COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease

Review Infectious Diseases

Comparing COVID-19 vaccines for their characteristics, efficacy and effectiveness against SARS-CoV-2 and variants of concern: a narrative review

Thibault Fiolet et al.

Summary: Overall, COVID-19 vaccines have high efficacy against the original strain and variants of concern, with rare serious adverse events. However, prices vary significantly for different vaccines.

CLINICAL MICROBIOLOGY AND INFECTION (2022)

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Article Biology

Atom counting method for determining elemental composition of viruses and its applications in biothermodynamics and environmental science

Marko Popovic

Summary: This paper proposes a new method for determining the elemental composition of viruses using atom counting. The method is found to be more accurate than existing molecular composition and geometric methods and can provide complementary information when compared with the other two.

COMPUTATIONAL BIOLOGY AND CHEMISTRY (2022)

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Review Cell Biology

Mechanisms of SARS-CoV-2 entry into cells

Cody B. Jackson et al.

Summary: The entry of SARS-CoV-2 into host cells is facilitated by the interaction between the viral spike protein and ACE2, leading to virus-cell membrane fusion, which has been extensively studied at the structural and cellular levels worldwide. This understanding has paved the way for the development of effective vaccines in response to the COVID-19 pandemic, caused by the infection with SARS-CoV-2.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2022)

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Article Infectious Diseases

Mechanistic Models of COVID-19: Insights into Disease Progression, Vaccines, and Therapeutics

Rajat Desikan et al.

Summary: The COVID-19 pandemic has had a severe impact on global health systems and economies. Efforts are underway to improve vaccine efficacy, optimize deployment, and develop new antiviral therapies. Mechanistic viral dynamics and pharmacology models have played a key role in advancing our understanding of SARS-CoV-2 and its variants, as well as the effectiveness of treatments and vaccines.

INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS (2022)

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Article Virology

Strain wars 2: Binding constants, enthalpies, entropies, Gibbs energies and rates of binding of SARS-CoV-2 variants

Marko Popovic

Summary: Mutations in the SARS-CoV-2 virus lead to changes in chemical composition, thermodynamic properties, and infectivity. Some mutated strains show higher infectivity and are capable of suppressing earlier strains through interference.

VIROLOGY (2022)

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Article Green & Sustainable Science & Technology

SARS-CoV-2 Dynamics in the Mucus Layer of the Human Upper Respiratory Tract Based on Host-Cell Dynamics

Hanyu Li et al.

Summary: This study investigated the infection dynamics of SARS-CoV-2 in the mucus layer of the human upper airway. By simulating the virus transmission process in the nasal cavity-nasopharynx, the study revealed the strong influence of diffusion, convection, and beta on the time series of SARS-CoV-2 concentration in the mucus layer.

SUSTAINABILITY (2022)

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Review Immunology

Biothermodynamics of Viruses from Absolute Zero (1950) to Virothermodynamics (2022)

Marko Popovic

Summary: Biothermodynamics of viruses is a young and rapidly developing scientific discipline, which has gained increased attention and research during the recent pandemic. Empirical formulas and thermodynamic properties have been published for multiple viruses and virus variants, providing important references for research and response to the pandemic.

VACCINES (2022)

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Article Biotechnology & Applied Microbiology

Omicron BA.2.75 Subvariant of SARS-CoV-2 Is Expected to Have the Greatest Infectivity Compared with the Competing BA.2 and BA.5, Due to Most Negative Gibbs Energy of Binding

Marko Popovic

Summary: Omicron BA.2.75, with the most spike protein and other gene mutations, is likely to become the globally dominant strain of COVID-19 in 2022. Its chemical composition and thermodynamic properties have changed compared to previous variants. The Gibbs energy of binding for Omicron BA.2.75 is more negative than competing variants BA.2 and BA.5.

BIOTECH (2022)

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Article Biochemistry & Molecular Biology

Why Does the Novel Coronavirus Spike Protein Interact so Strongly with the Human ACE2? A Thermodynamic Answer

Jones de Andrade et al.

Summary: The higher chemical affinity of SARS-CoV-2 for hACE2 compared to SARS-CoV makes it more difficult to treat SARS-CoV-2 with drugs targeting its spike protein. This research helps to explain the infectivity of SARS-CoV-2.

CHEMBIOCHEM (2021)

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Article Pharmacology & Pharmacy

Mechanistic Modeling of SARS-CoV-2 and Other Infectious Diseases and the Effects of Therapeutics

Alan S. Perelson et al.

Summary: Modern viral kinetic modeling and its application in therapeutics has attracted attention from various fields, such as AIDS, hepatitis C, hepatitis B, and other viruses, including the recent use in understanding and optimizing interventions for the COVID-19 pandemic caused by SARS-CoV-2.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2021)

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Article Mathematical & Computational Biology

Mechanistic modeling of the SARS-CoV-2 disease map

Kinza Rian et al.

Summary: The web interface presents a comprehensive mechanistic model of the SARS-CoV-2 disease map, allowing the inference of human signaling circuits' detailed activity from gene expression experiments. Additionally, it enables the study of potential interventions' effects and has the potential to be an invaluable asset in the search for efficient antiviral treatments.

BIODATA MINING (2021)

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Article Multidisciplinary Sciences

Mechanistic modelling of COVID-19 and the impact of lockdowns on a short-time scale

Danish A. Ahmed et al.

Summary: This study modeled the movement and infection process of host populations, finding that on a short-time scale, population diffusion and movement behavior type do not significantly affect infection levels. The efficacy of lockdown measures depends on the spatial distribution of susceptible and infectious individuals.

PLOS ONE (2021)

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Article Multidisciplinary Sciences

Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects

Lucas L. Maldonado et al.

Summary: The study analyzed the codon usage patterns of viral and human genes, revealing similarities that could facilitate viral infection. It highlights the impact of viral infection on genetic features and suggests further research into the mechanisms of gene deregulation under new viral infections.

SCIENTIFIC REPORTS (2021)

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Article Chemistry, Medicinal

Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro

Son Tung Ngo et al.

Summary: The COVID-19 pandemic caused by the SARS-CoV-2 virus has led to millions of deaths globally. Developing an effective therapy targeting the main protease (Mpro) of the virus is urgent, with different methods used to calculate ligand-binding affinity to SARS-CoV-2 Mpro. Results suggest that Vina is more accurate in docking calculations, while FEP is the most accurate free energy method.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

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Review Biochemistry & Molecular Biology

Extracellular Vesicle-Based Therapy for COVID-19: Promises, Challenges and Future Prospects

Vamika Karn et al.

Summary: The COVID-19 pandemic has had a serious impact on public health and the economy, prompting an urgent need for effective therapeutic strategies. Extracellular vesicles (EVs) have shown promise in suppressing the cytokine storm and aiding in the recovery and treatment of COVID-19.

BIOMEDICINES (2021)

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Review Chemistry, Physical

Inhaled aerosols: Their role in COVID-19 transmission, including biophysical interactions in the lungs

Tomasz R. Sosnowski

Summary: This review discusses the role of aerosols in the transmission of COVID-19, including virus transport, deposition in the respiratory system, and the importance of masks in reducing spreading. It also focuses on the physicochemical phenomena of the virus entering the surface of lung liquids.

CURRENT OPINION IN COLLOID & INTERFACE SCIENCE (2021)

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Article Chemistry, Multidisciplinary

Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket

Lucy Fallon et al.

Summary: The SARS-CoV-2 coronavirus spike protein plays a crucial role in viral entry and is a target for neutralizing antibodies. By using simulations, interactions influencing spike protein dynamics can be identified for potential therapeutic targeting. Small molecules binding to specific pockets may modulate the spike protein equilibrium and shed light on its conformational changes.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

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Article Chemistry, Analytical

Single virus inductively coupled plasma mass spectroscopy analysis: A comprehensive study

Claude Degueldre

Summary: The study proposes adapting the SP-ICP-MS method for identification and counting of single viruses, with analysis and identification achieved through counting of master and key ions. The counting of virus units can be completed in 20 seconds, with analysis of main and key ions recommended to be carried out in Ar torch.

TALANTA (2021)

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Article Biochemistry & Molecular Biology