1
|
Matveeva M, Lefebvre M, Chahinian H, Yahi N, Fantini J. Host Membranes as Drivers of Virus Evolution. Viruses 2023; 15:1854. [PMID: 37766261 PMCID: PMC10535233 DOI: 10.3390/v15091854] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The molecular mechanisms controlling the adaptation of viruses to host cells are generally poorly documented. An essential issue to resolve is whether host membranes, and especially lipid rafts, which are usually considered passive gateways for many enveloped viruses, also encode informational guidelines that could determine virus evolution. Due to their enrichment in gangliosides which confer an electronegative surface potential, lipid rafts impose a first control level favoring the selection of viruses with enhanced cationic areas, as illustrated by SARS-CoV-2 variants. Ganglioside clusters attract viral particles in a dynamic electrostatic funnel, the more cationic viruses of a viral population winning the race. However, electrostatic forces account for only a small part of the energy of raft-virus interaction, which depends mainly on the ability of viruses to form a network of hydrogen bonds with raft gangliosides. This fine tuning of virus-ganglioside interactions, which is essential to stabilize the virus on the host membrane, generates a second level of selection pressure driven by a typical induced-fit mechanism. Gangliosides play an active role in this process, wrapping around the virus spikes through a dynamic quicksand-like mechanism. Viruses are thus in an endless race for access to lipid rafts, and they are bound to evolve perpetually, combining speed (electrostatic potential) and precision (fine tuning of amino acids) under the selective pressure of the immune system. Deciphering the host membrane guidelines controlling virus evolution mechanisms may open new avenues for the design of innovative antivirals.
Collapse
Affiliation(s)
| | | | | | | | - Jacques Fantini
- Department of Biology, Faculty of Medicine, University of Aix-Marseille, INSERM UMR_S 1072, 13015 Marseille, France; (M.M.); (M.L.); (H.C.); (N.Y.)
| |
Collapse
|
2
|
Dai YC, Lin YC, Ching LL, Tsai JJ, Ishikawa K, Tsai WY, Chen JJ, Nerurkar VR, Wang WK. Determining the Time of Booster Dose Based on the Half-Life and Neutralization Titers against SARS-CoV-2 Variants of Concern in Fully Vaccinated Individuals. Microbiol Spectr 2023; 11:e0408122. [PMID: 37428104 PMCID: PMC10434144 DOI: 10.1128/spectrum.04081-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/20/2023] [Indexed: 07/11/2023] Open
Abstract
Although mRNA-based COVID-19 vaccines reduce the risk of severe disease, hospitalization and death, vaccine effectiveness (VE) against infection and disease from variants of concern (VOC) wanes over time. Neutralizing antibodies (NAb) are surrogates of protection and are enhanced by a booster dose, but their kinetics and durability remain understudied. Current recommendation of a booster dose does not consider the existing NAb in each individual. Here, we investigated 50% neutralization (NT50) titers against VOC among COVID-19-naive participants receiving the Moderna (n = 26) or Pfizer (n = 25) vaccine for up to 7 months following the second dose, and determined their half-lives. We found that the time it took for NT50 titers to decline to 24, equivalent to 50% inhibitory dilution of 10 international units/mL, was longer in the Moderna (325/324/235/274 days for the D614G/alpha/beta/delta variants) group than in the Pfizer (253/252/174/226 days) group, which may account for the slower decline in VE of the Moderna vaccine observed in real-world settings and supports our hypothesis that measuring the NT50 titers against VOC, together with information on NAb half-lives, can be used to dictate the time of booster vaccination. Our study provides a framework to determine the optimal time of a booster dose against VOC at the individual level. In response to future VOC with high morbidity and mortality, a quick evaluation of NAb half-lives using longitudinal serum samples from clinical trials or research programs of different primary-series vaccinations and/or one or two boosters could provide references for determining the time of booster in different individuals. IMPORTANCE Despite improved understanding of the biology of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the evolutionary trajectory of the virus is uncertain, and the concern of future antigenically distinct variants remains. Current recommendations for a COVID-19 vaccine booster dose are primarily based on neutralization capacity, effectiveness against circulating variants of concern (VOC), and other host factors. We hypothesized that measuring neutralizing antibody titers against SARS-CoV-2 VOC together with half-life information can be used to dictate the time of booster vaccination. Through detailed analysis of neutralizing antibodies against VOC among COVID-19-naive vaccinees receiving either of two mRNA vaccines, we found that the time it took for 50% neutralization titers to decline to a reference level of protection was longer in the Moderna than in the Pfizer group, which supports our hypothesis. In response to future VOC with potentially high morbidity and mortality, our proof-of-concept study provides a framework to determine the optimal time of a booster dose at the individual level.
Collapse
Affiliation(s)
- Yu-Ching Dai
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Yen-Chia Lin
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Lauren L. Ching
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
- Pacific Center for Emerging Infectious Diseases, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Jih-Jin Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kyle Ishikawa
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Wen-Yang Tsai
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
- Pacific Center for Emerging Infectious Diseases, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - John J. Chen
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Vivek R. Nerurkar
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
- Pacific Center for Emerging Infectious Diseases, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Wei-Kung Wang
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
- Pacific Center for Emerging Infectious Diseases, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| |
Collapse
|
3
|
Hickerson BT, Khalenkov AM, Xie T, Frucht DM, Scott DE, Ilyushina NA. Interchangeability of the Assays Used to Assess the Activity of Anti-SARS-CoV-2 Monoclonal Antibodies. Viruses 2023; 15:1698. [PMID: 37632039 PMCID: PMC10459467 DOI: 10.3390/v15081698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
The recent global COVID-19 pandemic caused by SARS-CoV-2 lasted for over three years. A key measure in combatting this pandemic involved the measurement of the monoclonal antibody (mAb)-mediated inhibition of binding between the spike receptor-binding domain (RBD) and hACE2 receptor. Potency assessments of therapeutic anti-SARS-CoV-2 mAbs typically include binding or cell-based neutralization assays. We assessed the inhibitory activity of five anti-SARS-CoV-2 mAbs using ELISA, surface plasmon resonance (SPR), and four cell-based neutralization assays using different pseudovirus particles and 293T or A549 cells expressing hACE2 with or without TMPRSS2. We assessed the interchangeability between cell-based and binding assays by applying the Bland-Altman method under certain assumptions. Our data demonstrated that the IC50 [nM] values determined by eight neutralization assays are independent of the cell line, presence of TMPRSS2 enzyme on the cell surface, and pseudovirus backbone used. Moreover, the Bland-Altman analysis showed that the IC50 [nM] and KD [nM] values determined by neutralization/ELISA or by SPR are equivalent and that the anti-spike mAb activity can be attributed to one variable directly related to its tertiary conformational structure conformation, rate dissociation constant Koff. This parameter is independent from the concentrations of the components of the mAb:RBD:hACE2 complexes and can be used for a comparison between the activities of the different mAbs.
Collapse
Affiliation(s)
- Brady T. Hickerson
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA; (B.T.H.); (T.X.); (D.M.F.)
| | - Alexey M. Khalenkov
- Division of Plasma Derivatives, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA; (A.M.K.); (D.E.S.)
| | - Tao Xie
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA; (B.T.H.); (T.X.); (D.M.F.)
| | - David M. Frucht
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA; (B.T.H.); (T.X.); (D.M.F.)
| | - Dorothy E. Scott
- Division of Plasma Derivatives, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA; (A.M.K.); (D.E.S.)
| | - Natalia A. Ilyushina
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA; (B.T.H.); (T.X.); (D.M.F.)
| |
Collapse
|
4
|
Convergent Evolution Dynamics of SARS-CoV-2 and HIV Surface Envelope Glycoproteins Driven by Host Cell Surface Receptors and Lipid Rafts: Lessons for the Future. Int J Mol Sci 2023; 24:ijms24031923. [PMID: 36768244 PMCID: PMC9915253 DOI: 10.3390/ijms24031923] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Although very different, in terms of their genomic organization, their enzymatic proteins, and their structural proteins, HIV and SARS-CoV-2 have an extraordinary evolutionary potential in common. Faced with various selection pressures that may be generated by treatments or immune responses, these RNA viruses demonstrate very high adaptive capacities, which result in the continuous emergence of variants and quasi-species. In this retrospective analysis of viral proteins, ensuring the adhesion of these viruses to the plasma membrane of host cells, we highlight many common points that suggest the convergent mechanisms of evolution. HIV and SARS-CoV-2 first recognize a lipid raft microdomain that acts as a landing strip for viral particles on the host cell surface. In the case of mucosal cells, which are the primary targets of both viruses, these microdomains are enriched in anionic glycolipids (gangliosides) forming a global electronegative field. Both viruses use lipid rafts to surf on the cell surface in search of a protein receptor able to trigger the fusion process. This implies that viral envelope proteins are both geometrically and electrically compatible to the biomolecules they select to invade host cells. In the present study, we identify the surface electrostatic potential as a critical parameter controlling the convergent evolution dynamics of HIV-1 and SARS-CoV-2 surface envelope proteins, and we discuss the impact of this parameter on the phenotypic properties of both viruses. The virological data accumulated since the emergence of HIV in the early 1980s should help us to face present and future virus pandemics.
Collapse
|
5
|
SARS-CoV-2 Spike Protein Induces Hemagglutination: Implications for COVID-19 Morbidities and Therapeutics and for Vaccine Adverse Effects. Int J Mol Sci 2022; 23:ijms232415480. [PMID: 36555121 PMCID: PMC9779393 DOI: 10.3390/ijms232415480] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
Experimental findings for SARS-CoV-2 related to the glycan biochemistry of coronaviruses indicate that attachments from spike protein to glycoconjugates on the surfaces of red blood cells (RBCs), other blood cells and endothelial cells are key to the infectivity and morbidity of COVID-19. To provide further insight into these glycan attachments and their potential clinical relevance, the classic hemagglutination (HA) assay was applied using spike protein from the Wuhan, Alpha, Delta and Omicron B.1.1.529 lineages of SARS-CoV-2 mixed with human RBCs. The electrostatic potential of the central region of spike protein from these four lineages was studied through molecular modeling simulations. Inhibition of spike protein-induced HA was tested using the macrocyclic lactone ivermectin (IVM), which is indicated to bind strongly to SARS-CoV-2 spike protein glycan sites. The results of these experiments were, first, that spike protein from these four lineages of SARS-CoV-2 induced HA. Omicron induced HA at a significantly lower threshold concentration of spike protein than the three prior lineages and was much more electropositive on its central spike protein region. IVM blocked HA when added to RBCs prior to spike protein and reversed HA when added afterward. These results validate and extend prior findings on the role of glycan bindings of viral spike protein in COVID-19. They furthermore suggest therapeutic options using competitive glycan-binding agents such as IVM and may help elucidate rare serious adverse effects (AEs) associated with COVID-19 mRNA vaccines, which use spike protein as the generated antigen.
Collapse
|
6
|
Fantini J, Chahinian H, Yahi N. A Vaccine Strategy Based on the Identification of an Annular Ganglioside Binding Motif in Monkeypox Virus Protein E8L. Viruses 2022; 14:v14112531. [PMID: 36423140 PMCID: PMC9693861 DOI: 10.3390/v14112531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
The recent outbreak of Monkeypox virus requires the development of a vaccine specifically directed against this virus as quickly as possible. We propose here a new strategy based on a two-step analysis combining (i) the search for binding domains of viral proteins to gangliosides present in lipid rafts of host cells, and (ii) B epitope predictions. Based on previous studies of HIV and SARS-CoV-2 proteins, we show that the Monkeypox virus cell surface-binding protein E8L possesses a ganglioside-binding motif consisting of several subsites forming a ring structure. The binding of the E8L protein to a cluster of gangliosides GM1 mimicking a lipid raft domain is driven by both shape and electrostatic surface potential complementarities. An induced-fit mechanism unmasks selected amino acid side chains of the motif without significantly affecting the secondary structure of the protein. The ganglioside-binding motif overlaps three potential linear B epitopes that are well exposed on the unbound E8L surface that faces the host cell membrane. This situation is ideal for generating neutralizing antibodies. We thus suggest using these three sequences derived from the E8L protein as immunogens in a vaccine formulation (recombinant protein, synthetic peptides or genetically based) specific for Monkeypox virus. This lipid raft/ganglioside-based strategy could be used for developing therapeutic and vaccine responses to future virus outbreaks, in parallel to existing solutions.
Collapse
|
7
|
Bayani F, Safaei Hashkavaei N, Uversky VN, Mozaffari-Jovin S, Sefidbakht Y. Insights into the structural peculiarities of the N-terminal and receptor binding domains of the spike protein from the SARS-CoV-2 Omicron variant. Comput Biol Med 2022; 147:105735. [PMID: 35767919 PMCID: PMC9220253 DOI: 10.1016/j.compbiomed.2022.105735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/26/2022] [Accepted: 06/11/2022] [Indexed: 11/03/2022]
|
8
|
Burel E, Colson P, Lagier JC, Levasseur A, Bedotto M, Lavrard-Meyer P, Fournier PE, La Scola B, Raoult D. Sequential Appearance and Isolation of a SARS-CoV-2 Recombinant between Two Major SARS-CoV-2 Variants in a Chronically Infected Immunocompromised Patient. Viruses 2022; 14:1266. [PMID: 35746737 PMCID: PMC9227898 DOI: 10.3390/v14061266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 02/05/2023] Open
Abstract
Genetic recombination is a major evolutionary mechanism among RNA viruses, and it is common in coronaviruses, including those infecting humans. A few SARS-CoV-2 recombinants have been reported to date whose genome harbored combinations of mutations from different mutants or variants, but only a single patient's sample was analyzed, and the virus was not isolated. Here, we report the gradual emergence of a hybrid genome of B.1.160 and Alpha variants in a lymphoma patient chronically infected for 14 months, and we isolated the recombinant virus. The hybrid genome was obtained by next-generation sequencing, and the recombination sites were confirmed by PCR. This consisted of a parental B.1.160 backbone interspersed with two fragments, including the spike gene, from an Alpha variant. An analysis of seven sequential samples from the patient decoded the recombination steps, including the initial infection with a B.1.160 variant, then a concurrent infection with this variant and an Alpha variant, the generation of hybrid genomes, and eventually the emergence of a predominant recombinant virus isolated at the end of the patient's follow-up. This case exemplifies the recombination process of SARS-CoV-2 in real life, and it calls for intensifying the genomic surveillance in patients coinfected with different SARS-CoV-2 variants, and more generally with several RNA viruses, as this may lead to the appearance of new viruses.
Collapse
Affiliation(s)
- Emilie Burel
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Marielle Bedotto
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
| | - Philippe Lavrard-Meyer
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| |
Collapse
|
9
|
Ghimire D, Han Y, Lu M. Structural Plasticity and Immune Evasion of SARS-CoV-2 Spike Variants. Viruses 2022; 14:1255. [PMID: 35746726 PMCID: PMC9229035 DOI: 10.3390/v14061255] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 01/27/2023] Open
Abstract
The global pandemic of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has significantly affected every human life and overloaded the health care system worldwide. Limited therapeutic options combined with the consecutive waves of the infection and emergence of novel SARS-CoV-2 variants, especially variants of concern (VOCs), have prolonged the COVID-19 pandemic and challenged its control. The Spike (S) protein on the surface of SARS-CoV-2 is the primary target exposed to the host and essential for virus entry into cells. The parental (Wuhan-Hu-1 or USA/WA1 strain) S protein is the virus-specific component of currently implemented vaccines. However, S is most prone to mutations, potentially shifting the dynamics of virus-host interactions by affecting S conformational/structural profiles. Scientists have rapidly resolved atomic structures of S VOCs and elucidated molecular details of these mutations, which can inform the design of S-directed novel therapeutics and broadly protective vaccines. Here, we discuss recent findings on S-associated virus transmissibility and immune evasion of SARS-CoV-2 VOCs and experimental approaches used to profile these properties. We summarize the structural studies that document the structural flexibility/plasticity of S VOCs and the potential roles of accumulated mutations on S structures and functions. We focus on the molecular interpretation of structures of the S variants and its insights into the molecular mechanism underlying antibody evasion and host cell-receptor binding.
Collapse
Affiliation(s)
- Dibya Ghimire
- Department of Cellular and Molecular Biology, University of Texas Health Science Center, Tyler, TX 75708, USA;
| | | | - Maolin Lu
- Department of Cellular and Molecular Biology, University of Texas Health Science Center, Tyler, TX 75708, USA;
| |
Collapse
|
10
|
Fantini J, Yahi N, Colson P, Chahinian H, La Scola B, Raoult D. The puzzling mutational landscape of the SARS-2-variant Omicron. J Med Virol 2022; 94:2019-2025. [PMID: 34997962 PMCID: PMC9015223 DOI: 10.1002/jmv.27577] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
The recently emerging SARS-CoV-2 variant omicron displays an unusual association of 30 mutations, 3 deletions, and 1 insertion. To analyze the impact of this atypic mutational landscape, we constructed a complete structure of the omicron spike protein. Compared with the delta variant, the receptor-binding domain (RBD) of omicron has an increased electrostatic surface potential, but a decreased affinity for the ACE-2 receptor. The N-terminal domain (NTD) has both a decreased surface potential and a lower affinity for lipid rafts. The omicron variant is predicted to be less fusogenic and thus less pathogenic than delta, due to a geometric reorganization of the S1-S2 cleavage site. Overall, these virological parameters suggest that omicron does not have a significant infectivity advantage over the delta variant. However, in omicron, neutralizing epitopes are greatly affected, suggesting that current vaccines will probably confer little protection against this variant. In conclusion, the puzzling mutational pattern of the omicron variant combines contradictory properties which may either decrease (virological properties) or increase (immunological escape/facilitation) the transmission of this variant in the human population. This Janus-like phenotype may explain some conflicting reports on the initial assessment of omicron and provide new insights about the molecular mechanisms controlling its dissemination and pathogenesis worldwide.
Collapse
Affiliation(s)
- Jacques Fantini
- Department of BiologyAix‐Marseille UniversitéMarseilleFrance
- INSERM UMR_S 1072MarseilleFrance
| | - Nouara Yahi
- Department of BiologyAix‐Marseille UniversitéMarseilleFrance
- INSERM UMR_S 1072MarseilleFrance
| | - Philippe Colson
- Department of BiologyAix‐Marseille UniversitéMarseilleFrance
- 3IHU Méditerranée InfectionMarseilleFrance
- MEPHI, Institut de Recherche pour le Développement (IRD)MarseilleFrance
- Assistance Publique—Hôpitaux de Marseille (AP‐HM)MarseilleFrance
| | - Henri Chahinian
- Department of BiologyAix‐Marseille UniversitéMarseilleFrance
- INSERM UMR_S 1072MarseilleFrance
| | - Bernard La Scola
- Department of BiologyAix‐Marseille UniversitéMarseilleFrance
- 3IHU Méditerranée InfectionMarseilleFrance
- MEPHI, Institut de Recherche pour le Développement (IRD)MarseilleFrance
- Assistance Publique—Hôpitaux de Marseille (AP‐HM)MarseilleFrance
| | - Didier Raoult
- Department of BiologyAix‐Marseille UniversitéMarseilleFrance
- 3IHU Méditerranée InfectionMarseilleFrance
- MEPHI, Institut de Recherche pour le Développement (IRD)MarseilleFrance
- Assistance Publique—Hôpitaux de Marseille (AP‐HM)MarseilleFrance
| |
Collapse
|
11
|
Delandre O, Gendrot M, Jardot P, Le Bideau M, Boxberger M, Boschi C, Fonta I, Mosnier J, Hutter S, Levasseur A, La Scola B, Pradines B. Antiviral Activity of Repurposing Ivermectin against a Panel of 30 Clinical SARS-CoV-2 Strains Belonging to 14 Variants. Pharmaceuticals (Basel) 2022; 15:445. [PMID: 35455442 PMCID: PMC9024598 DOI: 10.3390/ph15040445] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 02/05/2023] Open
Abstract
Over the past two years, several variants of SARS-CoV-2 have emerged and spread all over the world. However, infectivity, clinical severity, re-infection, virulence, transmissibility, vaccine responses and escape, and epidemiological aspects have differed between SARS-CoV-2 variants. Currently, very few treatments are recommended against SARS-CoV-2. Identification of effective drugs among repurposing FDA-approved drugs is a rapid, efficient and low-cost strategy against SARS-CoV-2. One of those drugs is ivermectin. Ivermectin is an antihelminthic agent that previously showed in vitro effects against a SARS-CoV-2 isolate (Australia/VI01/2020 isolate) with an IC50 of around 2 µM. We evaluated the in vitro activity of ivermectin on Vero E6 cells infected with 30 clinically isolated SARS-CoV-2 strains belonging to 14 different variants, and particularly 17 strains belonging to six variants of concern (VOC) (variants related to Wuhan, alpha, beta, gamma, delta and omicron). The in vitro activity of ivermectin was compared to those of chloroquine and remdesivir. Unlike chloroquine (EC50 from 4.3 ± 2.5 to 29.3 ± 5.2 µM) or remdesivir (EC50 from 0.4 ± 0.3 to 25.2 ± 9.4 µM), ivermectin showed a relatively homogeneous in vitro activity against SARS-CoV-2 regardless of the strains or variants (EC50 from 5.1 ± 0.5 to 6.7 ± 0.4 µM), except for one omicron strain (EC50 = 1.3 ± 0.5 µM). Ivermectin (No. EC50 = 219, mean EC50 = 5.7 ± 1.0 µM) was, overall, more potent in vitro than chloroquine (No. EC50 = 214, mean EC50 = 16.1 ± 9.0 µM) (p = 1.3 × 10-34) and remdesivir (No. EC50 = 201, mean EC50 = 11.9 ± 10.0 µM) (p = 1.6 × 10-13). These results should be interpreted with caution regarding the potential use of ivermectin in SARS-CoV-2-infected patients: it is difficult to translate in vitro study results into actual clinical treatment in patients.
Collapse
Affiliation(s)
- Océane Delandre
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
| | - Mathieu Gendrot
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
| | - Priscilla Jardot
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Marion Le Bideau
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Manon Boxberger
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Céline Boschi
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Isabelle Fonta
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Joel Mosnier
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Sébastien Hutter
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
| | - Anthony Levasseur
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| |
Collapse
|
12
|
Fahrner JE, Lahmar I, Goubet AG, Haddad Y, Carrier A, Mazzenga M, Drubay D, Alves Costa Silva C, de Sousa E, Thelemaque C, Melenotte C, Dubuisson A, Geraud A, Ferrere G, Birebent R, Bigenwald C, Picard M, Cerbone L, Lérias JR, Laparra A, Bernard-Tessier A, Kloeckner B, Gazzano M, Danlos FX, Terrisse S, Pizzato E, Flament C, Ly P, Tartour E, Benhamouda N, Meziani L, Ahmed-Belkacem A, Miyara M, Gorochov G, Barlesi F, Trubert A, Ungar B, Estrada Y, Pradon C, Gallois E, Pommeret F, Colomba E, Lavaud P, Deloger M, Droin N, Deutsch E, Gachot B, Spano JP, Merad M, Scotté F, Marabelle A, Griscelli F, Blay JY, Soria JC, Merad M, André F, Villemonteix J, Chevalier MF, Caillat-Zucman S, Fenollar F, Guttman-Yassky E, Launay O, Kroemer G, La Scola B, Maeurer M, Derosa L, Zitvogel L. The Polarity and Specificity of Antiviral T Lymphocyte Responses Determine Susceptibility to SARS-CoV-2 Infection in Patients with Cancer and Healthy Individuals. Cancer Discov 2022; 12:958-983. [PMID: 35179201 PMCID: PMC9394394 DOI: 10.1158/2159-8290.cd-21-1441] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/10/2022] [Accepted: 01/31/2022] [Indexed: 01/07/2023]
Abstract
Vaccination against coronavirus disease 2019 (COVID-19) relies on the in-depth understanding of protective immune responses to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). We characterized the polarity and specificity of memory T cells directed against SARS-CoV-2 viral lysates and peptides to determine correlates with spontaneous, virus-elicited, or vaccine-induced protection against COVID-19 in disease-free and cancer-bearing individuals. A disbalance between type 1 and 2 cytokine release was associated with high susceptibility to COVID-19. Individuals susceptible to infection exhibited a specific deficit in the T helper 1/T cytotoxic 1 (Th1/Tc1) peptide repertoire affecting the receptor binding domain of the spike protein (S1-RBD), a hotspot of viral mutations. Current vaccines triggered Th1/Tc1 responses in only a fraction of all subject categories, more effectively against the original sequence of S1-RBD than that from viral variants. We speculate that the next generation of vaccines should elicit Th1/Tc1 T-cell responses against the S1-RBD domain of emerging viral variants. SIGNIFICANCE This study prospectively analyzed virus-specific T-cell correlates of protection against COVID-19 in healthy and cancer-bearing individuals. A disbalance between Th1/Th2 recall responses conferred susceptibility to COVID-19 in both populations, coinciding with selective defects in Th1 recognition of the receptor binding domain of spike. See related commentary by McGary and Vardhana, p. 892. This article is highlighted in the In This Issue feature, p. 873.
Collapse
Affiliation(s)
- Jean-Eudes Fahrner
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.,Transgene S.A., Illkirch-Graffenstaden, France
| | - Imran Lahmar
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Anne-Gaëlle Goubet
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Yacine Haddad
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Agathe Carrier
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Marine Mazzenga
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Damien Drubay
- Gustave Roussy, Villejuif, France.,Département de Biostatistique et d'Epidémiologie, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Carolina Alves Costa Silva
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Lyon COVID Study Group
- Open Innovation & Partnerships (OIP), bioMérieux S.A., Marcy l'Etoile, France. R&D – Immunoassay, bioMérieux S.A., Marcy l'Etoile, France.,Joint Research Unit Hospices Civils de Lyon-bioMérieux, Civils Hospices of Lyon, Lyon Sud Hospital, Pierre-Bénite, France.,International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France.,Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France
| | - Eric de Sousa
- ImmunoTherapy/ImmunoSurgery, Champalimaud Centre for the Unknown, Lisboa, Portugal
| | - Cassandra Thelemaque
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Cléa Melenotte
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.,Aix-Marseille Université, Institut Hospitalo-Universitaire, Institut de Recherche pour le Développement, Assistance Publique – Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Marseille, France
| | - Agathe Dubuisson
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Arthur Geraud
- Gustave Roussy, Villejuif, France.,Département d'Innovation Thérapeutique et d'Essais Précoces (DITEP), Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Gladys Ferrere
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Roxanne Birebent
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Camille Bigenwald
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Marion Picard
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Luigi Cerbone
- Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Joana R. Lérias
- ImmunoTherapy/ImmunoSurgery, Champalimaud Centre for the Unknown, Lisboa, Portugal
| | - Ariane Laparra
- Gustave Roussy, Villejuif, France.,Département d'Innovation Thérapeutique et d'Essais Précoces (DITEP), Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Alice Bernard-Tessier
- Gustave Roussy, Villejuif, France.,Département d'Innovation Thérapeutique et d'Essais Précoces (DITEP), Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Benoît Kloeckner
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Marianne Gazzano
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - François-Xavier Danlos
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Safae Terrisse
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Eugenie Pizzato
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Caroline Flament
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Pierre Ly
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Eric Tartour
- Center of clinical investigations BIOTHERIS, INSERM CIC1428, Gustave Roussy, Villejuif, France.,Department of Immunology, Hôpital Européen Georges Pompidou, APHP, Paris, France
| | - Nadine Benhamouda
- Center of clinical investigations BIOTHERIS, INSERM CIC1428, Gustave Roussy, Villejuif, France.,Department of Immunology, Hôpital Européen Georges Pompidou, APHP, Paris, France
| | | | | | - Makoto Miyara
- Univ Paris Est Créteil, INSERM U955, IMRB, Créteil, France
| | - Guy Gorochov
- Univ Paris Est Créteil, INSERM U955, IMRB, Créteil, France
| | - Fabrice Barlesi
- Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France.,Sorbonne Université/Institut National de la Santé et de la Recherche Médicale, U1135, Centre d'Immunologie et des Maladies Infectieuses, Hôpital Pitié-Salpêtrière, Assistance Publique – Hôpitaux de Paris, Paris, France
| | - Alexandre Trubert
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Benjamin Ungar
- Aix Marseille University, CNRS, INSERM, CRCM, Marseille, France
| | - Yeriel Estrada
- Department of Dermatology, Center of Excellence in Eczema Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Caroline Pradon
- Gustave Roussy, Villejuif, France.,Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, New York.,Centre de Ressources Biologiques, ET-EXTRA, Gustave Roussy, Villejuif, France
| | - Emmanuelle Gallois
- Gustave Roussy, Villejuif, France.,Département de Biologie Médicale et Pathologie Médicales, Service de Biochimie, Gustave Roussy, Villejuif, France
| | - Fanny Pommeret
- Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Emeline Colomba
- Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Pernelle Lavaud
- Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Marc Deloger
- Département de Biologie Médicale et Pathologie Médicales, Service de Microbiologie, Gustave Roussy, Villejuif, France
| | - Nathalie Droin
- Gustave Roussy, Plateforme de Bioinformatique, Université Paris-Saclay, INSERM US23, CNRS UMS, Villejuif, France
| | - Eric Deutsch
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Gustave Roussy, Plateforme de génomique, Université Paris-Saclay, INSERM US23, CNRS UMS, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1030, Gustave Roussy, Villejuif, France
| | - Bertrand Gachot
- Gustave Roussy, Villejuif, France.,Département de Radiothérapie, Gustave Roussy, Villejuif, France
| | | | - Mansouria Merad
- Gustave Roussy, Villejuif, France.,Department of Medical Oncology, Pitié-Salpétrière Hospital, APHP, Sorbonne Université, Paris, France
| | - Florian Scotté
- Gustave Roussy, Villejuif, France.,Service de Médecine aigue d’Urgence en Cancérologie, Gustave Roussy, Villejuif, France
| | - Aurélien Marabelle
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.,Département d'Innovation Thérapeutique et d'Essais Précoces (DITEP), Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France.,Département Interdisciplinaire d'Organisation des Parcours Patients, Gustave Roussy, Villejuif, France
| | - Frank Griscelli
- Gustave Roussy, Villejuif, France.,Département de Biologie Médicale et Pathologie Médicales, Service de Biochimie, Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale – UMR935/UA9, Université Paris-Saclay, Villejuif, France.,INGESTEM National IPSC Infrastructure, Université de Paris-Saclay, Villejuif, France.,Université de Paris, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France
| | - Jean-Yves Blay
- Centre Léon Bérard, Lyon, France.,Université Claude Bernard, Lyon, France.,Unicancer, Paris, France
| | - Jean-Charles Soria
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Oncological Science, Icahn School of Medicine at Mount Sinai, New York, New York.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Fabrice André
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U981, Gustave Roussy, Villejuif, France
| | - Juliette Villemonteix
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint-Louis, APHP, Université de Paris, Paris, France
| | - Mathieu F. Chevalier
- INSERM UMR 976, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Sophie Caillat-Zucman
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint-Louis, APHP, Université de Paris, Paris, France.,INSERM UMR 976, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Florence Fenollar
- IHU Méditérranée Infection, VITROME, IRD, AP-HM, SSA, Aix-Marseille University, Marseille, France
| | - Emma Guttman-Yassky
- Department of Dermatology, Center of Excellence in Eczema Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Odile Launay
- Université de Paris, Inserm CIC 1417, I-Reivac, APHP, Hopital Cochin, Paris, France
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif, France.,Pôle de Biologie, Hôpital Européen George Pompidou, Assistance Publique – Hôpitaux de Paris, Paris, France
| | - Bernard La Scola
- Institut Hospitalo-Universitaire, Méditerranée Infection, Marseille, France
| | - Markus Maeurer
- ImmunoTherapy/ImmunoSurgery, Champalimaud Centre for the Unknown, Lisboa, Portugal.,Medizinische Klinik, Johannes Gutenberg University Mainz, Germany
| | - Lisa Derosa
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Laurence Zitvogel
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.,Center of clinical investigations BIOTHERIS, INSERM CIC1428, Gustave Roussy, Villejuif, France.,Corresponding Author: Laurence Zitvogel, University Paris-Saclay, Gustave Roussy Cancer Center, 114 rue Edouard Vaillant, Villejuif Cedex 94805, France. Phone: 331-4211-5041; E-mail:
| |
Collapse
|
13
|
Mackin RT, Edwards JV, Atuk EB, Beltrami N, Condon BD, Jayawickramarajah J, French AD. Structure/Function Analysis of Truncated Amino-Terminal ACE2 Peptide Analogs That Bind to SARS-CoV-2 Spike Glycoprotein. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072070. [PMID: 35408469 PMCID: PMC9000588 DOI: 10.3390/molecules27072070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022]
Abstract
The global burden of the SARS-CoV-2 pandemic is thought to result from a high viral transmission rate. Here, we consider mechanisms that influence host cell–virus binding between the SARS-CoV-2 spike glycoprotein (SPG) and the human angiotensin-converting enzyme 2 (ACE2) with a series of peptides designed to mimic key ACE2 hot spots through adopting a helical conformation analogous to the N-terminal α1 helix of ACE2, the region experimentally shown to bind to the SARS-CoV-2 receptor-binding domain (RBD). The approach examines putative structure/function relations by assessing SPG binding affinity with surface plasmon resonance (SPR). A cyclic peptide (c[KFNHEAEDLFEKLM]) was characterized in an α-helical conformation with micromolar affinity (KD = 500 µM) to the SPG. Thus, stabilizing the helical structure of the 14-mer through cyclization improves binding to SPG by an order of magnitude. In addition, end-group peptide analog modifications and residue substitutions mediate SPG binding, with net charge playing an apparent role. Therefore, we surveyed reported viral variants, and a correlation of increased positive charge with increased virulence lends support to the hypothesis that charge is relevant to enhanced viral fusion. Overall, the structure/function relationship informs the importance of conformation and charge for virus-binding analog design.
Collapse
Affiliation(s)
- Robert T. Mackin
- United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA 70124, USA; (R.T.M.); (B.D.C.); (A.D.F.)
| | - J. Vincent Edwards
- United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA 70124, USA; (R.T.M.); (B.D.C.); (A.D.F.)
- Correspondence: ; Tel.: +1-504-286-4360
| | - E. Berk Atuk
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA; (E.B.A.); (N.B.); (J.J.)
| | - Noah Beltrami
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA; (E.B.A.); (N.B.); (J.J.)
| | - Brian D. Condon
- United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA 70124, USA; (R.T.M.); (B.D.C.); (A.D.F.)
| | | | - Alfred D. French
- United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA 70124, USA; (R.T.M.); (B.D.C.); (A.D.F.)
| |
Collapse
|
14
|
Colson P, Delerce J, Burel E, Dahan J, Jouffret A, Fenollar F, Yahi N, Fantini J, La Scola B, Raoult D. Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. Arch Virol 2022; 167:1185-1190. [PMID: 35178586 PMCID: PMC8853869 DOI: 10.1007/s00705-022-05385-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/24/2022] [Indexed: 11/02/2022]
Abstract
SARS-CoV-2 variants have become a major virological, epidemiological, and clinical concern, particularly with regard to the risk of escape from vaccine-induced immunity. Here, we describe the emergence of a new variant, with the index case returning from travel in Cameroon. For 13 SARS-CoV-2-positive patients living in the same geographical area of southeastern France, a qPCR test for screening variant-associated mutations showed an atypical combination. The genome sequences were obtained by next-generation sequencing with Oxford Nanopore Technologies on GridION instruments within about 8 h. Analysis revealed 46 nucleotide substitutions and 37 deletions, resulting in 30 amino acid substitutions and 12 deletions. Fourteen of the amino acid substitutions, including N501Y and E484K, and nine deletions are located in the spike protein. This genotype pattern led to the establishment of a new Pangolin lineage, named B.1.640.2, that is a phylogenetic sister group to the old B.1.640 lineage, which has now been renamed B.1.640.1. The lineages differ by 25 nucleotide substitutions and 33 deletions. The combination of mutations in these isolates and their phylogenetic position indicate, based on our previous definition, that they represent a new variant, which we have named "IHU". These data are a further example of the unpredictability of the emergence of SARS-CoV-2 variants, and of their possible introduction into a given geographical area from abroad.
Collapse
Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Université, 27 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Jérémy Delerce
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Emilie Burel
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Jordan Dahan
- Laboratoire de Biologie Médicale, Synlab Provence Marseille, 25 rue Rabattu, 13015, Marseille, France
| | - Agnès Jouffret
- Laboratoire de Biologie Médicale Synlab Provence Forcalquier, rue du Souvenir Français, 04300, Forcalquier, France
| | - Florence Fenollar
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Université, 27 boulevard Jean Moulin, 13005, Marseille, France.,Institut de Recherche pour le Développement (IRD), Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Université, 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Nouara Yahi
- Aix-Marseille Université, INSERM UMR S 1072, 51 boulevard Pierre Dramard, 13015, Marseille, France
| | - Jacques Fantini
- Aix-Marseille Université, INSERM UMR S 1072, 51 boulevard Pierre Dramard, 13015, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Université, 27 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France. .,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Université, 27 boulevard Jean Moulin, 13005, Marseille, France.
| |
Collapse
|
15
|
Boschi C, Colson P, Bancod A, Moal V, La Scola B. Omicron variant escapes therapeutic mAbs including recently released Evusheld ®, contrary to eight prior main VOC. Clin Infect Dis 2022; 75:e534-e535. [PMID: 35171987 PMCID: PMC9402686 DOI: 10.1093/cid/ciac143] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Céline Boschi
- Microbes, Evolution, Phylogeny et Infection (MEPHI), Aix Marseille Univ, IRD, AP-HM, 13005 Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 13005 Marseille, France
| | - Philippe Colson
- Microbes, Evolution, Phylogeny et Infection (MEPHI), Aix Marseille Univ, IRD, AP-HM, 13005 Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 13005 Marseille, France
| | - Audrey Bancod
- Microbes, Evolution, Phylogeny et Infection (MEPHI), Aix Marseille Univ, IRD, AP-HM, 13005 Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 13005 Marseille, France
| | - Valérie Moal
- Microbes, Evolution, Phylogeny et Infection (MEPHI), Aix Marseille Univ, IRD, AP-HM, 13005 Marseille, France.,Department of Nephrology, Conception hospital, AP-HM, 13005 Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny et Infection (MEPHI), Aix Marseille Univ, IRD, AP-HM, 13005 Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 13005 Marseille, France
| |
Collapse
|
16
|
Colson P, Fournier PE, Chaudet H, Delerce J, Giraud-Gatineau A, Houhamdi L, Andrieu C, Brechard L, Bedotto M, Prudent E, Gazin C, Beye M, Burel E, Dudouet P, Tissot-Dupont H, Gautret P, Lagier JC, Million M, Brouqui P, Parola P, Fenollar F, Drancourt M, La Scola B, Levasseur A, Raoult D. Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics. Front Microbiol 2022; 12:786233. [PMID: 35197938 PMCID: PMC8859183 DOI: 10.3389/fmicb.2021.786233] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/15/2021] [Indexed: 01/05/2023] Open
Abstract
After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations along the whole genome shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47 and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analyzing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from farm minks. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.
Collapse
Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- French Armed Forces Center for Epidemiology and Public Health, Marseille, France
| | | | - Audrey Giraud-Gatineau
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- French Armed Forces Center for Epidemiology and Public Health, Marseille, France
| | | | | | | | | | | | | | | | | | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Gautret
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Brouqui
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Parola
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Florence Fenollar
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- *Correspondence: Didier Raoult,
| |
Collapse
|
17
|
Mukhopadhyay L, Gupta N, Yadav PD, Aggarwal N. Neutralization assays for SARS-CoV-2: Implications for assessment of protective efficacy of COVID-19 vaccines. Indian J Med Res 2022; 155:105-122. [PMID: 35859437 PMCID: PMC9552365 DOI: 10.4103/ijmr.ijmr_2544_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The WHO emergency use-listed (EUL) COVID-19 vaccines were developed against early strains of SARS-CoV-2. With the emergence of SARS-CoV-2 variants of concern (VOCs) - Alpha, Beta, Gamma, Delta and Omicron, it is necessary to assess the neutralizing activity of these vaccines against the VOCs. PubMed and preprint platforms were searched for literature on neutralizing activity of serum from WHO EUL vaccine recipients, against the VOCs, using appropriate search terms till November 30, 2021. Our search yielded 91 studies meeting the inclusion criteria. The analysis revealed a drop of 0-8.9-fold against Alpha variant, 0.3-42.4-fold against Beta variant, 0-13.8-fold against Gamma variant and 1.35-20-fold against Delta variant in neutralization titres of serum from the WHO EUL COVID-19 vaccine recipients, as compared to early SARS-CoV-2 isolates. The wide range of variability was due to differences in the choice of virus strains selected for neutralization assays (pseudovirus or live virus), timing of serum sample collection after the final dose of vaccine (day 0 to 8 months) and sample size (ranging from 5 to 470 vaccinees). The reasons for this variation have been discussed and the possible way forward to have uniformity across neutralization assays in different laboratories have been described, which will generate reliable data. Though in vitro neutralization studies are a valuable tool to estimate the performance of vaccines against the backdrop of emerging variants, the results must be interpreted with caution and corroborated with field-effectiveness studies.
Collapse
Affiliation(s)
- Labanya Mukhopadhyay
- Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Nivedita Gupta
- Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Pragya D Yadav
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Neeraj Aggarwal
- Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| |
Collapse
|
18
|
Astakhova EA, Byazrova MG, Yusubalieva GM, Larichev VF, Baklaushev VP, Filatov AV. High Heterogeneity of Virus-Neutralizing and RBD-Binding Activities of COVID-19 Convalescent Sera. Mol Biol 2022; 56:1028-1035. [PMCID: PMC9734827 DOI: 10.1134/s002689332206005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 12/14/2022]
Abstract
The parameters of the humoral response are an important immunological characteristic of donors who recovered from COVID-19 and vaccinated individuals. Analysis of the level of virus-binding antibodies has become widespread. The most accurate predictor of effective immune protection against symptomatic SARS-CoV-2 infection is the activity of virus-neutralizing antibodies. We determined virus-neutralizing activities in plasma samples of individuals (n = 111) who had COVID-19 from April to September 2020. Three independent methods were used: conventional with live virus, with virus-like particles pseudotyped with spike protein, and a surrogate virus-neutralization test (cVNT, pVNT and sVNT, respectively). For comparison, the levels of IgG, IgA and IgM antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein were also evaluated. The levels of virus-binding as well as virus-neutralizing antibodies in cVNT and pVNT showed high heterogeneity. A comparison of cVNT and pVNT results showed a high correlation, sVNT results also correlated well with both cVNT and pVNT. To the greatest extent, the level of IgG antibodies correlated with the results of cVNT, pVNT and sVNT. These results can be used in the selection of plasmas that are best suited for transfusion and treatment of acute COVID-19. In addition, data on the virus-neutralizing activity of plasma are important for the selection of potential donors, for the isolation of SARS-CoV-2-specific B-lymphocytes, in order to further generate monoclonal virus-neutralizing antibodies.
Collapse
Affiliation(s)
- E. A. Astakhova
- National Research Center “Institute of Immunology”, Federal Medical-Biological Agency, 115522 Moscow, Russia ,Immunology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| | - M. G. Byazrova
- National Research Center “Institute of Immunology”, Federal Medical-Biological Agency, 115522 Moscow, Russia ,Immunology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia ,Рeoples Friendship University of Russia (RUDN University) of Ministry of Science and Higher Education of Russia, 117198 Moscow, Russia
| | - G. M. Yusubalieva
- Federal Research and Clinical Center for Specialized Types of Medical Care and Medical Technologies, Federal Medical-Biological Agency, 115682 Moscow, Russia
| | - V. F. Larichev
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - V. P. Baklaushev
- Federal Research and Clinical Center for Specialized Types of Medical Care and Medical Technologies, Federal Medical-Biological Agency, 115682 Moscow, Russia
| | - A. V. Filatov
- National Research Center “Institute of Immunology”, Federal Medical-Biological Agency, 115522 Moscow, Russia ,Immunology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| |
Collapse
|