Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

Article Multidisciplinary Sciences

Functional evaluation of the P681 H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike

Bailey Lubinski et al.

Summary: The P681H mutation in the B.1.1.7 variant of SARS-CoV-2 does not significantly impact viral entry or cell-cell spread.

ISCIENCE (2022)

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Article Multidisciplinary Sciences

Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis

Bryan A. Johnson et al.

Summary: The genetic mutation in SARS-CoV-2 resulted in better fitness in some cells but lower replication capacity in human respiratory cell lines. Despite reducing disease symptoms, the Delta PRRA mutant provided protection against rechallenge with the wildtype SARS-CoV-2.

NATURE (2021)

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Article Biochemistry & Molecular Biology

A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent

Tianshu Xiao et al.

Summary: This study introduces a trimeric ACE2 ectodomain variant engineered using a structure-based approach, which has a high binding affinity for the spike protein of SARS-CoV-2, preserved peptidase activity, and the ability to block angiotensin II receptor activation. The engineered ACE2 also shows potent inhibition of SARS-CoV-2 infection in cell culture, suggesting it may be a promising therapeutic agent for COVID-19.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

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Article Microbiology

Furin cleavage of SARS-CoV-2 Spike promotes but is not essential for infection and cell-cell fusion

Guido Papa et al.

Summary: Research suggests that furin plays a promoting role in SARS-CoV-2 infectivity and cell-cell spread, but it is not essential, indicating that furin inhibitors may reduce but not completely prevent viral spread.

PLOS PATHOGENS (2021)

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Article Microbiology

SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells

Michihito Sasaki et al.

Summary: This study identified SARS-CoV-2 variants with mutations at the cleavage motif of the S protein (S gene mutants) that undergo inefficient proteolytic cleavage, leading to smaller plaques and less infectivity. These mutants emerged rapidly through virus propagation in Vero cells and may have been unknowingly used in experiments, antiviral screenings, and vaccine development. The mutations affect the virus' entry pathway and cell tropism, emphasizing the importance of monitoring de novo S gene mutations during tissue-culture propagation.

PLOS PATHOGENS (2021)

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Article Multidisciplinary Sciences

Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM

Cong Xu et al.

Summary: The recent global health emergency caused by SARS-CoV-2 outbreak is mediated by the interaction between the SARS-CoV-2 trimeric spike glycoprotein and the human ACE2 receptor. The SARS-CoV-2 S trimer is more sensitive to ACE2 receptor compared to SARS-CoV S trimer, potentially contributing to its superior infectivity. Research findings depict the mechanism of ACE2-induced conformational transitions in S trimer structure, aiding in the development of anti-SARS-CoV-2 vaccines and therapeutics.

SCIENCE ADVANCES (2021)

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Review Biochemistry & Molecular Biology

Binding Revisited-Avidity in Cellular Function and Signaling

Simon Erlendsson et al.

Summary: Avidity is a term used to describe the accumulated strength of multiple interactions between biomolecules, covering both specific and nonspecific interactions. Unlike affinity, which focuses on individual binding events, avidity is a macroscopic parameter linked to various microscopic events and can be influenced by reduced dimensionality and hindered diffusion. In biological systems, avidity plays a role in explaining discrepancies between cellular and in vitro binding strengths, and its effects on intracellular signaling processes are also important to consider.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Article Biochemistry & Molecular Biology

Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera

Piyada Supasa et al.

Summary: Research on the UK-dominant variant B.1.1.7 shows that it is harder to neutralize than the parental virus, but widespread escape from antibodies or monoclonal antibodies has not been observed yet.

CELL (2021)

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Article Biochemistry & Molecular Biology

Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera

Daming Zhou et al.

Summary: The race to develop vaccines against SARS-CoV-2 variants, such as B.1.1.7, B.1.351, and P.1, is ongoing as these variants have mutations in the spike protein, potentially leading to immune escape. A structure-function analysis of B.1.351 revealed tighter ACE2 binding and widespread evasion from monoclonal antibody neutralization, particularly driven by the E484K mutation.

CELL (2021)

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Article Multidisciplinary Sciences

Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant

Jun Zhang et al.

Summary: The Delta variant of SARS-CoV-2 is more efficient at fusing membranes at low levels of cellular receptor ACE2, possibly contributing to its heightened transmissibility. Each variant shows different rearrangement of the antigenic surface of the S protein, but only the changes in the RBD make it a better target for therapeutic antibodies.

SCIENCE (2021)

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Article Multidisciplinary Sciences

The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2

Donald J. Benton et al.

Summary: Studies indicate that the G614 mutant spike adopts more open conformations, which may facilitate binding to the SARS-CoV-2 receptor ACE2 and the subsequent structural rearrangements required for viral membrane fusion.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Multidisciplinary Sciences

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

Nicholas G. Davies et al.

Summary: A new variant of SARS-CoV-2 has emerged in England, with a higher reproduction number and potential for large resurgences of COVID-19 cases. Without stringent control measures, it is projected that COVID-19 hospitalizations and deaths in England for the first 6 months of 2021 will exceed those in 2020. The variant has spread globally and exhibited similar transmission increases in Denmark, Switzerland, and the United States.

SCIENCE (2021)

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Article Multidisciplinary Sciences

SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity

Seiya Ozono et al.

Summary: The naturally occurring mutations of SARS-CoV-2 spike protein can affect cell entry, with the D614G mutation resulting in increased cell entry and maintaining susceptibility to neutralization by antisera against prototypic viruses. Further global surveillance is needed to understand the transmissibility of SARS-CoV-2 among humans.

NATURE COMMUNICATIONS (2021)

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Article Biology

SARS-CoV-2 S protein:ACE2 interaction reveals novel allosteric targets

Palur V. Raghuvamsi et al.

Summary: The study reveals that the interaction between SARS-CoV-2 spike protein and ACE2 receptor triggers long-range allosteric propagation, affecting proteolytic processing and viral host entry. The dynamics map of the S:ACE2 interface provides mechanistic insights into how ACE2 binding is coupled to distal proteolysis sites. This indicates potential therapeutic targets for virus-host membrane fusion.

ELIFE (2021)

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Article Biophysics

The flexibility of ACE2 in the context of SARS-CoV-2 infection

Emilia P. Barros et al.

Summary: The COVID-19 pandemic has caused significant loss of life worldwide, and there are still unanswered questions regarding the viral association to ACE2 receptor. Molecular dynamics simulations reveal the flexibility of the ACE2 receptor and its dynamics on the cell surface, which could provide insights for the development of therapeutics against SARS-CoV-2.

BIOPHYSICAL JOURNAL (2021)

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Article Biophysics

A multiscale coarse-grained model of the SARS-CoV-2 virion

Alvin Yu et al.

Summary: This article presents the current status and ongoing development of a largely bottom-up coarse-grained (CG) model of the SARS-CoV-2 virion. The CG model was constructed using data from cryo-electron microscopy, x-ray crystallography, and computational predictions to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into the complete virion model. The CG model allows for capturing viral behavior that is difficult to observe in atomistic simulations and can be iteratively improved with new data.

BIOPHYSICAL JOURNAL (2021)

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Article Computer Science, Hardware & Architecture

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

Lorenzo Casalino et al.

Summary: The study introduced a generalizable AI-driven workflow that allows for more efficient exploration of the dynamics of molecular systems, particularly focusing on the mechanisms of infectivity of the SARS-CoV-2 virus. Several novel scientific discoveries were made, including the elucidation of the spike protein's full glycan shield, the role of spike glycans in modulating virus infectivity, and the characterization of flexible interactions between the spike protein and the human ACE2 receptor. The research also demonstrated the potential of AI in accelerating conformational sampling across different systems for future applications in SARS-CoV-2 and other molecular systems.

INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS (2021)

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Article Microbiology

The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways

Manon Laporte et al.

Summary: The high transmissibility of SARS-CoV-2 is related to the virus's abundant replication in the upper airways, which differs from other highly pathogenic coronaviruses. The spike protein of SARS-CoV-2 exhibits intrinsic temperature preference, optimizing the virus for the human respiratory tract and enhancing its transmission. Additionally, certain proteases in the human airways play a key role in activating the spike protein for virus entry, further increasing SARS-CoV-2's ability to spread.

PLOS PATHOGENS (2021)

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Article Multidisciplinary Sciences

The SARS-CoV-2 Spike variant D614G favors an open conformational state

Rachael A. Mansbach et al.

Summary: The emergence of the G-form variant of COVID-19 has led to a more infectious strain with increased viral loads, likely due to changes in protein energetics favoring infection-capable states and enhanced exposure of the receptor binding domain. These findings are crucial for vaccine design.

SCIENCE ADVANCES (2021)

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Article Biochemistry & Molecular Biology

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

Chang Liu et al.

Summary: Recent study examined the neutralizing ability of monoclonal antibodies, convalescent and vaccine sera against the Indian variants B.1.617.1 and B.1.617.2, showing that the neutralization of these variants is reduced compared to the ancestral strains, without widespread antibody escape as seen in other variants like B.1.351.

CELL (2021)

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Article Biochemistry & Molecular Biology

Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function

Tzu-Jing Yang et al.

Summary: The spike protein of the SARS-CoV-2 B.1.1.7 variant exhibits mutations that affect virus binding to the host ACE2 receptor and immune evasion. The A570D and N501Y mutations have been shown to impact the stability of the spike protein structure, and an introduced neutralizing antibody can effectively neutralize different strains of the virus.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

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Article Multidisciplinary Sciences

Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity

Sophie M-C Gobeil et al.

Summary: SARS-CoV-2 variants with multiple spike mutations have increased transmission and resistance to antibodies. Research showed that these variants have enhanced receptor binding and a preference for receptor binding domain up states. Different variants exhibit different mechanisms for resistance to neutralizing antibodies, which helps explain their transmission and resistance.

SCIENCE (2021)

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Article Multidisciplinary Sciences

Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants

Yongfei Cai et al.

Summary: The study found that the B.1.1.7 variant has increased receptor binding affinity, while the B.1.351 variant has developed resistance to some neutralizing antibodies by reshaping antigenic surfaces on the spike protein.

SCIENCE (2021)

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Article Multidisciplinary Sciences

Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2

Renhong Yan et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

Daniel Wrapp et al.

SCIENCE (2020)

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Article Biochemistry & Molecular Biology

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Alexandra C. Walls et al.

CELL (2020)

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Article Biochemistry & Molecular Biology

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

Markus Hoffmann et al.

CELL (2020)

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Article Multidisciplinary Sciences

Cell entry mechanisms of SARS-CoV-2

Jian Shang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Multidisciplinary Sciences

Site-specific glycan analysis of the SARS-CoV-2 spike

Yasunori Watanabe et al.

SCIENCE (2020)

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Article Biochemistry & Molecular Biology

A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells

Markus Hoffmann et al.

MOLECULAR CELL (2020)

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Article Biochemistry & Molecular Biology

A thermostable, closed SARS-CoV-2 spike protein trimer

Xiaoli Xiong et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

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Article Biochemistry & Molecular Biology

SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects

Antoni G. Wrobel et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

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Article Multidisciplinary Sciences

Distinct conformational states of SARS-CoV-2 spike protein

Yongfei Cai et al.

SCIENCE (2020)

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Article Chemistry, Physical

Conformational transition of SARS-CoV-2 spike glycoprotein between its closed and open states

Mert Gur et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

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Article Multidisciplinary Sciences

Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion

Donald J. Benton et al.

NATURE (2020)

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Article Multidisciplinary Sciences

Structures and distributions of SARS-CoV-2 spike proteins on intact virions

Zunlong Ke et al.

NATURE (2020)

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Article Multidisciplinary Sciences

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

Beata Turonova et al.

SCIENCE (2020)

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Article Virology

Interaction of Human ACE2 to Membrane-Bound SARS-CoV-1 and SARS-CoV-2 S Glycoproteins

Sai Priya Anand et al.

VIRUSES-BASEL (2020)

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Article Multidisciplinary Sciences

Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor

Jinsung Yang et al.

NATURE COMMUNICATIONS (2020)

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Article Chemistry, Multidisciplinary

Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein

Lorenzo Casalino et al.

ACS CENTRAL SCIENCE (2020)

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Article Microbiology

Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles

Maolin Lu et al.

CELL HOST & MICROBE (2020)

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SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity

Lizhou Zhang et al.

NATURE COMMUNICATIONS (2020)

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Review Medicine, Research & Experimental

ACE2 and ACE: structure-based insights into mechanism, regulation and receptor recognition by SARS-CoV

Lizelle Lubbe et al.

CLINICAL SCIENCE (2020)

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Article Chemistry, Physical

Multiconfigurational Coarse-Grained Molecular Dynamics

Morris E. Sharp et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

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CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Jing Huang et al.

NATURE METHODS (2017)

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Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion

Alexandra C. Walls et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

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Article Biophysics

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

Robert T. McGibbon et al.

BIOPHYSICAL JOURNAL (2015)

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Meeting Abstract Biophysics

Moltemplate a Coarse-Grained Model Assembly Tool

Andrew I. Jewett et al.

BIOPHYSICAL JOURNAL (2013)

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Article Chemistry, Physical

On the 'Dielectric Constant of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi

Lin Li et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

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Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric

Ting Zhou et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

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Article Chemistry, Physical

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions

Yusuke Naritomi et al.

JOURNAL OF CHEMICAL PHYSICS (2011)

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Article Chemistry, Physical

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

Kyle A. Beauchamp et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

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Isothermal-isobaric molecular dynamics using stochastic velocity rescaling

Giovanni Bussi et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

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PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations

L. Martinez et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

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Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins

Edward Lyman et al.

BIOPHYSICAL JOURNAL (2008)

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A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules

Zhiyong Zhang et al.

BIOPHYSICAL JOURNAL (2008)

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The relative entropy is fundamental to multiscale and inverse thermodynamic problems

M. Scott Shell

JOURNAL OF CHEMICAL PHYSICS (2008)

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Article Chemistry, Multidisciplinary

Software news and updates - CHARNIM-GUI: A web-based grraphical user interface for CHARMM

Sunhwan Jo et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

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Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase

P Maragakis et al.

JOURNAL OF MOLECULAR BIOLOGY (2005)

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Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

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