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Processes
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Modeling, Control and Pathogenesis Process in Virus Infection
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Modeling, Control and Pathogenesis Process in Virus Infection

A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Biological Processes and Systems".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 16217

Special Issue Editors

Dr. Katarzyna Otulak-Kozieł

E-Mail Website
Guest Editor
Institute of Biology, Department of Botany, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
Interests: physiological; molecular and cellular processes in plants; plant-microbe interaction; plant virology; plant defense; cell biology; cell signaling
Special Issues, Collections and Topics in MDPI journals
Dr. Edmund Kozieł

E-Mail Website
Guest Editor
Institute of Biology, Department of Botany, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
Interests: bioinformatic; virus phylogenetics; molecular biology of bromoviridae; plant-virus interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Viruses are a numerous, highly diverse, and economically important group of plant, animal, and human pathogens. Viruses are small in size, but cause an enormous amount of pathological changes/modifications in different types of host cells to sustain. Viruses are pathogens that are a fundamentally varied form of life, which makes them interesting objects for research. Unlike all other living organisms, viruses are non-cellular. In contrast to cells, which multiply by dividing into daughter cells, viruses assemble from their structural components (genome and proteins). Consequently, plant, animal, and human viruses need cells and are dependent on the cellular machinery of their hosts to reproduce and also use elements of cell/tissue to transport themselves from cell to cell or for systemic transport. As a rule, virus particles are immobile outside the infected host; they rely on the aid of other organisms or the environment for their dissemination/translocation.

The forthcoming Special Issue of Processes on the “Modeling, Control, and Pathogenesis Process in Virus Infection” will publish a collection of the latest original research articles, short communications, and reviews concerning recent progress in research into virus–host interactions. It will emphasize that the problem of viral infection in various organisms is emerging and has an upward tendency. New strains of viruses are evolving to oppose the immune system of plant, animal, and human hosts.

Therefore, this Special Issue will focus on present new insights and aspects of modeling, control, and molecular and cellular mechanisms of the pathogenesis process of viral infection ongoing in plant, animal, and human hosts.

Dr. Katarzyna Otulak-Kozieł
Dr. Edmund Kozieł
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Processes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • viral pathogenesis
  • viral infection
  • plant viruses
  • animal viruses
  • human viruses
  • infection modeling
  • molecular and cellular mechanism of viral infection
  • infection control
  • cell biology
  • cell signaling
  • pathogenesis changes in host cells

Published Papers (5 papers)

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Research

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13 pages, 1549 KiB  
Article
Follow-Up of Liver Stiffness with Shear Wave Elastography in Chronic Hepatitis C Patients in Sustained Virological Response Augments Clinical Risk Assessment
by Anikó Folhoffer, Aladár D. Rónaszéki, Bettina K. Budai, Petra Borsos, Vince Orbán, Gabriella Győri, Ferenc Szalay and Pál N. Kaposi
Processes 2021, 9(5), 753; https://0-doi-org.brum.beds.ac.uk/10.3390/pr9050753 - 24 Apr 2021
Cited by 2 | Viewed by 2273
Abstract
This study aimed to observe the effect of the direct-acting antiviral (DAA) therapy on liver stiffness (LS) and serum biomarkers. We prospectively observed 35 patients with chronic hepatitis C infection and attained a sustained virological response (SVR) after antiviral therapy. Shear wave elastography [...] Read more.
This study aimed to observe the effect of the direct-acting antiviral (DAA) therapy on liver stiffness (LS) and serum biomarkers. We prospectively observed 35 patients with chronic hepatitis C infection and attained a sustained virological response (SVR) after antiviral therapy. Shear wave elastography (SWE) measurement was performed at the beginning of DAA treatment and at 48 weeks after the end of treatment (EOT48w). The METAVIR score and the score for varices needing treatment (VNT) were determined based on the LS values; the fibrosis-4 (FIB4) score was calculated from laboratory tests. The baseline LS (mean ± standard deviation = 2.59 ± 0.89 m/s) decreased significantly after successful DAA therapy (1.90 ± 0.50 m/s; p < 0.001). The METAVIR score showed significant improvement at EOT48w (F0/1 = 9, F2 = 2, F3 = 10, F4 = 14) compared to the initial status (F0/1 = 2, F2 = 1, F3 = 7, F4 = 25; p < 0.028). The FIB4 score indicated less fibrosis after therapy (2.04 ± 1.12) than at baseline (3.51 ± 2.24; p < 0.018). Meanwhile, the number of patients with a high-risk of VNT was significantly less at EOT48w (4 vs. 15 at baseline; OR = 0.17 95% confidence interval (CI) = 0.05–0.59, p < 0.007). SWE indicates a significant resolution of liver fibrosis when chronic hepatitis C patients are in SVR, coinciding with a lower risk of VNT. Full article
(This article belongs to the Special Issue Modeling, Control and Pathogenesis Process in Virus Infection)
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13 pages, 4444 KiB  
Article
Modeling the Spread of Epidemics Based on Cellular Automata
by Jindong Dai, Chi Zhai, Jiali Ai, Jiaying Ma, Jingde Wang and Wei Sun
Processes 2021, 9(1), 55; https://0-doi-org.brum.beds.ac.uk/10.3390/pr9010055 - 29 Dec 2020
Cited by 20 | Viewed by 4243
Abstract
Mathematical modeling is a powerful tool to study the process of the spread of infectious diseases. Among various mathematical methods for describing the spread of infectious diseases, the cellular automaton makes it possible to explicitly simulate both the spatial and temporal evolution of [...] Read more.
Mathematical modeling is a powerful tool to study the process of the spread of infectious diseases. Among various mathematical methods for describing the spread of infectious diseases, the cellular automaton makes it possible to explicitly simulate both the spatial and temporal evolution of epidemics with intuitive local rules. In this paper, a model is proposed and realized on a cellular automata platform, which is applied to simulate the spread of coronavirus disease 2019 (COVID-19) for different administrative districts. A simplified social community is considered with varying parameters, e.g., sex ratio, age structure, population movement, incubation and treatment period, immunity, etc. COVID-19 confirmation data from New York City and Iowa are adopted for model validation purpose. It can be observed that the disease exhibits different spread patterns in different cities, which could be well accommodated by this model. Then, scenarios under different control strategies in the next 100 days in Iowa are simulated, which could provide a valuable reference for decision makers in identifying the critical factors for future infection control in Iowa. Full article
(This article belongs to the Special Issue Modeling, Control and Pathogenesis Process in Virus Infection)
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16 pages, 1583 KiB  
Article
Modeling, Control, and Prediction of the Spread of COVID-19 Using Compartmental, Logistic, and Gauss Models: A Case Study in Iraq and Egypt
by Mahmoud A. Ibrahim and Amenah Al-Najafi
Processes 2020, 8(11), 1400; https://0-doi-org.brum.beds.ac.uk/10.3390/pr8111400 - 02 Nov 2020
Cited by 19 | Viewed by 4837
Abstract
In this paper, we study and investigate the spread of the coronavirus disease 2019 (COVID-19) in Iraq and Egypt by using compartmental, logistic regression, and Gaussian models. We developed a generalized SEIR model for the spread of COVID-19, taking into account mildly and [...] Read more.
In this paper, we study and investigate the spread of the coronavirus disease 2019 (COVID-19) in Iraq and Egypt by using compartmental, logistic regression, and Gaussian models. We developed a generalized SEIR model for the spread of COVID-19, taking into account mildly and symptomatically infected individuals. The logistic and Gaussian models were utilized to forecast and predict the numbers of confirmed cases in both countries. We estimated the parameters that best fit the incidence data. The results provide discouraging forecasts for Iraq from 22 February to 8 October 2020 and for Egypt from 15 February to 8 October 2020. To provide a forecast of the spread of COVID-19 in Iraq, we present various simulation scenarios for the expected peak and its timing using Gaussian and logistic regression models, where the predicted cases showed a reasonable agreement with the officially reported cases. We apply our compartmental model with a time-periodic transmission rate to predict the possible start of the second wave of the COVID-19 epidemic in Egypt and the possible control measures. Our sensitivity analyses of the basic reproduction number allow us to conclude that the most effective way to prevent COVID-19 cases is by decreasing the transmission rate. The findings of this study could therefore assist Iraqi and Egyptian officials to intervene with the appropriate safety measures to cope with the increase of COVID-19 cases. Full article
(This article belongs to the Special Issue Modeling, Control and Pathogenesis Process in Virus Infection)
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15 pages, 543 KiB  
Article
Influence of Fermented Diets on In Vitro Survival Rate of Some Artificially Inoculated Pathogens—A Preliminary Study
by Sebastian Bunte, Birgit Keller, Bussarakam Chuppava, Josef Kamphues, Christian Visscher and Amr Abd El-Wahab
Processes 2020, 8(11), 1345; https://0-doi-org.brum.beds.ac.uk/10.3390/pr8111345 - 24 Oct 2020
Cited by 6 | Viewed by 1595
Abstract
Improving the hygienic status of feed ingredients by biotechnological processes as fermentation is of the greatest concern. This preliminary study aimed to investigate whether there are relevant effects of fermented liquid feed (FLF) on the survival of potential pathogens in vitro. The feed [...] Read more.
Improving the hygienic status of feed ingredients by biotechnological processes as fermentation is of the greatest concern. This preliminary study aimed to investigate whether there are relevant effects of fermented liquid feed (FLF) on the survival of potential pathogens in vitro. The feed (fresh basis) consisted of 50% rye, 30% rapeseed extracted meal, 10% barley and 10% wheat. Glass bottles were filled about 14.1 g water (38 °C) containing the diluted starter culture and feed (8.81 g). Fermentation led to high levels of lactate (5–7% of dry matter), low pH values (<4.0) and low levels of acetic acid (<1% of dry matter) in the FLF. The survival rate of pathogens added, such as Salmonella enterica serovar Typhimurium, Escherichia coli and Clostridium perfringens after 6 h of controlled fermentation, was significantly reduced (<2 log10 CFU/g). The counts of Candida krusei in FLF at 3 h and 6 h post inoculation remained almost unchanged regardless of the incubation time. Even adding sodium-benzoate at a concentration of up to 0.25% in the liquid feed did not reduce the survival of C.krusei during fermentation. Based on this in vitro study, feeding of FLF seems a promising strategy to reduce pathogen transmission but has to be confirmed on natural feeds by pathogens for increasing the hygienic properties. Full article
(This article belongs to the Special Issue Modeling, Control and Pathogenesis Process in Virus Infection)
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Review

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23 pages, 391 KiB  
Review
Diversity of Plant Virus Movement Proteins: What Do They Have in Common?
by Yuri L. Dorokhov, Ekaterina V. Sheshukova, Tatiana E. Byalik and Tatiana V. Komarova
Processes 2020, 8(12), 1547; https://0-doi-org.brum.beds.ac.uk/10.3390/pr8121547 - 26 Nov 2020
Cited by 4 | Viewed by 2473
Abstract
The modern view of the mechanism of intercellular movement of viruses is based largely on data from the study of the tobacco mosaic virus (TMV) 30-kDa movement protein (MP). The discovered properties and abilities of TMV MP, namely, (a) in vitro binding of [...] Read more.
The modern view of the mechanism of intercellular movement of viruses is based largely on data from the study of the tobacco mosaic virus (TMV) 30-kDa movement protein (MP). The discovered properties and abilities of TMV MP, namely, (a) in vitro binding of single-stranded RNA in a non-sequence-specific manner, (b) participation in the intracellular trafficking of genomic RNA to the plasmodesmata (Pd), and (c) localization in Pd and enhancement of Pd permeability, have been used as a reference in the search and analysis of candidate proteins from other plant viruses. Nevertheless, although almost four decades have passed since the introduction of the term “movement protein” into scientific circulation, the mechanism underlying its function remains unclear. It is unclear why, despite the absence of homology, different MPs are able to functionally replace each other in trans-complementation tests. Here, we consider the complexity and contradictions of the approaches for assessment of the ability of plant viral proteins to perform their movement function. We discuss different aspects of the participation of MP and MP/vRNA complexes in intra- and intercellular transport. In addition, we summarize the essential MP properties for their functioning as “conditioners”, creating a favorable environment for viral reproduction. Full article
(This article belongs to the Special Issue Modeling, Control and Pathogenesis Process in Virus Infection)
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