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Miller NL, Raman R, Clark T, Sasisekharan R. Complexity of Viral Epitope Surfaces as Evasive Targets for Vaccines and Therapeutic Antibodies. Front Immunol 2022; 13:904609. [PMID: 35784339 PMCID: PMC9247215 DOI: 10.3389/fimmu.2022.904609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/16/2022] [Indexed: 11/29/2022] Open
Abstract
The dynamic interplay between virus and host plays out across many interacting surfaces as virus and host evolve continually in response to one another. In particular, epitope-paratope interactions (EPIs) between viral antigen and host antibodies drive much of this evolutionary race. In this review, we describe a series of recent studies examining aspects of epitope complexity that go beyond two interacting protein surfaces as EPIs are typically understood. To structure our discussion, we present a framework for understanding epitope complexity as a spectrum along a series of axes, focusing primarily on 1) epitope biochemical complexity (e.g., epitopes involving N-glycans) and 2) antigen conformational/dynamic complexity (e.g., epitopes with differential properties depending on antigen state or fold-axis). We highlight additional epitope complexity factors including epitope tertiary/quaternary structure, which contribute to epistatic relationships between epitope residues within- or adjacent-to a given epitope, as well as epitope overlap resulting from polyclonal antibody responses, which is relevant when assessing antigenic pressure against a given epitope. Finally, we discuss how these different forms of epitope complexity can limit EPI analyses and therapeutic antibody development, as well as recent efforts to overcome these limitations.
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Affiliation(s)
- Nathaniel L. Miller
- Harvard Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Rahul Raman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas Clark
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ram Sasisekharan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
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152
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Morobe JM, Pool B, Marie L, Didon D, Lambisia AW, Makori T, Mohammed KS, de Laurent ZR, Ndwiga L, Mburu MW, Moraa E, Murunga N, Musyoki J, Mwacharo J, Nyamako L, Riako D, Ephnatus P, Gambo F, Naimani J, Namulondo J, Tembo SZ, Ogendi E, Balde T, Dratibi FA, Yahaya AA, Gumede N, Achilla RA, Borus PK, Wanjohi DW, Tessema SK, Mwangangi J, Bejon P, Nokes DJ, Ochola-Oyier LI, Githinji G, Biscornet L, Agoti CN. Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021. Viruses 2022; 14:1318. [PMID: 35746789 PMCID: PMC9231335 DOI: 10.3390/v14061318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/13/2022] [Accepted: 06/03/2022] [Indexed: 12/13/2022] Open
Abstract
Seychelles, an archipelago of 155 islands in the Indian Ocean, had confirmed 24,788 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the 31st of December 2021. The first SARS-CoV-2 cases in Seychelles were reported on the 14th of March 2020, but cases remained low until January 2021, when a surge was observed. Here, we investigated the potential drivers of the surge by genomic analysis of 1056 SARS-CoV-2 positive samples collected in Seychelles between 14 March 2020 and 31 December 2021. The Seychelles genomes were classified into 32 Pango lineages, 1042 of which fell within four variants of concern, i.e., Alpha, Beta, Delta and Omicron. Sporadic cases of SARS-CoV-2 detected in Seychelles in 2020 were mainly of lineage B.1 (lineage predominantly observed in Europe) but this lineage was rapidly replaced by Beta variant starting January 2021, and which was also subsequently replaced by the Delta variant in May 2021 that dominated till November 2021 when Omicron cases were identified. Using the ancestral state reconstruction approach, we estimated that at least 78 independent SARS-CoV-2 introduction events occurred in Seychelles during the study period. The majority of viral introductions into Seychelles occurred in 2021, despite substantial COVID-19 restrictions in place during this period. We conclude that the surge of SARS-CoV-2 cases in Seychelles in January 2021 was primarily due to the introduction of more transmissible SARS-CoV-2 variants into the islands.
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Affiliation(s)
- John Mwita Morobe
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Brigitte Pool
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health, Victoria P.O. Box 52, Seychelles; (B.P.); (L.M.); (D.D.); (L.B.)
| | - Lina Marie
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health, Victoria P.O. Box 52, Seychelles; (B.P.); (L.M.); (D.D.); (L.B.)
| | - Dwayne Didon
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health, Victoria P.O. Box 52, Seychelles; (B.P.); (L.M.); (D.D.); (L.B.)
| | - Arnold W. Lambisia
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Timothy Makori
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Khadija Said Mohammed
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Zaydah R. de Laurent
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Leonard Ndwiga
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Maureen W. Mburu
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Edidah Moraa
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Nickson Murunga
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Jennifer Musyoki
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Jedida Mwacharo
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Lydia Nyamako
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Debra Riako
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Pariken Ephnatus
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Faith Gambo
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Josephine Naimani
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Joyce Namulondo
- World Health Organization-Seychelles Country Office, Victoria P.O. Box 1217, Seychelles; (J.N.); (S.Z.T.); (E.O.)
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases—Uganda Virus Research Institution (UVRI), Entebbe P.O. Box 49, Uganda
| | - Susan Zimba Tembo
- World Health Organization-Seychelles Country Office, Victoria P.O. Box 1217, Seychelles; (J.N.); (S.Z.T.); (E.O.)
| | - Edwin Ogendi
- World Health Organization-Seychelles Country Office, Victoria P.O. Box 1217, Seychelles; (J.N.); (S.Z.T.); (E.O.)
| | - Thierno Balde
- World Health Organization Regional Center for Africa, Brazzaville P.O. Box 06, Congo; (T.B.); (F.A.D.); (A.A.Y.); (N.G.); (R.A.A.)
| | - Fred Athanasius Dratibi
- World Health Organization Regional Center for Africa, Brazzaville P.O. Box 06, Congo; (T.B.); (F.A.D.); (A.A.Y.); (N.G.); (R.A.A.)
| | - Ali Ahmed Yahaya
- World Health Organization Regional Center for Africa, Brazzaville P.O. Box 06, Congo; (T.B.); (F.A.D.); (A.A.Y.); (N.G.); (R.A.A.)
| | - Nicksy Gumede
- World Health Organization Regional Center for Africa, Brazzaville P.O. Box 06, Congo; (T.B.); (F.A.D.); (A.A.Y.); (N.G.); (R.A.A.)
| | - Rachel A. Achilla
- World Health Organization Regional Center for Africa, Brazzaville P.O. Box 06, Congo; (T.B.); (F.A.D.); (A.A.Y.); (N.G.); (R.A.A.)
| | - Peter K. Borus
- World Health Organization-Kenya Country Office, Gigiri, Nairobi P.O. Box 45335, Kenya;
| | - Dorcas W. Wanjohi
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa P.O. Box 3243, Ethiopia; (D.W.W.); (S.K.T.)
| | - Sofonias K. Tessema
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa P.O. Box 3243, Ethiopia; (D.W.W.); (S.K.T.)
| | - Joseph Mwangangi
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - Philip Bejon
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - David J. Nokes
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry CV4 7AL, UK
| | - Lynette Isabella Ochola-Oyier
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
| | - George Githinji
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi P.O. Box 195-80108, Kenya
| | - Leon Biscornet
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health, Victoria P.O. Box 52, Seychelles; (B.P.); (L.M.); (D.D.); (L.B.)
| | - Charles N. Agoti
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; (A.W.L.); (T.M.); (K.S.M.); (Z.R.d.L.); (L.N.); (M.W.M.); (E.M.); (N.M.); (J.M.); (J.M.); (L.N.); (D.R.); (P.E.); (F.G.); (J.N.); (J.M.); (P.B.); (D.J.N.); (L.I.O.-O.); (G.G.); (C.N.A.)
- Department of Public Health, Pwani University, Kilifi P.O. Box 195-80108, Kenya
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Li C, Marton I, Harari D, Shemesh M, Kalchenko V, Pardo M, Schreiber G, Rudich Y. Gelatin Stabilizes Nebulized Proteins in Pulmonary Drug Delivery against COVID-19. ACS Biomater Sci Eng 2022; 8:2553-2563. [PMID: 35608934 PMCID: PMC9159517 DOI: 10.1021/acsbiomaterials.2c00419] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022]
Abstract
Delivering medication to the lungs via nebulization of pharmaceuticals is a noninvasive and efficient therapy route, particularly for respiratory diseases. The recent worldwide severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic urges the development of such therapies as an effective alternative to vaccines. The main difficulties in using inhalation therapy are the development of effective medicine and methods to stabilize the biological molecules and transfer them to the lungs efficiently following nebulization. We have developed a high-affinity angiotensin-converting enzyme 2 (ACE2) receptor-binding domain (RBD-62) that can be used as a medication to inhibit infection with SARS-CoV-2 and its variants. In this study, we established a nebulization protocol for drug delivery by inhalation using two commercial vibrating mesh (VM) nebulizers (Aerogen Solo and PARI eFlow) that generate similar mist size distribution in a size range that allows efficient deposition in the small respiratory airway. In a series of experiments, we show the high activity of RBD-62, interferon-α2 (IFN-α2), and other proteins following nebulization. The addition of gelatin significantly stabilizes the proteins and enhances the fractions of active proteins after nebulization, minimizing the medication dosage. Furthermore, hamster inhalation experiments verified the feasibility of the protocol in pulmonary drug delivery. In short, the gelatin-modified RBD-62 formulation in coordination with VM nebulizer can be used as a therapy to cure SARS-CoV-2.
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Affiliation(s)
- Chunlin Li
- Department
of Earth and Planetary Sciences, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Ira Marton
- Department
of Earth and Planetary Sciences, Weizmann
Institute of Science, Rehovot 76100, Israel
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Daniel Harari
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Maya Shemesh
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Vyacheslav Kalchenko
- Department
of Veterinary Resources, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Michal Pardo
- Department
of Earth and Planetary Sciences, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Gideon Schreiber
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Yinon Rudich
- Department
of Earth and Planetary Sciences, Weizmann
Institute of Science, Rehovot 76100, Israel
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154
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Saad-Roy CM, Metcalf CJE, Grenfell BT. Immuno-epidemiology and the predictability of viral evolution. Science 2022; 376:1161-1162. [PMID: 35679395 DOI: 10.1126/science.abn9410] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Understanding viral evolution depends on a synthesis of evolutionary biology and immuno-epidemiology.
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Affiliation(s)
- Chadi M Saad-Roy
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
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155
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Hoteit R, Yassine HM. Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences. Vaccines (Basel) 2022; 10:919. [PMID: 35746526 PMCID: PMC9230982 DOI: 10.3390/vaccines10060919] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that belongs to the coronavirus family and is the cause of coronavirus disease 2019 (COVID-19). As of May 2022, it had caused more than 500 million infections and more than 6 million deaths worldwide. Several vaccines have been produced and tested over the last two years. The SARS-CoV-2 virus, on the other hand, has mutated over time, resulting in genetic variation in the population of circulating variants during the COVID-19 pandemic. It has also shown immune-evading characteristics, suggesting that vaccinations against these variants could be potentially ineffective. The purpose of this review article is to investigate the key variants of concern (VOCs) and mutations of the virus driving the current pandemic, as well as to explore the transmission rates of SARS-CoV-2 VOCs in relation to epidemiological factors and to compare the virus's transmission rate to that of prior coronaviruses. We examined and provided key information on SARS-CoV-2 VOCs in this study, including their transmissibility, infectivity rate, disease severity, affinity for angiotensin-converting enzyme 2 (ACE2) receptors, viral load, reproduction number, vaccination effectiveness, and vaccine breakthrough.
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Affiliation(s)
- Reem Hoteit
- Clinical Research Institute, Faculty of Medicine, American University of Beirut, Beirut 110236, Lebanon;
| | - Hadi M. Yassine
- Biomedical Research Center and College of Health Sciences-QU Health, Qatar University, Doha 2713, Qatar
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156
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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: 30] [Impact Index Per Article: 15.0] [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.
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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;
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Yamasoba D, Kimura I, Nasser H, Morioka Y, Nao N, Ito J, Uriu K, Tsuda M, Zahradnik J, Shirakawa K, Suzuki R, Kishimoto M, Kosugi Y, Kobiyama K, Hara T, Toyoda M, Tanaka YL, Butlertanaka EP, Shimizu R, Ito H, Wang L, Oda Y, Orba Y, Sasaki M, Nagata K, Yoshimatsu K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Kuramochi J, Seki M, Fujiki R, Kaneda A, Shimada T, Nakada TA, Sakao S, Suzuki T, Ueno T, Takaori-Kondo A, Ishii KJ, Schreiber G, Sawa H, Saito A, Irie T, Tanaka S, Matsuno K, Fukuhara T, Ikeda T, Sato K. Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike. Cell 2022; 185:2103-2115.e19. [PMID: 35568035 DOI: 10.1101/2022.02.14.480335] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/24/2022] [Accepted: 04/26/2022] [Indexed: 05/23/2023]
Abstract
Soon after the emergence and global spread of the SARS-CoV-2 Omicron lineage BA.1, another Omicron lineage, BA.2, began outcompeting BA.1. The results of statistical analysis showed that the effective reproduction number of BA.2 is 1.4-fold higher than that of BA.1. Neutralization experiments revealed that immunity induced by COVID vaccines widely administered to human populations is not effective against BA.2, similar to BA.1, and that the antigenicity of BA.2 is notably different from that of BA.1. Cell culture experiments showed that the BA.2 spike confers higher replication efficacy in human nasal epithelial cells and is more efficient in mediating syncytia formation than the BA.1 spike. Furthermore, infection experiments using hamsters indicated that the BA.2 spike-bearing virus is more pathogenic than the BA.1 spike-bearing virus. Altogether, the results of our multiscale investigations suggest that the risk of BA.2 to global health is potentially higher than that of BA.1.
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Affiliation(s)
- Daichi Yamasoba
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Faculty of Medicine, Kobe University, Kobe, Japan
| | - Izumi Kimura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan; Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Yuhei Morioka
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Mai Kishimoto
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kouji Kobiyama
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Teppei Hara
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Mako Toyoda
- Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Yuri L Tanaka
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Erika P Butlertanaka
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Hayato Ito
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kayoko Nagata
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | | | - Motoaki Seki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ryoji Fujiki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tadanaga Shimada
- Department of Emergency and Critical Care Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Taka-Aki Nakada
- Department of Emergency and Critical Care Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Seiichiro Sakao
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takuji Suzuki
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takamasa Ueno
- Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken J Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Hirofumi Sawa
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan; Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan; Center for Animal Disease Control, University of Miyazaki, Chiba, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.
| | - Takashi Irie
- Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Keita Matsuno
- One Health Research Center, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
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158
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Yamasoba D, Kimura I, Nasser H, Morioka Y, Nao N, Ito J, Uriu K, Tsuda M, Zahradnik J, Shirakawa K, Suzuki R, Kishimoto M, Kosugi Y, Kobiyama K, Hara T, Toyoda M, Tanaka YL, Butlertanaka EP, Shimizu R, Ito H, Wang L, Oda Y, Orba Y, Sasaki M, Nagata K, Yoshimatsu K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Kuramochi J, Seki M, Fujiki R, Kaneda A, Shimada T, Nakada TA, Sakao S, Suzuki T, Ueno T, Takaori-Kondo A, Ishii KJ, Schreiber G, Sawa H, Saito A, Irie T, Tanaka S, Matsuno K, Fukuhara T, Ikeda T, Sato K. Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike. Cell 2022; 185:2103-2115.e19. [PMID: 35568035 PMCID: PMC9057982 DOI: 10.1016/j.cell.2022.04.035] [Citation(s) in RCA: 199] [Impact Index Per Article: 99.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/24/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
Soon after the emergence and global spread of the SARS-CoV-2 Omicron lineage BA.1, another Omicron lineage, BA.2, began outcompeting BA.1. The results of statistical analysis showed that the effective reproduction number of BA.2 is 1.4-fold higher than that of BA.1. Neutralization experiments revealed that immunity induced by COVID vaccines widely administered to human populations is not effective against BA.2, similar to BA.1, and that the antigenicity of BA.2 is notably different from that of BA.1. Cell culture experiments showed that the BA.2 spike confers higher replication efficacy in human nasal epithelial cells and is more efficient in mediating syncytia formation than the BA.1 spike. Furthermore, infection experiments using hamsters indicated that the BA.2 spike-bearing virus is more pathogenic than the BA.1 spike-bearing virus. Altogether, the results of our multiscale investigations suggest that the risk of BA.2 to global health is potentially higher than that of BA.1.
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Affiliation(s)
- Daichi Yamasoba
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Faculty of Medicine, Kobe University, Kobe, Japan
| | - Izumi Kimura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan; Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Yuhei Morioka
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Mai Kishimoto
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kouji Kobiyama
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Teppei Hara
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Mako Toyoda
- Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Yuri L Tanaka
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Erika P Butlertanaka
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Hayato Ito
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kayoko Nagata
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | | | - Motoaki Seki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ryoji Fujiki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tadanaga Shimada
- Department of Emergency and Critical Care Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Taka-Aki Nakada
- Department of Emergency and Critical Care Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Seiichiro Sakao
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takuji Suzuki
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takamasa Ueno
- Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken J Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Hirofumi Sawa
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan; Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan; Center for Animal Disease Control, University of Miyazaki, Chiba, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.
| | - Takashi Irie
- Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Keita Matsuno
- One Health Research Center, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
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159
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A comprehensive review of Artificial Intelligence and Network based approaches to drug repurposing in Covid-19. Biomed Pharmacother 2022; 153:113350. [PMID: 35777222 PMCID: PMC9236981 DOI: 10.1016/j.biopha.2022.113350] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022] Open
Abstract
Conventional drug discovery and development is tedious and time-taking process; because of which it has failed to keep the required pace to mitigate threats and cater demands of viral and re-occurring diseases, such as Covid-19. The main reasons of this delay in traditional drug development are: high attrition rates, extensive time requirements, and huge financial investment with significant risk. The effective solution to de novo drug discovery is drug repurposing. Previous studies have shown that the network-based approaches and analysis are versatile platform for repurposing as the network biology is used to model the interactions between variety of biological concepts. Herein, we provide a comprehensive background of machine learning and deep learning in drug repurposing while specifically focusing on the applications of network-based approach to drug repurposing in Covid-19, data sources, and tools used. Furthermore, use of network proximity, network diffusion, and AI on network-based drug repurposing for Covid-19 is well-explained. Finally, limitations of network-based approaches in general and specific to network are stated along with future recommendations for better network-based models.
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160
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Yang H, Liu P, Zhang Y, Du T, Zhou Y, Lu S, Peng X. Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. MedComm (Beijing) 2022; 3:e129. [PMID: 35434714 PMCID: PMC8994548 DOI: 10.1002/mco2.129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 12/19/2022] Open
Abstract
In view of the rapid development of the COVID-19 pandemic and SARS-CoV-2 mutation, we characterized the emerging SARS-CoV-2 variants of concern (VOCs) by both bioinformatics methods and experiments. The representative genomic sequences of SARS-CoV-2 VOCs were first downloaded from NCBI, including the prototypic strain, Alpha (B.1.1.7) strain, Beta (B.1.351) strain, Delta (B.1.617.2), and Omicron (B1.1.529) strain. Bioinformatics analysis revealed that the D614G mutation led to formation of a protruding spike (S) in the tertiary structure of spike protein, which could be responsible for the enhanced binding to angiotensin-converting enzyme 2 (ACE2) receptor. The epitope analysis further showed that the S protein antigenicity of the Omicron variant changed dramatically, which was possibly associated with its enhanced ability of immune escape. To verify the bioinformatics results, we performed experiments of pseudovirus infection and protein affinity assay. Notably, we found that the spike protein of Omicron variant showed the weakest infectivity and binding ability among all tested strains. Finally, we also proved this through virus infection experiments, and found that the cytotoxicity of Omicron seems to be not strong enough. The results in this study provide guidelines for prevention and control of COVID-19.
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Affiliation(s)
- Hao Yang
- Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeKunmingYunnanChina
| | - Penghui Liu
- Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeKunmingYunnanChina
| | - Yong Zhang
- Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeKunmingYunnanChina
| | - Tingfu Du
- Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeKunmingYunnanChina
| | - Yanan Zhou
- Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeKunmingYunnanChina
| | - Shuaiyao Lu
- Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeKunmingYunnanChina
| | - Xiaozhong Peng
- Institute of Medical BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeKunmingYunnanChina
- State Key Laboratory of Medical Molecular BiologyDepartment of Molecular Biology and BiochemistryInstitute of Basic Medical SciencesMedical Primate Research CenterNeuroscience CenterChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
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161
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Tian D, Sun Y, Xu H, Ye Q. The emergence and epidemic characteristics of the highly mutated SARS-CoV-2 Omicron variant. J Med Virol 2022; 94:2376-2383. [PMID: 35118687 PMCID: PMC9015498 DOI: 10.1002/jmv.27643] [Citation(s) in RCA: 268] [Impact Index Per Article: 134.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/07/2022]
Abstract
Recently, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (B.1.1.529) was first identified in Botswana in November 2021. It was first reported to the World Health Organization (WHO) on November 24. On November 26, 2021, according to the advice of scientists who are part of the WHO's Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE), the WHO defined the strain as a variant of concern (VOC) and named it Omicron. Compared to the other four VOCs (Alpha, Beta, Gamma, and Delta), the Omicron variant was the most highly mutated strain, with 50 mutations accumulated throughout the genome. The Omicron variant contains at least 32 mutations in the spike protein, which was twice as many as the Delta variant. Studies have shown that carrying many mutations can increase infectivity and immune escape of the Omicron variant compared with the early wild-type strain and the other four VOCs. The Omicron variant is becoming the dominant strain in many countries worldwide and brings new challenges to preventing and controlling coronavirus disease 2019 (COVID-19). The current review article aims to analyze and summarize information data about the biological characteristics of amino acid mutations, the epidemic characteristics, immune escape, and vaccine reactivity of the Omicron variant, hoping to provide a scientific reference for monitoring, prevention, and vaccine development strategies for the Omicron variant.
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Affiliation(s)
- Dandan Tian
- Department of clinical laboratoryNational Clinical Research Center for Child Health, National Children's Regional Medical Center, The Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - Yanhong Sun
- Department of clinical laboratoryNational Clinical Research Center for Child Health, National Children's Regional Medical Center, The Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - Huihong Xu
- Department of clinical laboratoryNational Clinical Research Center for Child Health, National Children's Regional Medical Center, The Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - Qing Ye
- Department of clinical laboratoryNational Clinical Research Center for Child Health, National Children's Regional Medical Center, The Children's HospitalZhejiang University School of MedicineHangzhouChina
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Hsieh CL, McLellan JS. Protein engineering responses to the COVID-19 pandemic. Curr Opin Struct Biol 2022; 74:102385. [PMID: 35533563 PMCID: PMC9075828 DOI: 10.1016/j.sbi.2022.102385] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 02/06/2023]
Abstract
Antigen design guided by high-resolution viral glycoprotein structures has successfully generated diverse vaccine candidates for COVID-19. Using conjugation systems to combine antigen design with computationally optimized nanoparticles, researchers have been able to display multivalent antigens with beneficial substitutions that elicited robust humoral immunity with enhanced neutralization potency and breadth. Here, we discuss strategies that have been used for structure-based design and nanoparticle display to develop COVID-19 vaccine candidates as well as potential next-generation vaccine candidates to protect against SARS-CoV-2 variants and other coronaviruses that emerge into the human population.
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163
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Gerges D, Kapps S, Hernández-Carralero E, Freire R, Aiad M, Schmidt S, Winnicki W, Reiter T, Pajenda S, Schmidt A, Sunder-Plassmann G, Wagner L. Vaccination with BNT162b2 and ChAdOx1 nCoV-19 Induces Cross-Reactive Anti-RBD IgG against SARS-CoV-2 Variants including Omicron. Viruses 2022; 14:1181. [PMID: 35746653 PMCID: PMC9231407 DOI: 10.3390/v14061181] [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: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023] Open
Abstract
SARS-CoV-2 variants of concern (VOCs) have caused a significant increase in infections worldwide. Despite high vaccination rates in industrialized countries, the fourth VOC, Omicron, has outpaced the Delta variant and is causing breakthrough infections in individuals with two booster vaccinations. While the magnitude of morbidity and lethality is lower in Omicron, the infection rate and global spread are rapid. Using a specific IgG multipanel-ELISA with the spike protein’s receptor-binding domain (RBD) from recombinant Alpha, Gamma, Delta, and Omicron variants, sera from health-care workers from the Medical University of Vienna were tested pre-pandemic and post-vaccination (BNT162b2; ChAdOx1 nCoV-19). The cohort was continuously monitored by SARS-CoV-2 testing and commercial nucleocapsid IgG ELISA. RBD IgG ELISA showed significantly lower reactivity against the Omicron-RBD compared to the Alpha variant in all individuals (p < 0.001). IgG levels were independent of sex, but were significantly higher in BNT162b2 recipients <45 years of age for Alpha, Gamma, and Delta (p < 0.001; p = 0.040; p = 0.004, respectively). Pre-pandemic cross-reactive anti-Omicron IgG was detected in 31 individuals and was increased 8.78-fold after vaccination, regardless of vaccine type. The low anti-RBD Omicron IgG level could explain the breakthrough infections and their presence could also contribute to a milder COVID-19 course by cross-reactivity and broadening the adaptive immunity.
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Affiliation(s)
- Daniela Gerges
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (S.K.); (M.A.); (S.S.); (W.W.); (T.R.); (S.P.); (A.S.); (G.S.-P.)
| | - Sebastian Kapps
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (S.K.); (M.A.); (S.S.); (W.W.); (T.R.); (S.P.); (A.S.); (G.S.-P.)
| | - Esperanza Hernández-Carralero
- Unidad de Investigacion, Hospital Universitario de Canarias-FIISC, 38320 La Laguna, Spain; (E.H.-C.); (R.F.)
- Instituto de Tecnologías Biomedicas, Universidad de La Laguna, 38200 La Laguna, Spain
| | - Raimundo Freire
- Unidad de Investigacion, Hospital Universitario de Canarias-FIISC, 38320 La Laguna, Spain; (E.H.-C.); (R.F.)
- Instituto de Tecnologías Biomedicas, Universidad de La Laguna, 38200 La Laguna, Spain
- Universidad Fernando Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
| | - Monika Aiad
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (S.K.); (M.A.); (S.S.); (W.W.); (T.R.); (S.P.); (A.S.); (G.S.-P.)
| | - Sophie Schmidt
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (S.K.); (M.A.); (S.S.); (W.W.); (T.R.); (S.P.); (A.S.); (G.S.-P.)
| | - Wolfgang Winnicki
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (S.K.); (M.A.); (S.S.); (W.W.); (T.R.); (S.P.); (A.S.); (G.S.-P.)
| | - Thomas Reiter
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (S.K.); (M.A.); (S.S.); (W.W.); (T.R.); (S.P.); (A.S.); (G.S.-P.)
| | - Sahra Pajenda
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (S.K.); (M.A.); (S.S.); (W.W.); (T.R.); (S.P.); (A.S.); (G.S.-P.)
| | - Alice Schmidt
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (S.K.); (M.A.); (S.S.); (W.W.); (T.R.); (S.P.); (A.S.); (G.S.-P.)
| | - Gere Sunder-Plassmann
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (S.K.); (M.A.); (S.S.); (W.W.); (T.R.); (S.P.); (A.S.); (G.S.-P.)
| | - Ludwig Wagner
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (D.G.); (S.K.); (M.A.); (S.S.); (W.W.); (T.R.); (S.P.); (A.S.); (G.S.-P.)
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164
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Zahradník J, Nunvar J, Schreiber G. Perspectives: SARS-CoV-2 Spike Convergent Evolution as a Guide to Explore Adaptive Advantage. Front Cell Infect Microbiol 2022; 12:748948. [PMID: 35711666 PMCID: PMC9197234 DOI: 10.3389/fcimb.2022.748948] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 04/19/2022] [Indexed: 01/22/2023] Open
Abstract
Viruses rapidly co-evolve with their hosts. The 9 million sequenced SARS-CoV-2 genomes by March 2022 provide a detailed account of viral evolution, showing that all amino acids have been mutated many times. However, only a few became prominent in the viral population. Here, we investigated the emergence of the same mutations in unrelated parallel lineages and the extent of such convergent evolution on the molecular level in the spike (S) protein. We found that during the first phase of the pandemic (until mid 2021, before mass vaccination) 31 mutations evolved independently ≥3-times within separated lineages. These included all the key mutations in SARS-CoV-2 variants of concern (VOC) at that time, indicating their fundamental adaptive advantage. The omicron added many more mutations not frequently seen before, which can be attributed to the synergistic nature of these mutations, which is more difficult to evolve. The great majority (24/31) of S-protein mutations under convergent evolution tightly cluster in three functional domains; N-terminal domain, receptor-binding domain, and Furin cleavage site. Furthermore, among the S-protein receptor-binding motif mutations, ACE2 affinity-improving substitutions are favoured. Next, we determined the mutation space in the S protein that has been covered by SARS-CoV-2. We found that all amino acids that are reachable by single nucleotide changes have been probed multiple times in early 2021. The substitutions requiring two nucleotide changes have recently (late 2021) gained momentum and their numbers are increasing rapidly. These provide a large mutation landscape for SARS-CoV-2 future evolution, on which research should focus now.
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Affiliation(s)
- Jiri Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jaroslav Nunvar
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czechia
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Vestec, Czechia
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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165
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Riddell AC, Kele B, Harris K, Bible J, Murphy M, Dakshina S, Storey N, Owoyemi D, Pade C, Gibbons JM, Harrington D, Alexander E, McKnight Á, Cutino-Moguel T. Generation of Novel Severe Acute Respiratory Syndrome Coronavirus 2 Variants on the B.1.1.7 Lineage in 3 Patients With Advanced Human Immunodeficiency Virus-1 Disease. Clin Infect Dis 2022; 75:2016-2018. [PMID: 35616095 PMCID: PMC9213850 DOI: 10.1093/cid/ciac409] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Indexed: 01/17/2023] Open
Abstract
The emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is of public health concern in case of vaccine escape. Described are 3 patients with advanced human immunodeficiency virus (HIV)-1 and chronic SARS-CoV-2 infection in whom there is evidence of selection and persistence of novel mutations that are associated with increased transmissibility and immune escape.
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Affiliation(s)
- Anna C Riddell
- Correspondence: A. C. Riddell, Department of Infection, 3rd Floor Pathology and Pharmacy Building, Royal London Hospital, 80 Newark Street, London, UK, E1 2ES ()
| | - Beatrix Kele
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
| | - Kathryn Harris
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
| | - Jon Bible
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
| | - Maurice Murphy
- Department of Infection and Immunity, Barts Health NHS Trust, London, United Kingdom
| | - Subathira Dakshina
- Department of Infection and Immunity, Barts Health NHS Trust, London, United Kingdom
| | - Nathaniel Storey
- Microbiology, Virology, and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Dola Owoyemi
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
| | - Corinna Pade
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Joseph M Gibbons
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - David Harrington
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
| | - Eliza Alexander
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
| | - Áine McKnight
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Teresa Cutino-Moguel
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
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166
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Dang S, Ren L, Wang J. Functional mutations of SARS-CoV-2: implications to viral transmission, pathogenicity and immune escape. Chin Med J (Engl) 2022; 135:1213-1222. [PMID: 35788093 PMCID: PMC9337262 DOI: 10.1097/cm9.0000000000002158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Indexed: 11/27/2022] Open
Abstract
ABSTRACT The pandemic of coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to major public health challenges globally. The increasing viral lineages identified indicate that the SARS-CoV-2 genome is evolving at a rapid rate. Viral genomic mutations may cause antigenic drift or shift, which are important ways by which SARS-CoV-2 escapes the human immune system and changes its transmissibility and virulence. Herein, we summarize the functional mutations in SARS-CoV-2 genomes to characterize its adaptive evolution to inform the development of vaccination, treatment as well as control and intervention measures.
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Affiliation(s)
- Shengyuan Dang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lili Ren
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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167
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Melanker O, Goloubinoff P, Schreiber G. In vitro evolution of uracil glycosylase towards DnaKJ and GroEL binding evolves different misfolded states. J Mol Biol 2022; 434:167627. [PMID: 35597550 DOI: 10.1016/j.jmb.2022.167627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022]
Abstract
Natural evolution is driven by random mutations that improve fitness. In vitro evolution mimics this process, however, on a short time-scale and is driven by the given bait. Here, we used directed in vitro evolution of a random mutant library of Uracil glycosylase (eUNG) displayed on yeast surface to select for binding to chaperones GroEL, DnaK+DnaJ+ATP (DnaKJ) or E.coli cell extract (CE), using binding to the eUNG inhibitor Ugi as probe for native fold. The CE selected population was further divided to Ugi binders (+U) or non-binders (-U). The aim here was to evaluate the sequence space and physical state of the evolved protein binding the different baits. We found that GroEL, DnaKJ and CE-U select and enrich for mutations causing eUNG to misfold, with the three being enriched in mutations in buried and conserved positions, with a tendency to increase positive charge. Still, each selection had its own trajectory, with GroEL and CE-U selecting mutants highly sensitive to protease cleavage while DnaKJ selected partially structured misfolded species with a tendency to refold, making them less sensitive to proteases. More general, our results show that GroEL has a higher tendency to purge promiscuous misfolded protein mutants from the system, while DnaKJ binds misfolding-prone mutant species that are, upon chaperone release, more likely to natively refold. CE-U shares some of the properties of GroEL- and DnaKJ-selected populations, while harboring also unique properties that can be explained by the presence of additional chaperones in CE, such as Trigger factor, HtpG and ClpB.
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Affiliation(s)
- Oran Melanker
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Lausanne University, 1015 Lausanne, Switzerland
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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168
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Roessler J, Pich D, Albanese M, Wratil PR, Krähling V, Hellmuth JC, Scherer C, von Bergwelt-Baildon M, Becker S, Keppler OT, Brisson A, Zeidler R, Hammerschmidt W. Quantitation of SARS-CoV-2 neutralizing antibodies with a virus-free, authentic test. PNAS NEXUS 2022; 1:pgac045. [PMID: 36382127 PMCID: PMC9645495 DOI: 10.1093/pnasnexus/pgac045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/02/2022] [Accepted: 04/11/2022] [Indexed: 06/16/2023]
Abstract
Neutralizing antibodies (NAbs), and their concentration in sera of convalescents and vaccinees are a correlate of protection from COVID-19. The antibody concentrations in clinical samples that neutralize SARS-CoV-2 are difficult and very cumbersome to assess with conventional virus neutralization tests (cVNTs), which require work with the infectious virus and biosafety level 3 containment precautions. Alternative virus neutralization tests currently in use are mostly surrogate tests based on direct or competitive enzyme immunoassays or use viral vectors with the spike protein as the single structural component of SARS-CoV-2. To overcome these obstacles, we developed a virus-free, safe and very fast (4.5 h) in vitro diagnostic test based on engineered yet authentic SARS-CoV-2 virus-like-particles (VLPs). They share all features of the original SARS-CoV-2 but lack the viral RNA genome and thus are non-infectious. NAbs induced by infection or vaccination, but also potentially neutralizing monoclonal antibodies can be reliably quantified and assessed with ease and within hours with our test, because they interfere and block the ACE2-mediated uptake of VLPs by recipient cells. Results from the VLP neutralization test (VLPNT) showed excellent specificity and sensitivity and correlated very well with a cVNT using fully infectious SARS-CoV-2. The results also demonstrated the reduced neutralizing capacity of COVID-19 vaccinee sera against variants of concern of SARS-CoV-2 including omicron B.1.1.529, BA.1.
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Affiliation(s)
- Johannes Roessler
- Department of Otorhinolaryngology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Dagmar Pich
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Manuel Albanese
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paul R Wratil
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Verena Krähling
- Institute of Virology, Faculty of Medicine, Philipps-Universität Marburg, Marburg, Germany
- German Centre for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Marburg, Germany
| | - Johannes C Hellmuth
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Clemens Scherer
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Medicine I, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael von Bergwelt-Baildon
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- German Cancer Consortium (DKTK), Munich, Germany
| | - Stephan Becker
- Institute of Virology, Faculty of Medicine, Philipps-Universität Marburg, Marburg, Germany
- German Centre for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Marburg, Germany
| | - Oliver T Keppler
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Alain Brisson
- UMR-CBMN CNRS-University of Bordeaux-INP, Pessac, France
| | - Reinhard Zeidler
- Department of Otorhinolaryngology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
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169
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Sharma V, Rai H, Gautam DNS, Prajapati PK, Sharma R. Emerging evidence on Omicron (B.1.1.529) SARS-CoV-2 variant. J Med Virol 2022; 94:1876-1885. [PMID: 35083761 PMCID: PMC9015596 DOI: 10.1002/jmv.27626] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 11/24/2022]
Abstract
COVID's Omicron variant has sparked a slew of concerns across the globe. This review aims to provide a brief overview of what we know about the Omicron variant right now. The new variant has been discovered in 149 countries across all six World Health Organization (WHO) regions since its discovery in South Africa on November 24, 2021 and became the dominant variant in the country in less than 3 weeks. The WHO has warned that the B.1.1.529 variant is spreading at an unprecedented rate, and has urged countries to prepare for the worst. Over the course of this time, researchers from Africa and around the world have uncovered a wealth of information about the virus's epidemiology and biological properties. Case numbers are increasing exponentially in hard-hit areas such as South Africa, United Kingdom, and USA (overtaking the delta variant), implying that the variant is highly transmissible. Initial research has provided some insights into the efficacy of vaccines against the Omicron variant and whether it produces major illness, however, much remains unknown, and additional work is needed to investigate what the initial reports represent in real-world situations.
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Affiliation(s)
- Vineet Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical SciencesBanaras Hindu UniversityVaranasiIndia
| | - Himanshu Rai
- DST‐Centre for Interdisciplinary Mathematical Sciences, Institute of ScienceBanaras Hindu UniversityVaranasiIndia
| | - Dev N. S. Gautam
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical SciencesBanaras Hindu UniversityVaranasiIndia
| | - Pradeep K. Prajapati
- Department of Rasa Shastra and Bhaishajya KalpanaAll India Institute of AyurvedaNew DelhiIndia
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical SciencesBanaras Hindu UniversityVaranasiIndia
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170
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Gunnels TF, Stranford DM, Mitrut RE, Kamat NP, Leonard JN. Elucidating Design Principles for Engineering Cell-Derived Vesicles to Inhibit SARS-CoV-2 Infection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200125. [PMID: 35388947 PMCID: PMC9106922 DOI: 10.1002/smll.202200125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/21/2022] [Indexed: 06/14/2023]
Abstract
The ability of pathogens to develop drug resistance is a global health challenge. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents an urgent need wherein several variants of concern resist neutralization by monoclonal antibody (mAb) therapies and vaccine-induced sera. Decoy nanoparticles-cell-mimicking particles that bind and inhibit virions-are an emerging class of therapeutics that may overcome such drug resistance challenges. To date, quantitative understanding as to how design features impact performance of these therapeutics is lacking. To address this gap, this study presents a systematic, comparative evaluation of various biologically derived nanoscale vesicles, which may be particularly well suited to sustained or repeated administration in the clinic due to low toxicity, and investigates their potential to inhibit multiple classes of model SARS-CoV-2 virions. A key finding is that such particles exhibit potent antiviral efficacy across multiple manufacturing methods, vesicle subclasses, and virus-decoy binding affinities. In addition, these cell-mimicking vesicles effectively inhibit model SARS-CoV-2 variants that evade mAbs and recombinant protein-based decoy inhibitors. This study provides a foundation of knowledge that may guide the design of decoy nanoparticle inhibitors for SARS-CoV-2 and other viral infections.
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Affiliation(s)
- Taylor F. Gunnels
- Department of Biomedical EngineeringNorthwestern UniversityEvanstonIL60208USA
- Center for Synthetic BiologyNorthwestern UniversityEvanstonIL60208USA
| | - Devin M. Stranford
- Center for Synthetic BiologyNorthwestern UniversityEvanstonIL60208USA
- Department of Chemical and Biological EngineeringNorthwestern UniversityEvanstonIL60208USA
| | - Roxana E. Mitrut
- Center for Synthetic BiologyNorthwestern UniversityEvanstonIL60208USA
- Department of Chemical and Biological EngineeringNorthwestern UniversityEvanstonIL60208USA
| | - Neha P. Kamat
- Department of Biomedical EngineeringNorthwestern UniversityEvanstonIL60208USA
- Center for Synthetic BiologyNorthwestern UniversityEvanstonIL60208USA
- Chemistry of Life Processes InstituteNorthwestern UniversityEvanstonIL60208USA
| | - Joshua N. Leonard
- Center for Synthetic BiologyNorthwestern UniversityEvanstonIL60208USA
- Department of Chemical and Biological EngineeringNorthwestern UniversityEvanstonIL60208USA
- Chemistry of Life Processes InstituteNorthwestern UniversityEvanstonIL60208USA
- Robert H. Lurie Comprehensive Cancer CenterNorthwestern UniversityEvanstonIL60208USA
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171
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Strohl WR, Ku Z, An Z, Carroll SF, Keyt BA, Strohl LM. Passive Immunotherapy Against SARS-CoV-2: From Plasma-Based Therapy to Single Potent Antibodies in the Race to Stay Ahead of the Variants. BioDrugs 2022; 36:231-323. [PMID: 35476216 PMCID: PMC9043892 DOI: 10.1007/s40259-022-00529-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic is now approaching 2 years old, with more than 440 million people infected and nearly six million dead worldwide, making it the most significant pandemic since the 1918 influenza pandemic. The severity and significance of SARS-CoV-2 was recognized immediately upon discovery, leading to innumerable companies and institutes designing and generating vaccines and therapeutic antibodies literally as soon as recombinant SARS-CoV-2 spike protein sequence was available. Within months of the pandemic start, several antibodies had been generated, tested, and moved into clinical trials, including Eli Lilly's bamlanivimab and etesevimab, Regeneron's mixture of imdevimab and casirivimab, Vir's sotrovimab, Celltrion's regdanvimab, and Lilly's bebtelovimab. These antibodies all have now received at least Emergency Use Authorizations (EUAs) and some have received full approval in select countries. To date, more than three dozen antibodies or antibody combinations have been forwarded into clinical trials. These antibodies to SARS-CoV-2 all target the receptor-binding domain (RBD), with some blocking the ability of the RBD to bind human ACE2, while others bind core regions of the RBD to modulate spike stability or ability to fuse to host cell membranes. While these antibodies were being discovered and developed, new variants of SARS-CoV-2 have cropped up in real time, altering the antibody landscape on a moving basis. Over the past year, the search has widened to find antibodies capable of neutralizing the wide array of variants that have arisen, including Alpha, Beta, Gamma, Delta, and Omicron. The recent rise and dominance of the Omicron family of variants, including the rather disparate BA.1 and BA.2 variants, demonstrate the need to continue to find new approaches to neutralize the rapidly evolving SARS-CoV-2 virus. This review highlights both convalescent plasma- and polyclonal antibody-based approaches as well as the top approximately 50 antibodies to SARS-CoV-2, their epitopes, their ability to bind to SARS-CoV-2 variants, and how they are delivered. New approaches to antibody constructs, including single domain antibodies, bispecific antibodies, IgA- and IgM-based antibodies, and modified ACE2-Fc fusion proteins, are also described. Finally, antibodies being developed for palliative care of COVID-19 disease, including the ramifications of cytokine release syndrome (CRS) and acute respiratory distress syndrome (ARDS), are described.
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Affiliation(s)
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
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172
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Guo Y, Han J, Zhang Y, He J, Yu W, Zhang X, Wu J, Zhang S, Kong Y, Guo Y, Lin Y, Zhang J. SARS-CoV-2 Omicron Variant: Epidemiological Features, Biological Characteristics, and Clinical Significance. Front Immunol 2022; 13:877101. [PMID: 35572518 PMCID: PMC9099228 DOI: 10.3389/fimmu.2022.877101] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/07/2022] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 Omicron (B.1.1529) variant was designated as a variant of concern (VOC) by the World Health Organization (WHO) on November 26, 2021. Within two months, it had replaced the Delta variant and had become the dominant circulating variant around the world. The Omicron variant possesses an unprecedented number of mutations, especially in the spike protein, which may be influencing its biological and clinical aspects. Preliminary studies have suggested that increased transmissibility and the reduced protective effects of neutralizing antibodies have contributed to the rapid spread of this variant, posing a significant challenge to control the coronavirus disease 2019 (COVID-19) pandemic. There is, however, a silver lining for this wave of the Omicron variant. A lower risk of hospitalization and mortality has been observed in prevailing countries. Booster vaccination also has ameliorated a significant reduction in neutralization. Antiviral drugs are minimally influenced. Moreover, the functions of Fc-mediated and T-cell immunity have been retained to a great extent, both of which play a key role in preventing severe disease.
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Affiliation(s)
- Yifei Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiajia Han
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yao Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jingjing He
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Weien Yu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xueyun Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jingwen Wu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shenyan Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yide Kong
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yue Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yanxue Lin
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiming Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China
- Department of Infectious Diseases, Jing’An Branch of Huashan Hospital, Fudan University, Shanghai, China
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Alkhatib M, Salpini R, Carioti L, Ambrosio FA, D’Anna S, Duca L, Costa G, Bellocchi MC, Piermatteo L, Artese A, Santoro MM, Alcaro S, Svicher V, Ceccherini-Silberstein F. Update on SARS-CoV-2 Omicron Variant of Concern and Its Peculiar Mutational Profile. Microbiol Spectr 2022; 10:e0273221. [PMID: 35352942 PMCID: PMC9045195 DOI: 10.1128/spectrum.02732-21] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/11/2022] [Indexed: 12/24/2022] Open
Abstract
The process of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversification is still ongoing and has very recently led to the emergence of a new variant of concern (VOC), defined as Omicron or B.1.1.529. Omicron VOC is the most divergent variant identified so far and has generated immediate concern for its potential capability to increase SARS-CoV-2 transmissibility and, more worryingly, to escape therapeutic and vaccine-induced antibodies. Nevertheless, a clear definition of the Omicron VOC mutational spectrum is still missing. Herein, we provide a comprehensive definition and functional characterization (in terms of infectivity and/or antigenicity) of mutations characterizing the Omicron VOC. In particular, 887,475 SARS-CoV-2 Omicron VOC whole-genome sequences were retrieved from the GISAID database and used to precisely define its specific patterns of mutations across the different viral proteins. In addition, the functional characterization of Omicron VOC spike mutations was finely discussed according to published manuscripts. Lastly, residues characterizing the Omicron VOC and the previous four VOCs (Alpha, Beta, Gamma, and Delta) were mapped on the three-dimensional structure of the SARS-CoV-2 spike protein to assess their localization in the different spike domains. Overall, our study will assist with deciphering the Omicron VOC mutational profile and will shed more light on its clinical implications. This is critical considering that Omicron VOC is currently the predominant variant worldwide. IMPORTANCE The Omicron variant of concern (VOC) has a peculiar spectrum of mutations characterized by the acquisition of mutations or deletions rarely detected in previously identified variants, particularly in the spike glycoprotein. Such mutations, mostly residing in the receptor-binding domain, could play a pivotal role in enhancing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity (by increasing binding affinity for ACE2), jeopardizing spike recognition by therapeutic and vaccine-induced antibodies and causing diagnostic assay failure. To our knowledge, this is one of the first exhaustive descriptions of newly emerged mutations underlying the Omicron VOC and its biological and clinical implications.
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Affiliation(s)
- Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Romina Salpini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Francesca Alessandra Ambrosio
- Dipartimento di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Campus S. Venuta, Catanzaro, Italy
| | - Stefano D’Anna
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Leonardo Duca
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Campus S. Venuta, Catanzaro, Italy
- Net4Science Academic Spin-Off, Università Magna Græcia di Catanzaro, Campus S. Venuta, Catanzaro, Italy
| | | | - Lorenzo Piermatteo
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Campus S. Venuta, Catanzaro, Italy
- Net4Science Academic Spin-Off, Università Magna Græcia di Catanzaro, Campus S. Venuta, Catanzaro, Italy
| | | | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Campus S. Venuta, Catanzaro, Italy
- Net4Science Academic Spin-Off, Università Magna Græcia di Catanzaro, Campus S. Venuta, Catanzaro, Italy
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Bartsch YC, Tong X, Kang J, Avendaño MJ, Serrano EF, García-Salum T, Pardo-Roa C, Riquelme A, Cai Y, Renzi I, Stewart-Jones G, Chen B, Medina RA, Alter G. Omicron variant Spike-specific antibody binding and Fc activity are preserved in recipients of mRNA or inactivated COVID-19 vaccines. Sci Transl Med 2022; 14:eabn9243. [PMID: 35289637 PMCID: PMC8995028 DOI: 10.1126/scitranslmed.abn9243] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/07/2022] [Indexed: 01/05/2023]
Abstract
The Omicron variant of SARS-CoV-2 has been shown to evade neutralizing antibodies elicited by vaccination or infection. Despite the global spread of the Omicron variant, even among highly vaccinated populations, death rates have not increased concomitantly. These data suggest that immune mechanisms beyond antibody-mediated virus neutralization may protect against severe disease. In addition to neutralizing pathogens, antibodies contribute to control and clearance of infections through Fc effector mechanisms. Here, we probed the ability of vaccine-induced antibodies to drive Fc effector activity against the Omicron variant using samples from individuals receiving one of three SARS-CoV-2 vaccines. Despite a substantial loss of IgM, IgA, and IgG binding to the Omicron variant receptor binding domain (RBD) in samples from individuals receiving BNT162b2, mRNA-1273, and CoronaVac vaccines, stable binding was maintained against the full-length Omicron Spike protein. Compromised RBD binding IgG was accompanied by a loss of RBD-specific antibody Fcγ receptor (FcγR) binding in samples from individuals who received the CoronaVac vaccine, but RBD-specific FcγR2a and FcγR3a binding was preserved in recipients of mRNA vaccines. Conversely, Spike protein-specific antibodies exhibited persistent but reduced binding to FcγRs across all three vaccines, although higher binding was observed in samples from recipients of mRNA vaccines. This was associated with preservation of FcγR2a and FcγR3a binding antibodies and maintenance of Spike protein-specific antibody-dependent natural killer cell activation. Thus, despite the loss of Omicron neutralization, vaccine-induced Spike protein-specific antibodies continue to drive Fc effector functions, suggesting a capacity for extraneutralizing antibodies to contribute to disease control.
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Affiliation(s)
| | - Xin Tong
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA 02138, USA
| | - Jaewon Kang
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA 02138, USA
| | - María José Avendaño
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
| | - Eileen F. Serrano
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
| | - Tamara García-Salum
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
- Advanced Interdisciplinary Rehabilitation Register (AIRR) – COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
| | - Catalina Pardo-Roa
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
- Advanced Interdisciplinary Rehabilitation Register (AIRR) – COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
| | - Arnoldo Riquelme
- Advanced Interdisciplinary Rehabilitation Register (AIRR) – COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
- Department of Health Sciences, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
| | - Yongfei Cai
- Division of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rafael A. Medina
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
- Advanced Interdisciplinary Rehabilitation Register (AIRR) – COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA 02138, USA
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175
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Geng Q, Shi K, Ye G, Zhang W, Aihara H, Li F. Structural Basis for Human Receptor Recognition by SARS-CoV-2 Omicron Variant BA.1. J Virol 2022; 96:e0024922. [PMID: 35343765 PMCID: PMC9044962 DOI: 10.1128/jvi.00249-22] [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: 02/04/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
The highly contagious and fast-spreading omicron variant of SARS-CoV-2 infects the respiratory tracts efficiently. The receptor-binding domain (RBD) of the omicron spike protein recognizes human angiotensin-converting enzyme 2 (ACE2) as its receptor and plays a critical role in the tissue tropism of SARS-CoV-2. Here, we showed that the omicron RBD (strain BA.1) binds to ACE2 more strongly than does the prototypic RBD from the original Wuhan strain. We also measured how individual omicron mutations affect ACE2 binding. We further determined the crystal structure of the omicron RBD (engineered to facilitate crystallization) complexed with ACE2 at 2.6 Å. The structure shows that omicron mutations caused significant structural rearrangements of two mutational hot spots at the RBD/ACE2 interface, elucidating how each omicron mutation affects ACE2 binding. The enhanced ACE2 binding by the omicron RBD may facilitate the omicron variant's infection of the respiratory tracts where ACE2 expression level is low. Our study provides insights into the receptor recognition and tissue tropism of the omicron variant. IMPORTANCE Despite the scarcity of the SARS-CoV-2 receptor-human angiotensin-converting enzyme 2 (ACE2)-in the respiratory tract, the omicron variant efficiently infects the respiratory tract, causing rapid and widespread infections of COVID-19. The omicron variant contains extensive mutations in the receptor-binding domain (RBD) of its spike protein that recognizes human ACE2. Here, using a combination of biochemical and X-ray crystallographic approaches, we showed that the omicron RBD binds to ACE2 with enhanced affinity and also elucidated the role of each of the omicron mutations in ACE2 binding. The enhanced ACE2 binding by the omicron RBD may contribute to the omicron variant's new viral tropism in the respiratory tract despite the low level of ACE2 expression in the tissue. These findings help us to understand tissue tropism of the omicron variant and shed light on the molecular evolution of SARS-CoV-2.
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Affiliation(s)
- Qibin Geng
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Saint Paul, Minnesota, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Gang Ye
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Saint Paul, Minnesota, USA
| | - Wei Zhang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Saint Paul, Minnesota, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Fang Li
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Saint Paul, Minnesota, USA
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176
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Ballesteros-Sanabria L, Pelaez-Prestel HF, Ras-Carmona A, Reche PA. Resilience of Spike-Specific Immunity Induced by COVID-19 Vaccines against SARS-CoV-2 Variants. Biomedicines 2022; 10:biomedicines10050996. [PMID: 35625733 PMCID: PMC9138591 DOI: 10.3390/biomedicines10050996] [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: 04/07/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 12/10/2022] Open
Abstract
The outbreak of SARS-CoV-2 leading to the declaration of the COVID-19 global pandemic has led to the urgent development and deployment of several COVID-19 vaccines. Many of these new vaccines, including those based on mRNA and adenoviruses, are aimed to generate neutralizing antibodies against the spike glycoprotein, which is known to bind to the receptor angiotensin converting enzyme 2 (ACE2) in host cells via the receptor-binding domain (RBD). Antibodies binding to this domain can block the interaction with the receptor and prevent viral entry into the cells. Additionally, these vaccines can also induce spike-specific T cells which could contribute to providing protection against the virus. However, the emergence of new SARS-CoV-2 variants can impair the immunity generated by COVID-19 vaccines if mutations occur in cognate epitopes, precluding immune recognition. Here, we evaluated the chance of five SARS-CoV-2 variants of concern (VOCs), Alpha, Beta, Gamma, Delta and Omicron, to escape spike-specific immunity induced by vaccines. To that end, we examined the impact of the SARS-CoV-2 variant mutations on residues located on experimentally verified spike-specific epitopes, deposited at the Immune Epitope Database, that are targeted by neutralizing antibodies or recognized by T cells. We found about 300 of such B cell epitopes, which were largely overlapping, and could be grouped into 54 B cell epitope clusters sharing ≥ 7 residues. Most of the B cell epitope clusters map in the RBD domain (39 out of 54) and 20%, 50%, 37%, 44% and 57% of the total are mutated in SARS-CoV-2 Alpha, Beta, Gamma, Delta and Omicron variants, respectively. We also found 234 experimentally verified CD8 and CD4 T cell epitopes that were distributed evenly throughout the spike protein. Interestingly, in each SARS-CoV-2 VOC, over 87% and 79% of CD8 and CD4 T cell epitopes, respectively, are not mutated. These observations suggest that SARS-CoV-2 VOCs—particularly the Omicron variant—may be prone to escape spike-specific antibody immunity, but not cellular immunity, elicited by COVID-19 vaccines.
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177
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The E484K Substitution in a SARS-CoV-2 Spike Protein Subunit Vaccine Resulted in Limited Cross-Reactive Neutralizing Antibody Responses in Mice. Viruses 2022; 14:v14050854. [PMID: 35632595 PMCID: PMC9146450 DOI: 10.3390/v14050854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 01/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially emerging variants, poses an increased threat to global public health. The significant reduction in neutralization activity against the variants such as B.1.351 in the serum of convalescent patients and vaccinated people calls for the design of new potent vaccines targeting the emerging variant. However, since most vaccines approved and in clinical trials are based on the sequence of the original SARS-CoV-2 strain, the immunogenicity and protective efficacy of vaccines based on the B.1.351 variant remain largely unknown. In this study, we evaluated the immunogenicity, induced neutralization activity, and protective efficacy of wild-type spike protein nanoparticle (S-2P) and mutant spike protein nanoparticle (S-4M-2P) carrying characteristic mutations of B.1.351 variant in mice. Although there was no significant difference in the induction of spike-specific IgG responses in S-2P- and S-4M-2P-immunized mice, neutralizing antibodies elicited by S-4M-2P exhibited noteworthy, narrower breadth of reactivity with SARS-CoV-2 variants compared with neutralizing antibodies elicited by S-2P. Furthermore, the decrease of induced neutralizing antibody breadth at least partly resulted from the amino acid substitution at position 484. Moreover, S-4M-2P vaccination conferred insufficient protection against live SARS-CoV-2 virus infection, while S-2P vaccination gave definite protection against SARS-CoV-2 challenge in mice. Together, our study provides direct evidence that the E484K substitution in a SARS-CoV-2 subunit protein vaccine limited the cross-reactive neutralizing antibody breadth in mice and, more importantly, draws attention to the unfavorable impact of this mutation in spike protein of SARS-CoV-2 variants on the induction of potent neutralizing antibody responses.
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178
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Verkhivker G, Agajanian S, Kassab R, Krishnan K. Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. Int J Mol Sci 2022; 23:4376. [PMID: 35457196 PMCID: PMC9032413 DOI: 10.3390/ijms23084376] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 02/01/2023] Open
Abstract
In this study, we combine all-atom MD simulations and comprehensive mutational scanning of S-RBD complexes with the angiotensin-converting enzyme 2 (ACE2) host receptor in the native form as well as the S-RBD Delta and Omicron variants to (a) examine the differences in the dynamic signatures of the S-RBD complexes and (b) identify the critical binding hotspots and sensitivity of the mutational positions. We also examined the differences in allosteric interactions and communications in the S-RBD complexes for the Delta and Omicron variants. Through the perturbation-based scanning of the allosteric propensities of the SARS-CoV-2 S-RBD residues and dynamics-based network centrality and community analyses, we characterize the global mediating centers in the complexes and the nature of local stabilizing communities. We show that a constellation of mutational sites (G496S, Q498R, N501Y and Y505H) correspond to key binding energy hotspots and also contribute decisively to the key interfacial communities that mediate allosteric communications between S-RBD and ACE2. These Omicron mutations are responsible for both favorable local binding interactions and long-range allosteric interactions, providing key functional centers that mediate the high transmissibility of the virus. At the same time, our results show that other mutational sites could provide a "flexible shield" surrounding the stable community network, thereby allowing the Omicron virus to modulate immune evasion at different epitopes, while protecting the integrity of binding and allosteric interactions in the RBD-ACE2 complexes. This study suggests that the SARS-CoV-2 S protein may exploit the plasticity of the RBD to generate escape mutants, while engaging a small group of functional hotspots to mediate efficient local binding interactions and long-range allosteric communications with ACE2.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (S.A.); (R.K.); (K.K.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Steve Agajanian
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (S.A.); (R.K.); (K.K.)
| | - Ryan Kassab
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (S.A.); (R.K.); (K.K.)
| | - Keerthi Krishnan
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (S.A.); (R.K.); (K.K.)
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Chekol Abebe E, Tiruneh G/Medhin M, Behaile T/Mariam A, Asmamaw Dejenie T, Mengie Ayele T, Tadele Admasu F, Tilahun Muche Z, Asmare Adela G. Mutational Pattern, Impacts and Potential Preventive Strategies of Omicron SARS-CoV-2 Variant Infection. Infect Drug Resist 2022; 15:1871-1887. [PMID: 35450114 PMCID: PMC9017707 DOI: 10.2147/idr.s360103] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/08/2022] [Indexed: 01/18/2023] Open
Abstract
Since the emergence of COVID 19, the authentic SARS-CoV-2 has evolved into a range of novel variants that are of more global concern. In late November 2021, the Omicron (lineage B.1.1.529) variant was identified as a new variant and considered as the fifth variant of concern. Omicron harbors a genetic profile that is exceedingly unusual, with a huge number of mutations. Above thirty mutations are localized in the S protein, while some are found in other structural and non-structural proteins. Half of the mutations in the S protein are in the RBD, which is a major target of antibodies, showing that Omicron mutations may affect antibody binding affinity to the S protein. The Omicron variant has been found to result in immune escape, therapeutic or vaccine escape, as well as increased transmissibility and reinfection risk, explaining its rapid international spread that sparks a global alarm even more serious than the previously reported variants. Omicron has the capability to bypass at least some of the multi-faceted immune responses induced by prior infection or vaccination. It is shown to extensively escape neutralizing antibodies while evading cell mediated immune defense to a lesser extent. The efficacy of COVID 19 vaccines against Omicron variant is decreased with primary vaccination, showing that the vaccine is less efficient in preventing Omicron infections. However, after receiving a booster vaccine dose, the immunological response to Omicron significantly improved and hold promising results. Despite the mild nature of the disease in most vaccinated people, the rapid spread of Omicron, as well as the increased risk of re-infection, poses yet another major public health concern. Therefore, effort should be devoted to maintaining the existing COVID 19 preventive measures as well as developing new vaccination strategies in order to control the fast dissemination of Omicron.
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Affiliation(s)
- Endeshaw Chekol Abebe
- Department of Medical Biochemistry, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Markeshaw Tiruneh G/Medhin
- Department of Medical Biochemistry, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Awgichew Behaile T/Mariam
- Department of Medical Biochemistry, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Tadesse Asmamaw Dejenie
- Department of Medical Biochemistry, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Teklie Mengie Ayele
- Department of Pharmacy, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Fitalew Tadele Admasu
- Department of Medical Biochemistry, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Zelalem Tilahun Muche
- Department of Physiology, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Getachew Asmare Adela
- Department of Reproductive Health and Nutrition, School of Public Health, Wolaita Sodo University, Wolaita Sodo, Ethiopia
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180
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Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins GW, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A, Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL. Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function. Mol Biol Evol 2022; 39:msac061. [PMID: 35325204 PMCID: PMC9037384 DOI: 10.1093/molbev/msac061] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (1) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (2) interactions of Spike with ACE2 receptors, and (3) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any virus within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and, in combination with other mutations, adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron overall previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.
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Affiliation(s)
- Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Division of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Alexander G. Lucaci
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Wolfgang Maier
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany, usegalaxy.eu
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany, usegalaxy.eu
| | - Stephen D. Shank
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Oscar A. MacLean
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Richard J. Orton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Maciej F. Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gordon W. Harkins
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
| | - Carolyn Williamson
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
- Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Nei-yuan Hsiao
- Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Arne De Klerk
- Institute of Infectious Diseases and Molecular Medicine, Division of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Robert J. Wilkinson
- Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Cape Town, South Africa
- Francis Crick Institute, London, United Kingdom
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - B. Trevor Sewell
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anton Nekrutenko
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA, usegalaxy.org
| | - Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science, Stellenbosch University, Stellenbosch, South Africa
| | - Ravindra K. Gupta
- Africa Health Research Institute, Durban, South Africa
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science, Stellenbosch University, Stellenbosch, South Africa
| | - Sergei L. Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
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181
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Gómez SA, Rojas‐Valencia N, Gómez S, Cappelli C, Restrepo A. The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. Chembiochem 2022; 23:e202100393. [PMID: 34529328 PMCID: PMC8652971 DOI: 10.1002/cbic.202100393] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/14/2021] [Indexed: 12/24/2022]
Abstract
Specific S477N, N501Y, K417N, K417T, E484K mutations in the receptor binding domain (RBD) of the spike protein in the wild type SARS-COV-2 virus have resulted, among others, in the following variants: B.1.160 (20A or EU2, first reported in continental Europe), B1.1.7 (α or 20I501Y.V1, first reported in the United Kingdom), B.1.351 (β or 20H/501Y.V2, first reported in South Africa), B.1.1.28.1 (γ or P.1 or 20J/501Y.V3, first reported in Brazil), and B.1.1.28.2 (ζ, or P.2 or 20B/S484K, also first reported in Brazil). From the analysis of a set of bonding descriptors firmly rooted in the formalism of quantum mechanics, including Natural Bond Orbitals (NBO), Quantum Theory of Atoms In Molecules (QTAIM) and highly correlated energies within the Domain Based Local Pair Natural Orbital Coupled Cluster Method (DLPNO-CCSD(T)), and from a set of computed electronic spectral patterns with environmental effects, we show that the new variants improve their ability to recognize available sites to either hydrogen bond or to form salt bridges with residues in the ACE2 receptor of the host cells. This results in significantly improved initial virus⋅⋅⋅cell molecular recognition and attachment at the microscopic level, which trigger the infectious cycle.
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Affiliation(s)
- Santiago A. Gómez
- Instituto de QuímicaUniversidad de Antioquia UdeACalle 70 No. 52–21050010MedellínColombia
| | - Natalia Rojas‐Valencia
- Instituto de QuímicaUniversidad de Antioquia UdeACalle 70 No. 52–21050010MedellínColombia
- Escuela de Ciencias y HumanidadesDepartamento de Ciencias B'ásicasUniversidad Eafit AA3300MedellínColombia
| | - Sara Gómez
- Scuola Normale SuperioreClasse di ScienzePiazza dei Cavalieri 756126PisaItaly
| | - Chiara Cappelli
- Scuola Normale SuperioreClasse di ScienzePiazza dei Cavalieri 756126PisaItaly
| | - Albeiro Restrepo
- Instituto de QuímicaUniversidad de Antioquia UdeACalle 70 No. 52–21050010MedellínColombia
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182
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Zhou H, Ni WJ, Huang W, Wang Z, Cai M, Sun YC. Advances in Pathogenesis, Progression, Potential Targets and Targeted Therapeutic Strategies in SARS-CoV-2-Induced COVID-19. Front Immunol 2022; 13:834942. [PMID: 35450063 PMCID: PMC9016159 DOI: 10.3389/fimmu.2022.834942] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/07/2022] [Indexed: 01/18/2023] Open
Abstract
As the new year of 2020 approaches, an acute respiratory disease quietly caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as coronavirus disease 2019 (COVID-19) was reported in Wuhan, China. Subsequently, COVID-19 broke out on a global scale and formed a global public health emergency. To date, the destruction that has lasted for more than two years has not stopped and has caused the virus to continuously evolve new mutant strains. SARS-CoV-2 infection has been shown to cause multiple complications and lead to severe disability and death, which has dealt a heavy blow to global development, not only in the medical field but also in social security, economic development, global cooperation and communication. To date, studies on the epidemiology, pathogenic mechanism and pathological characteristics of SARS-CoV-2-induced COVID-19, as well as target confirmation, drug screening, and clinical intervention have achieved remarkable effects. With the continuous efforts of the WHO, governments of various countries, and scientific research and medical personnel, the public's awareness of COVID-19 is gradually deepening, a variety of prevention methods and detection methods have been implemented, and multiple vaccines and drugs have been developed and urgently marketed. However, these do not appear to have completely stopped the pandemic and ravages of this virus. Meanwhile, research on SARS-CoV-2-induced COVID-19 has also seen some twists and controversies, such as potential drugs and the role of vaccines. In view of the fact that research on SARS-CoV-2 and COVID-19 has been extensive and in depth, this review will systematically update the current understanding of the epidemiology, transmission mechanism, pathological features, potential targets, promising drugs and ongoing clinical trials, which will provide important references and new directions for SARS-CoV-2 and COVID-19 research.
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Affiliation(s)
- Hong Zhou
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei-Jian Ni
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei Huang
- The Third People’s Hospital of Hefei, The Third Clinical College of Anhui Medical University, Hefei, China
| | - Zhen Wang
- Anhui Provincial Children’s Hospital, Children’s Hospital of Fudan University-Anhui Campus, Hefei, China
| | - Ming Cai
- Department of Pharmacy, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Yan-Cai Sun
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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183
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Sokal A, Broketa M, Barba-Spaeth G, Meola A, Fernández I, Fourati S, Azzaoui I, de La Selle A, Vandenberghe A, Roeser A, Bouvier-Alias M, Crickx E, Languille L, Michel M, Godeau B, Gallien S, Melica G, Nguyen Y, Zarrouk V, Canoui-Poitrine F, Noizat-Pirenne F, Megret J, Pawlotsky JM, Fillatreau S, Simon-Lorière E, Weill JC, Reynaud CA, Rey FA, Bruhns P, Chappert P, Mahévas M. Analysis of mRNA vaccination-elicited RBD-specific memory B cells reveals strong but incomplete immune escape of the SARS-CoV-2 Omicron variant. Immunity 2022; 55:1096-1104.e4. [PMID: 35483354 PMCID: PMC8986479 DOI: 10.1016/j.immuni.2022.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/16/2022] [Accepted: 04/04/2022] [Indexed: 11/05/2022]
Abstract
The SARS-CoV-2 Omicron variant can escape neutralization by vaccine-elicited and convalescent antibodies. Memory B cells (MBCs) represent another layer of protection against SARS-CoV-2, as they persist after infection and vaccination and improve their affinity. Whether MBCs elicited by mRNA vaccines can recognize the Omicron variant remains unclear. We assessed the affinity and neutralization potency against the Omicron variant of several hundred naturally expressed MBC-derived monoclonal IgG antibodies from vaccinated COVID-19-recovered and -naive individuals. Compared with other variants of concern, Omicron evaded recognition by a larger proportion of MBC-derived antibodies, with only 30% retaining high affinity against the Omicron RBD, and the reduction in neutralization potency was even more pronounced. Nonetheless, neutralizing MBC clones could be found in all the analyzed individuals. Therefore, despite the strong immune escape potential of the Omicron variant, these results suggest that the MBC repertoire generated by mRNA vaccines still provides some protection against the Omicron variant in vaccinated individuals.
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184
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Pierros V, Kontopodis E, Stravopodis DJ, Tsangaris GT. Unique peptide signatures of SARS-CοV-2 virus against human proteome reveal variants’ immune escape and infectiveness. Heliyon 2022; 8:e09222. [PMID: 35399374 PMCID: PMC8979629 DOI: 10.1016/j.heliyon.2022.e09222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/19/2021] [Accepted: 03/21/2022] [Indexed: 10/29/2022] Open
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185
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Ahmed S, Manjunath K, Chattopadhyay G, Varadarajan R. Identification of stabilizing point mutations through mutagenesis of destabilized protein libraries. J Biol Chem 2022; 298:101785. [PMID: 35247389 PMCID: PMC8971944 DOI: 10.1016/j.jbc.2022.101785] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/18/2022] [Accepted: 02/26/2022] [Indexed: 01/22/2023] Open
Abstract
Although there have been recent transformative advances in the area of protein structure prediction, prediction of point mutations that improve protein stability remains challenging. It is possible to construct and screen large mutant libraries for improved activity or ligand binding. However, reliable screens for mutants that improve protein stability do not yet exist, especially for proteins that are well folded and relatively stable. Here, we demonstrate that incorporation of a single, specific, destabilizing mutation termed parent inactivating mutation into each member of a single-site saturation mutagenesis library, followed by screening for suppressors, allows for robust and accurate identification of stabilizing mutations. We carried out fluorescence-activated cell sorting of such a yeast surface display, saturation suppressor library of the bacterial toxin CcdB, followed by deep sequencing of sorted populations. We found that multiple stabilizing mutations could be identified after a single round of sorting. In addition, multiple libraries with different parent inactivating mutations could be pooled and simultaneously screened to further enhance the accuracy of identification of stabilizing mutations. Finally, we show that individual stabilizing mutations could be combined to result in a multi-mutant that demonstrated an increase in thermal melting temperature of about 20 °C, and that displayed enhanced tolerance to high temperature exposure. We conclude that as this method is robust and employs small library sizes, it can be readily extended to other display and screening formats to rapidly isolate stabilized protein mutants.
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Affiliation(s)
- Shahbaz Ahmed
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kavyashree Manjunath
- Centre for Chemical Biology and Therapeutics, Institute of Stem Cell Science and Regenerative Medicine, Bangalore, India
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186
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Rajah MM, Bernier A, Buchrieser J, Schwartz O. The Mechanism and Consequences of SARS-CoV-2 Spike-Mediated Fusion and Syncytia Formation. J Mol Biol 2022; 434:167280. [PMID: 34606831 PMCID: PMC8485708 DOI: 10.1016/j.jmb.2021.167280] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022]
Abstract
Syncytia are formed when individual cells fuse. SARS-CoV-2 induces syncytia when the viral spike (S) protein on the surface of an infected cell interacts with receptors on neighboring cells. Syncytia may potentially contribute to pathology by facilitating viral dissemination, cytopathicity, immune evasion, and inflammatory response. SARS-CoV-2 variants of concern possess several mutations within the S protein that enhance receptor interaction, fusogenicity and antibody binding. In this review, we discuss the molecular determinants of S mediated fusion and the antiviral innate immunity components that counteract syncytia formation. Several interferon-stimulated genes, including IFITMs and LY6E act as barriers to S protein-mediated fusion by altering the composition or biophysical properties of the target membrane. We also summarize the effect that the mutations associated with the variants of concern have on S protein fusogenicity. Altogether, this review contextualizes the current understanding of Spike fusogenicity and the role of syncytia during SARS-CoV-2 infection and pathology.
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Affiliation(s)
- Maaran Michael Rajah
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France; Université de Paris, Sorbonne Paris Cité, Paris, France. https://twitter.com/MaaranRajah
| | - Annie Bernier
- Institut Curie, INSERM U932, Paris, France. https://twitter.com/nini_bernier
| | - Julian Buchrieser
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France. https://twitter.com/JBuchrieser
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France; Université de Paris, Sorbonne Paris Cité, Paris, France; Vaccine Research Institute, Creteil, France.
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187
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Hertanto DM, Sutanto H, Lusida MI, Kuntaman K, Santoso D. The genomic and clinical features of the COVID-19 Omicron variant: a narrative review. F1000Res 2022. [DOI: 10.12688/f1000research.110647.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a major cause of morbidity and mortality worldwide. Since late November 2021, the Omicron variant has emerged as the primary cause of COVID-19 and caused a huge increase in the reported incidence around the world. To date, 32-34 spike mutations have been reported to be present in the Omicron variant, 15 of which were located in the receptor-binding domain that interacts with the cell surface of the host cells, while the rest were located in the N-terminal domain and around the furin cleavage site. Recent studies have suggested that those mutations could have a major role in the transmissibility and pathogenicity of the Omicron variant. Additionally, some mutations might contribute to the change of viral tropism of this novel variant. Here, we aim to discuss the recent reports on the transmissibility and severity of the Omicron variant from both the genetic and clinical perspectives. Afterward, we also take the chance to deliver our personal view on the topic.
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188
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Chen C, Boorla VS, Chowdhury R, Nissly RH, Gontu A, Chothe SK, LaBella L, Jakka P, Ramasamy S, Vandegrift KJ, Nair MS, Kuchipudi SV, Maranas CD. A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.03.22.485413. [PMID: 35350198 PMCID: PMC8963690 DOI: 10.1101/2022.03.22.485413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The cellular entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involves the association of its receptor binding domain (RBD) with human angiotensin converting enzyme 2 (hACE2) as the first crucial step. Efficient and reliable prediction of RBD-hACE2 binding affinity changes upon amino acid substitutions can be valuable for public health surveillance and monitoring potential spillover and adaptation into non-human species. Here, we introduce a convolutional neural network (CNN) model trained on protein sequence and structural features to predict experimental RBD-hACE2 binding affinities of 8,440 variants upon single and multiple amino acid substitutions in the RBD or ACE2. The model achieves a classification accuracy of 83.28% and a Pearson correlation coefficient of 0.85 between predicted and experimentally calculated binding affinities in five-fold cross-validation tests and predicts improved binding affinity for most circulating variants. We pro-actively used the CNN model to exhaustively screen for novel RBD variants with combinations of up to four single amino acid substitutions and suggested candidates with the highest improvements in RBD-ACE2 binding affinity for human and animal ACE2 receptors. We found that the binding affinity of RBD variants against animal ACE2s follows similar trends as those against human ACE2. White-tailed deer ACE2 binds to RBD almost as tightly as human ACE2 while cattle, pig, and chicken ACE2s bind weakly. The model allows testing whether adaptation of the virus for increased binding with other animals would cause concomitant increases in binding with hACE2 or decreased fitness due to adaptation to other hosts.
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Affiliation(s)
- Chen Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Abhinay Gontu
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shubhada K. Chothe
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lindsey LaBella
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Padmaja Jakka
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Santhamani Ramasamy
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kurt J. Vandegrift
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Suresh V. Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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Tiberti M, Terkelsen T, Degn K, Beltrame L, Cremers TC, da Piedade I, Di Marco M, Maiani E, Papaleo E. MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles. Brief Bioinform 2022; 23:6552273. [PMID: 35323860 DOI: 10.1093/bib/bbac074] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/28/2022] [Accepted: 02/16/2022] [Indexed: 12/26/2022] Open
Abstract
Mutations, which result in amino acid substitutions, influence the stability of proteins and their binding to biomolecules. A molecular understanding of the effects of protein mutations is both of biotechnological and medical relevance. Empirical free energy functions that quickly estimate the free energy change upon mutation (ΔΔG) can be exploited for systematic screenings of proteins and protein complexes. In silico saturation mutagenesis can guide the design of new experiments or rationalize the consequences of known mutations. Often software such as FoldX, while fast and reliable, lack the necessary automation features to apply them in a high-throughput manner. We introduce MutateX, a software to automate the prediction of ΔΔGs associated with the systematic mutation of each residue within a protein, or protein complex to all other possible residue types, using the FoldX energy function. MutateX also supports ΔΔG calculations over protein ensembles, upon post-translational modifications and in multimeric assemblies. At the heart of MutateX lies an automated pipeline engine that handles input preparation, parallelization and outputs publication-ready figures. We illustrate the MutateX protocol applied to different case studies. The results of the high-throughput scan provided by our tools can help in different applications, such as the analysis of disease-associated mutations, to complement experimental deep mutational scans, or assist the design of variants for industrial applications. MutateX is a collection of Python tools that relies on open-source libraries. It is available free of charge under the GNU General Public License from https://github.com/ELELAB/mutatex.
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Affiliation(s)
- Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Thilde Terkelsen
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Kristine Degn
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ludovica Beltrame
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Tycho Canter Cremers
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Isabelle da Piedade
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Miriam Di Marco
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Emiliano Maiani
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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190
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Kumar R, Murugan NA, Srivastava V. Improved Binding Affinity of Omicron's Spike Protein for the Human Angiotensin-Converting Enzyme 2 Receptor Is the Key behind Its Increased Virulence. Int J Mol Sci 2022; 23:3409. [PMID: 35328828 PMCID: PMC8955673 DOI: 10.3390/ijms23063409] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/24/2022] [Accepted: 03/14/2022] [Indexed: 01/27/2023] Open
Abstract
The new variant of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), Omicron, has been quickly spreading in many countries worldwide. Compared to the original virus, Omicron is characterized by several mutations in its genomic region, including the spike protein's receptor-binding domain (RBD). We have computationally investigated the interaction between the RBD of both the wild type and Omicron variant of SARS-CoV-2 with the human angiotensin-converting enzyme 2 (hACE2) receptor using molecular dynamics and molecular mechanics-generalized Born surface area (MM-GBSA)-based binding free energy calculations. The mode of the interaction between Omicron's RBD with the hACE2 receptor is similar to the original SARS-CoV-2 RBD except for a few key differences. The binding free energy difference shows that the spike protein of Omicron has an increased affinity for the hACE2 receptor. The mutated residues in the RBD showed strong interactions with a few amino acid residues of hACE2. More specifically, strong electrostatic interactions (salt bridges) and hydrogen bonding were observed between R493 and R498 residues of the Omicron RBD with D30/E35 and D38 residues of the hACE2, respectively. Other mutated amino acids in the Omicron RBD, e.g., S496 and H505, also exhibited hydrogen bonding with the hACE2 receptor. A pi-stacking interaction was also observed between tyrosine residues (RBD-Tyr501: hACE2-Tyr41) in the complex, which contributes majorly to the binding free energies and suggests that this is one of the key interactions stabilizing the formation of the complex. The resulting structural insights into the RBD:hACE2 complex, the binding mode information within it, and residue-wise contributions to the free energy provide insight into the increased transmissibility of Omicron and pave the way to design and optimize novel antiviral agents.
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Affiliation(s)
- Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 106 91 Stockholm, Sweden;
| | - Natarajan Arul Murugan
- Department of Computer Science, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 106 91 Stockholm, Sweden;
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191
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Cheng MH, Krieger JM, Banerjee A, Xiang Y, Kaynak B, Shi Y, Arditi M, Bahar I. Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions. iScience 2022; 25:103939. [PMID: 35194576 PMCID: PMC8851820 DOI: 10.1016/j.isci.2022.103939] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/31/2022] [Accepted: 02/14/2022] [Indexed: 12/29/2022] Open
Abstract
The emergence of SARS-CoV-2 variants necessitates rational assessment of their impact on the recognition and neutralization of the virus by the host cell. We present a comparative analysis of the interactions of Alpha, Beta, Gamma, and Delta variants with cognate molecules (ACE2 and/or furin), neutralizing nanobodies (Nbs), and monoclonal antibodies (mAbs) using in silico methods, in addition to Nb-binding assays. Our study elucidates the molecular origin of the ability of Beta and Delta variants to evade selected antibodies, such as REGN10933, LY-CoV555, B38, C105, or H11-H4, while being insensitive to others including REGN10987. Experiments confirm that nanobody Nb20 retains neutralizing activity against the Delta variant. The substitutions T478K and L452R in the Delta variant enhance associations with ACE2, whereas P681R promotes recognition by proteases, thus facilitating viral entry. The Ab-specific responses of variants highlight how full-atomic structure and dynamics analyses are required for assessing the response to newly emerging variants.
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Affiliation(s)
- Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - James M. Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anupam Banerjee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yufei Xiang
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Burak Kaynak
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yi Shi
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Moshe Arditi
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, and Biomedical Sciences, Infectious and Immunologic Diseases Research Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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192
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Cochin M, Luciani L, Touret F, Driouich JS, Petit PR, Moureau G, Baronti C, Laprie C, Thirion L, Maes P, Boudewijns R, Neyts J, de Lamballerie X, Nougairède A. The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model. Commun Biol 2022; 5:225. [PMID: 35273335 PMCID: PMC8913834 DOI: 10.1038/s42003-022-03171-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/14/2022] [Indexed: 12/14/2022] Open
Abstract
Late 2020, SARS-CoV-2 Alpha variant emerged in United Kingdom and gradually replaced G614 strains initially involved in the global spread of the pandemic. In this study, we use a Syrian hamster model to compare a clinical strain of Alpha variant with an ancestral G614 strain. The Alpha variant succeed to infect animals and to induce a pathology that mimics COVID-19. However, both strains replicate to almost the same level and induced a comparable disease and immune response. A slight fitness advantage is noted for the G614 strain during competition and transmission experiments. These data do not corroborate the epidemiological situation observed during the first half of 2021 in humans nor reports that showed a more rapid replication of Alpha variant in human reconstituted bronchial epithelium. This study highlights the need to combine data from different laboratories using various animal models to decipher the biological properties of newly emerging SARS-CoV-2 variants.
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Affiliation(s)
- Maxime Cochin
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Léa Luciani
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Jean-Sélim Driouich
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Paul-Rémi Petit
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Grégory Moureau
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Cécile Baronti
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | | | - Laurence Thirion
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Piet Maes
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Leuven, Belgium
| | - Robbert Boudewijns
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Antoine Nougairède
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.
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Schubert M, Bertoglio F, Steinke S, Heine PA, Ynga-Durand MA, Maass H, Sammartino JC, Cassaniti I, Zuo F, Du L, Korn J, Milošević M, Wenzel EV, Krstanović F, Polten S, Pribanić-Matešić M, Brizić I, Baldanti F, Hammarström L, Dübel S, Šustić A, Marcotte H, Strengert M, Protić A, Piralla A, Pan-Hammarström Q, Čičin-Šain L, Hust M. Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. BMC Med 2022; 20:102. [PMID: 35236358 PMCID: PMC8890955 DOI: 10.1186/s12916-022-02312-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/21/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic is caused by the betacoronavirus SARS-CoV-2. In November 2021, the Omicron variant was discovered and immediately classified as a variant of concern (VOC), since it shows substantially more mutations in the spike protein than any previous variant, especially in the receptor-binding domain (RBD). We analyzed the binding of the Omicron RBD to the human angiotensin-converting enzyme-2 receptor (ACE2) and the ability of human sera from COVID-19 patients or vaccinees in comparison to Wuhan, Beta, or Delta RBD variants. METHODS All RBDs were produced in insect cells. RBD binding to ACE2 was analyzed by ELISA and microscale thermophoresis (MST). Similarly, sera from 27 COVID-19 patients, 81 vaccinated individuals, and 34 booster recipients were titrated by ELISA on RBDs from the original Wuhan strain, Beta, Delta, and Omicron VOCs. In addition, the neutralization efficacy of authentic SARS-CoV-2 wild type (D614G), Delta, and Omicron by sera from 2× or 3× BNT162b2-vaccinated persons was analyzed. RESULTS Surprisingly, the Omicron RBD showed a somewhat weaker binding to ACE2 compared to Beta and Delta, arguing that improved ACE2 binding is not a likely driver of Omicron evolution. Serum antibody titers were significantly lower against Omicron RBD compared to the original Wuhan strain. A 2.6× reduction in Omicron RBD binding was observed for serum of 2× BNT162b2-vaccinated persons. Neutralization of Omicron SARS-CoV-2 was completely diminished in our setup. CONCLUSION These results indicate an immune escape focused on neutralizing antibodies. Nevertheless, a boost vaccination increased the level of anti-RBD antibodies against Omicron, and neutralization of authentic Omicron SARS-CoV-2 was at least partially restored. This study adds evidence that current vaccination protocols may be less efficient against the Omicron variant.
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Affiliation(s)
- Maren Schubert
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Federico Bertoglio
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Stephan Steinke
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Philip Alexander Heine
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Mario Alberto Ynga-Durand
- Helmholtz Centre for Infection Research, Department of Viral Immunology, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Henrike Maass
- Helmholtz Centre for Infection Research, Department of Viral Immunology, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Josè Camilla Sammartino
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
| | - Irene Cassaniti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
| | - Fanglei Zuo
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Likun Du
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Janin Korn
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
- Abcalis GmbH, Science Campus Braunschweig-Süd, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Marko Milošević
- Department of Anesthesiology, Reanimation, Intensive Care and Emergency Medicine, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Esther Veronika Wenzel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
- Abcalis GmbH, Science Campus Braunschweig-Süd, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Fran Krstanović
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Saskia Polten
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | | | - Ilija Brizić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Stefan Dübel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Alan Šustić
- Department of Anesthesiology, Reanimation, Intensive Care and Emergency Medicine, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Harold Marcotte
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Monika Strengert
- Department of Epidemiology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Alen Protić
- Department of Anesthesiology, Reanimation, Intensive Care and Emergency Medicine, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | | | - Luka Čičin-Šain
- Helmholtz Centre for Infection Research, Department of Viral Immunology, Inhoffenstr. 7, 38124, Braunschweig, Germany
- Centre for Individualised Infection Medicine (CIIM), a joint venture of Helmholtz Centre for Infection Research and Medical School Hannover, Hannover, Germany
| | - Michael Hust
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany.
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Li J, Wu YN, Zhang S, Kang XP, Jiang T. Deep learning based on biologically interpretable genome representation predicts two types of human adaptation of SARS-CoV-2 variants. Brief Bioinform 2022; 23:6540151. [PMID: 35233612 PMCID: PMC9116219 DOI: 10.1093/bib/bbac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/27/2022] Open
Abstract
Explosively emerging SARS-CoV-2 variants challenge current nomenclature schemes based on genetic diversity and biological significance. Genomic composition-based machine learning methods have recently performed well in identifying phenotype–genotype relationships. We introduced a framework involving dinucleotide (DNT) composition representation (DCR) to parse the general human adaptation of RNA viruses and applied a three-dimensional convolutional neural network (3D CNN) analysis to learn the human adaptation of other existing coronaviruses (CoVs) and predict the adaptation of SARS-CoV-2 variants of concern (VOCs). A markedly separable, linear DCR distribution was observed in two major genes—receptor-binding glycoprotein and RNA-dependent RNA polymerase (RdRp)—of six families of single-stranded (ssRNA) viruses. Additionally, there was a general host-specific distribution of both the spike proteins and RdRps of CoVs. The 3D CNN based on spike DCR predicted a dominant type II adaptation of most Beta, Delta and Omicron VOCs, with high transmissibility and low pathogenicity. Type I adaptation with opposite transmissibility and pathogenicity was predicted for SARS-CoV-2 Alpha VOCs (77%) and Kappa variants of interest (58%). The identified adaptive determinants included D1118H and A570D mutations and local DNTs. Thus, the 3D CNN model based on DCR features predicts SARS-CoV-2, a major type II human adaptation and is qualified to predict variant adaptation in real time, facilitating the risk-assessment of emerging SARS-CoV-2 variants and COVID-19 control.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology 10 and Epidemiology, Beijing 100071, China
| | - Ya-Nan Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology 10 and Epidemiology, Beijing 100071, China
| | - Sen Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology 10 and Epidemiology, Beijing 100071, China
| | - Xiao-Ping Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology 10 and Epidemiology, Beijing 100071, China
| | - Tao Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology 10 and Epidemiology, Beijing 100071, China
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Zhang W, He Y, Feng Z, Zhang J. Recent advances of functional nucleic acid-based sensors for point-of-care detection of SARS-CoV-2. Mikrochim Acta 2022; 189:128. [PMID: 35235065 PMCID: PMC8889384 DOI: 10.1007/s00604-022-05242-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/21/2022] [Indexed: 12/18/2022]
Abstract
This review focuses on critical scientific barriers that the field of point-of-care (POC) testing of SARS-CoV-2 is facing and possible solutions to overcome these barriers using functional nucleic acid (FNA)-based technology. Beyond the summary of recent advances in FNA-based sensors for COVID-19 diagnostics, our goal is to outline how FNA might serve to overcome the scientific barriers that currently available diagnostic approaches are suffering. The first introductory section on the operationalization of the COVID-19 pandemic in historical view and its clinical features contextualizes essential SARS-CoV-2-specific biomarkers. The second part highlights three major scientific barriers for POC COVID-19 diagnosis, that is, the lack of a general method for (1) designing receptors of SARS-CoV-2 variants; (2) improving sensitivity to overcome false negatives; and (3) signal readout in resource-limited settings. The subsequent part provides fundamental insights into FNA and technical tricks to successfully achieve effective COVID-19 diagnosis by using in vitro selection of FNA to overcome receptor design barriers, combining FNA with multiple DNA signal amplification strategies to improve sensitivity, and interfacing FNA with portable analyzers to overcome signal readout barriers. This review concludes with an overview of further opportunities and emerging applications for FNA-based sensors against COVID-19.
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Affiliation(s)
- Wenxian Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Ying He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zhe Feng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Jingjing Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China.
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196
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Kim YI, Casel MAB, Choi YK. Transmissibility and pathogenicity of SARS-CoV-2 variants in animal models. J Microbiol 2022; 60:255-267. [PMID: 35235177 PMCID: PMC8890026 DOI: 10.1007/s12275-022-2033-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 12/13/2022]
Abstract
As of February 2022, SARS-CoV-2 is still one of the most serious public health threats due to its high mortality rate and rapid spread of novel variants. Since the first outbreak in 2019, general understanding of SARS-CoV-2 has been improved through basic and clinical studies; however, knowledge gaps still exist in our understanding of the emerging novel SARSCoV-2 variants, which impacts the corresponding development of vaccines and therapeutics. Especially, accumulation of mutations in SARS-CoV-2 and rapid spread in populations with previous immunity has resulted in selection of variants that evade the host immune response. This phenomenon threatens to render current SARS-CoV-2 vaccines ineffective for controlling the pandemic. Proper animal models are essential for detailed investigations into the viral etiology, transmission and pathogenesis mechanisms, as well as evaluation of the efficacy of vaccine candidates against recent SARS-CoV-2 variants. Further, the choice of animal model for each research topic is important for researchers to gain better knowledge of recent SARS-CoV-2 variants. Here, we review the advantages and limitations of each animal model, including mice, hamsters, ferrets, and non-human primates, to elucidate variant SARS-CoV-2 etiology and transmission and to evaluate therapeutic and vaccine efficacy.
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Affiliation(s)
- Young-Il Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Mark Anthony B Casel
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Young Ki Choi
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea.
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Aghamirza Moghim Aliabadi H, Eivazzadeh‐Keihan R, Beig Parikhani A, Fattahi Mehraban S, Maleki A, Fereshteh S, Bazaz M, Zolriasatein A, Bozorgnia B, Rahmati S, Saberi F, Yousefi Najafabadi Z, Damough S, Mohseni S, Salehzadeh H, Khakyzadeh V, Madanchi H, Kardar GA, Zarrintaj P, Saeb MR, Mozafari M. COVID-19: A systematic review and update on prevention, diagnosis, and treatment. MedComm (Beijing) 2022; 3:e115. [PMID: 35281790 PMCID: PMC8906461 DOI: 10.1002/mco2.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 01/09/2023] Open
Abstract
Since the rapid onset of the COVID-19 or SARS-CoV-2 pandemic in the world in 2019, extensive studies have been conducted to unveil the behavior and emission pattern of the virus in order to determine the best ways to diagnosis of virus and thereof formulate effective drugs or vaccines to combat the disease. The emergence of novel diagnostic and therapeutic techniques considering the multiplicity of reports from one side and contradictions in assessments from the other side necessitates instantaneous updates on the progress of clinical investigations. There is also growing public anxiety from time to time mutation of COVID-19, as reflected in considerable mortality and transmission, respectively, from delta and Omicron variants. We comprehensively review and summarize different aspects of prevention, diagnosis, and treatment of COVID-19. First, biological characteristics of COVID-19 were explained from diagnosis standpoint. Thereafter, the preclinical animal models of COVID-19 were discussed to frame the symptoms and clinical effects of COVID-19 from patient to patient with treatment strategies and in-silico/computational biology. Finally, the opportunities and challenges of nanoscience/nanotechnology in identification, diagnosis, and treatment of COVID-19 were discussed. This review covers almost all SARS-CoV-2-related topics extensively to deepen the understanding of the latest achievements (last updated on January 11, 2022).
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Affiliation(s)
- Hooman Aghamirza Moghim Aliabadi
- Protein Chemistry LaboratoryDepartment of Medical BiotechnologyBiotechnology Research CenterPasteur Institute of IranTehranIran
- Advance Chemical Studies LaboratoryFaculty of ChemistryK. N. Toosi UniversityTehranIran
| | | | - Arezoo Beig Parikhani
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | | | - Ali Maleki
- Department of ChemistryIran University of Science and TechnologyTehranIran
| | | | - Masoume Bazaz
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | | | | | - Saman Rahmati
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | - Fatemeh Saberi
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineShahid Beheshti University of Medical SciencesTehranIran
| | - Zeinab Yousefi Najafabadi
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineTehran University of Medical SciencesTehranIran
- ImmunologyAsthma & Allergy Research InstituteTehran University of Medical SciencesTehranIran
| | - Shadi Damough
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | - Sara Mohseni
- Non‐metallic Materials Research GroupNiroo Research InstituteTehranIran
| | | | - Vahid Khakyzadeh
- Department of ChemistryK. N. Toosi University of TechnologyTehranIran
| | - Hamid Madanchi
- School of MedicineSemnan University of Medical SciencesSemnanIran
- Drug Design and Bioinformatics UnitDepartment of Medical BiotechnologyBiotechnology Research CenterPasteur Institute of IranTehranIran
| | - Gholam Ali Kardar
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineTehran University of Medical SciencesTehranIran
- ImmunologyAsthma & Allergy Research InstituteTehran University of Medical SciencesTehranIran
| | - Payam Zarrintaj
- School of Chemical EngineeringOklahoma State UniversityStillwaterOklahomaUSA
| | - Mohammad Reza Saeb
- Department of Polymer TechnologyFaculty of ChemistryGdańsk University of TechnologyGdańskPoland
| | - Masoud Mozafari
- Department of Tissue Engineering & Regenerative MedicineIran University of Medical SciencesTehranIran
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Tragni V, Preziusi F, Laera L, Onofrio A, Mercurio I, Todisco S, Volpicella M, De Grassi A, Pierri CL. Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. EPMA J 2022; 13:149-175. [PMID: 35013687 PMCID: PMC8732965 DOI: 10.1007/s13167-021-00267-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/04/2021] [Indexed: 12/12/2022]
Abstract
Aims The rapid spread of new SARS-CoV-2 variants has highlighted the crucial role played in the infection by mutations occurring at the SARS-CoV-2 spike receptor binding domain (RBD) in the interactions with the human ACE2 receptor. In this context, it urgently needs to develop new rapid tools for quickly predicting the affinity of ACE2 for the SARS-CoV-2 spike RBD protein variants to be used with the ongoing SARS-CoV-2 genomic sequencing activities in the clinics, aiming to gain clues about the transmissibility and virulence of new variants, to prevent new outbreaks and to quickly estimate the severity of the disease in the context of the 3PM. Methods In our study, we used a computational pipeline for calculating the interaction energies at the SARS-CoV-2 spike RBD/ACE2 protein-protein interface for a selected group of characterized infectious variants of concern/interest (VoC/VoI). By using our pipeline, we built 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for the VoC B.1.1.7-United Kingdom (carrying the mutations of concern/interest N501Y, S494P, E484K at the RBD), P.1-Japan/Brazil (RBD mutations: K417T, E484K, N501Y), B.1.351-South Africa (RBD mutations: K417N, E484K, N501Y), B.1.427/B.1.429-California (RBD mutations: L452R), the B.1.141 (RBD mutations: N439K), and the recent B.1.617.1-India (RBD mutations: L452R; E484Q) and the B.1.620 (RBD mutations: S477N; E484K). Then, we used the obtained 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for predicting the interaction energies at the protein-protein interface. Results Along SARS-CoV-2 mutation database screening and mutation localization analysis, it was ascertained that the most dangerous mutations at VoC/VoI spike proteins are located mainly at three regions of the SARS-CoV-2 spike "boat-shaped" receptor binding motif, on the RBD domain. Notably, the P.1 Japan/Brazil variant present three mutations, K417T, E484K, N501Y, located along the entire receptor binding motif, which apparently determines the highest interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein-protein interface, among those calculated. Conversely, it was also observed that the replacement of a single acidic/hydrophilic residue with a basic residue (E484K or N439K) at the "stern" or "bow" regions, of the boat-shaped receptor binding motif on the RBD, appears to determine an interaction energy with ACE2 receptor higher than that observed with single mutations occurring at the "hull" region or with other multiple mutants. In addition, our pipeline allowed searching for ACE2 structurally related proteins, i.e., THOP1 and NLN, which deserve to be investigated for their possible involvement in interactions with the SARS-CoV-2 spike protein, in those tissues showing a low expression of ACE2, or as a novel receptor for future spike variants. A freely available web-tool for the in silico calculation of the interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein-protein interface, starting from the sequences of the investigated spike and/or ACE2 variants, was made available for the scientific community at: https://www.mitoairm.it/covid19affinities. Conclusion In the context of the PPPM/3PM, the employment of the described pipeline through the provided webservice, together with the ongoing SARS-CoV-2 genomic sequencing, would help to predict the transmissibility of new variants sequenced from future patients, depending on SARS-CoV-2 genomic sequencing activities and on the specific amino acid replacement and/or on its location on the SARS-CoV-2 spike RBD, to put in play all the possible counteractions for preventing the most deleterious scenarios of new outbreaks, taking into consideration that a greater transmissibility has not to be necessarily related to a more severe manifestation of the disease. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-021-00267-w.
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Affiliation(s)
- Vincenzo Tragni
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Francesca Preziusi
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Luna Laera
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Angelo Onofrio
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Ivan Mercurio
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Simona Todisco
- Department of Sciences, University of Basilicata, Viale dell’Ateneo Lucano, 10-85100 Potenza, Italy
| | - Mariateresa Volpicella
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
- BROWSer S.r.l. at Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70126 Bari, Italy
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
- BROWSer S.r.l. at Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70126 Bari, Italy
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Ao D, Lan T, He X, Liu J, Chen L, Baptista‐Hon DT, Zhang K, Wei X. SARS-CoV-2 Omicron variant: Immune escape and vaccine development. MedComm (Beijing) 2022; 3:e126. [PMID: 35317190 PMCID: PMC8925644 DOI: 10.1002/mco2.126] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 02/05/2023] Open
Abstract
New genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) constantly emerge through unmitigated spread of the virus in the ongoing Coronavirus disease 2019 pandemic. Omicron (B.1.1.529), the latest variant of concern (VOC), has so far shown exceptional spread and infectivity and has established itself as the dominant variant in recent months. The SARS-CoV-2 spike glycoprotein is a key component for the recognition and binding to host cell angiotensin-converting enzyme 2 receptors. The Omicron variant harbors a cluster of substitutions/deletions/insertions, and more than 30 mutations are located in spike. Some noticeable mutations, including K417N, T478K, N501Y, and P681H, are shared with the previous VOCs Alpha, Beta, Gamma, or Delta variants and have been proven to be associated with higher transmissibility, viral infectivity, and immune evasion potential. Studies have revealed that the Omicron variant is partially resistant to the neutralizing activity of therapeutic antibodies and convalescent sera, which poses significant challenges for the clinical effectiveness of the current vaccines and therapeutic antibodies. We provide a comprehensive analysis and summary of the epidemiology and immune escape mechanisms of the Omicron variant. We also suggest some therapeutic strategies against the Omicron variant. This review, therefore, aims to provide information for further research efforts to prevent and contain the impact of new VOCs during the ongoing pandemic.
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Affiliation(s)
- Danyi Ao
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Tianxia Lan
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Xuemei He
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Jian Liu
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Li Chen
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Daniel T. Baptista‐Hon
- Center for Biomedicine and InnovationsFaculty of MedicineMacau University of Science and TechnologyMacauChina
| | - Kang Zhang
- Center for Biomedicine and InnovationsFaculty of MedicineMacau University of Science and TechnologyMacauChina
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
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200
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Ri H, Chen X. The updated strategy to overcome new challenge: Omicron variant (B.1.1.529) pandemic. CLINICAL AND TRANSLATIONAL DISCOVERY 2022; 2:e28. [PMID: 35572364 PMCID: PMC9087120 DOI: 10.1002/ctd2.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 11/20/2022]
Abstract
The new variant was discovered in South Africa and threatened the word of concerning new pandemic coming from this variant. The Omicron variant likely would spread more easily than the original SARS‐CoV‐2 virus, and can spread the virus to others, even if they are vaccinated or don't have symptoms. WHO first reported the new strain on November 24, 2021, after a case was reported in South Africa in November, later calling it a ‘variant of concern’ and that early evidence ‘suggests an increased risk of reinfection’. Following the discovery of the SARS‐CoV‐2 Omicron variant (B.1.1.529), the global COVID‐19 outbreak has resurfaced after appearing to be relentlessly spreading over the past two years.
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Affiliation(s)
- HyokJu Ri
- The Second Hospital Dalian Medical University Dalian China.,The Hospital of Pyongyang Medical College Pyongyang DPR of Korea
| | - Xin Chen
- The Second Hospital Dalian Medical University Dalian China
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