Physicochemical tools for studying virus interactions with targeted cell membranes in a molecular and spatiotemporally resolved context

AbstractThe objective of this critical review is to provide an overview of how emerging bioanalytical techniques are expanding our understanding of the complex physicochemical nature of virus interactions with host cell surfaces. Herein, selected model viruses representing both non-enveloped (simian virus 40 and human norovirus) and enveloped (influenza A virus, human herpes simplex virus, and human immunodeficiency virus type 1) viruses are highlighted. The technologies covered utilize a wide range of cell membrane mimics, from supported lipid bilayers (SLBs) containing a single purified host membrane component to SLBs derived from the plasma membrane of a target cell, which can be compared with live-cell experiments to better understand the role of individual interaction pairs in virus attachment and entry. These platforms are used to quantify binding strengths, residence times, diffusion characteristics, and binding kinetics down to the single virus particle and single receptor, and even to provide assessments of multivalent interactions. The technologies covered herein are surface plasmon resonance (SPR), quartz crystal microbalance with dissipation (QCM-D), dynamic force spectroscopy (DFS), total internal reflection fluorescence (TIRF) microscopy combined with equilibrium fluctuation analysis (EFA) and single particle tracking (SPT), and finally confocal microscopy using multi-labeling techniques to visualize entry of individual virus particles in live cells. Considering the growing scientific and societal needs for untangling, and interfering with, the complex mechanisms of virus binding and entry, we hope that this review will stimulate the community to implement these emerging tools and strategies in conjunction with more traditional methods. The gained knowledge will not only contribute to a better understanding of the virus biology, but may also facilitate the design of effective inhibitors to block virus entry.

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Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations

Physical Chemistry Chemical Physics ◽

10.1039/c7cp01921a ◽

2017 ◽

Vol 19 (25) ◽

pp. 16806-16818 ◽

Cited By ~ 31

Author(s):

M. Doktorova ◽

D. Harries ◽

G. Khelashvili

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Lipid Bilayers ◽

Lipid Membranes ◽

Real Space ◽

Fluctuation Analysis ◽

Bending Rigidity ◽

Wide Range ◽

Dynamics Simulations

Computational methodology that allows to extract bending rigidity and tilt modulus for a wide range of single and multi-component lipid bilayers from real-space analysis of fluctuations in molecular dynamics simulations.

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Rearrangement of Simian Virus 40 Regulatory Region Is Not Required for Induction of Progressive Multifocal Leukoencephalopathy in Immunosuppressed Rhesus Monkeys

Journal of Virology ◽

10.1128/jvi.79.3.1361-1366.2005 ◽

2005 ◽

Vol 79 (3) ◽

pp. 1361-1366 ◽

Cited By ~ 11

Author(s):

Xin Dang ◽

Michael K. Axthelm ◽

Norman L. Letvin ◽

Igor J. Koralnik

Keyword(s):

Progressive Multifocal Leukoencephalopathy ◽

Jc Virus ◽

Regulatory Region ◽

Simian Virus 40 ◽

Simian Virus ◽

T Antigen ◽

C Terminus ◽

Wide Range ◽

Disease Induction ◽

The Brain

ABSTRACT Rearrangements of the JC virus (JCV) regulatory region (RR) are consistently found in the brains of patients with progressive multifocal leukoencephalopathy (PML), whereas the archetype RR is present in their kidneys. In addition, the C terminus of the large T antigen (T-Ag) shows greater variability in PML than does the rest of the coding region. To determine whether similar changes in simian virus 40 (SV40) are necessary for disease induction in monkeys, we sequenced the SV40 RR and the C terminus of the T-Ag from the brain of simian/human immunodeficiency virus (SHIV)-infected monkey 18429, which presented spontaneously with an SV40-associated PML-like disease, as well as from the peripheral blood mononuclear cells (PBMC), kidneys, and brains of SV40-seronegative, SHIV-infected monkeys 21289 and 21306, which were inoculated with the 18429 brain SV40 isolate. These animals developed both SV40-associated PML and meningoencephalitis. Thirteen types of SV40 RR were characterized. Compared to the SV40 archetype, we identified RRs with variable deletions in either the origin of replication, the 21-bp repeat elements, or the late promoter, as well as deletions or duplications of the 72-bp enhancer. The archetype was the most prominent RR in the brain of monkey 18429. Shortly after inoculation, a wide range of RRs could be found in the PBMC of monkeys 21289 and 21306. However, the archetype RR became the predominant type in their blood, kidneys, and brains at the time of sacrifice. On the contrary, the T-Ag C termini remained identical in all compartments of the three animals. These results indicate that unlike JCV in humans, rearrangements of SV40 RR are not required for brain disease induction in immunosuppressed monkeys.

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Induction of adaptive immune responses against antigens incorporated within the capsid of simian virus 40

Journal of General Virology ◽

10.1099/jgv.0.001445 ◽

2020 ◽

Vol 101 (8) ◽

pp. 853-862

Author(s):

Kikue Saika ◽

Masahiko Kato ◽

Hideaki Sanada ◽

Sho Matsushita ◽

Masanori Matsui ◽

...

Keyword(s):

Immune Responses ◽

Influenza A ◽

Matrix Protein ◽

Insect Cells ◽

Simian Virus 40 ◽

Simian Virus ◽

Vaccine Platform ◽

Adaptive Immune Responses ◽

Adaptive Immune ◽

Ctl Epitope

Simian virus 40 (SV40) is a monkey polyomavirus. The capsid structure is icosahedral and comprises VP1 units that measure 45 nm in diameter. Five SV40 VP1 molecules form one pentamer subunit, and a single icosahedral subunit comprises 72 pentamers; a single SV40 VP1 capsid comprises 360 SV40 VP1 molecules. In a previous study, we showed that an influenza A virus matrix protein 1 (M1) CTL epitope inserted within SV40 virus-like particles (VLPs) induced cytotoxic T lymphocytes (CTLs) without the need for an adjuvant. Here, to address whether SV40 VLPs induce adaptive immune responses against VLP-incorporated antigens, we prepared SV40 VLPs containing M1 or chicken ovalbumin (OVA). This was done by fusing M1 or OVA with the carboxyl terminus of SV40 VP2 and co-expressing them with SV40 VP1 in insect cells using a baculovirus vector. Intraperitoneal (i.p.) or intranasal administration of SV40 VLPs incorporating M1 induced the production of CTLs specific for the M1 epitope without the requirement for adjuvant. The production of antibodies against SV40 VLPs was also induced by i.p. administration of SV40 VLPs in the absence of adjuvant. Finally, the administration of SV40 VLPs incorporating OVA induced anti-OVA antibodies in the absence of adjuvant; in addition, the level of antibody production was comparable with that after i.p. administration of OVA plus alum adjuvant. These results suggest that the SV40 capsid incorporating foreign antigens can be used as a vaccine platform to induce adaptive immune responses without the need for adjuvant.

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Non-coronavirus Genome Sequences Identified from Metagenomic Analysis of Clinical Samples from COVID-19 Infected Patients: An Evidence for Co-infection

10.20944/preprints202005.0505.v2 ◽

2020 ◽

Author(s):

Mohamed Abouelkhair

Keyword(s):

Influenza A ◽

Hepatitis Virus ◽

Simian Virus 40 ◽

Simian Virus ◽

Viral Fitness ◽

World Health ◽

Clinical Samples ◽

Genome Sequences ◽

Epidemic Disease ◽

Critical Determinant

In December 2019, pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection emerged in Wuhan City, Hubei Province, China. Early in 2020, the World Health Organization (WHO) announced a new name for the 2019-nCoV-caused epidemic disease: coronavirus disease 2019 (COVID-19) and declared COVID-19 to be the sixth international public health emergency. Cellular co-infection is a critical determinant of both viral fitness and infection outcome and plays a crucial role in shaping the host immune response to infections. In this study, sixty-eight public next-generation sequencing libraries from SARS-CoV-2 infected patients were retrieved from the NCBI Sequence Read Archive database using SRA-Toolkit. Using an alignment-free method based on K-mer mapping and extension, SARS-CoV-2 was identified in all except three patients. Influenza A H7N9 (3/68), Human immunodeficiency virus 1 (1/68), rhabdovirus isolate (3/68), Human metapneumovirus (1/68), coronaviruses NL63 (1/68), Parvovirus (1/68), Simian virus 40 (1/68), and hepatitis virus (1/68) genome sequences were detected in SARS-CoV-2 infected patients.

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