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Keywords = virus-host co-evolution

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10 pages, 1037 KiB  
Conference Report
Thirteenth International Foamy Virus Conference—Meeting Report
by Arifa S. Khan, Martin Löchelt, Florence Buseyne, Ottmar Herchenröder, Dirk Lindemann, William M. Switzer, André F. A. Santos and Marcelo A. Soares
Viruses 2025, 17(8), 1071; https://doi.org/10.3390/v17081071 - 31 Jul 2025
Viewed by 166
Abstract
The 13th International Foamy Virus (FV) Conference was held from 8 to 10 November 2023 at the BioParque/Zoological Garden in Rio de Janeiro, Brazil. This was the first conference on spumaretroviruses to be held in the Southern Hemisphere and in the unique environment [...] Read more.
The 13th International Foamy Virus (FV) Conference was held from 8 to 10 November 2023 at the BioParque/Zoological Garden in Rio de Janeiro, Brazil. This was the first conference on spumaretroviruses to be held in the Southern Hemisphere and in the unique environment of the rainforest. New developments and current perspectives in FV research were presented. Highlights of the conference included the structural biology of the envelope protein (Env) and insights into its function and evolution, epidemiologic identification of Amazonian indigenous people with a high prevalence of simian FV (SFV) infections, investigations of virus biology and genomics using synthetic FV DNAs, studies of humoral immune response, and development and applications of SFV vectors. The last day of the meeting was a special tour of the Centro de Primatologia do Rio de Janeiro, located northeast of Rio de Janeiro amidst the protected rainforest, where New World primate hosts of spumaretroviruses are rescued and studied. Our report summarizes the meeting highlights and outcomes for future discussions. Full article
(This article belongs to the Special Issue Spumaretroviruses: Research and Applications)
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19 pages, 4184 KiB  
Article
Host–Virus Interface in Persistent SARS-CoV-2 Infections: Viral Characteristic Evolution and Gene Expression Profiling Analysis
by Athok Shofiudin Maarif, Yukari Nishikawa, Miyako Takata, Kyosuke Kanai, Edo Riyandani, Kengo Mukuda, Momone Mimura, Kosuke Yamaguchi, Hiroyuki Kato, Ryo Okamoto, Kensaku Okada, Tsuyoshi Kitaura, Masaki Nakamoto, Akira Yamasaki, Seiji Kageyama and Hiroki Chikumi
Int. J. Mol. Sci. 2025, 26(13), 6221; https://doi.org/10.3390/ijms26136221 - 27 Jun 2025
Viewed by 490
Abstract
Persistent SARS-CoV-2 infections involve prolonged viral replication and immune system interactions, potentially driving viral evolution and immune escape. This study examines viral characteristics and host gene expression changes in persistent infections. The nasopharyngeal samples from four patients with persistent SARS-CoV-2 infections at Tottori [...] Read more.
Persistent SARS-CoV-2 infections involve prolonged viral replication and immune system interactions, potentially driving viral evolution and immune escape. This study examines viral characteristics and host gene expression changes in persistent infections. The nasopharyngeal samples from four patients with persistent SARS-CoV-2 infections at Tottori University Hospital, Japan, were analyzed. Viral isolates were cultured, and infectivity was assessed using TCID50 assays. To investigate host responses, RNA sequencing (RNA-seq) was performed to identify differentially expressed genes (DEGs), and Gene Ontology (GO) enrichment analysis mapped affected biological pathways. Viral genome sequencing detected mutations associated with prolonged infection. The results showed significant infectivity differences between early- and late-phase infection. Gene expression analysis revealed a strong early phase of pro-inflammatory response (IL6, TNF, IL1B, CXCL10) followed by immune suppression. GO enrichment analysis highlighted inflammation and cytokine-mediated immune pathways. Genomic sequencing identified mutations in ORF1ab and the spike (S) protein, potentially aiding immune escape. The findings underscore that SARS-CoV-2 adapts during persistent infections, altering infectivity and immune responses. These highlight the need for continued monitoring of prolonged infections to mitigate immune escape and viral evolution. Full article
(This article belongs to the Special Issue Advanced Perspectives on Virus–Host Interactions)
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33 pages, 5228 KiB  
Review
Human Cytomegalovirus Immune Evasion of Natural Killer Cells: A Virus for All Seasons?
by Hannah Preston, Rowan Casey, Elizabeth Ferris, Lauren Kerr-Jones, Lauren Jones, Farah Latif, Mathew Clement, Rebecca J. Aicheler, Eddie C. Y. Wang, Richard J. Stanton and Ceri A. Fielding
Pathogens 2025, 14(7), 629; https://doi.org/10.3390/pathogens14070629 - 24 Jun 2025
Viewed by 797
Abstract
Human cytomegalovirus (HCMV) is a ubiquitous member of the herpesvirus family, of significant clinical importance, and highly adapted to its host, resulting from millions of years of co-evolution. As a result, the virus systematically subverts almost all aspects of antiviral immune defence to [...] Read more.
Human cytomegalovirus (HCMV) is a ubiquitous member of the herpesvirus family, of significant clinical importance, and highly adapted to its host, resulting from millions of years of co-evolution. As a result, the virus systematically subverts almost all aspects of antiviral immune defence to successfully establish a lifelong persistent infection, and in the process, dramatically reshapes the phenotype and function of host immunity to both HCMV and other diseases. Natural killer (NK) cells are a critical component of successful herpesvirus control. Here, we discuss their role in modulating HCMV disease and the multitude of ways that HCMV has evolved to prevent and manipulate this process. We also consider how antibody-dependent cellular cytotoxicity by NK cells directed against HCMV might overcome NK immune evasion mechanisms and be useful therapeutically. Full article
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14 pages, 3241 KiB  
Article
Evolutionary Dynamics of Codon Usage Bias in Tomato Spotted Wilt Virus: Insights into Viral Adaptation and Host Interactions
by Haiting Zhao, Lang Qin, Xiaolong Deng, Stuart Reitz, Shengyong Wu and Zhen He
Horticulturae 2025, 11(7), 721; https://doi.org/10.3390/horticulturae11070721 - 20 Jun 2025
Viewed by 405
Abstract
Tomato spotted wilt virus (TSWV), belonging to the genus Orthotospovirus, is a significant pathogen through its infection of economically vital crops including tomato, tobacco, pepper, and other species worldwide. Given its substantial influence on the agricultural industry, in-depth research on TSWV is [...] Read more.
Tomato spotted wilt virus (TSWV), belonging to the genus Orthotospovirus, is a significant pathogen through its infection of economically vital crops including tomato, tobacco, pepper, and other species worldwide. Given its substantial influence on the agricultural industry, in-depth research on TSWV is of great necessity. Several studies have been conducted on the dinucleotide preference of TSWV previously; however, the information regarding codon usage bias (CUB) and the virus’s adaptive evolution remains inconclusive. Here, a thorough analysis of TSWV was performed by utilizing five protein-coding sequences in order to investigate the characteristics of CUB. It has been observed that the TSWV protein-coding sequences are AU-rich, and codons ending with A or U are also preferred in these sequences. A consistently stable and preserved genomic composition characterized by a lower codon usage preference was also observed. Principal Component Analysis (PCA), neutrality analysis, and ENC-plot indicated that, in comparison to mutational pressure, natural selection has a more dominant influence on the CUB of TSWV. The codon adaptation index (CAI) demonstrated a more significant correlation between TSWV and Nicotiana tabacum. Meanwhile, the relative codon deoptimization index (RCDI) indicated a stronger correlation between TSWV and Solanum lycopersicum. This study is the first to systematically characterize the CUB of TSWV based on its protein-coding sequences, providing critical insights into viral genetic diversity, evolution mechanisms, and host adaptation. The findings advance understanding of plant-virus coevolution and inform virus-resistant crop breeding and antiviral strategies. Full article
(This article belongs to the Special Issue Disease Diagnosis and Control for Fruit Crops)
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13 pages, 2394 KiB  
Article
Molecular Epidemiology of SARS-CoV-2 in Bangladesh
by Abu Sayeed Mohammad Mahmud, Patiyan Andersson, Dieter Bulach, Sebastian Duchene, Anders Goncalves da Silva, Chantel Lin, Torsten Seemann, Benjamin P. Howden, Timothy P. Stinear, Tarannum Taznin, Md. Ahashan Habib, Shahina Akter, Tanjina Akhtar Banu, Md. Murshed Hasan Sarkar, Barna Goswami, Iffat Jahan and Md. Salim Khan
Viruses 2025, 17(4), 517; https://doi.org/10.3390/v17040517 - 1 Apr 2025
Viewed by 779
Abstract
Mutation is one of the most important drivers of viral evolution and genome variability, allowing viruses to potentially evade host immune responses and develop drug resistance. In the context of COVID-19, local genomic surveillance of circulating virus populations is therefore critical. The goals [...] Read more.
Mutation is one of the most important drivers of viral evolution and genome variability, allowing viruses to potentially evade host immune responses and develop drug resistance. In the context of COVID-19, local genomic surveillance of circulating virus populations is therefore critical. The goals of this study were to describe the distribution of different SARS-CoV-2 lineages, assess their genomic differences, and infer virus importation events in Bangladesh. We individually aligned 1965 SARS-CoV-2 genome sequences obtained between April 2020 and June 2021 to the Wuhan-1 sequence and used the resulting multiple sequence alignment as input to infer a maximum likelihood phylogenetic tree. Sequences were assigned to lineages as described by the hierarchical Pangolin nomenclature scheme. We built a phylogeographic model using the virus population genome sequence variation to infer the number of virus importation events. We observed thirty-four lineages and sub-lineages in Bangladesh, with B.1.1.25 and its sub-lineages D.* (979 sequences) dominating, as well as the Beta variant of concern (VOC) B.1.351 and its sub-lineages B.1.351.* (403 sequences). The earliest B.1.1.25/D.* lineages likely resulted from multiple introductions, some of which led to larger outbreak clusters. There were 570 missense mutations, 426 synonymous mutations, 18 frameshift mutations, 7 deletions, 2 insertions, 10 changes at start/stop codons, and 64 mutations in intergenic or untranslated regions. According to phylogeographic modeling, there were 31 importation events into Bangladesh (95% CI: 27–36). Like elsewhere, Bangladesh has experienced distinct waves of dominant lineages during the COVID-19 pandemic; this study focuses on the emergence and displacement of the first wave-dominated lineage, which contains mutations seen in several VOCs and may have had a transmission advantage over the extant lineages. Full article
(This article belongs to the Section Coronaviruses)
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19 pages, 3982 KiB  
Article
Comparative Interactome Profiling of Nonstructural Protein 3 Across SARS-CoV-2 Variants Emerged During the COVID-19 Pandemic
by Valeria Garcia Lopez and Lars Plate
Viruses 2025, 17(3), 447; https://doi.org/10.3390/v17030447 - 20 Mar 2025
Viewed by 770
Abstract
SARS-CoV-2 virus and its variants remain a global health threat, due to their capacity for rapid evolution. Variants throughout the COVID-19 pandemic exhibited variations in virulence, impacting vaccine protection and disease severity. Investigating nonstructural protein variants is critical to understanding viral evolution and [...] Read more.
SARS-CoV-2 virus and its variants remain a global health threat, due to their capacity for rapid evolution. Variants throughout the COVID-19 pandemic exhibited variations in virulence, impacting vaccine protection and disease severity. Investigating nonstructural protein variants is critical to understanding viral evolution and manipulation of host protein interactions. We focus on nonstructural protein 3 (nsp3), with multiple domains with different activities, including viral polyprotein cleavage, host deubiquitylation, de-ISGylation, and double-membrane vesicle formation. Using affinity purification–mass spectrometry (AP-MS), we identify differential protein interactions in nsp3 caused by mutations found in variants identified between 2019 and 2024: Alpha 20I, Beta 20H, Delta 21I, Delta 21J, Gamma 20J, Kappa 21B, Lambda 21G, Omicron 21K, and Omicron 21L. A small set of amino acid substitutions in the N-terminal region of nsp3 (nsp3.1) could be traced to increased interactions with RNA-binding proteins, which are vital in viral replication. Meanwhile, variants of the central region of nsp3 (nsp3.2) were found to share interactions with protein quality control machinery, including ER-associated degradation. In this construct, shared trends in interactor enrichment are observed between Omicron 21K and Delta 21I. These results underscore how minor mutations reshape host interactions, emphasizing the evolutionary arms race between the host and virus. We provide a roadmap to track the interaction changes driven by SARS-CoV-2 variant evolution. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variants, Vaccines, and Immune Responses)
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43 pages, 12081 KiB  
Article
Coevolution of Lentiviral Vif with Host A3F and A3G: Insights from Computational Modelling and Ancestral Sequence Reconstruction
by David Nicolas Giuseppe Huebert, Atefeh Ghorbani, Shaw Yick Brian Lam and Mani Larijani
Viruses 2025, 17(3), 393; https://doi.org/10.3390/v17030393 - 10 Mar 2025
Viewed by 846
Abstract
The evolutionary arms race between host restriction factors and viral antagonists provides crucial insights into immune system evolution and viral adaptation. This study investigates the structural and evolutionary dynamics of the double-domain restriction factors A3F and A3G and their viral inhibitor, Vif, across [...] Read more.
The evolutionary arms race between host restriction factors and viral antagonists provides crucial insights into immune system evolution and viral adaptation. This study investigates the structural and evolutionary dynamics of the double-domain restriction factors A3F and A3G and their viral inhibitor, Vif, across diverse primate species. By constructing 3D structural homology models and integrating ancestral sequence reconstruction (ASR), we identified patterns of sequence diversity, structural conservation, and functional adaptation. Inactive CD1 (Catalytic Domain 1) domains displayed greater sequence diversity and more positive surface charges than active CD2 domains, aiding nucleotide chain binding and intersegmental transfer. Despite variability, the CD2 DNA-binding grooves remained structurally consistent with conserved residues maintaining critical functions. A3F and A3G diverged in loop 7’ interaction strategies, utilising distinct molecular interactions to facilitate their roles. Vif exhibited charge variation linked to host species, reflecting its coevolution with A3 proteins. These findings illuminate how structural adaptations and charge dynamics enable both restriction factors and their viral antagonists to adapt to selective pressures. Our results emphasize the importance of studying structural evolution in host–virus interactions, with implications for understanding immune defense mechanisms, zoonotic risks, and viral evolution. This work establishes a foundation for further exploration of restriction factor diversity and coevolution across species. Full article
(This article belongs to the Special Issue Host-Mediated Viral Mutations: APOBECs, ADARs, and Beyond)
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17 pages, 2448 KiB  
Article
Genetic Diversity and Molecular Evolution of Hepatitis E Virus Within the Genus Chirohepevirus in Bats
by Bo Wang, Peter Cronin, Marcus G. Mah, Xing-Lou Yang and Yvonne C. F. Su
Viruses 2025, 17(3), 339; https://doi.org/10.3390/v17030339 - 28 Feb 2025
Viewed by 905
Abstract
Hepatitis E virus (HEV) is a major zoonotic pathogen causing hepatitis E, with strains identified in various animal species, including pigs, wild boar, rabbits, deer, camels, and rats. These variants are capable of crossing species barriers and infecting humans. HEV belongs to the [...] Read more.
Hepatitis E virus (HEV) is a major zoonotic pathogen causing hepatitis E, with strains identified in various animal species, including pigs, wild boar, rabbits, deer, camels, and rats. These variants are capable of crossing species barriers and infecting humans. HEV belongs to the family Hepeviridae, which has recently divided into two subfamilies: Orthohepevirinae and Parahepevirinae, and five genera: Paslahepevirus, Avihepevirus, Rocahepevirus, Chirohepevirus, and Piscihepevirus. Recent advances in high-throughput sequencing, particularly of bat viromes, have revealed numerous HEV-related viruses, raising concerns about their zoonotic potential. Bat-derived HEVs have been classified into the genus Chirohepevirus, which includes three distinct species. In this study, we analyzed 64 chirohepevirus sequences from 22 bat species across six bat families collected from nine countries. Twelve sequences represent complete or nearly complete viral genomes (>6410 nucleotides) containing the characteristic three HEV open reading frames (ORFs). These strains exhibited high sequence divergence (>25%) within their respective host genera or species. Phylogenetic analyses with maximum likelihood methods identified at least seven distinct subclades within Chirohepevirus, each potentially representing an independent species. Additionally, the close phylogenetic relationship between chirohepevirus strains and their bat hosts indicates a pattern of virus–host co-speciation. Our findings expand the known diversity within the family Hepeviridae and provide new insights into the evolution of bat-associated HEV. Continued surveillance of chirohepevirus will be essential for understanding its potential for zoonotic transmission and public health risks. Full article
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12 pages, 2855 KiB  
Perspective
Evolutionary Mechanisms of the Emergence of the Variants of Concern of SARS-CoV-2
by Igor M. Rouzine
Viruses 2025, 17(2), 197; https://doi.org/10.3390/v17020197 - 30 Jan 2025
Cited by 2 | Viewed by 1468
Abstract
The evolutionary origin of the variants of concern (VOCs) of SARS-CoV-2, characterized by a large number of new substitutions and strong changes in virulence and transmission rate, is intensely debated. The leading explanation in the literature is a chronic infection in immunocompromised individuals, [...] Read more.
The evolutionary origin of the variants of concern (VOCs) of SARS-CoV-2, characterized by a large number of new substitutions and strong changes in virulence and transmission rate, is intensely debated. The leading explanation in the literature is a chronic infection in immunocompromised individuals, where the virus evolves before returning into the main population. The present article reviews less-investigated hypotheses of VOC emergence with transmission between acutely infected hosts, with a focus on the mathematical models of stochastic evolution that have proved to be useful for other viruses, such as HIV and influenza virus. The central message is that understanding the acting factors of VOC evolution requires the framework of stochastic multi-locus evolution models, and that alternative hypotheses can be effectively verified by fitting results of computer simulation to empirical data. Full article
(This article belongs to the Section Animal Viruses)
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15 pages, 1502 KiB  
Article
Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients
by Su Myat Han, Yoshiano Kubo, Alexis Robert, Marc Baguelin and Koya Ariyoshi
Viruses 2025, 17(2), 152; https://doi.org/10.3390/v17020152 - 23 Jan 2025
Viewed by 1161
Abstract
Numerous studies have documented the evidence of virus–virus interactions at the population, host, and cellular levels. However, the impact of these interactions on the within-host diversity of influenza viral populations remains unexplored. Our study identified 13 respiratory viral pathogens from the nasopharyngeal swab [...] Read more.
Numerous studies have documented the evidence of virus–virus interactions at the population, host, and cellular levels. However, the impact of these interactions on the within-host diversity of influenza viral populations remains unexplored. Our study identified 13 respiratory viral pathogens from the nasopharyngeal swab samples (NPSs) of influenza-like-illness (ILI) patients during the 2012/13 influenza season using multiplex RT-PCR. Subsequent next-generation sequencing (NGS) of RT-PCR-confirmed influenza A infections revealed all samples as subtype A/H3N2. Out of the 2305 samples tested, 538 (23.3%) were positive for the influenza A virus (IAV), while rhinovirus (RV) and adenoviruses (Adv) were detected in 264 (11.5%) and 44 (1.9%) samples, respectively. Among these, the co-detection of more than one virus was observed in ninety-six samples, and five samples showed co-detections involving more than two viruses. The most frequent viral co-detection was IAV–RV, identified in 48 out of the 96 co-detection cases. Of the total samples, 150 were processed for whole-genome sequencing (WGS), and 132 met the criteria for intra-host single-nucleotide variant (iSNV) calling. Across the genome, 397 unique iSNVs were identified, with most samples containing fewer than five iSNVs at frequencies below 10%. Seven samples had no detectable iSNVs. Notably, the majority of iSNVs (86%) were unique and rarely shared across samples. We conducted a negative binomial regression analysis to examine factors associated with the number of iSNVs detected within hosts. Two age groups—elderly individuals (>64 years old) and school-aged children (6–18 years old)—were significantly associated with higher iSNV counts, with incidence rate ratios (IRR) of 1.80 (95% confidence interval [CI]: 1.09–3.06) and 1.38 (95% CI: 1.01–1.90), respectively. Our findings suggest a minor or negligible contribution of these viral co-detections to the evolution of influenza viruses. However, the data available in this study may not be exhaustive, warranting further, more in-depth investigations to conclusively determine the impact of virus–virus interactions on influenza virus genetic diversity. Full article
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16 pages, 1914 KiB  
Article
Co-Infection of Culex tarsalis Mosquitoes with Rift Valley Fever Phlebovirus Strains Results in Efficient Viral Reassortment
by Emma K. Harris, Velmurugan Balaraman, Cassidy C. Keating, Chester McDowell, J. Brian Kimble, Alina De La Mota-Peynado, Erin M. Borland, Barbara Graham, William C. Wilson, Juergen A. Richt, Rebekah C. Kading and Natasha N. Gaudreault
Viruses 2025, 17(1), 88; https://doi.org/10.3390/v17010088 - 11 Jan 2025
Viewed by 1417
Abstract
Rift Valley fever phlebovirus (RVFV) is a zoonotic mosquito-borne pathogen endemic to sub-Saharan Africa and the Arabian Peninsula which causes Rift Valley fever in ruminant livestock and humans. Co-infection with divergent viral strains can produce reassortment among the L, S, and M segments [...] Read more.
Rift Valley fever phlebovirus (RVFV) is a zoonotic mosquito-borne pathogen endemic to sub-Saharan Africa and the Arabian Peninsula which causes Rift Valley fever in ruminant livestock and humans. Co-infection with divergent viral strains can produce reassortment among the L, S, and M segments of the RVFV genome. Reassortment events can produce novel genotypes with altered virulence, transmission dynamics, and/or mosquito host range. This can have severe implications in areas where RVFV is endemic and convolutes our ability to anticipate transmission and circulation in novel geographic regions. Previously, we evaluated the frequency of RVFV reassortment in a susceptible ruminant host and observed low rates of reassortment (0–1.7%). Here, we tested the hypothesis that reassortment occurs predominantly in the mosquito using a highly permissive vector, Culex tarsalis. Cells derived from Cx. tarsalis or adult mosquitoes were co-infected with either two virulent (Kenya-128B-15 and SA01-1322) or a virulent and attenuated (Kenya-128B-15 and MP-12) strain of RVFV. Our results showed approximately 2% of virus genotypes isolated from co-infected Cx. tarsalis-derived cells were reassortant. Co-infected mosquitoes infected via infectious bloodmeal resulted in a higher percentage of reassortant virus (2–60%) isolated from midgut and salivary tissues at 14 days post-infection. The percentage of reassortant genotypes isolated from the midguts of mosquitoes co-infected with Kenya-128B-15 and SA01-1322 was similar to that of mosquitoes co-infected with Kenya-128B-15 and MP-12- strains (60 vs. 47%). However, only 2% of virus isolated from the salivary glands of Kenya-128B-15 and SA01-1322 co-infected mosquitoes represented reassortant genotypes. This was contrasted by 54% reassortment in the salivary glands of mosquitoes co-infected with Kenya-128B-15 and MP-12 strains. Furthermore, we observed preferential inclusion of genomic segments from the three parental strains among the reassorted viruses. Replication curves of select reassorted genotypes were significantly higher in Vero cells but not in Culex—derived cells. These data imply that mosquitoes play a crucial role in the reassortment of RVFV and potentially contribute to driving evolution of the virus. Full article
(This article belongs to the Special Issue Emerging Highlights in the Study of Rift Valley Fever Virus)
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24 pages, 1408 KiB  
Review
Advances and Challenges in Antiviral Development for Respiratory Viruses
by Luis Adrián De Jesús-González, Moisés León-Juárez, Flor Itzel Lira-Hernández, Bruno Rivas-Santiago, Manuel Adrián Velázquez-Cervantes, Iridiana Monserrat Méndez-Delgado, Daniela Itzel Macías-Guerrero, Jonathan Hernández-Castillo, Ximena Hernández-Rodríguez, Daniela Nahomi Calderón-Sandate, Willy Salvador Mata-Martínez, José Manuel Reyes-Ruíz, Juan Fidel Osuna-Ramos and Ana Cristina García-Herrera
Pathogens 2025, 14(1), 20; https://doi.org/10.3390/pathogens14010020 - 31 Dec 2024
Cited by 6 | Viewed by 5284
Abstract
The development of antivirals for respiratory viruses has advanced markedly in response to the growing threat of pathogens such as Influenzavirus (IAV), respiratory syncytial virus (RSV), and SARS-CoV-2. This article reviews the advances and challenges in this field, highlighting therapeutic strategies that target [...] Read more.
The development of antivirals for respiratory viruses has advanced markedly in response to the growing threat of pathogens such as Influenzavirus (IAV), respiratory syncytial virus (RSV), and SARS-CoV-2. This article reviews the advances and challenges in this field, highlighting therapeutic strategies that target critical stages of the viral replication cycle, including inhibitors of viral entry, replication, and assembly. In addition, innovative approaches such as inhibiting host cellular proteins to reduce viral resistance and repurposing existing drugs are explored, using advanced bioinformatics tools that optimize the identification of antiviral candidates. The analysis also covers emerging technologies such as nanomedicine and CRISPR gene editing, which promise to improve the stability and efficacy of treatments. While current antivirals offer valuable options, they face challenges such as viral evolution and the need for accessible treatments for vulnerable populations. This article underscores the importance of continued innovation in biotechnology to overcome these limitations and provide safe and effective treatments. Combining traditional and advanced approaches in developing antivirals is essential in order to address respiratory viral diseases that affect global health. Full article
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42 pages, 2428 KiB  
Review
SARS-CoV-2 Evolution: Implications for Diagnosis, Treatment, Vaccine Effectiveness and Development
by Fabrizio Angius, Silvia Puxeddu, Silvio Zaimi, Serena Canton, Sepehr Nematollahzadeh, Andrea Pibiri, Ilenia Delogu, Gualtiero Alvisi, Meng Ling Moi and Aldo Manzin
Vaccines 2025, 13(1), 17; https://doi.org/10.3390/vaccines13010017 - 28 Dec 2024
Cited by 4 | Viewed by 2572
Abstract
The COVID-19 pandemic, driven by the rapid evolution of the SARS-CoV-2 virus, presents ongoing challenges to global public health. SARS-CoV-2 is characterized by rapidly evolving mutations, especially in (but not limited to) the spike protein, complicating predictions about its evolutionary trajectory. These mutations [...] Read more.
The COVID-19 pandemic, driven by the rapid evolution of the SARS-CoV-2 virus, presents ongoing challenges to global public health. SARS-CoV-2 is characterized by rapidly evolving mutations, especially in (but not limited to) the spike protein, complicating predictions about its evolutionary trajectory. These mutations have significantly affected transmissibility, immune evasion, and vaccine efficacy, leading to multiple pandemic waves with over half a billion cases and seven million deaths globally. Despite several strategies, from rapid vaccine development and administration to the design and availability of antivirals, including monoclonal antibodies, already having been employed, the persistent circulation of the virus and the emergence of new variants continue to result in high case numbers and fatalities. In the past four years, immense research efforts have contributed much to our understanding of the viral pathogenesis mechanism, the COVID-19 syndrome, and the host–microbe interactions, leading to the development of effective vaccines, diagnostic tools, and treatments. The focus of this review is to provide a comprehensive analysis of the functional impact of mutations on diagnosis, treatments, and vaccine effectiveness. We further discuss vaccine safety in pregnancy and the implications of hybrid immunity on long-term protection against infection, as well as the latest developments on a pan-coronavirus vaccine and nasal formulations, emphasizing the need for continued surveillance, research, and adaptive public health strategies in response to the ongoing SARS-CoV-2 evolution race. Full article
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13 pages, 7705 KiB  
Communication
Novel Betaherpesviruses in Neotropical Bats on the Caribbean Island of St. Kitts: First Report from Antillean Tree Bats (Ardops nichollsi) and Evidence for Cross-Species Transmission
by Jessica L. Kulberg, Sarah Hooper, Yashpal S. Malik and Souvik Ghosh
Microorganisms 2024, 12(12), 2603; https://doi.org/10.3390/microorganisms12122603 - 16 Dec 2024
Viewed by 1115
Abstract
To date, limited information is available on herpesviruses in bats from the Caribbean region. We report here high detection rates (24.24%, n = 66) of herpesviruses in oral samples from apparently healthy bats (Ardops nichollsi (75%, 9/12) and Molossus molossus (28%, 7/25)) [...] Read more.
To date, limited information is available on herpesviruses in bats from the Caribbean region. We report here high detection rates (24.24%, n = 66) of herpesviruses in oral samples from apparently healthy bats (Ardops nichollsi (75%, 9/12) and Molossus molossus (28%, 7/25)) on the Lesser Antillean Island of St. Kitts. Based on analysis of partial DNA polymerase (DPOL) sequences (~225 amino acid (aa) residues), we identified two distinct groups of herpesviruses (BO-I and -II) that were unique to A. nichollsi and M. molossus, respectively. Within the subfamily Betaherpesvirinae, the BO-I DPOL sequences shared low deduced aa identities (<70%) with other herpesviruses, and phylogenetically, they formed a distinct cluster, representing a putative novel betaherpesvirus. The BO-II DPOL sequences were closely related to a putative novel betaherpesvirus from a M. molossus in Lesser Antillean Island of Martinique, indicating possible transmission of herpesviruses by bat movement between the Caribbean Islands. Phylogenetically, the BO-I and -II betaherpesviruses exhibited species-specific (A. nichollsi and M. molossus, respectively) as well as family-specific (Phyllostomidae and Molossidae, respectively) clustering patterns, corroborating the hypothesis on host specificity of betaherpesviruses. Interestingly, a single M. molossus betaherpesvirus strain clustered with the A. nichollsi betaherpesviruses, indicating possible interspecies transmission of herpesviruses between Phyllostomidae and Molossidae. To our knowledge, this is the first report on detection of herpesviruses from Antillean tree bats (A. nichollsi), expanding the host range of betaherpesviruses. Taken together, the present study identified putative novel betaherpesviruses that might be unique to chiropteran species (A. nichollsi and M. molossus), indicating virus–host coevolution, and provided evidence for interspecies transmission of betaherpesviruses between chiropteran families. Full article
(This article belongs to the Special Issue New Progress in Animal Herpesviruses)
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18 pages, 4865 KiB  
Review
Evasion of the Antiviral Innate Immunity by PRV
by Chenlong Wang, Longxi Li, Xinyu Zhai, Hongtao Chang and Huimin Liu
Int. J. Mol. Sci. 2024, 25(23), 13140; https://doi.org/10.3390/ijms252313140 - 6 Dec 2024
Viewed by 1775
Abstract
Pseudorabies virus (PRV) establishes persistent latent infections by effectively evading the host’s antiviral innate immune response. PRV has developed sophisticated strategies to bypass immune surveillance through coevolution with its host. Currently, no effective vaccine exists to prevent or treat infections caused by emerging [...] Read more.
Pseudorabies virus (PRV) establishes persistent latent infections by effectively evading the host’s antiviral innate immune response. PRV has developed sophisticated strategies to bypass immune surveillance through coevolution with its host. Currently, no effective vaccine exists to prevent or treat infections caused by emerging PRV variants, and the interactions between PRV and the host’s innate immune defenses remain incompletely understood. Nevertheless, ongoing research is uncovering insights that may lead to novel treatments and preventive approaches for herpesvirus-related diseases. This review summarizes recent advances in understanding how PRV disrupts key adaptors in immune signaling pathways to evade antiviral immunity. Additionally, we explored the intrinsic cellular defenses that play crucial roles in combating viral invasion. A deeper understanding of the immune evasion strategies of PRV could inform the development of new therapeutic targets and vaccines. Full article
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