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Pathogens
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Pathogen-Host Interactions in Viral Infections
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Pathogen-Host Interactions in Viral Infections

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Viral Pathogens".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 13572

Special Issue Editors

Dr. Timokratis Karamitros

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Guest Editor
Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
Interests: bioinformatics; applied genomics; molecular virology; phylogenenomics; virus host interactions
Dr. Tara Patricia Hurst

E-Mail Website
Guest Editor
School of Health Sciences, Birmingham City University, Edgbaston, Birmingham B15 3TN, UK
Interests: immunology; molecular virology; viral pathogenesis and virus-host interactions
Dr. Lemonia Skoura

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Guest Editor
Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, S. Kyriakidi Str., 54636 Thessaloniki, Greece
Interests: medical microbiology; antibicrobial resistace; infection control; medical virology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Virus–host interactions are processes that occur during infections when both parties respond to each other at the cellular and molecular level.

Since viruses rely on their host cells for the biochemical and metabolic pathways used in genome replication and particle assembly, they have adopted a myriad of different strategies for exploiting the host resources and—at the same time—evading, escaping or manipulating host immune defenses.

The past few decades have witnessed a tremendous expansion in our knowledge of viral infections. These developments have enhanced our understanding of the structure and the architecture of the viral genome, viral proteins, and their assembly. They have enabled new insights into viral replication processes and the regulation of viral gene expression. Additionally, recent advances in next-generation sequencing technologies and bioinformatics algorithms, the development of high-end automated platforms for screening of serum biomarkers, as well as the establishment of sophisticated systems for patient monitoring, have revolutionized the study of host responses during viral infections. This has permitted multi-omics analyses based on machine learning algorithms. These new methodologies have allowed a more global view of host–pathogen interactions which were previously not possible with more targeted approaches.

In this exciting context, Pathogens is launching a Special Issue devoted to host–pathogen interactions during viral infections, focusing on respiratory and blood-borne viruses. Both original research and review articles are welcomed. This issue aims to cover the wide spectrum of virus–host interactions, including topics such as profiling of immunological responses in viral infections and vaccinations, antiviral drug resistance, transcriptomic signatures, virus versus host genomics (e.g., HLA typing), biomarkers, diverse clinical manifestations as a result of infections from different viral genotypes, intra-host variability (quasispecies), and viral immune evasion.

Dr. Timokratis Karamitros
Dr. Tara Patricia Hurst
Dr. Lemonia Skoura
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. Pathogens 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 2700 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.

Published Papers (5 papers)

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Research

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26 pages, 22006 KiB  
Article
Comparative Analysis of Human Hepatic Lesions in Dengue, Yellow Fever, and Chikungunya: Revisiting Histopathological Changes in the Light of Modern Knowledge of Cell Pathology
by Yasmin Pacheco Ribeiro, Luiz Fabio Magno Falcão, Vanessa Cavaleiro Smith, Jorge Rodrigues de Sousa, Carla Pagliari, Edna Cristina Santos Franco, Ana Cecília Ribeiro Cruz, Janniffer Oliveira Chiang, Livia Carício Martins, Juliana Abreu Lima Nunes, Fellipe Souza da Silva Vilacoert, Lais Carneiro dos Santos, Matheus Perini Furlaneto, Hellen Thais Fuzii, Marcos Virgilio Bertonsin Filho, Luccas Delgado da Costa, Maria Irma Seixas Duarte, Ismari Perini Furlaneto, Arnaldo Jorge Martins Filho, Tinara Leila de Souza Aarão, Pedro Fernando da Costa Vasconcelos and Juarez Antônio Simões Quaresmaadd Show full author list remove Hide full author list
Pathogens 2023, 12(5), 680; https://doi.org/10.3390/pathogens12050680 - 4 May 2023
Cited by 2 | Viewed by 2189
Abstract
Arboviruses, such as yellow fever virus (YFV), dengue virus (DENV), and chikungunya virus (CHIKV), present wide global dissemination and a pathogenic profile developed in infected individuals, from non-specific clinical conditions to severe forms, characterised by the promotion of significant lesions in different organs [...] Read more.
Arboviruses, such as yellow fever virus (YFV), dengue virus (DENV), and chikungunya virus (CHIKV), present wide global dissemination and a pathogenic profile developed in infected individuals, from non-specific clinical conditions to severe forms, characterised by the promotion of significant lesions in different organs of the harbourer, culminating in multiple organ dysfunction. An analytical cross-sectional study was carried out via the histopathological analysis of 70 samples of liver patients, collected between 2000 and 2017, with confirmed laboratory diagnoses, who died due to infection and complications due to yellow fever (YF), dengue fever (DF), and chikungunya fever (CF), to characterise, quantify, and compare the patterns of histopathological alterations in the liver between the samples. Of the histopathological findings in the human liver samples, there was a significant difference between the control and infection groups, with a predominance of alterations in the midzonal area of the three cases analysed. Hepatic involvement in cases of YF showed a greater intensity of histopathological changes. Among the alterations evaluated, cell swelling, microvesicular steatosis, and apoptosis were classified according to the degree of tissue damage from severe to very severe. Pathological abnormalities associated with YFV, DENV, and CHIKV infections showed a predominance of changes in the midzonal area. We also noted that, among the arboviruses studied, liver involvement in cases of YFV infection was more intense. Full article
(This article belongs to the Special Issue Pathogen-Host Interactions in Viral Infections)
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8 pages, 527 KiB  
Article
Viral Infection Profile in Children Treated for Acute Lymphoblastic Leukemia—Results of Nationwide Study
by Joanna Zawitkowska, Katarzyna Drabko, Krzysztof Czyżewski, Magdalena Dziedzic, Kamila Jaremek, Patrycja Zalas-Więcek, Anna Szmydki-Baran, Łukasz Hutnik, Michał Matysiak, Wojciech Czogała, Walentyna Balwierz, Iwona Żak, Małgorzata Salamonowicz-Bodzioch, Bernarda Kazanowska, Grażyna Wróbel, Krzysztof Kałwak, Renata Tomaszewska, Tomasz Szczepański, Olga Zając-Spychała, Jacek Wachowiak, Marcin Płonowski, Maryna Krawczuk-Rybak, Aleksandra Królak, Tomasz Ociepa, Tomasz Urasiński, Filip Pierlejewski, Wojciech Młynarski, Justyna Urbańska-Rakus, Katarzyna Machnik, Sonia Pająk, Wanda Badowska, Tomasz Brzeski, Katarzyna Mycko, Hanna Mańko-Glińska, Agnieszka Urbanek-Dądela, Grażyna Karolczyk, Agnieszka Mizia-Malarz, Weronika Stolpa, Katarzyna Skowron-Kandzia, Jakub Musiał, Radosław Chaber, Ninela Irga-Jaworska, Ewa Bień and Jan Styczyńskiadd Show full author list remove Hide full author list
Pathogens 2022, 11(10), 1091; https://doi.org/10.3390/pathogens11101091 - 24 Sep 2022
Cited by 1 | Viewed by 1920
Abstract
Viral infections can be a serious complication of therapy in children with acute lymphoblastic leukemia (ALL). In this study, we focused on the incidence and the profile of viral infection in children with ALL treated in 17 pediatric oncology centers in Poland in [...] Read more.
Viral infections can be a serious complication of therapy in children with acute lymphoblastic leukemia (ALL). In this study, we focused on the incidence and the profile of viral infection in children with ALL treated in 17 pediatric oncology centers in Poland in the two-year periods of 2018–2019 and 2020–2021. We also compared the frequency of viral infections in 2018–2019 to that in 2020–2021. In 2020–2021, a total of 192 children with ALL had a viral infection during intensive chemotherapy. A total number of 312 episodes of viral infections were diagnosed. The most common infections detected in the samples were: COVID-19 (23%), rhinovirus (18%), and respiratory syncytial virus (14%). COVID-19 and BK virus infections were the reason for the death 1% of all patients. In 2018–2019, a total of 53 ALL patients who had a viral infection were reported and 72 viral events were observed, mainly adenovirus (48.6%), rotavirus (31.9%), and herpes zoster (8.3%). No deaths were reported during this period. The cumulative incidence of viral infections in 2018–2019 was 10.4%, while for 2020–2021, it was 36.7%. In conclusion, a high incidence of COVID-19 infection was observed among pediatric patients with ALL in Poland. The mortality rate in our material was low. The viral profile in ALL children undergoing chemotherapy can be useful for clinicians to improve prophylactic and therapeutic strategies. Full article
(This article belongs to the Special Issue Pathogen-Host Interactions in Viral Infections)
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19 pages, 4452 KiB  
Article
InfectionCMA: A Cell MicroArray Approach for Efficient Biomarker Screening in In Vitro Infection Assays
by Ana C. Magalhães, Sara Ricardo, Ana C. Moreira, Mariana Nunes, Margarida Tavares, Ricardo J. Pinto, Maria Salomé Gomes and Luisa Pereira
Pathogens 2022, 11(3), 313; https://doi.org/10.3390/pathogens11030313 - 3 Mar 2022
Cited by 3 | Viewed by 2531
Abstract
The recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has forced the scientific community to acquire knowledge in real-time, when total lockdowns and the interruption of flights severely limited access to reagents as the global pandemic became established. This unique reality made [...] Read more.
The recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has forced the scientific community to acquire knowledge in real-time, when total lockdowns and the interruption of flights severely limited access to reagents as the global pandemic became established. This unique reality made researchers aware of the importance of designing efficient in vitro set-ups to evaluate infectious kinetics. Here, we propose a histology-based method to evaluate infection kinetics grounded in cell microarray (CMA) construction, immunocytochemistry and in situ hybridization techniques. We demonstrate that the chip-like organization of the InfectionCMA has several advantages, allowing side-by-side comparisons between diverse cell lines, infection time points, and biomarker expression and cytolocalization evaluation in the same slide. In addition, this methodology has the potential to be easily adapted for drug screening. Full article
(This article belongs to the Special Issue Pathogen-Host Interactions in Viral Infections)
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10 pages, 508 KiB  
Article
The Significance of Circulating Cell-Free DNA Markers in Chronic Hepatitis B Patients with Hepatocellular Carcinoma
by Alkistis Papatheodoridi, Nikolaos Karakousis, Panagiotis Lembessis, Antonios Chatzigeorgiou and George V. Papatheodoridis
Pathogens 2021, 10(11), 1524; https://doi.org/10.3390/pathogens10111524 - 22 Nov 2021
Cited by 2 | Viewed by 2208
Abstract
(1) Background: Hepatocellular carcinoma (HCC) is the most serious complication of chronic hepatitis B (CHB). Recently, the detection of circulating cell-free (cf) DNA and nucleosomes has found numerous applications in oncology. This study aimed to examine the levels of serum cfDNA markers and [...] Read more.
(1) Background: Hepatocellular carcinoma (HCC) is the most serious complication of chronic hepatitis B (CHB). Recently, the detection of circulating cell-free (cf) DNA and nucleosomes has found numerous applications in oncology. This study aimed to examine the levels of serum cfDNA markers and nucleosomes in CHB patients with and without HCC and assess their potential association with HCC patients’ survival. (2) Methods: Nineteen patients with CHB and HCC and 38 matched patients with CHB without cancer development during 5 years of antiviral therapy were included. Stored serum samples were analyzed for cfDNA species, including the cfDNA concentration and levels of Alu115, Alu247, and nucleosomes. DNA integrity was expressed as the Alu247/Alu115 ratio. (3) Results: Compared to controls, HCC patients had higher median Alu247 levels (64.2 vs. 23.2 genomic equivalent, p = 0.004) and DNA integrity (1.0 vs. 0.7, p < 0.001) and a trend for a higher median cfDNA concentration (36.0 vs. 19.5 ng/mL, p = 0.064). Increased DNA integrity (Alu247/Alu115 > 1) was associated with an increased risk of death during the first year after HCC diagnosis (p = 0.016). (4) Conclusions: Levels of Alu247 and DNA integrity in serum cfDNA are elevated in CHB patients with HCC, whereas increased DNA integrity seems to be associated with a worse short-term prognosis in this setting. Full article
(This article belongs to the Special Issue Pathogen-Host Interactions in Viral Infections)
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Review

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18 pages, 1493 KiB  
Review
Molecular and Clinical Prognostic Biomarkers of COVID-19 Severity and Persistence
by Gethsimani Papadopoulou, Eleni Manoloudi, Nikolena Repousi, Lemonia Skoura, Tara Hurst and Timokratis Karamitros
Pathogens 2022, 11(3), 311; https://doi.org/10.3390/pathogens11030311 - 2 Mar 2022
Cited by 18 | Viewed by 3487
Abstract
The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), poses several challenges to clinicians, due to its unpredictable clinical course. The identification of laboratory biomarkers, specific cellular, and molecular mediators of immune response could contribute to the prognosis [...] Read more.
The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), poses several challenges to clinicians, due to its unpredictable clinical course. The identification of laboratory biomarkers, specific cellular, and molecular mediators of immune response could contribute to the prognosis and management of COVID-19 patients. Of utmost importance is also the detection of differentially expressed genes, which can serve as transcriptomic signatures, providing information valuable to stratify patients into groups, based on the severity of the disease. The role of biomarkers such as IL-6, procalcitonin, neutrophil–lymphocyte ratio, white blood cell counts, etc. has already been highlighted in recently published studies; however, there is a notable amount of new evidence that has not been summarized yet, especially regarding transcriptomic signatures. Hence, in this review, we assess the latest cellular and molecular data and determine the significance of abnormalities in potential biomarkers for COVID-19 severity and persistence. Furthermore, we applied Gene Ontology (GO) enrichment analysis using the genes reported as differentially expressed in the literature in order to investigate which biological pathways are significantly enriched. The analysis revealed a number of processes, such as inflammatory response, and monocyte and neutrophil chemotaxis, which occur as part of the complex immune response to SARS-CoV-2. Full article
(This article belongs to the Special Issue Pathogen-Host Interactions in Viral Infections)
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