV-2 that has altered some crucial characteristics of coronaviruses, such as rate of infection and binding affinities. The binding affinity of different antiviral drugs was evaluated using rigid molecular docking. The reliability of the docking results was evaluated with the induced-fit docking method, and a better understanding of the drug-protein interactions was performed using molecular dynamics simulation. The results show that the D614G variant could change the binding affinity of antiviral drugs and spike protein remarkably. Although Cytarabine showed an appropriate interaction with the wild spike protein, Ribavirin and PMEG diphosphate exhibited a significant binding affinity to the mutated spike protein. The parameters of the ADME/T analysis showed that these drugs are suitable for further in-vitro and in-vivo investigation. D614G alteration affected the binding affinity of the RBD and its receptor on the cell surface.
Collapse
Affiliation(s)
- Alireza Poustforoosh
- Chemical Engineering Department, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hassan Hashemipour
- Chemical Engineering Department, Faculty of Engineering, Vali-e-Asr, University of Rafsanjan, Rafsanjan, Iran.
| | - Burak Tüzün
- Department of Chemistry, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Mahdiyeh Azadpour
- Chemical Engineering Department, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Sanaz Faramarz
- Department of Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Abbas Pardakhty
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehrnaz Mehrabani
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hadi Nematollahi
- Department of Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran. .,Herbal and Traditional Medicines Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| |
Collapse
|
9
|
Kashani NR, Azadbakht J, Ehteram H, Kashani HH, Rajabi-Moghadam H, Ahmad E, Nikzad H, Hosseini ES. Molecular and Clinical Investigation of COVID-19: From Pathogenesis and Immune Responses to Novel Diagnosis and Treatment. Front Mol Biosci 2022; 9:770775. [PMID: 35664675 PMCID: PMC9161360 DOI: 10.3389/fmolb.2022.770775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 04/04/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus-related severe acute respiratory syndrome (SARS-CoV) in 2002/2003, the Middle East respiratory syndrome (MERS-CoV) in 2012/2013, and especially the current 2019/2021 severe acute respiratory syndrome-2 (SARS-CoV-2) negatively affected the national health systems worldwide. Different SARS-CoV-2 variants, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and recently Omicron (B.1.1.529), have emerged resulting from the high rate of genetic recombination and S1-RBD/S2 mutation/deletion in the spike protein that has an impact on the virus activity. Furthermore, genetic variability in certain genes involved in the immune system might impact the level of SARS-CoV-2 recognition and immune response against the virus among different populations. Understanding the molecular mechanism and function of SARS-CoV-2 variants and their different epidemiological outcomes is a key step for effective COVID-19 treatment strategies, including antiviral drug development and vaccine designs, which can immunize people with genetic variabilities against various strains of SARS-CoV-2. In this review, we center our focus on the recent and up-to-date knowledge on SARS-CoV-2 (Alpha to Omicron) origin and evolution, structure, genetic diversity, route of transmission, pathogenesis, new diagnostic, and treatment strategies, as well as the psychological and economic impact of COVID-19 pandemic on individuals and their lives around the world.
Collapse
Affiliation(s)
- Narjes Riahi Kashani
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Javid Azadbakht
- Department of Radiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hassan Ehteram
- Department of Pathology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Haddad Kashani
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Hassan Rajabi-Moghadam
- Department of Cardiovascular Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Ejaz Ahmad
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Hossein Nikzad
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Elahe Seyed Hosseini
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
- *Correspondence: Elahe Seyed Hosseini,
| |
Collapse
|
10
|
Gong S, Gautam S, Coneglio JD, Scinto HB, Ruprecht RM. Antibody Light Chains: Key to Increased Monoclonal Antibody Yields in Expi293 Cells? Antibodies (Basel) 2022; 11:37. [PMID: 35645210 PMCID: PMC9149950 DOI: 10.3390/antib11020037] [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: 03/19/2022] [Revised: 04/19/2022] [Accepted: 05/10/2022] [Indexed: 02/04/2023] Open
Abstract
When constructing isogenic recombinant IgM-IgG pairs, we discovered that μ heavy chains strongly prefer partnering with λ light chains for optimal IgM expression in transiently cotransfected Expi293 cells. When μ chains were paired with κ light chains, IgM yields were low but increased by logs-up to 20,000 X-by using λ chains instead. Switching light chains did not alter epitope specificity. For dimeric IgA2, optimal expression involved pairing with λ chains, whereas light-chain preference varied for other immunoglobulin classes. In summary, recombinant IgM production can be drastically increased by using λ chains, an important finding in the use of IgM for mucosal immunoprophylaxis.
Collapse
Affiliation(s)
- Siqi Gong
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA 70560, USA or (S.G.); (S.G.); (J.D.C.)
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA;
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Seijal Gautam
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA 70560, USA or (S.G.); (S.G.); (J.D.C.)
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - Joshua D. Coneglio
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA 70560, USA or (S.G.); (S.G.); (J.D.C.)
| | - Hanna B. Scinto
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA;
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Ruth M. Ruprecht
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA 70560, USA or (S.G.); (S.G.); (J.D.C.)
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA;
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| |
Collapse
|
11
|
Zhang M, Gong Y, Jiao S. Neutralization heterogeneity of circulating SARS-CoV-2 variants to sera elicited by a vaccinee or convalescent. Future Virol 2022. [PMID: 35492429 PMCID: PMC9041375 DOI: 10.2217/fvl-2021-0100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 03/18/2022] [Indexed: 12/14/2022]
Abstract
COVID-19, which was first reported in December 2019 in China, has caused a global outbreak. Five variants of concern (VOCs) have been identified in different countries since the global pandemic, namely, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.529). Although multiple vaccines have been found to be effective, some of the amino acid changes may increase the infectivity of virus and decrease the sensitivity to antibodies. Here we characterize the VOCs and discuss their sensitivity to antibodies elicited by convalescent and vaccinee sera. In conclusion, several variants display a reduction in the susceptibility to neutralization antibodies generated by natural infection or vaccination, which threatens the containment of the epidemic.
Collapse
Affiliation(s)
- Meng Zhang
- Department of Research & Development, Beijing DCTY® Biotech Co., Ltd, 86 Shuangying West Road, Beijing, 102200, People's Republic of China
| | - Yixin Gong
- Department of Research & Development, Beijing DCTY® Biotech Co., Ltd, 86 Shuangying West Road, Beijing, 102200, People's Republic of China
| | - Shunchang Jiao
- Department of Oncology, Chinese PLA General Hospital, 28 Fuxing Road, Haidian, Beijing, 100853, People's Republic of China
| |
Collapse
|
12
|
Okoh OS, Nii-Trebi NI, Jakkari A, Olaniran TT, Senbadejo TY, Kafintu-Kwashie AA, Dairo EO, Ganiyu TO, Akaninyene IE, Ezediuno LO, Adeosun IJ, Ockiya MA, Jimah EM, Spiro DJ, Oladipo EK, Trovão NS. Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa. iScience 2022; 25:103880. [PMID: 35156006 PMCID: PMC8817759 DOI: 10.1016/j.isci.2022.103880] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/29/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
There is a dearth of information on COVID-19 disease dynamics in Africa. To fill this gap, we investigated the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in the continent. We retrieved 5229 complete genomes collected in 33 African countries from the GISAID database. We investigated the circulating diversity, reconstructed the viral evolutionary divergence and history, and studied the case and death trends in the continent. Almost a fifth (144/782, 18.4%) of Pango lineages found worldwide circulated in Africa, with five different lineages dominating over time. Phylogenetic analysis revealed that African viruses cluster more closely with those from Europe. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the epidemiological and evolutionary dynamics of the circulating viral diversity in Africa. They also emphasize the need to expand surveillance efforts in Africa to help inform and implement better public health measures. SARS-CoV-2 viruses from Africa cluster predominantly with European strains Lower viral diversity observed in Africa is likely due to genomic under-surveillance Number of cases, deaths, and testing show substantial heterogeneity across Africa Two motifs could function as integrin-binding sites and N-glycosylation domains
Collapse
Affiliation(s)
| | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Abdulrokeeb Jakkari
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | - Tosin Titus Olaniran
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria.,Helix Biogen Institute, Ogbomoso, Nigeria
| | - Tosin Yetunde Senbadejo
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Anna Aba Kafintu-Kwashie
- Department of Medical Microbiology, Clinical Virology Unit, University of Ghana Medical School, Accra, Ghana
| | - Emmanuel Oluwatobi Dairo
- Helix Biogen Institute, Ogbomoso, Nigeria.,Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tajudeen Oladunni Ganiyu
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Ifiokakaninyene Ekpo Akaninyene
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria.,Helix Biogen Institute, Ogbomoso, Nigeria
| | - Louis Odinakaose Ezediuno
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin,1515 P.M.B, Ilorin, Nigeria
| | - Idowu Jesulayomi Adeosun
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun, Nigeria.,Division of Microbiology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield Pretoria 0028, South Africa
| | - Michael Asebake Ockiya
- Department of Animal Science, Niger Delta University, Wilberforce Island, Bayelsa, Nigeria
| | - Esther Moradeyo Jimah
- Helix Biogen Institute, Ogbomoso, Nigeria.,Department of Medical Microbiology and Parasitology, University of Ilorin 1515, P.M.B, Ilorin, Nigeria
| | - David J Spiro
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Elijah Kolawole Oladipo
- Helix Biogen Institute, Ogbomoso, Nigeria.,Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun, Nigeria
| | - Nídia S Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
13
|
Abstract
Since the COVID-19 pandemic first began in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has continuously evolved with many variants emerging across the world. These variants are categorized as the variant of interest (VOI), variant of concern (VOC), and variant under monitoring (VUM). As of September 15, 2021, there are four SARS-CoV-2 lineages designated as the VOC (alpha, beta, gamma, and delta variants). VOCs have increased transmissibility compared to the original virus, and have the potential for increasing disease severity. In addition, VOCs exhibit decreased susceptibility to vaccine-induced and infection-induced immune responses, and thus possess the ability to reinfect previously infected and recovered individuals. Given their ability to evade immune responses, VOC are less susceptible to monoclonal antibody treatments. VOCs can also impact the effectiveness of mRNA and adenovirus vector vaccines, although the currently authorized COVID-19 vaccines are still effective in preventing infection and severe disease. Current measures to reduce transmission as well as efforts to monitor and understand the impact of variants should be continued. Here, we review the molecular features, epidemiology, impact on transmissibility, disease severity, and vaccine effectiveness of VOCs.
Collapse
Affiliation(s)
- Jun Yong Choi
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea.
| | - Davey M Smith
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| |
Collapse
|
14
|
Sarker MT, Hasan AQF, Rafi MO, Hossain MJ, El-Mageed HRA, Elsapagh RM, Capasso R, Emran TB. A Comprehensive Overview of the Newly Emerged COVID-19 Pandemic: Features, Origin, Genomics, Epidemiology, Treatment, and Prevention. BIOLOGICS 2021; 1:357-383. [DOI: 10.3390/biologics1030021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The coronavirus disease 2019 (COVID-19), a life-threatening pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has resulted in massive destruction and is still continuously adding to its death toll. The advent of this global outbreak has not yet been confirmed; however, investigation for suitable prophylaxis against this lethal virus is being carried out by experts all around the globe. The SARS-CoV-2 belongs to the Coronaviridae superfamily, like the other previously occurring human coronavirus variants. To better understand a new virus variant, such as the SARS-CoV-2 delta variant, it is vital to investigate previous virus strains, including their genomic composition and functionality. Our study aimed at addressing the basic overview of the virus’ profile that may provide the scientific community with evidence-based insights into COVID-19. Therefore, this study accomplished a comprehensive literature review that includes the virus’ origin, classification, structure, life cycle, genome, mutation, epidemiology, and subsequent essential factors associated with host–virus interaction. Moreover, we summarized the considerable diagnostic measures, treatment options, including multiple therapeutic approaches, and prevention, as well as future directions that may reduce the impact and misery caused by this devastating pandemic. The observations and data provided here have been screened and accumulated through extensive literature study, hence this study will help the scientific community properly understand this new virus and provide further leads for therapeutic interventions.
Collapse
|
15
|
Ysrafil Y, Mus R, Gama NI, Rahmaisyah D, Nur'amalia R. Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Biomed J 2021; 44:570-581. [PMID: 34271250 PMCID: PMC8275844 DOI: 10.1016/j.bj.2021.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 05/20/2021] [Accepted: 07/07/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Recently, differences in mortality rates of COVID-19 in different geographic areas have become an important subject of research because these different mortality rates appear to be associated with mutations that appeared in SARS-CoV-2. The part of the viral body called the spike protein plays a critical role in the viral attachment and entry of the virus into the host cell. Accordingly, we hypothesized that mutations in this area will affect viral infectivity. METHODS A total of 193 sequences of spike SARS-CoV-2 were randomly retrieved from five different geographic areas and collection dates (from December 2019 until July 2020). Multiple sequence alignment for mutation and phylogenetic analyses was conducted using Bioedit, UniProt, and MEGA X. RESULTS We found 169 total mutations with 37 different mutations across the included samples. The D614G is the first and most frequently established mutation in different regions including Europe, Asia, America, Africa and Australia with the number of mutations of 49, 33, 17, 16 and 4, respectively. Furthermore, we also found mutations in several important domains in this virus including NTD and CTR/RBD of S1 subunit and at S2 subunit area, namely the peptide fusion (FP), and both heptad repetition (HR1 and 2) domains that suggested this could influence virus binding and virus-host cell membrane fusion. CONCLUSION In summary, we concluded that mutation had generated diversity of spike SARS-CoV-2 sequences worldwide and is still growing. This analysis may provide important evidence that should be considered in vaccine development in different geographic areas.
Collapse
Affiliation(s)
- Ysrafil Ysrafil
- Department of Pharmacy, Health Polytechnic of Gorontalo, Ministry of Health, Gorontalo, Indonesia,Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia,Corresponding author. Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Bulaksumur Yogyakarta 55281, Indonesia.
| | - Rosdiana Mus
- Diploma Degree Technology of Medical Laboratory, Faculty of Health Technology, Universitas Megarezky, Makassar, Indonesia
| | - Noviyanty Indjar Gama
- Department of Clinical Pharmacy, Faculty of Pharmacy, University of Mulawarman, Samarinda, Indonesia
| | - Dwi Rahmaisyah
- Master Program in Biomedical Science, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Riskah Nur'amalia
- Department of Physiotherapy, Faculty of Nursing, Universitas Hasanuddin, Makassar, Indonesia
| |
Collapse
|
16
|
Lorenzo R, Defelipe LA, Aliperti L, Niebling S, Custódio TF, Löw C, Schwarz JJ, Remans K, Craig PO, Otero LH, Klinke S, García-Alai M, Sánchez IE, Alonso LG. Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif. J Biol Chem 2021; 297:101175. [PMID: 34499924 PMCID: PMC8421091 DOI: 10.1016/j.jbc.2021.101175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 01/22/2023] Open
Abstract
The spike protein is the main protein component of the SARS-CoV-2 virion surface. The spike receptor-binding motif mediates recognition of the human angiotensin-converting enzyme 2 receptor, a critical step in infection, and is the preferential target for spike-neutralizing antibodies. Posttranslational modifications of the spike receptor-binding motif have been shown to modulate viral infectivity and host immune response, but these modifications are still being explored. Here we studied asparagine deamidation of the spike protein, a spontaneous event that leads to the appearance of aspartic and isoaspartic residues, which affect both the protein backbone and its charge. We used computational prediction and biochemical experiments to identify five deamidation hotspots in the SARS-CoV-2 spike protein. Asparagine residues 481 and 501 in the receptor-binding motif deamidate with a half-life of 16.5 and 123 days at 37 °C, respectively. Deamidation is significantly slowed at 4 °C, indicating a strong dependence of spike protein molecular aging on environmental conditions. Deamidation of the spike receptor-binding motif decreases the equilibrium constant for binding to the human angiotensin-converting enzyme 2 receptor more than 3.5-fold, yet its high conservation pattern suggests some positive effect on viral fitness. We propose a model for deamidation of the full SARS-CoV-2 virion illustrating how deamidation of the spike receptor-binding motif could lead to the accumulation on the virion surface of a nonnegligible chemically diverse spike population in a timescale of days. Our findings provide a potential mechanism for molecular aging of the spike protein with significant consequences for understanding virus infectivity and vaccine development.
Collapse
Affiliation(s)
- Ramiro Lorenzo
- Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CICPBA-UNCPBA, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro (FCV-UNCPBA), Tandil, Argentina
| | - Lucas A Defelipe
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Lucio Aliperti
- Laboratorio de Fisiología de Proteínas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Stephan Niebling
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Tânia F Custódio
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Christian Löw
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | | | - Kim Remans
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Patricio O Craig
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - María García-Alai
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Ignacio E Sánchez
- Laboratorio de Fisiología de Proteínas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Leonardo G Alonso
- Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
| |
Collapse
|
17
|
Zhou W, Xu C, Wang P, Luo M, Xu Z, Cheng R, Jin X, Guo Y, Xue G, Juan L, Anashkina AA, Nie H, Jiang Q. N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Front Cell Dev Biol 2021; 9:697035. [PMID: 34414185 PMCID: PMC8369991 DOI: 10.3389/fcell.2021.697035] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/09/2021] [Indexed: 11/28/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing an outbreak of coronavirus disease 2019 (COVID-19), has been undergoing various mutations. The analysis of the structural and energetic effects of mutations on protein-protein interactions between the receptor binding domain (RBD) of SARS-CoV-2 and angiotensin converting enzyme 2 (ACE2) or neutralizing monoclonal antibodies will be beneficial for epidemic surveillance, diagnosis, and optimization of neutralizing agents. According to the molecular dynamics simulation, a key mutation N439K in the SARS-CoV-2 RBD region created a new salt bridge with Glu329 of hACE2, which resulted in greater electrostatic complementarity, and created a weak salt bridge with Asp442 of RBD. Furthermore, the N439K-mutated RBD bound hACE2 with a higher affinity than wild-type, which may lead to more infectious. In addition, the N439K-mutated RBD was markedly resistant to the SARS-CoV-2 neutralizing antibody REGN10987, which may lead to the failure of neutralization. The results show consistent with the previous experimental conclusion and clarify the structural mechanism under affinity changes. Our methods will offer guidance on the assessment of the infection efficiency and antigenicity effect of continuing mutations in SARS-CoV-2.
Collapse
Affiliation(s)
- Wenyang Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Chang Xu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Pingping Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Meng Luo
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zhaochun Xu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Rui Cheng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Xiyun Jin
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yu Guo
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Guangfu Xue
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Liran Juan
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.,Key Laboratory of Biological Big Data (Harbin Institute of Technology), Ministry of Education, Harbin, China
| | - Anastasia A Anashkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.,Key Laboratory of Biological Big Data (Harbin Institute of Technology), Ministry of Education, Harbin, China
| |
Collapse
|
18
|
Ding C, He J, Zhang X, Jiang C, Sun Y, Zhang Y, Chen Q, He H, Li W, Xie J, Liu Z, Gao Y. Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Front Immunol 2021; 12:693775. [PMID: 34484190 PMCID: PMC8416052 DOI: 10.3389/fimmu.2021.693775] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
Small number of SARS-CoV-2 epidemic lineages did not efficiently exhibit a neutralization profile, while single amino acid mutation in the spike protein has not been confirmed in altering viral antigenicity resulting in immune escape. To identify crucial mutations in spike protein that escape humoral immune response, we evaluated the cross-neutralization of convalescent plasmas and RBD-specific monoclonal antibodies (mAbs) against various spike protein-based pseudoviruses. Three of 24 SARS-CoV-2 pseudoviruses containing different mutations in spike protein, including D614G, A475V, and E484Q, consistently showed an altered sensitivity to neutralization by convalescent plasmas. A475V and E484Q mutants are highly resistant to neutralization by mAb B38 and 2-4, suggesting that some crucial mutations in spike protein might evolve SARS-CoV-2 variants capable of escaping humoral immune response.
Collapse
Affiliation(s)
- Chengchao Ding
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Jun He
- Department of Microbiology, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Xiangyu Zhang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Chengcheng Jiang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Yong Sun
- Department of Microbiology, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Yuqing Zhang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Qingqing Chen
- Department of Microbiology, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Hongliang He
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Wenting Li
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Jiajia Xie
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Zhirong Liu
- Department of Microbiology, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Yong Gao
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| |
Collapse
|
19
|
Wang C, Zheng Y, Niu Z, Jiang X, Sun Q. The virological impacts of SARS-CoV-2 D614G mutation. J Mol Cell Biol 2021; 13:712-720. [PMID: 34289053 PMCID: PMC8344946 DOI: 10.1093/jmcb/mjab045] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 11/12/2022] Open
Abstract
The coronavirus diseases 2019 (COVID-19) caused by the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in December 2019 has caused more than 140 million infections worldwide by the end of April 2021. As an enveloped single-stranded positive-sense RNA virus, SARS-CoV-2 underwent constant evolution that produced novel variants carrying mutation conferring fitness advantages. The current prevalent D614G variant, with glycine substituted for aspartic acid at position 614 in the spike glycoprotein, is one of such variants that became the main circulating strain worldwide in a short period of time. Over the past year, intensive studies from all over the world had defined the epidemiological characteristics of this highly contagious variant and revealed the underlying mechanisms. This review aims at presenting an overall picture of the impacts of D614G mutation on virus transmission, elucidating the underlying mechanisms of D614G in virus pathogenicity, and providing insights into the development of effective therapeutics.
Collapse
Affiliation(s)
- Chenxi Wang
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| | - You Zheng
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| | - Zubiao Niu
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| | - Xiaoyi Jiang
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| | - Qiang Sun
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| |
Collapse
|
20
|
Sohrabi F, Saeidifard S, Ghasemi M, Asadishad T, Hamidi SM, Hosseini SM. Role of plasmonics in detection of deadliest viruses: a review. EUROPEAN PHYSICAL JOURNAL PLUS 2021; 136:675. [PMID: 34178567 PMCID: PMC8214556 DOI: 10.1140/epjp/s13360-021-01657-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/08/2021] [Indexed: 05/09/2023]
Abstract
Viruses have threatened animal and human lives since a long time ago all over the world. Some of these tiny particles have caused disastrous pandemics that killed a large number of people with subsequent economic downturns. In addition, the quarantine situation itself encounters the challenges like the deficiency in the online educational system, psychiatric problems and poor international relations. Although viruses have a rather simple protein structure, they have structural heterogeneity with a high tendency to mutation that impedes their study. On top of the breadth of such worldwide worrying issues, there are profound scientific gaps, and several unanswered questions, like lack of vaccines or antivirals to combat these pathogens. Various detection techniques like the nucleic acid test, immunoassay, and microscopy have been developed; however, there is a tradeoff between their advantages and disadvantages like safety in sample collecting, invasiveness, sensitivity, response time, etc. One of the highly resolved techniques that can provide early-stage detection with fast experiment duration is plasmonics. This optical technique has the capability to detect viral proteins and genomes at the early stage via highly sensitive interaction between the biological target and the plasmonic chip. The efficiency of this technique could be proved using commercialized techniques like reverse transcription polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assay (ELISA) techniques. In this study, we aim to review the role of plasmonic technique in the detection of 11 deadliest viruses besides 2 common genital viruses for the human being. This is a rapidly moving topic of research, and a review article that encompasses the current findings may be useful for guiding strategies to deal with the pandemics. By investigating the potential aspects of this technique, we hope that this study could open new avenues toward the application of point-of-care techniques for virus detection at early stage that may inhibit the progressively hygienic threats.
Collapse
Affiliation(s)
- Foozieh Sohrabi
- Magneto-Plasmonic Lab, Laser and Plasma Research Institute, Shahid Beheshti University, Daneshju Boulevard, 1983969411 Tehran, Iran
| | - Sajede Saeidifard
- Magneto-Plasmonic Lab, Laser and Plasma Research Institute, Shahid Beheshti University, Daneshju Boulevard, 1983969411 Tehran, Iran
| | - Masih Ghasemi
- Magneto-Plasmonic Lab, Laser and Plasma Research Institute, Shahid Beheshti University, Daneshju Boulevard, 1983969411 Tehran, Iran
| | - Tannaz Asadishad
- Magneto-Plasmonic Lab, Laser and Plasma Research Institute, Shahid Beheshti University, Daneshju Boulevard, 1983969411 Tehran, Iran
| | - Seyedeh Mehri Hamidi
- Magneto-Plasmonic Lab, Laser and Plasma Research Institute, Shahid Beheshti University, Daneshju Boulevard, 1983969411 Tehran, Iran
| | - Seyed Masoud Hosseini
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Evin, Tehran, Iran
| |
Collapse
|
21
|
Garrett ME, Galloway J, Chu HY, Itell HL, Stoddard CI, Wolf CR, Logue JK, McDonald D, Weight H, Matsen FA, Overbaugh J. High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies. Cell 2021; 184:2927-2938.e11. [PMID: 34010620 PMCID: PMC8096189 DOI: 10.1016/j.cell.2021.04.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/26/2021] [Accepted: 04/23/2021] [Indexed: 01/02/2023]
Abstract
Defining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, spike (S). Here, we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using coronavirus disease 2019 (COVID-19) convalescent plasma. Antibody binding was common in two regions, the fusion peptide and the linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.
Collapse
Affiliation(s)
- Meghan E Garrett
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA; Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| | - Jared Galloway
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hannah L Itell
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA; Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| | - Caitlin I Stoddard
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer K Logue
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dylan McDonald
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Haidyn Weight
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Frederick A Matsen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA; Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA.
| |
Collapse
|
22
|
Riley TP, Chou HT, Hu R, Bzymek KP, Correia AR, Partin AC, Li D, Gong D, Wang Z, Yu X, Manzanillo P, Garces F. Enhancing the Prefusion Conformational Stability of SARS-CoV-2 Spike Protein Through Structure-Guided Design. Front Immunol 2021; 12:660198. [PMID: 33968063 PMCID: PMC8100506 DOI: 10.3389/fimmu.2021.660198] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/30/2021] [Indexed: 01/08/2023] Open
Abstract
The worldwide pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented and the impact on public health and the global economy continues to be devastating. Although early therapies such as prophylactic antibodies and vaccines show great promise, there are concerns about the long-term efficacy and universal applicability of these therapies as the virus continues to mutate. Thus, protein-based immunogens that can quickly respond to viral changes remain of continued interest. The Spike protein, the main immunogen of this virus, displays a highly dynamic trimeric structure that presents a challenge for therapeutic development. Here, guided by the structure of the Spike trimer, we rationally design new Spike constructs that show a uniquely high stability profile while simultaneously remaining locked into the immunogen-desirable prefusion state. Furthermore, our approach emphasizes the relationship between the highly conserved S2 region and structurally dynamic Receptor Binding Domains (RBD) to enable vaccine development as well as the generation of antibodies able to resist viral mutation.
Collapse
Affiliation(s)
- Timothy P. Riley
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Hui-Ting Chou
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Ruozhen Hu
- Department of Inflammation and Oncology, Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Krzysztof P. Bzymek
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Ana R. Correia
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Alexander C. Partin
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Danqing Li
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Danyang Gong
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Zhulun Wang
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Xinchao Yu
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Paolo Manzanillo
- Department of Inflammation and Oncology, Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Fernando Garces
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| |
Collapse
|
23
|
Kwarteng A, Asiedu E, Sylverken AA, Larbi A, Sakyi SA, Asiedu SO. Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. INFECTION GENETICS AND EVOLUTION 2021; 91:104815. [PMID: 33774178 PMCID: PMC7987576 DOI: 10.1016/j.meegid.2021.104815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/10/2021] [Accepted: 03/20/2021] [Indexed: 12/21/2022]
Abstract
The D614G variant of SARS-CoV-2 S-protein emerged in early 2020 and quickly became the dominant circulating strain in Europe and its environs. The variant was characterized by the higher viral load, which is not associated with disease severity, higher incorporation into the virion, and high cell entry via ACE-2 and TMPRSS2. Previous strains of the coronavirus and the current SARS-CoV-2 have demonstrated the selection of mutations as a mechanism of escaping immune responses. In this study, we used molecular dynamics simulation and MM-PBSA binding energy analysis to provide insights into the behaviour of the D614G S-protein at the molecular level and describe the neutralization mechanism of this variant. Our results show that the D614G S-protein adopts distinct conformational dynamics which is skewed towards the open-state conformation more than the closed-state conformation of the wild-type S-protein. Residue-specific variation of amino acid flexibility and domain-specific RMSD suggest that the mutation causes an allosteric conformational change in the RBD. Evaluation of the interaction energies between the S-protein and neutralizing antibodies show that the mutation may enhance, reduce or not affect the neutralizing interactions depending on the neutralizing antibody, especially if it targets the RBD. The results of this study have shed insights into the behaviour of the D614G S-protein at the molecular level and provided a glimpse of the neutralization mechanism of this variant.
Collapse
Affiliation(s)
- Alexander Kwarteng
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana; Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana.
| | - Ebenezer Asiedu
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana; Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Amma Larbi
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Samuel Asamoah Sakyi
- Department of Molecular Medicine, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Samuel Opoku Asiedu
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana; Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| |
Collapse
|
24
|
SARS-CoV-2 evolution in an immunocompromised host reveals shared neutralization escape mechanisms. Cell 2021; 184:2605-2617.e18. [PMID: 33831372 PMCID: PMC7962548 DOI: 10.1016/j.cell.2021.03.027] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/23/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023]
Abstract
Many individuals mount nearly identical antibody responses to SARS-CoV-2. To gain insight into how the viral spike (S) protein receptor-binding domain (RBD) might evolve in response to common antibody responses, we studied mutations occurring during virus evolution in a persistently infected immunocompromised individual. We use antibody Fab/RBD structures to predict, and pseudotypes to confirm, that mutations found in late-stage evolved S variants confer resistance to a common class of SARS-CoV-2 neutralizing antibodies we isolated from a healthy COVID-19 convalescent donor. Resistance extends to the polyclonal serum immunoglobulins of four out of four healthy convalescent donors we tested and to monoclonal antibodies in clinical use. We further show that affinity maturation is unimportant for wild-type virus neutralization but is critical to neutralization breadth. Because the mutations we studied foreshadowed emerging variants that are now circulating across the globe, our results have implications to the long-term efficacy of S-directed countermeasures.
Collapse
|
25
|
Lee CY, Amrun SN, Chee RS, Goh YS, Mak T, Octavia S, Yeo NK, Chang ZW, Tay MZ, Torres‐Ruesta A, Carissimo G, Poh CM, Fong S, Bei W, Lee S, Young BE, Tan S, Leo Y, Lye DC, Lin RTP, Maurer‐Stroh S, Lee B, Wang C, Renia L, Ng LFP. Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Clin Transl Immunology 2021; 10:e1241. [PMID: 33628442 PMCID: PMC7899292 DOI: 10.1002/cti2.1241] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVES The emergence of a SARS-CoV-2 variant with a point mutation in the spike (S) protein, D614G, has taken precedence over the original Wuhan isolate by May 2020. With an increased infection and transmission rate, it is imperative to determine whether antibodies induced against the D614 isolate may cross-neutralise against the G614 variant. METHODS Antibody profiling against the SARS-CoV-2 S protein of the D614 variant by flow cytometry and assessment of neutralising antibody titres using pseudotyped lentiviruses expressing the SARS-CoV-2 S protein of either the D614 or G614 variant tagged with a luciferase reporter were performed on plasma samples from COVID-19 patients with known D614G status (n = 44 infected with D614, n = 6 infected with G614, n = 7 containing all other clades: O, S, L, V, G, GH or GR). RESULTS Profiling of the anti-SARS-CoV-2 humoral immunity reveals similar neutralisation profiles against both S protein variants, albeit waning neutralising antibody capacity at the later phase of infection. Of clinical importance, patients infected with either the D614 or G614 clade elicited a similar degree of neutralisation against both pseudoviruses, suggesting that the D614G mutation does not impact the neutralisation capacity of the elicited antibodies. CONCLUSIONS Cross-reactivity occurs at the functional level of the humoral response on both the S protein variants, which suggests that existing serological assays will be able to detect both D614 and G614 clades of SARS-CoV-2. More importantly, there should be negligible impact towards the efficacy of antibody-based therapies and vaccines that are currently being developed.
Collapse
Affiliation(s)
- Cheryl Yi‐Pin Lee
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Siti Naqiah Amrun
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Rhonda Sin‐Ling Chee
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Yun Shan Goh
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Tze‐Minn Mak
- National Centre for Infectious DiseasesSingapore
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
| | - Sophie Octavia
- National Centre for Infectious DiseasesSingapore
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
| | - Nicholas Kim‐Wah Yeo
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Zi Wei Chang
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Matthew Zirui Tay
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Anthony Torres‐Ruesta
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Guillaume Carissimo
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Chek Meng Poh
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Siew‐Wai Fong
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Wang Bei
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Sandy Lee
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Barnaby Edward Young
- National Centre for Infectious DiseasesSingapore
- Department of Infectious DiseasesTan Tock Seng HospitalSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore
| | - Seow‐Yen Tan
- Department of Infectious DiseasesChangi General HospitalSingapore
| | - Yee‐Sin Leo
- National Centre for Infectious DiseasesSingapore
- Department of Infectious DiseasesTan Tock Seng HospitalSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore
- Yong Loo Lin School of MedicineNational University of Singapore and National University Health SystemSingapore
| | - David C Lye
- National Centre for Infectious DiseasesSingapore
- Department of Infectious DiseasesTan Tock Seng HospitalSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore
- Yong Loo Lin School of MedicineNational University of Singapore and National University Health SystemSingapore
| | - Raymond TP Lin
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
- Department of Microbiology and ImmunologyYong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Sebastien Maurer‐Stroh
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- National Centre for Infectious DiseasesSingapore
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
- Department of Biological SciencesNational University of SingaporeSingapore
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR)Singapore
| | - Bernett Lee
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Cheng‐I Wang
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Lisa FP Ng
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingapore
- National Institute of Health ResearchHealth Protection Research Unit in Emerging and Zoonotic InfectionsUniversity of LiverpoolLiverpoolUK
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolLiverpoolUK
| |
Collapse
|
26
|
Zhou Y, Liu Z, Li S, Xu W, Zhang Q, Silva IT, Li C, Wu Y, Jiang Q, Liu Z, Wang Q, Guo Y, Wu J, Gu C, Cai X, Qu D, Mayer CT, Wang X, Jiang S, Ying T, Yuan Z, Xie Y, Wen Y, Lu L, Wang Q. Enhancement versus neutralization by SARS-CoV-2 antibodies from a convalescent donor associates with distinct epitopes on the RBD. Cell Rep 2021; 34:108699. [PMID: 33485405 PMCID: PMC7802522 DOI: 10.1016/j.celrep.2021.108699] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/27/2020] [Accepted: 01/06/2021] [Indexed: 12/20/2022] Open
Abstract
Several potent neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus have been identified. However, antibody-dependent enhancement (ADE) has not been comprehensively studied for SARS-CoV-2, and the relationship between enhancing versus neutralizing activities and antibody epitopes remains unknown. Here, we select a convalescent individual with potent IgG neutralizing activity and characterize his antibody response. Monoclonal antibodies isolated from memory B cells target four groups of five non-overlapping receptor-binding domain (RBD) epitopes. Antibodies to one group of these RBD epitopes mediate ADE of entry in Raji cells via an Fcγ receptor-dependent mechanism. In contrast, antibodies targeting two other distinct epitope groups neutralize SARS-CoV-2 without ADE, while antibodies against the fourth epitope group are poorly neutralizing. One antibody, XG014, potently cross-neutralizes SARS-CoV-2 variants, as well as SARS-CoV-1, with respective IC50 (50% inhibitory concentration) values as low as 5.1 and 23.7 ng/mL, while not exhibiting ADE. Therefore, neutralization and ADE of human SARS-CoV-2 antibodies correlate with non-overlapping RBD epitopes.
Collapse
Affiliation(s)
- Yunjiao Zhou
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zezhong Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Shibo Li
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan 316021, China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qianqian Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Israel T Silva
- Laboratory of Bioinformatics and Computational Biology, A. C. Camargo Cancer Center, São Paulo 01509-010, Brazil
| | - Cheng Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yanling Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qingling Jiang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Zhenmi Liu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Qiujing Wang
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan 316021, China
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Jianbo Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chengjian Gu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xia Cai
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Di Qu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Christian T Mayer
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Tianlei Ying
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Yumei Wen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| |
Collapse
|
27
|
The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. Biochem Biophys Res Commun 2021; 538:104-107. [PMID: 33199022 PMCID: PMC7643658 DOI: 10.1016/j.bbrc.2020.10.109] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
The development of the SARS-CoV-2 pandemic has prompted an extensive worldwide sequencing effort to characterise the geographical spread and molecular evolution of the virus. A point mutation in the spike protein, D614G, emerged as the virus spread from Asia into Europe and the USA, and has rapidly become the dominant form worldwide. Here we review how the D614G variant was identified and discuss recent evidence about the effect of the mutation on the characteristics of the virus, clinical outcome of infection and host immune response.
Collapse
|
28
|
Sharma A, Ahmad Farouk I, Lal SK. COVID-19: A Review on the Novel Coronavirus Disease Evolution, Transmission, Detection, Control and Prevention. Viruses 2021. [PMID: 33572857 DOI: 10.3390/v13020202]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Three major outbreaks of the coronavirus, a zoonotic virus known to cause respiratory disease, have been reported since 2002, including SARS-CoV, MERS-CoV and the most recent 2019-nCoV, or more recently known as SARS-CoV-2. Bats are known to be the primary animal reservoir for coronaviruses. However, in the past few decades, the virus has been able to mutate and adapt to infect humans, resulting in an animal-to-human species barrier jump. The emergence of a novel coronavirus poses a serious global public health threat and possibly carries the potential of causing a major pandemic outbreak in the naïve human population. The recent outbreak of COVID-19, the disease caused by SARS-CoV-2, in Wuhan, Hubei Province, China has infected over 36.5 million individuals and claimed over one million lives worldwide, as of 8 October 2020. The novel virus is rapidly spreading across China and has been transmitted to 213 other countries/territories across the globe. Researchers have reported that the virus is constantly evolving and spreading through asymptomatic carriers, further suggesting a high global health threat. To this end, current up-to-date information on the coronavirus evolution and SARS-CoV-2 modes of transmission, detection techniques and current control and prevention strategies are summarized in this review.
Collapse
Affiliation(s)
- Anshika Sharma
- School of Science, Monash University Malaysia, Bandar Sunway 47500, Selangor DE, Malaysia
| | - Isra Ahmad Farouk
- School of Science, Monash University Malaysia, Bandar Sunway 47500, Selangor DE, Malaysia
| | - Sunil Kumar Lal
- School of Science, Monash University Malaysia, Bandar Sunway 47500, Selangor DE, Malaysia
- Tropical Medicine & Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway 47500, Selangor DE, Malaysia
| |
Collapse
|
29
|
Sharma A, Ahmad Farouk I, Lal SK. COVID-19: A Review on the Novel Coronavirus Disease Evolution, Transmission, Detection, Control and Prevention. Viruses 2021; 13:202. [PMID: 33572857 PMCID: PMC7911532 DOI: 10.3390/v13020202] [Citation(s) in RCA: 225] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/10/2020] [Accepted: 11/27/2020] [Indexed: 02/07/2023] Open
Abstract
Three major outbreaks of the coronavirus, a zoonotic virus known to cause respiratory disease, have been reported since 2002, including SARS-CoV, MERS-CoV and the most recent 2019-nCoV, or more recently known as SARS-CoV-2. Bats are known to be the primary animal reservoir for coronaviruses. However, in the past few decades, the virus has been able to mutate and adapt to infect humans, resulting in an animal-to-human species barrier jump. The emergence of a novel coronavirus poses a serious global public health threat and possibly carries the potential of causing a major pandemic outbreak in the naïve human population. The recent outbreak of COVID-19, the disease caused by SARS-CoV-2, in Wuhan, Hubei Province, China has infected over 36.5 million individuals and claimed over one million lives worldwide, as of 8 October 2020. The novel virus is rapidly spreading across China and has been transmitted to 213 other countries/territories across the globe. Researchers have reported that the virus is constantly evolving and spreading through asymptomatic carriers, further suggesting a high global health threat. To this end, current up-to-date information on the coronavirus evolution and SARS-CoV-2 modes of transmission, detection techniques and current control and prevention strategies are summarized in this review.
Collapse
Affiliation(s)
- Anshika Sharma
- School of Science, Monash University Malaysia, Bandar Sunway 47500, Selangor DE, Malaysia; (A.S.); (I.A.F.)
| | - Isra Ahmad Farouk
- School of Science, Monash University Malaysia, Bandar Sunway 47500, Selangor DE, Malaysia; (A.S.); (I.A.F.)
| | - Sunil Kumar Lal
- School of Science, Monash University Malaysia, Bandar Sunway 47500, Selangor DE, Malaysia; (A.S.); (I.A.F.)
- Tropical Medicine & Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway 47500, Selangor DE, Malaysia
| |
Collapse
|
30
|
Structural Analysis of Neutralizing Epitopes of the SARS-CoV-2 Spike to Guide Therapy and Vaccine Design Strategies. Viruses 2021; 13:v13010134. [PMID: 33477902 PMCID: PMC7833398 DOI: 10.3390/v13010134] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/01/2021] [Accepted: 01/14/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus research has gained tremendous attention because of the COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus (nCoV or SARS-CoV-2). In this review, we highlight recent studies that provide atomic-resolution structural details important for the development of monoclonal antibodies (mAbs) that can be used therapeutically and prophylactically and for vaccines against SARS-CoV-2. Structural studies with SARS-CoV-2 neutralizing mAbs have revealed a diverse set of binding modes on the spike's receptor-binding domain and N-terminal domain and highlight alternative targets on the spike. We consider this structural work together with mAb effects in vivo to suggest correlations between structure and clinical applications. We also place mAbs against severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses in the context of the SARS-CoV-2 spike to suggest features that may be desirable to design mAbs or vaccines capable of conferring broad protection.
Collapse
|
31
|
Duner P, Salehi A. COVID-19 and Possible Pharmacological Preventive Options. J Clin Med Res 2021; 12:758-772. [PMID: 33447309 PMCID: PMC7781281 DOI: 10.14740/jocmr4383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/11/2020] [Indexed: 12/22/2022] Open
Abstract
The dreadful fear of the coronavirus disease 2019 (COVID-19), which is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with the deadly consequences, requires rapid development of pharmacological cures. The objective of this review is to speculate about possible pharmacological options, already available today to prevent or treat the COVID-19 in the early stage of its outbreak. A literature search across PubMed and internet was conducted. A number of studies dealing with COVID-19 were identified. The data elucidated that increased pro-inflammatory and decreased anti-inflammatory cytokines in combination with hypoxia, thromboembolism and pneumonia are involved in the pathogenesis of SARS-CoV-2 infection. Although many drugs has been tested in monotherapy regimen with varying outcome or without desirable effect, there is still hope for better results by simultaneously targeting the virus itself and its symptoms. Theoretically, a mixture of at least two available antiviral drugs in combination with other anti-pathogenic and immune system-enhancing drugs or combination of antiviral drugs with convalescent plasma seems likely to have much better effect than the monotherapy regimen of either of these drugs.
Collapse
Affiliation(s)
- Pontus Duner
- Department of Clinical Science, SUS, Experimental Cardiovascular research, University of Lund, Sweden
| | - Albert Salehi
- Department of Clinical Science, Division of Islet Cell Physiology, University of Lund, Sweden
| |
Collapse
|
32
|
Boson B, Legros V, Zhou B, Siret E, Mathieu C, Cosset FL, Lavillette D, Denolly S. The SARS-CoV-2 envelope and membrane proteins modulate maturation and retention of the spike protein, allowing assembly of virus-like particles. J Biol Chem 2021; 296:100111. [PMID: 33229438 PMCID: PMC7833635 DOI: 10.1074/jbc.ra120.016175] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/13/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a β-coronavirus, is the causative agent of the COVID-19 pandemic. Like for other coronaviruses, its particles are composed of four structural proteins: spike (S), envelope (E), membrane (M), and nucleoprotein (N) proteins. The involvement of each of these proteins and their interactions are critical for assembly and production of β-coronavirus particles. Here, we sought to characterize the interplay of SARS-CoV-2 structural proteins during the viral assembly process. By combining biochemical and imaging assays in infected versus transfected cells, we show that E and M regulate intracellular trafficking of S as well as its intracellular processing. Indeed, the imaging data reveal that S is relocalized at endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC) or Golgi compartments upon coexpression of E or M, as observed in SARS-CoV-2-infected cells, which prevents syncytia formation. We show that a C-terminal retrieval motif in the cytoplasmic tail of S is required for its M-mediated retention in the ERGIC, whereas E induces S retention by modulating the cell secretory pathway. We also highlight that E and M induce a specific maturation of N-glycosylation of S, independently of the regulation of its localization, with a profile that is observed both in infected cells and in purified viral particles. Finally, we show that E, M, and N are required for optimal production of virus-like-particles. Altogether, these results highlight how E and M proteins may influence the properties of S proteins and promote the assembly of SARS-CoV-2 viral particles.
Collapse
Affiliation(s)
- Bertrand Boson
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Vincent Legros
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Lyon, France; Université de Lyon, VetAgro Sup, Marcy-l'Étoile, France
| | - Bingjie Zhou
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Eglantine Siret
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Cyrille Mathieu
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - François-Loïc Cosset
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Dimitri Lavillette
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai Chinese Academy of Sciences, Pasteurien College, Soochow University, Jiangsu, China
| | - Solène Denolly
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Lyon, France.
| |
Collapse
|
33
|
Salvamani S, Tan HZ, Thang WJ, Ter HC, Wan MS, Gunasekaran B, Rhodes A. Understanding the dynamics of COVID-19; implications for therapeutic intervention, vaccine development and movement control. Br J Biomed Sci 2020; 77:168-184. [PMID: 32942955 DOI: 10.1080/09674845.2020.1826136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The COVID-19 disease is caused by the SARS-CoV-2 virus, which is highly infective within the human population. The virus is widely disseminated to almost every continent with over twenty-seven million infections and over ninety-thousand reported deaths attributed to COVID-19 disease. SARS-CoV-2 is a single stranded RNA virus, comprising three main viral proteins; membrane, spike and envelope. The clinical features of COVID-19 disease can be classified according to different degrees of severity, with some patients progressing to acute respiratory distress syndrome, which can be fatal. In addition, many infections are asymptomatic or only cause mild symptoms. As there is no specific treatment for COVID-19 there is considerable endeavour to raise a vaccine against SARS-CoV-2, in addition to engineering neutralizing antibody interventions. In the absence of an effective vaccine, movement controls of varying stringencies have been imposed. Whilst enforced lockdown measures have been effective, they may be less effective against the current strain of SARS-CoV-2, the G614 clade. Conversely, other mutations of the virus, such as the Δ382 variant could reduce the clinical relevance of infection. The front runners in the race to develop an effective vaccine focus on the SARS-Co-V-2 Spike protein. However, vaccines that produce a T-cell response to a wider range of SARS-Co-V-2 viral proteins, may be more effective. Population based studies that determine the level of innate immunity to SARS-CoV-2, from prior exposure to the virus or to other coronaviruses, will have important implications for government imposed movement control and the strategic delivery of vaccination programmes.
Collapse
Affiliation(s)
- S Salvamani
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University , Kuala Lumpur, Malaysia
| | - H Z Tan
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University , Kuala Lumpur, Malaysia
| | - W J Thang
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University , Kuala Lumpur, Malaysia
| | - H C Ter
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University , Kuala Lumpur, Malaysia
| | - M S Wan
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University , Kuala Lumpur, Malaysia
| | - B Gunasekaran
- Dept of Biotechnology, Faculty of Applied Sciences, UCSI University , Kuala Lumpur, Malaysia
| | - A Rhodes
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University , Kuala Lumpur, Malaysia.,Dept of Pathology, Faculty of Medicine, University of Malaya , Kuala Lumpur, Malaysia
| |
Collapse
|
34
|
Salazar E, Kuchipudi SV, Christensen PA, Eagar T, Yi X, Zhao P, Jin Z, Long SW, Olsen RJ, Chen J, Castillo B, Leveque C, Towers D, Lavinder J, Gollihar J, Cardona J, Ippolito G, Nissly R, Bird I, Greenawalt D, Rossi RM, Gontu A, Srinivasan S, Poojary I, Cattadori IM, Hudson PJ, Josleyn NM, Prugar L, Huie K, Herbert A, Bernard DW, Dye JM, Kapur V, Musser JM. Convalescent plasma anti-SARS-CoV-2 spike protein ectodomain and receptor-binding domain IgG correlate with virus neutralization. J Clin Invest 2020; 130:6728-6738. [PMID: 32910806 PMCID: PMC7685744 DOI: 10.1172/jci141206] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 12/13/2022] Open
Abstract
The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the urgent need for assays that detect protective levels of neutralizing antibodies. We studied the relationship among anti-spike ectodomain (anti-ECD), anti-receptor-binding domain (anti-RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by 2 in vitro assays using convalescent plasma samples from 68 patients with COVID-19. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers and in vitro VN titers. The probability of a VN titer of ≥160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment, was ≥80% when anti-RBD or anti-ECD titers were ≥1:1350. Of all donors, 37% lacked VN titers of ≥160. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease VN or IgG titers. Analysis of 2814 asymptomatic adults found 73 individuals with anti-ECD IgG titers of ≥1:50 and strong positive correlation with anti-RBD and VN titers. Fourteen of these individuals had VN titers of ≥1:160, and all of them had anti-RBD titers of ≥1:1350. We conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titers of ≥1:1350 may provide critical information about protection against COVID-19 disease.
Collapse
Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Suresh V. Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Paul A. Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Todd Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Xin Yi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Picheng Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Zhicheng Jin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - S. Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Dalton Towers
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Jason Lavinder
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Jimmy Gollihar
- Combat Capabilities Development Command Army Research Laboratory — South, University of Texas, Austin, Texas, USA
| | - Jose Cardona
- Combat Capabilities Development Command Army Research Laboratory — South, University of Texas, Austin, Texas, USA
| | - Gregory Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, Texas, USA
| | - Ruth Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | - Ian Bird
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | - Denver Greenawalt
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | | | - Abhinay Gontu
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | | | | | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Nicole M. Josleyn
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Laura Prugar
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Kathleen Huie
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Andrew Herbert
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - David W. Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - John M. Dye
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences and
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, USA
| | - James M. Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| |
Collapse
|
35
|
Garrett ME, Galloway J, Chu HY, Itell HL, Stoddard CI, Wolf CR, Logue JK, McDonald D, Matsen FA, Overbaugh J. High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.16.385278. [PMID: 33236010 PMCID: PMC7685320 DOI: 10.1101/2020.11.16.385278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Defining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, Spike (S). Here we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using COVID-19 convalescent plasma. Antibody binding was common in two regions: the fusion peptide and linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.
Collapse
Affiliation(s)
- Meghan E Garrett
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jared Galloway
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hannah L Itell
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Caitlin I Stoddard
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer K Logue
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Dylan McDonald
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Frederick A Matsen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| |
Collapse
|
36
|
Ghorbani M, Brooks BR, Klauda JB. Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations. J Phys Chem B 2020; 124:10034-10047. [PMID: 33112147 PMCID: PMC7605337 DOI: 10.1021/acs.jpcb.0c05994] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/07/2020] [Indexed: 12/11/2022]
Abstract
The novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virion's surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier severe acute respiratory syndrome coronavirus (SARS-COV) in 2002 via extensive molecular dynamics (MD) simulations. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of the RBD/ACE2 complex. It is found that most of the naturally occurring mutations to the RBD either slightly strengthen or have the same binding affinity to ACE2 as the wild-type nCOV-2019. This means that the virus had sufficient binding affinity to its receptor at the beginning of the crisis. This also has implications for any vaccine design endeavors since these mutations could act as antibody escape mutants. Furthermore, in silico Ala-scanning and long-timescale MD simulations highlight the crucial role of the residues at the interface of RBD and ACE2 that may be used as potential pharmacophores for any drug development endeavors. From an evolutional perspective, this study also identifies how the virus has evolved from its predecessor SARS-COV and how it could further evolve to become even more infectious.
Collapse
Affiliation(s)
- Mahdi Ghorbani
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA
| |
Collapse
|
37
|
Owji H, Negahdaripour M, Hajighahramani N. Immunotherapeutic approaches to curtail COVID-19. Int Immunopharmacol 2020; 88:106924. [PMID: 32877828 PMCID: PMC7441891 DOI: 10.1016/j.intimp.2020.106924] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/16/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023]
Abstract
COVID-19, the disease induced by the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has imposed an unpredictable burden on the world. Drug repurposing has been employed to rapidly find a cure; but despite great efforts, no drug or vaccine is presently available for treating or prevention of COVID-19. Apart from antivirals, immunotherapeutic strategies are suggested considering the role of the immune response as the host defense against the virus, and the fact that SARS-CoV-2 suppresses interferon induction as an immune evasion strategy. Active immunization through vaccines, interferon administration, passive immunotherapy by convalescent plasma or synthesized monoclonal and polyclonal antibodies, as well as immunomodulatory drugs, are different immunotherapeutic approaches that will be mentioned in this review. The focus would be on passive immunotherapeutic interventions. Interferons might be helpful in some stages. Vaccine development has been followed with unprecedented speed. Some of these vaccines have been advanced to human clinical trials. Convalescent plasma therapy is already practiced in many countries to help save the lives of severely ill patients. Different antibodies that target various steps of SARS-CoV-2 pathogenesis or the associated immune responses are also proposed. For treating the cytokine storm induced at a late stage of the disease in some patients, immune modulation through JAK inhibitors, corticosteroids, and some other cognate classes are evaluated. Given the changing pattern of cytokine induction and immune responses throughout the COVID-19 disease course, different adapted approaches are needed to help patients. Gaining more knowledge about the detailed pathogenesis of SARS-CoV-2, its interplay with the immune system, and viral-mediated responses are crucial to identify efficient preventive and therapeutic approaches. A systemic approach seems essential in this regard.
Collapse
Affiliation(s)
- Hajar Owji
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Nasim Hajighahramani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| |
Collapse
|
38
|
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020. [PMID: 32697968 DOI: 10.1016/j.cell.2020.06.043s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
Collapse
Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| |
Collapse
|
39
|
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020; 182:812-827.e19. [PMID: 32697968 PMCID: PMC7332439 DOI: 10.1016/j.cell.2020.06.043] [Citation(s) in RCA: 2778] [Impact Index Per Article: 694.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/10/2020] [Accepted: 06/26/2020] [Indexed: 02/08/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
Collapse
Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| |
Collapse
|
40
|
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020. [PMID: 32697968 DOI: 10.1016/j.cell.2020.06.043%0asummary] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
Collapse
Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| |
Collapse
|
41
|
Tong PBV, Lin LY, Tran TH. Coronaviruses pandemics: Can neutralizing antibodies help? Life Sci 2020; 255:117836. [PMID: 32450171 PMCID: PMC7243778 DOI: 10.1016/j.lfs.2020.117836] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022]
Abstract
For the first time in Homo sapiens history, possibly, most of human activities is stopped by coronavirus disease 2019 (COVID-19). Nearly eight billion people of this world are facing a great challenge, maybe not "to be or not to be" yet, but unpredictable. What happens to other major pandemics in the past, and how human beings went through these hurdles? The human body is equipped with the immune system that can recognize, respond and fight against pathogens such as viruses. Following the innate response, immune system processes the adaptive response by which each pathogen is encoded and recorded in memory system. The humoral reaction containing cytokines and antibodies is expected to activate when the pathogens come back. Exploiting this nature of body protection, neutralizing antibodies have been investigated. Learning from past, in parallel to SARS-CoV-2, other coronaviruses SARS-CoV and MERS-CoV who caused previous pandemics, are recalled in this review. We here propose insights of origin and characteristics and perspective for the future of antibodies development.
Collapse
Affiliation(s)
- Phuoc-Bao-Viet Tong
- INSERM U1109, Fédération Hospitalo-Universitaire (FHU) OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Li-Yun Lin
- INSERM U1109, Fédération Hospitalo-Universitaire (FHU) OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Tuan Hiep Tran
- Faculty of Pharmacy, PHENIKAA University, Yen Nghia, Ha Dong, Hanoi 12116, Viet Nam; PHENIKAA Research and Technology Institute (PRATI), A&A Green Phoenix Group JSC, No.167 Hoang Ngan, Trung Hoa, Cau Giay, Hanoi 11313, Viet Nam.
| |
Collapse
|
42
|
Salazar E, Kuchipudi SV, Christensen PA, Eagar TN, Yi X, Zhao P, Jin Z, Long SW, Olsen RJ, Chen J, Castillo B, Leveque C, Towers DM, Lavinder J, Gollihar JD, Cardona J, Ippolito GC, Nissly RH, Bird IM, Greenawalt D, Rossi RM, Gontu A, Srinivasan S, Poojary IB, Cattadori IM, Hudson PJ, Joselyn N, Prugar L, Huie K, Herbert A, Bernard DW, Dye J, Kapur V, Musser JM. Relationship between Anti-Spike Protein Antibody Titers and SARS-CoV-2 In Vitro Virus Neutralization in Convalescent Plasma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.08.138990. [PMID: 32577662 PMCID: PMC7302218 DOI: 10.1101/2020.06.08.138990] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Newly emerged pathogens such as SARS-CoV-2 highlight the urgent need for assays that detect levels of neutralizing antibodies that may be protective. We studied the relationship between anti-spike ectodomain (ECD) and anti-receptor binding domain (RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by two different in vitro assays using convalescent plasma samples obtained from 68 COVID-19 patients, including 13 who donated plasma multiple times. Only 23% (16/68) of donors had been hospitalized. We also studied 16 samples from subjects found to have anti-spike protein IgG during surveillance screening of asymptomatic individuals. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers, and in vitro VN titer. Anti-RBD plasma IgG correlated slightly better than anti-ECD IgG titer with VN titer. The probability of a VN titer ≥160 was 80% or greater with anti-RBD or anti-ECD titers of ≥1:1350. Thirty-seven percent (25/68) of convalescent plasma donors lacked VN titers ≥160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease either VN or IgG titers. Analysis of 2,814 asymptomatic adults found 27 individuals with anti-RBD or anti-ECD IgG titers of ≥1:1350, and evidence of VN ≥1:160. Taken together, we conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titer of ≥1:1350 may provide critical information about protection against COVID-19 disease.
Collapse
Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Suresh V. Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
| | - Paul A. Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Todd N. Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Xin Yi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Picheng Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Zhicheng Jin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - S. Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Dalton M. Towers
- Department of Molecular Biosciences, University of Texas at Austin
| | - Jason Lavinder
- Department of Molecular Biosciences, University of Texas at Austin
| | - Jimmy D. Gollihar
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas
| | - Jose Cardona
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas
| | - Gregory C. Ippolito
- Department of Molecular Biosciences, University of Texas at Austin
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Ruth H. Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Ian M. Bird
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Denver Greenawalt
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Randall M. Rossi
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Abinhay Gontu
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Sreenidhi Srinivasan
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - Indira B. Poojary
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Nicole Joselyn
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Laura Prugar
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Kathleen Huie
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Andrew Herbert
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - David W. Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - John Dye
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - James M. Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| |
Collapse
|
43
|
Giurgea LT, Han A, Memoli MJ. Universal coronavirus vaccines: the time to start is now. NPJ Vaccines 2020; 5:43. [PMID: 32528732 PMCID: PMC7256035 DOI: 10.1038/s41541-020-0198-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/14/2020] [Indexed: 11/08/2022] Open
Abstract
The continued explosive spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) despite aggressive public health measures has triggered an unprecedented international vaccine effort. However, correlates of protection, which can help guide intelligent vaccine design, are not known for SARS-CoV-2. Research on influenza immunity and vaccine development may provide valuable lessons for coronavirus efforts, especially considering similarities in rapid evolutionary potential. The apparent inevitability of future novel coronavirus outbreaks must prompt work on a universal coronavirus vaccine.
Collapse
Affiliation(s)
- Luca T. Giurgea
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Alison Han
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Matthew J. Memoli
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| |
Collapse
|
44
|
Liu H, Zheng S, Hou X, Liu X, Du K, Lv X, Li Y, Yang F, Li W, Sui J. Novel Abs targeting the N-terminus of fibroblast growth factor 19 inhibit hepatocellular carcinoma growth without bile-acid-related side-effects. Cancer Sci 2020; 111:1750-1760. [PMID: 32061104 PMCID: PMC7226213 DOI: 10.1111/cas.14353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a common and particularly fatal form of cancer for which very few drugs are effective. The fibroblast growth factor 19 (FGF19) has been viewed as a driver of HCC development and a potential Ab target for developing novel HCC therapy. However, a previously developed anti‐FGF19 Ab disrupted FGF19’s normal regulatory function and caused severe bile‐acid‐related side‐effects despite of having potent antitumor effects in preclinical models. Here, we developed novel human Abs (G1A8 and HS29) that specifically target the N‐terminus of FGF19. Both Abs inhibited FGF19‐induced HCC cell proliferation in vitro and significantly suppressed HCC tumor growth in mouse models. Importantly, no bile‐acid‐related side effects were observed in preclinical cynomolgus monkeys. Fundamentally, our study demonstrates that it is possible to target FGF19 for anti‐HCC therapies without adversely affecting its normal bile acid regulatory function, and highlights the exciting promise of G1A8 or HS29 as potential therapy for HCC.
Collapse
Affiliation(s)
- Huisi Liu
- National Institute of Biological Sciences (NIBS), Beijing, China.,Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint Graduate Program, School of Life Sciences, Peking University, Beijing, China
| | - Sanduo Zheng
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Xinfeng Hou
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Ximing Liu
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Kaixin Du
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Xueyuan Lv
- National Institute of Biological Sciences (NIBS), Beijing, China.,PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yulu Li
- National Institute of Biological Sciences (NIBS), Beijing, China.,Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint Graduate Program, School of Life Sciences, Peking University, Beijing, China
| | - Fang Yang
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Wenhui Li
- National Institute of Biological Sciences (NIBS), Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Jianhua Sui
- National Institute of Biological Sciences (NIBS), Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| |
Collapse
|
45
|
Yu F, Du L, Ojcius DM, Pan C, Jiang S. Measures for diagnosing and treating infections by a novel coronavirus responsible for a pneumonia outbreak originating in Wuhan, China. Microbes Infect 2020; 22:74-79. [PMID: 32017984 PMCID: PMC7102556 DOI: 10.1016/j.micinf.2020.01.003] [Citation(s) in RCA: 192] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 01/24/2020] [Indexed: 11/03/2022]
Abstract
On 10 January 2020, a new coronavirus causing a pneumonia outbreak in Wuhan City in central China was denoted as 2019-nCoV by the World Health Organization (WHO). As of 24 January 2020, there were 887 confirmed cases of 2019-nCoV infection, including 26 deaths, reported in China and other countries. Therefore, combating this new virus and stopping the epidemic is a matter of urgency. Here, we focus on advances in research and development of fast diagnosis methods, as well as potential prophylactics and therapeutics to prevent or treat 2019-nCoV infection.
Collapse
Affiliation(s)
- Fei Yu
- The College of Life and Sciences, Hebei Agricultural University, Bao Ding, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, USA
| | - David M Ojcius
- Department of Biomedical Sciences, University of the Pacific, School of Dentistry, San Francisco, USA
| | - Chungen Pan
- Guangdong Haid Institute of Animal Husbandry & Veterinary, Haid Research Institute, Guangdong Haid Group Co., Ltd, Guangzhou, China.
| | - Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, USA; Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China.
| |
Collapse
|
46
|
Li D, He W, Liu X, Zheng S, Qi Y, Li H, Mao F, Liu J, Sun Y, Pan L, Du K, Ye K, Li W, Sui J. A potent human neutralizing antibody Fc-dependently reduces established HBV infections. eLife 2017; 6. [PMID: 28949917 PMCID: PMC5614562 DOI: 10.7554/elife.26738] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/04/2017] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a major global health problem. Currently-available therapies are ineffective in curing chronic HBV infection. HBV and its satellite hepatitis D virus (HDV) infect hepatocytes via binding of the preS1 domain of its large envelope protein to sodium taurocholate cotransporting polypeptide (NTCP). Here, we developed novel human monoclonal antibodies that block the engagement of preS1 with NTCP and neutralize HBV and HDV with high potency. One antibody, 2H5-A14, functions at picomolar level and exhibited neutralization-activity-mediated prophylactic effects. It also acts therapeutically by eliciting antibody-Fc-dependent immunological effector functions that impose durable suppression of viral infection in HBV-infected mice, resulting in reductions in the levels of the small envelope antigen and viral DNA, with no emergence of escape mutants. Our results illustrate a novel antibody-Fc-dependent approach for HBV treatment and suggest 2H5-A14 as a novel clinical candidate for HBV prevention and treatment of chronic HBV infection.
Collapse
Affiliation(s)
- Dan Li
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Wenhui He
- National Institute of Biological Sciences, Beijing, China
| | - Ximing Liu
- National Institute of Biological Sciences, Beijing, China.,PTN Joint Graduate Program, College of Life Sciences, Peking University, Beijing, China
| | - Sanduo Zheng
- National Institute of Biological Sciences, Beijing, China
| | - Yonghe Qi
- National Institute of Biological Sciences, Beijing, China
| | - Huiyu Li
- National Institute of Biological Sciences, Beijing, China
| | - Fengfeng Mao
- National Institute of Biological Sciences, Beijing, China.,Graduate Program in College of Life Sciences, Beijing Normal University, Beijing, China
| | - Juan Liu
- National Institute of Biological Sciences, Beijing, China
| | - Yinyan Sun
- National Institute of Biological Sciences, Beijing, China
| | - Lijing Pan
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Kaixin Du
- National Institute of Biological Sciences, Beijing, China.,Graduate Program in College of Life Sciences, Beijing Normal University, Beijing, China
| | - Keqiong Ye
- National Institute of Biological Sciences, Beijing, China
| | - Wenhui Li
- National Institute of Biological Sciences, Beijing, China
| | - Jianhua Sui
- National Institute of Biological Sciences, Beijing, China
| |
Collapse
|
47
|
Pallesen J, Wang N, Corbett KS, Wrapp D, Kirchdoerfer RN, Turner HL, Cottrell CA, Becker MM, Wang L, Shi W, Kong WP, Andres EL, Kettenbach AN, Denison MR, Chappell JD, Graham BS, Ward AB, McLellan JS. Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen. Proc Natl Acad Sci U S A 2017; 114:E7348-E7357. [PMID: 28807998 PMCID: PMC5584442 DOI: 10.1073/pnas.1707304114] [Citation(s) in RCA: 781] [Impact Index Per Article: 111.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As in other coronaviruses, the spike (S) glycoprotein of MERS-CoV mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. Here we use structure-based design to develop a generalizable strategy for retaining coronavirus S proteins in the antigenically optimal prefusion conformation and demonstrate that our engineered immunogen is able to elicit high neutralizing antibody titers against MERS-CoV. We also determined high-resolution structures of the trimeric MERS-CoV S ectodomain in complex with G4, a stem-directed neutralizing antibody. The structures reveal that G4 recognizes a glycosylated loop that is variable among coronaviruses and they define four conformational states of the trimer wherein each receptor-binding domain is either tightly packed at the membrane-distal apex or rotated into a receptor-accessible conformation. Our studies suggest a potential mechanism for fusion initiation through sequential receptor-binding events and provide a foundation for the structure-based design of coronavirus vaccines.
Collapse
Affiliation(s)
- Jesper Pallesen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Nianshuang Wang
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755;
| | - Kizzmekia S Corbett
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Daniel Wrapp
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Robert N Kirchdoerfer
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Michelle M Becker
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Lingshu Wang
- Virology Core, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Wei Shi
- Virology Core, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Wing-Pui Kong
- Virology Core, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Erica L Andres
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756
| | - Mark R Denison
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Barney S Graham
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037;
| | - Jason S McLellan
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755;
| |
Collapse
|
48
|
Abstract
Outbreaks from zoonotic sources represent a threat to both human disease as well as the global economy. Despite a wealth of metagenomics studies, methods to leverage these datasets to identify future threats are underdeveloped. In this study, we describe an approach that combines existing metagenomics data with reverse genetics to engineer reagents to evaluate emergence and pathogenic potential of circulating zoonotic viruses. Focusing on the severe acute respiratory syndrome (SARS)-like viruses, the results indicate that the WIV1-coronavirus (CoV) cluster has the ability to directly infect and may undergo limited transmission in human populations. However, in vivo attenuation suggests additional adaptation is required for epidemic disease. Importantly, available SARS monoclonal antibodies offered success in limiting viral infection absent from available vaccine approaches. Together, the data highlight the utility of a platform to identify and prioritize prepandemic strains harbored in animal reservoirs and document the threat posed by WIV1-CoV for emergence in human populations.
Collapse
|
49
|
McKimm-Breschkin JL, Fry AM. Meeting report: 4th ISIRV antiviral group conference: Novel antiviral therapies for influenza and other respiratory viruses. Antiviral Res 2016; 129:21-38. [PMID: 26872862 PMCID: PMC7132401 DOI: 10.1016/j.antiviral.2016.01.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 01/22/2016] [Indexed: 01/08/2023]
Abstract
The International Society for Influenza and other Respiratory Virus Diseases (isirv) held its 4th Antiviral Group Conference at the University of Texas on 2–4 June, 2015. With emerging resistance to the drugs currently licensed for treatment and prophylaxis of influenza viruses, primarily the neuraminidase inhibitor oseltamivir phosphate (Tamiflu) and the M2 inhibitors amantadine and rimantadine, and the lack of effective interventions against other respiratory viruses, the 3-day programme focused on the discovery and development of inhibitors of several virus targets and key host cell factors involved in virus replication or mediating the inflammatory response. Virus targets included the influenza haemagglutinin, neuraminidase and M2 proteins, and both the respiratory syncytial virus and influenza polymerases and nucleoproteins. Therapies for rhinoviruses and MERS and SARS coronaviruses were also discussed. With the emerging development of monoclonal antibodies as therapeutics, the potential implications of antibody-dependent enhancement of disease were also addressed. Topics covered all aspects from structural and molecular biology to preclinical and clinical studies. The importance of suitable clinical trial endpoints and regulatory issues were also discussed from the perspectives of both industry and government. This meeting summary provides an overview, not only for the conference participants, but also for those interested in the current status of antivirals for respiratory viruses. The International Society for Influenza and other Respiratory Viruses held an Antiviral Group conference in June, 2015. This report covers oral presentations, including therapies against influenza and respiratory syncytial virus infections. Therapies for rhinovirus, MERS and SARS coronavirus infections were also topics at the conference. Some speakers focused on monoclonal antibodies as therapeutics and antibody-dependent enhancement of disease. The importance of suitable clinical trial endpoints and regulatory issues were also discussed.
Collapse
Affiliation(s)
| | - Alicia M Fry
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| |
Collapse
|
50
|
Abstract
Purpose of review This review highlights recent developments in HIV-1 antibody engineering and discusses the effects of increased polyreactivity on serum half-lives of engineered antibodies. Recent findings Recent studies have uncovered a wealth of information about the relationship between the sequences and efficacies of anti-HIV-1 antibodies through a combination of bioinformatics, structural characterization and in vivo studies. This knowledge has stimulated efforts to enhance antibody breadth and potency for therapeutic use. Although some engineered antibodies have shown increased polyreactivity and short half-lives, promising efforts are circumventing these problems. Summary Antibodies are desirable as therapeutics due to their ability to recognize targets with both specificity and high affinity. Furthermore, the ability of antibodies to stimulate Fc-mediated effector functions can increase their utility. Thus, mAbs have become central to strategies for the treatment of various diseases. Using both targeted and library-based approaches, antibodies can be engineered to improve their therapeutic properties. This article will discuss recent antibody engineering efforts to improve the breadth and potency of anti-HIV-1 antibodies. The polyreactivity of engineered HIV-1 bNAbs and the effect on serum half-life will be explored along with strategies to overcome problems introduced by engineering antibodies. Finally, advances in creating bispecific anti-HIV-1 reagents are discussed.
Collapse
|