Viruses

16 pages, 2085 KiB

Open AccessArticle

Genetic Profiles of Ten African Swine Fever Virus Strains from Outbreaks in Select Provinces of Luzon, Visayas, and Mindanao, Philippines, Between 2021 and 2023

by Andrew D. Montecillo, Zyne K. Baybay, Jimwel Bryan Christopher Ferrer, Wreahlen Cariaso, Airish Pantua, John Paulo Jose, Rachel Madera, Jishu Shi, Karla Cristine Doysabas, Alan Dargantes, Kassey Alsylle T. Dargantes, Anna Rochelle A. Boongaling, Alfredo P. Manglicmot, Lucille C. Villegas and Homer D. Pantua

Viruses 2025, 17(4), 588; https://doi.org/10.3390/v17040588 - 21 Apr 2025

Abstract

An African Swine Fever (ASF) outbreak was first recorded in the Philippines in July 2019. Since then, the disease has spread across provinces in Luzon, Visayas, and Mindanao, causing severe economic consequences for the country’s swine industry. Here, we report the genome sequencing [...] Read more.

An African Swine Fever (ASF) outbreak was first recorded in the Philippines in July 2019. Since then, the disease has spread across provinces in Luzon, Visayas, and Mindanao, causing severe economic consequences for the country’s swine industry. Here, we report the genome sequencing of ASF virus strains from outbreaks in several provinces of the Philippines between 2021 and 2023, using a long-read tiled amplicon sequencing approach. The coding-complete genomes generated ranged from 187,609 to 189,540 bp in length, with GC contents of 38.4% to 38.5%. Notably, a strain from the Bataan province had a 1.9 kb deletion at the 5′-end, affecting several coding regions. The strains were characterized using 13 genes and regions; namely the B646L gene, the CD2v serogroup, the central variable region (CVR) of the B602L gene, the intergenic region (IGR) between the I73R and I329L genes, the IGR between A179L and A137R, O174L, K145R, Bt/Sj, J268L, and ECO2, the multigene family (MGF) 505-5R, and the MGF 505-9R and 10R regions. The ASFV strains were mostly related to Asian and European p72 genotype II strains. Genetic profiling provides valuable information on the diversity of local strains of ASFV in the Philippines, which are useful for epidemiology, diagnostics, and vaccine development. Full article

(This article belongs to the Collection African Swine Fever Virus (ASFV))

16 pages, 1632 KiB

Open AccessReview

Innate Immune Sensing of Parapoxvirus Orf Virus and Viral Immune Evasion

by Basheer A. AlDaif and Stephen B. Fleming

Viruses 2025, 17(4), 587; https://doi.org/10.3390/v17040587 - 19 Apr 2025

Viewed by 35

Abstract

Orf virus (ORFV) is the type species of Parapoxvirus of the Poxviridae family that induces cutaneous pustular skin lesions in sheep and goats, and causes zoonotic infections in humans. Pattern recognition receptors (PRRs) sense pathogen-associated molecular patterns (PAMPs), leading to the triggering of [...] Read more.

Orf virus (ORFV) is the type species of Parapoxvirus of the Poxviridae family that induces cutaneous pustular skin lesions in sheep and goats, and causes zoonotic infections in humans. Pattern recognition receptors (PRRs) sense pathogen-associated molecular patterns (PAMPs), leading to the triggering of the innate immune response through multiple signalling pathways involving type I interferons (IFNs). The major PAMPs generated during viral infection are nucleic acids, which are the most important molecules that are recognized by the host. The induction of type l IFNs leads to activation of the Janus kinase (JAK)-signal transducer activator of transcription (STAT) pathway, which results in the induction of hundreds of interferon-stimulated genes (ISGs), many of which encode proteins that have antiviral roles in eliminating virus infection and create an antiviral state. Genetic and functional analyses have revealed that ORFV, as found for other poxviruses, has evolved multiple immunomodulatory genes and strategies that manipulate the innate immune sensing response. Full article

(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)

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19 pages, 1794 KiB

Open AccessArticle

Pathogen Profile of Children Hospitalised with Viral Respiratory Infections in Galati County, Romania

by Elena-Roxana Matache (Vasilache), Gabriela Gurau, Cosmin-Raducu Raileanu, Anamaria Zaharescu, Gabriel Valeriu Popa, Nicoleta-Maricica Maftei, Camelia Busila, Madalina Nicoleta Matei and Dana Tutunaru

Viruses 2025, 17(4), 586; https://doi.org/10.3390/v17040586 - 19 Apr 2025

Viewed by 55

Abstract

Respiratory infections are the most common infectious diseases among children, representing a cause of death and generating a significant number of hospitalisations. The aim of the study was to analyse the epidemiological and clinical characteristics of viral pathogens causing respiratory tract infections in [...] Read more.

Respiratory infections are the most common infectious diseases among children, representing a cause of death and generating a significant number of hospitalisations. The aim of the study was to analyse the epidemiological and clinical characteristics of viral pathogens causing respiratory tract infections in newborns and young children admitted to Galati pediatric hospital between October 2022 and December 2023. The diagnosis was performed using multiplex RT-PCR panels, which allowed simultaneous identification of respiratory pathogens (viruses and bacteria). From a total of 803 hospitalised patients with respiratory diseases, 607 (75.6%) children had a positive result for at least one respiratory virus and 96 patients (11.9%) were identified with bacterial infections. Mixed coinfections were found in almost half of the patients (44.5%). Most of RSV positive children had an increased length of stay, more than 7 days. It was shown a decline in severe cases of viral respiratory infections with prolonged hospitalisation as patients age up to 5 years. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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13 pages, 2937 KiB

Open AccessArticle

Detection of Avian Influenza Virus in Pigeons

by Ning Cui, Peipei Wang, Qinghua Huang, Zihao Yuan, Shuai Su, Chuantian Xu and Lihong Qi

Viruses 2025, 17(4), 585; https://doi.org/10.3390/v17040585 - 18 Apr 2025

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Abstract

Pigeons (Columba livia) are usually kept as free-ranging or racing birds, and they have direct contact with livestock, poultry, and humans. Therefore, they may have an important role in the ecology of influenza virus among various species. In the present study, we bring [...] Read more.

Pigeons (Columba livia) are usually kept as free-ranging or racing birds, and they have direct contact with livestock, poultry, and humans. Therefore, they may have an important role in the ecology of influenza virus among various species. In the present study, we bring together all available sequence data of pigeon avian influenza virus (AIV) from public databases to address the current understanding of the genomic characteristics and emergence of each subtype of AIV in pigeons. Collectively, we identified 658 pigeon AIV strains in 21 countries across the world, which were mainly distributed in Europe, Asia, and North America. H1 (2), H2 (1), H3 (8), H5 (71), H6 (16), H7 (16), H9 (543), and H11 (1) AIV subtypes have been identified in pigeons. In addition, we interrogate features of the H5, H6, H7, and H9 subtypes of pigeon AIV, which are relatively common in pigeons. It is particularly noteworthy that the H5 AIV strains identified in pigeons are all classified as HPAIV. For the first time, this study presents a complete overview of the multiple AIV subtypes that have been circulating in pigeons, providing information on their distribution and genomic characteristics. This study will help to understand the molecular evolution of AIV in pigeons. Full article

(This article belongs to the Section Animal Viruses)

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15 pages, 3308 KiB

Open AccessArticle

Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification

by Mengfei Peng, Morgan L. Davis, Meghan L. Bentz, Alex Burgin, Mark Burroughs, Jasmine Padilla, Sarah Nobles, Yvette Unoarumhi and Kevin Tang

Viruses 2025, 17(4), 584; https://doi.org/10.3390/v17040584 - 18 Apr 2025

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Abstract

Genomic surveillance of SARS-CoV-2 is crucial for detecting emerging variants and informing public health responses. Various sequencing technologies are used for whole genome sequencing of SARS-CoV-2. This cross-platform benchmark study applied established bioinformatics tools to assess and improve the performance of Illumina NovaSeq, [...] Read more.

Genomic surveillance of SARS-CoV-2 is crucial for detecting emerging variants and informing public health responses. Various sequencing technologies are used for whole genome sequencing of SARS-CoV-2. This cross-platform benchmark study applied established bioinformatics tools to assess and improve the performance of Illumina NovaSeq, Oxford Nanopore Technologies MinION, and Pacific Biosciences Sequel II sequencing platforms in identifying SARS-CoV-2 variants and lineage assignment. NovaSeq produced the highest number of reads and bases, depth of coverage, completeness of consensus genomes, stable mapping coverage across open reading frames in the genome, and consistent lineage assignments. The long-read sequencing platforms had lower yields, sequencing depth, and mapping coverage, limiting the number of qualified sequences for lineage assignment and variant identification. However, implementing proper quality controls on sequence data overcame these limitations and achieved consistent SARS-CoV-2 lineage assignments across all three sequencing platforms. The advancements in library preparation and technology for long-read sequencing are likely to enhance sequence quality and expand genome coverage, effectively addressing current limitations in genome analysis. By merging the unique advantages of both short- and long-read methods, we can significantly improve SARS-CoV-2 genomic surveillance and provide insights into sequencing strategies for other RNA viruses, pending further validation. This may lead to precise tracking of viral evolution and support public health policy decisions. Full article

(This article belongs to the Section Coronaviruses)

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15 pages, 1603 KiB

Open AccessArticle

Quantifying Impact of HIV Receptor Surface Density Reveals Differences in Fusion Dynamics of HIV Strains

by Anthony Gerg and Hana M. Dobrovolny

Viruses 2025, 17(4), 583; https://doi.org/10.3390/v17040583 - 18 Apr 2025

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Abstract

Human Immunodeficiency Virus (HIV) Type-1 has been studied heavily for decades, yet one area that is still poorly understood is the virus’ ability to cause cell–cell fusion. In HIV, the fusion process is mediated by viral surface glycoproteins that bind to CD4 cell [...] Read more.

Human Immunodeficiency Virus (HIV) Type-1 has been studied heavily for decades, yet one area that is still poorly understood is the virus’ ability to cause cell–cell fusion. In HIV, the fusion process is mediated by viral surface glycoproteins that bind to CD4 cell receptors. This virus-mediated cell fusion creates multi-nucleated cells called syncytia that can affect infection dynamics. Syncytia formation is often studied using a cell–cell fusion assay, in which donor cells expressing the viral surface protein fuse with acceptor cells expressing the cell receptor. A mathematical model capable of reproducing the dynamics of the cell–cell fusion assay was recently developed and can be used to quantify changes in syncytia formation. In this study, we use this mathematical model to quantify the changes in syncytia formation in HIV as the surface density of the glycoproteins is varied. We find that we need to modify the model to explicitly include a density-dependent syncytia formation rate that allows us to capture the dynamics of the cell–cell fusion assay as the density of the glycoproteins changes. With this modification, we find that cell–cell fusion of the HXB2 strain, which uses the CXCR4 coreceptor, shows a threshold-like behavior, while cell–cell fusion of the Sf162 strain, which uses the CCR5 co-receptor, shows a more gradual change as surface density decreases. Full article

(This article belongs to the Special Issue Computational Biology of Viruses: From Molecules to Epidemics, Volume 2)

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13 pages, 2782 KiB

Open AccessArticle

Complete Genome Sequencing of the Divergent Guiana Dolphin Morbillivirus (GDMV), Brazil

by Kátia Regina Groch, Sueli Akemi Taniwaki Miyagi, Josué Díaz-Delgado, Elitieri B. Santos-Neto, José Lailson-Brito, Paulo Eduardo Brandão and José Luiz Catão-Dias

Viruses 2025, 17(4), 582; https://doi.org/10.3390/v17040582 - 18 Apr 2025

Viewed by 170

Abstract

Cetacean morbillivirus (CeMV) is a major threat to cetaceans worldwide, causing individual deaths and outbreaks of mass mortality. Based on partial sequences of the viral phosphoprotein, CeMV is subclassified into seven strains and two distinct lineages. To date, only CeMV-1 strains, including the [...] Read more.

Cetacean morbillivirus (CeMV) is a major threat to cetaceans worldwide, causing individual deaths and outbreaks of mass mortality. Based on partial sequences of the viral phosphoprotein, CeMV is subclassified into seven strains and two distinct lineages. To date, only CeMV-1 strains, including the dolphin morbillivirus (DMV), have been completely sequenced. The CeMV-2 lineage was first reported in Guiana dolphins (Sotalia guianensis) in Brazil and was associated with an unusual mortality event in 2017–2018. Here we provide the nearly complete Guiana dolphin morbillivirus (GDMV) genome sequence, representing the first within the CeMV-2 lineage. GDMV was isolated using Vero.DogSLAMtag cells, the viral RNA was extracted, and deep sequencing analysis was performed. Gaps in the viral genome were completed by Sanger sequencing. The final genome length was 15,607 nucleotides covering 99.3% of the DMV reference genome, including full sequences of the six structural proteins encoded by morbillivirus. The sequence similarity was 74–77.9% to other CeMV strains, with highest identity to the DMV. The complete L protein amino acid sequence comparison-based taxonomy indicates that GDMV is a distinct morbillivirus species; however, as GDMV and CeMV-1 strains infect a similar host spectrum, our findings support that GDMV represents a new CeMV-2 lineage. Full article

(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity)

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20 pages, 1493 KiB

Open AccessReview

Advances in the Drug Development and Quality Evaluation Principles of Oncolytic Herpes Simplex Virus

by Basma Eid Abdullah Ghorab, Tongtan Liu, Min Ying, Ping Wang, Meirong Qin, Jiayong Xing, Huadong Wang and Fuqiang Xu

Viruses 2025, 17(4), 581; https://doi.org/10.3390/v17040581 - 18 Apr 2025

Viewed by 170

Abstract

Oncolytic herpes simplex virus (oHSV) represents a promising therapeutic approach to treating cancers by virtue of its selective replication in and lysis of tumor cells, with stimulation of host antitumor immunity. At present, four OV drugs have been approved for the treatment of [...] Read more.

Oncolytic herpes simplex virus (oHSV) represents a promising therapeutic approach to treating cancers by virtue of its selective replication in and lysis of tumor cells, with stimulation of host antitumor immunity. At present, four OV drugs have been approved for the treatment of cancers worldwide, two of which are oHSV drugs that have received extensive attention, known as T-VEC and Delytact. This review discusses the history, mechanism of action, clinical development, quality control, and evaluation principles of oHSV products, including viral species and genetic modifications that have improved these products’ therapeutic potential, limitations, and future directions. Integration of oHSVs with immunotherapeutic agents and conventional therapies has a promising future in the field of treatment of malignant tumors. Although much progress has been achieved, there is still much work to be done regarding the optimization of treatment protocols and the quality control of oncolytic virus drugs. The approval of various oncolytic virus therapies underlines their clinical relevance, safety, and efficacy, thereby paving the way for further research aimed at overcoming the existing limitations and enhancing patient responses. Full article

(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)

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23 pages, 4464 KiB

Open AccessArticle

Expression Profiles of lncRNAs and mRNAs in the Mouse Brain Infected with Pseudorabies Virus: A Bioinformatic Analysis

by Yanwei Li, Teng Tu, Yan Luo, Xueping Yao, Zexiao Yang and Yin Wang

Viruses 2025, 17(4), 580; https://doi.org/10.3390/v17040580 - 17 Apr 2025

Viewed by 201

Abstract

Pseudorabies virus (PRV) is a pathogen that causes severe neurological dysfunction in the host, leading to extensive neuronal damage and inflammation. Despite extensive research on the neuropathogenesis of α-herpesvirus infections, many scientific questions remain unresolved, such as the largely unknown functions of long [...] Read more.

Pseudorabies virus (PRV) is a pathogen that causes severe neurological dysfunction in the host, leading to extensive neuronal damage and inflammation. Despite extensive research on the neuropathogenesis of α-herpesvirus infections, many scientific questions remain unresolved, such as the largely unknown functions of long non-coding RNAs (lncRNAs) in herpesvirus-infected nervous systems. To address these questions, we used RNA sequencing (RNA-seq) to investigate the expression profiles of lncRNAs and mRNAs in the brains of mice infected with PRV. Through bioinformatic analysis, we identified 316 differentially expressed lncRNAs and 886 differentially expressed mRNAs. We predicted the biological functions of these differentially expressed lncRNAs and mRNAs using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and the results showed that the differentially expressed transcripts were mainly involved in the innate immune response. Finally, we validated the differential expression trends of lncRNAs and mRNAs using quantitative real-time PCR (q-PCR), which were consistent with the sequencing data. To our knowledge, this is the first report analyzing the lncRNA expression profile in the central nervous system (CNS) of mice infected with PRV. Our findings provide new insights into the roles of lncRNAs and mRNAs during PRV infection of the host CNS. Full article

(This article belongs to the Special Issue Pseudorabies Virus, Third Edition)

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19 pages, 5015 KiB

Open AccessArticle

Superior Potency of Synthetic Virus-like Structures in Vaccine-Induced Antibody Responses Compared to Qβ Bacteriophage Virus-like Particles

by Alexander R. Meyer, Libo Li, Wei-Yun Wholey, Bryce Chackerian and Wei Cheng

Viruses 2025, 17(4), 579; https://doi.org/10.3390/v17040579 - 17 Apr 2025

Viewed by 155

Abstract

Virus-like particles are a well-established platform for vaccines, although the molecular mechanisms that underlie the extraordinary potency of many virus-like particles in eliciting strong antibody responses remain incompletely understood. Here, we show that synthetic virus-like structures, a new platform that we have recently [...] Read more.

Virus-like particles are a well-established platform for vaccines, although the molecular mechanisms that underlie the extraordinary potency of many virus-like particles in eliciting strong antibody responses remain incompletely understood. Here, we show that synthetic virus-like structures, a new platform that we have recently developed, are superior to bacteriophage Qβ-based virus-like particles for the induction of long-term neutralizing antibody responses. For the same antigen, both platforms induced antibodies with comparable affinities. The resulting antigen-specific antibodies had similar binding on-rates and off-rates. However, synthetic virus-like structures induced a much higher concentration of functional antibodies in the serum than Qβ-based virus-like particles, suggesting that synthetic virus-like structures are more potent than Qβ-based virus-like particles in the induction of long-lived plasma cells. Full article

(This article belongs to the Special Issue B Cell-Mediated Immunity to Viruses)

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12 pages, 814 KiB

Open AccessReview

Clinical Manifestations of Hemorrhagic Fever with Renal Syndrome, Various Nosologic Forms and Issues of Hantavirus Infections Terminology

by Evgeniy Tkachenko, Tamara Dzagurova, Guzel Galieva, Victoria Ivanis, Svetlana Kurashova, Petr Tkachenko, Alexandra Balkina, Dmitriy Trankvilevsky and Aydar Ishmukhametov

Viruses 2025, 17(4), 578; https://doi.org/10.3390/v17040578 - 17 Apr 2025

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Abstract

Hemorrhagic fever with renal syndrome (HFRS) is the result of acute, zoonotic, natural foci hantavirus infections. It has serious social and medical importance due to its widespread distribution and the disease’s severity. There is a lack of effective etiotropic therapy and specific prophylaxis [...] Read more.

Hemorrhagic fever with renal syndrome (HFRS) is the result of acute, zoonotic, natural foci hantavirus infections. It has serious social and medical importance due to its widespread distribution and the disease’s severity. There is a lack of effective etiotropic therapy and specific prophylaxis available. The aim of this review is to observe the etiological, clinical, and epidemiological features of nosologic HFRS forms in Russia, as well as differences and similarities with hantavirus pulmonary syndrome (HPS). The various clinical HFRS manifestations characterized diseases associated with Puumala, Kurkino, and Sochi hantaviruses in the Russian European part, and with Hantaan, Amur, and Seoul hantaviruses in the Russian Far East. Differences were observed for HFRS foci types based on biological characteristics and natural host population dynamics. As a result of clinical and epidemiological analysis six nosological forms were established, all of which were classified as “hemorrhagic fever with renal syndrome” according to the WHO’s expert recommendation from 1983 year. The study showed comparable taxonomic characteristics and determined the mechanism of human infection course for HFRS and HPS. The accumulated knowledge of this study allows for the combination of HFRS and HPS names into a common logical disease name “Hantavirus fever”. Full article

(This article belongs to the Special Issue Hantavirus 2024)

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19 pages, 3132 KiB

Open AccessArticle

Molecular Epidemiology of Human Adenovirus from Acute Gastroenteritis Cases in Brazil After the COVID-19 Pandemic Period, 2021–2023

by Mateus de Souza Mello, Fábio Correia Malta, Alexandre Madi Fialho, Fernanda Marcicano Burlandy and Tulio Machado Fumian

Viruses 2025, 17(4), 577; https://doi.org/10.3390/v17040577 - 17 Apr 2025

Viewed by 185

Abstract

Human enteric adenoviruses (HAdV-F40/41) play a crucial role as causative agents of acute gastroenteritis (AGE), particularly affecting children in low-and middle-income countries. This study investigated the prevalence, genetic diversity, and molecular characteristics of HAdV-F40/41 in AGE cases reported in Brazil from 2021 to [...] Read more.

Human enteric adenoviruses (HAdV-F40/41) play a crucial role as causative agents of acute gastroenteritis (AGE), particularly affecting children in low-and middle-income countries. This study investigated the prevalence, genetic diversity, and molecular characteristics of HAdV-F40/41 in AGE cases reported in Brazil from 2021 to 2023, a period after the COVID-19 pandemic. A total of 1980 stool samples collected from medically attended AGE patients from nine states were analyzed by TaqMan-based qPCR. Overall, HAdV was detected in 16.6% (n = 328/1980) of cases, with the highest prevalence observed in children under five years of age. The positive HAdV samples were genotyped through partial sequencing of the hexon and/or fiber genes followed by phylogenetic analysis. Enteric HAdVs (HAdV-F40/41) were detected in 3.2% (n = 63/1980) of samples, with HAdV-F41 (44.1%) being the most common genotype. Among the non-enteric types, HAdV-C (29.4%) was the most prevalent, followed by HAdV-B (13.2%), HAdV-A (10.3%), and HAdV-D (2.9%). Phylogenetic analysis of the hexon (HVR1–HVR6) and fiber (Shaft) gene regions identified two major clusters, H-GTC1 and F-GTC2, showing close genetic relationships with global strains. HAdV-F40/41 demonstrated significantly higher viral loads compared to non-enteric HAdVs. These findings highlight the importance of continued surveillance of HAdV-F to better understand its role in AGE cases and support public health strategies, including potential vaccine development. Full article

(This article belongs to the Special Issue Viruses Associated with Gastroenteritis)

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17 pages, 4082 KiB

Open AccessArticle

Transmission and Characterization of Creutzfeldt–Jakob Disease and Chronic Wasting Disease in the North American Deer Mouse

by Jennifer Myskiw, Lise Lamoureux, Kathy Frost, Rebecca Fox, Jessy A. Slota, Gordon Mitchell, Ben A. Bailey-Elkin and Stephanie A. Booth

Viruses 2025, 17(4), 576; https://doi.org/10.3390/v17040576 - 16 Apr 2025

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Abstract

Prion transmission into rodents is essential for understanding prion strains. However, it is often limited by a “species barrier” that makes transmission challenging and complicates the study of animal and human prion diseases. Here, we report that North American deer mice (Peromyscus [...] Read more.

Prion transmission into rodents is essential for understanding prion strains. However, it is often limited by a “species barrier” that makes transmission challenging and complicates the study of animal and human prion diseases. Here, we report that North American deer mice (Peromyscus maniculatus) are susceptible to infection with both human sporadic Creutzfeldt–Jakob disease (sCJD) and chronic wasting disease (CWD). Experimental transmission of both sCJD and CWD in deer mice resulted in 100% attack rates, albeit with differing incubation times, with CWD-inoculated mice taking nearly three times longer than sCJD-inoculated mice to succumb. We observed distinct patterns of spongiform vacuolation and prion-protein deposition in the brain, as well as distinct protein-glycosylation profiles and seeding kinetics in RT-QuIC for each strain. Adaptation on the second passage led to reduced incubation periods and marked strain-specific pathology, as seen predominantly in the cortex in sCJD and the thalamus in CWD. Notably, primary transmission of CWD resulted in infrequent vacuoles and widespread punctate deposits of prion protein in the brain, while diffuse staining and remarkable vacuolation of the thalamus were seen on passage. Prion seeding kinetics for sCJD and CWD were indistinguishable in the second passage; however, the distinct glycosylation patterns seen on immunoblot of the prion protein were maintained. Adaptation also resulted in extraneural dissemination of prion seeding activity distinct to CWD infection. Overall, the ability to transmit both CWD and sCJD to this model, resulting in clear differences in incubation period, biochemical properties, clinical signs, pathology and seeding kinetics, indicates that the model has the potential for use as a tool to investigate atypical cases of sCJD that may indicate CWD spillover to humans. Full article

(This article belongs to the Section Prions)

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19 pages, 3858 KiB

Open AccessArticle

Flow Virometry in Wastewater Monitoring: Comparison of Virus-like Particles to Coliphage, Pepper Mild Mottle Virus, CrAssphage, and Tomato Brown Rugose Fruit Virus

by Melis M. Johnson, C. Winston Bess, Rachel Olson and Heather N. Bischel

Viruses 2025, 17(4), 575; https://doi.org/10.3390/v17040575 - 16 Apr 2025

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Abstract

Flow virometry (FVM) offers a promising approach for monitoring viruses and virus-like particles (VLPs) in environmental samples. This study compares levels of non-specific VLPs across a wastewater treatment plant (WWTP) with levels of somatic coliphage, (F+) specific coliphage, Pepper Mild Mottle Virus (PMMoV), [...] Read more.

Flow virometry (FVM) offers a promising approach for monitoring viruses and virus-like particles (VLPs) in environmental samples. This study compares levels of non-specific VLPs across a wastewater treatment plant (WWTP) with levels of somatic coliphage, (F+) specific coliphage, Pepper Mild Mottle Virus (PMMoV), CrAssphage (CrAss), and Tomato Brown Rugose Fruit Virus (ToBRFV). All targets were quantified in influent, secondary-treated effluent, and tertiary-treated effluent at the University of California, Davis Wastewater Treatment Plant (UCDWWTP) over 11 weeks. We established an FVM-gating boundary for VLPs using bacteriophages T4 and ϕ6 as well as four phages isolated from wastewater. We then utilize T4 alongside three submicron beads as quality controls in the FVM assay. Coliphage was measured by standard plaque assays, and genome copies of PMMoV, CrAss, and ToBRFV were measured by digital droplet (dd)PCR. FVM results for wastewater revealed distinct microbial profiles at each treatment stage. However, correlations between VLPs and targeted viruses were poor. Trends for virus inactivation and removal, observed for targeted viruses during wastewater treatment, were consistent with expectations. Conversely, VLP counts were elevated in the WWTP effluent relative to the influent. Additional sampling revealed a decrease in VLP counts during the filtration treatment step following secondary treatment but a substantial increase in VLPs following ultraviolet disinfection. Defining application boundaries remain crucial to ensuring meaningful data interpretation as flow cytometry and virometry take on greater significance in water quality monitoring. Full article

(This article belongs to the Special Issue Flow Virometry: A New Tool for Studying Viruses)

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13 pages, 12987 KiB

Open AccessArticle

Environmental Suitability of Kazakhstan to Highly Pathogenic Avian Influenza Using Data on Eurasian Outbreaks, 2020–2024

by Asem Zh. Abenova, Yersyn Y. Mukhanbetkaliyev, Ablaikhan S. Kadyrov, Igor I. Sytnik, Alexander B. Shevtsov, Fedor I. Korennoy, Irene Iglesias Martin, Andres M. Perez and Sarsenbay K. Abdrakhmanov

Viruses 2025, 17(4), 574; https://doi.org/10.3390/v17040574 - 16 Apr 2025

Viewed by 255

Abstract

Highly pathogenic avian influenza (HPAI) is a highly contagious disease of domestic, synanthropic, and wild birds that has demonstrated a sharp rise globally since 2020. This study intends to examine environmental and demographic factors most significantly associated with HPAI (H5N1 and H5N8) outbreaks [...] Read more.

Highly pathogenic avian influenza (HPAI) is a highly contagious disease of domestic, synanthropic, and wild birds that has demonstrated a sharp rise globally since 2020. This study intends to examine environmental and demographic factors most significantly associated with HPAI (H5N1 and H5N8) outbreaks in Kazakhstan, 2020–2024, and to identify areas of potential underreporting of the disease. Two ecological niche models were developed, namely an “occurrence model” (considering climatic and environmental factors influencing the likelihood of HPAI occurrence) and a “reporting model” (that assesses the probability of disease reporting based on human and poultry population demography). Both models were trained using outbreak locations in countries neighboring Kazakhstan (Afghanistan, China, Hong Kong, Iran, Iraq, Pakistan and Russia), and then tested using the HPAI outbreak locations in Kazakhstan. Results suggested a good fit for both models to Kazakhstani outbreaks (test AUC = 0.894 vs. training AUC = 0.915 for “occurrence model”, and test AUC = 0.869 vs. training AUC = 0.872 for “reporting model”). A cluster of high occurrence-to-reporting ratio was detected in the south-western region of Kazakhstan, close to the Caspian Sea, suggesting a need for enhancing surveillance efforts in this zone as well as in some other areas of Pavlodar, Northern Kazakhstan, Western Kazakhstan, Qyzylorda, and Eastern Kazakhstan. Results presented here will help inform the design and implementation of control strategies for HPAI in Kazakhstan with the ultimate goal of promoting disease prevention and control in the country. Full article

(This article belongs to the Special Issue Advances in Animal Influenza Virus Research: Third Edition)

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20 pages, 14004 KiB

Open AccessArticle

Ephrin B1 and B2 Mediate Cedar Virus Entry into Egyptian Fruit Bat Cells

by Lea Lenhard, Martin Müller, Sandra Diederich, Lisa Loerzer, Virginia Friedrichs, Bernd Köllner, Stefan Finke, Anca Dorhoi and Gang Pei

Viruses 2025, 17(4), 573; https://doi.org/10.3390/v17040573 - 16 Apr 2025

Viewed by 214

Abstract

Cedar virus (CedV), closely related to the Hendra and Nipah viruses, is a novel Henipavirus that was originally isolated from flying foxes in Australia in 2012. Although its glycoprotein G exhibits relatively low sequence similarity with its counterparts of the Hendra and Nipah [...] Read more.

Cedar virus (CedV), closely related to the Hendra and Nipah viruses, is a novel Henipavirus that was originally isolated from flying foxes in Australia in 2012. Although its glycoprotein G exhibits relatively low sequence similarity with its counterparts of the Hendra and Nipah viruses, CedV also uses ephrin receptors, i.e., ephrins B1, B2, A2 and A5, to enters human cells. Nevertheless, the entry mechanism of CedV into bat cells remains unexplored. Considering that Rousettus aegyptiacus (Egyptian Rousette bat, ERB) is postulated to be a reservoir host for henipaviruses, we aim to reveal the receptors utilized by CedV to enable its entry into ERB cells. To this end, we cloned the class A and B ephrins of ERB and generated CHO-K1 cells stably expressing individual ephrins. We also developed a lentivirus-based pseudovirus system containing the firefly luciferase reporter. Assessment of the luciferase activity in cells expressing single ephrins demonstrated that the ERB ephrin B1 and B2 mediated CedV pseudovirus entry. Further, we generated a recombinant CedV expressing the fluorescent protein TurboFP635 (rCedV-nTurbo635). By performing high-content microscopy and flow cytometry, we unveiled that, in addition to ephrin B1 and B2, ephrin A5 was also able to mediate rCedV-nTurbo635 entry, although to a much lesser extent. In contrast to human ephrin A2, ERB ephrin A2 failed to mediate rCedV-nTurbo635 entry. Finally, we generated ERB epithelial cells with ephrin B1 and/or ephrin B2 knockdown (KD). The entry of rCedV-nTurbo635 into ERB epithelial cells was drastically impaired by ephrin B1/B2 KD, validating the importance of ephrin B1 and B2 in its entry. Altogether, we conclude that CedV primarily employs ERB ephrin B1, B2 and, possibly, A5 for its entry into ERB cells. Full article

(This article belongs to the Special Issue Antiviral Immune Responses of Bat)

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26 pages, 1668 KiB

Open AccessReview

Neuroinflammation, Blood–Brain Barrier, and HIV Reservoirs in the CNS: An In-Depth Exploration of Latency Mechanisms and Emerging Therapeutic Strategies

by Noor Said and Vishwanath Venketaraman

Viruses 2025, 17(4), 572; https://doi.org/10.3390/v17040572 - 16 Apr 2025

Viewed by 315

Abstract

Despite the success of antiretroviral therapy (ART) in suppressing viral replication in the blood, HIV persists in the central nervous system (CNS) and causes chronic neurocognitive impairment, a hallmark of HIV-associated neurocognitive disorders (HAND). This review looks at the complex interactions among HIV, [...] Read more.

Despite the success of antiretroviral therapy (ART) in suppressing viral replication in the blood, HIV persists in the central nervous system (CNS) and causes chronic neurocognitive impairment, a hallmark of HIV-associated neurocognitive disorders (HAND). This review looks at the complex interactions among HIV, the blood–brain barrier (BBB), neuroinflammation, and the roles of viral proteins, immune cell trafficking, and pro-inflammatory mediators in establishing and maintaining latent viral reservoirs in the CNS, particularly microglia and astrocytes. Key findings show disruption of the BBB, monocyte infiltration, and activation of CNS-resident cells by HIV proteins like Tat and gp120, contributing to the neuroinflammatory environment and neuronal damage. Advances in epigenetic regulation of latency have identified targets like histone modifications and DNA methylation, and new therapeutic strategies like latency-reversing agents (LRAs), gene editing (CRISPR/Cas9), and nanoparticle-based drug delivery also offer hope. While we have made significant progress in understanding the molecular basis of HIV persistence in the CNS, overcoming the challenges of BBB penetration and neuroinflammation is key to developing effective therapies. Further research into combination therapies and novel drug delivery systems will help improve outcomes for HAND patients and bring us closer to a functional cure for HIV. Full article

(This article belongs to the Special Issue HIV Neurological Disorders: 2nd Edition)

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17 pages, 3611 KiB

Open AccessArticle

Characterization of Nanobody Binding to Distinct Regions of the SARS-CoV-2 Spike Protein by Flow Virometry

by Mariam Maltseva, Martin A. Rossotti, Jamshid Tanha and Marc-André Langlois

Viruses 2025, 17(4), 571; https://doi.org/10.3390/v17040571 - 15 Apr 2025

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Abstract

Nanobodies, or single-domain antibodies (V_HHs) from camelid heavy-chain-only antibodies, offer significant advantages in therapeutic and diagnostic applications due to their small size and ability to bind cryptic protein epitopes inaccessible to conventional antibodies. In this study, we examined nanobodies specific to [...] Read more.

Nanobodies, or single-domain antibodies (V_HHs) from camelid heavy-chain-only antibodies, offer significant advantages in therapeutic and diagnostic applications due to their small size and ability to bind cryptic protein epitopes inaccessible to conventional antibodies. In this study, we examined nanobodies specific to regions of the SARS-CoV-2 spike glycoprotein, including the receptor-binding domain (RBD), N-terminal domain (NTD), and subunit 2 (S2). Using flow virometry, a high-throughput technique for viral quantification, we achieved the efficient detection of pseudotyped viruses expressing the spike glycoprotein. RBD-targeting nanobodies showed the most effective staining, followed by NTD-targeting ones, while S2-specific nanobodies exhibited limited resolution. The simple genetic structure of nanobodies enables the creation of multimeric formats, improving binding specificity and avidity. Bivalent V_HH-Fc constructs (V_HHs fused to the Fc region of human IgG) outperformed monovalent formats in resolving viral particles from background noise. However, S2-specific monovalent V_HHs demonstrated improved staining efficiency, suggesting their smaller size better accesses restricted antigenic sites. Furthermore, direct staining of cell supernatants was possible without virus purification. This versatile nanobody platform, initially developed for antiviral therapy against SARS-CoV-2, can be readily adapted for flow virometry applications and other diagnostic assays. Full article

(This article belongs to the Special Issue Flow Virometry: A New Tool for Studying Viruses)

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13 pages, 5151 KiB

Open AccessArticle

First Report of Paralytic Rabies in a Lowland Tapir (Tapirus terrestris) in Argentina

by Matías Castillo Giraudo, María Marcela Orozco, Marcelo Juan Zabalza, Leonardo Minatel, Laura Patricia Novaro, Gabriela Alejandra Centurión, Marcos Adolfo Fabeiro, Luciano Coppola, Vanina Daniela Marchione, María Carolina Artuso, Pablo Daniel Aon and Susana Elida Russo

Viruses 2025, 17(4), 570; https://doi.org/10.3390/v17040570 - 15 Apr 2025

Viewed by 393

Abstract

As a significant zoonotic disease, rabies poses substantial economic challenges for the livestock sector, highlighting the need for effective wildlife monitoring as part of a One Health approach. This study documents the first case of paralytic rabies in a lowland tapir (Tapirus [...] Read more.

As a significant zoonotic disease, rabies poses substantial economic challenges for the livestock sector, highlighting the need for effective wildlife monitoring as part of a One Health approach. This study documents the first case of paralytic rabies in a lowland tapir (Tapirus terrestris) at the Guaycolec Wildlife Station in Formosa, Argentina. The 12-year-old male tapir exhibited neurological symptoms, including limb paralysis and dysphagia, leading to its death. The rabies virus was confirmed through direct immunofluorescence, virus isolation in BHK-21 cells, and molecular diagnostics via real-time RT-PCR and conventional PCR. Antigenic variant 3, associated with Desmodus rotundus, was identified. Histopathological examination revealed non-suppurative encephalitis with lymphocytic perivascular cuffs, neuronal vacuolization, and acidophilic intracytoplasmic inclusion bodies in the grey matter. This case underscores the importance of expanded surveillance for non-traditional hosts, as it demonstrates the potential for rabies transmission in changing environments. The findings highlight the need to maintain epidemiological surveillance systems at the wildlife–livestock–human interface and to develop targeted control strategies to mitigate the spread of rabies, particularly in areas where vampire bat populations are subject to anthropogenic pressures. Comprehensive monitoring and early detection are essential for effective rabies management in both wildlife and urban contexts. Full article

(This article belongs to the Special Issue Advances in Rabies Research 2024)

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26 pages, 2312 KiB

Open AccessArticle

Impact of SARS-CoV-2 Wuhan and Omicron Variant Proteins on Type I Interferon Response

by Marija Janevska, Evelien Naessens and Bruno Verhasselt

Viruses 2025, 17(4), 569; https://doi.org/10.3390/v17040569 - 15 Apr 2025

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Abstract

SARS-CoV-2 has demonstrated a remarkable capacity for immune evasion. While initial studies focused on the Wuhan variant and adaptive immunity, later emerging strains such as Omicron exhibit mutations that may alter their immune-modulatory properties. We performed a comprehensive review of immune evasion mechanisms [...] Read more.

SARS-CoV-2 has demonstrated a remarkable capacity for immune evasion. While initial studies focused on the Wuhan variant and adaptive immunity, later emerging strains such as Omicron exhibit mutations that may alter their immune-modulatory properties. We performed a comprehensive review of immune evasion mechanisms associated with SARS-CoV-2 viral proteins to focus on the evolutionary dynamics of immune modulation. We systematically analyzed and compared the impact of all currently known Wuhan and Omicron SARS-CoV-2 proteins on type I interferon (IFN) responses using a dual-luciferase reporter assay carrying an interferon-inducible promoter. Results revealed that Nsp1, Nsp5, Nsp14, and ORF6 are potent type I IFN inhibitors conserved across Wuhan and Omicron strains. Notably, we identified strain-specific differences, with Nsp6 and Spike proteins exhibiting enhanced IFN suppression in Omicron, whereas the Envelope protein largely retained this function. To extend these findings, we investigated selected proteins in primary human endothelial cells and also observed strain-specific differences in immune response with higher type I IFN response in cells expressing the Wuhan strain variant, suggesting that Omicron’s adaptational mutations may contribute to a damped type I IFN response in the course of the pandemic’s trajectory. Full article

(This article belongs to the Section Coronaviruses)

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11 pages, 796 KiB

Open AccessArticle

Investigation of Hepatitis C, D, and HIV Seroprevalence and Evaluation of APRI and FIB-4 Scores in HbsAg-Positive Patients

by Fatih Mehmet Akıllı, Elif Nur Özbay Haliloğlu, Mehmet Mücahit Güncü and Dilara Turan Gökçe

Viruses 2025, 17(4), 568; https://doi.org/10.3390/v17040568 - 15 Apr 2025

Viewed by 161

Abstract

This study aimed to assess the prevalence of HDV (hepatitis delta virus), HCV (hepatitis C virus), and HIV (human immunodeficiency virus) coinfections among HBsAg-positive patients and to determine the severity of liver fibrosis and biochemical markers. Furthermore, the study sought to evaluate the [...] Read more.

This study aimed to assess the prevalence of HDV (hepatitis delta virus), HCV (hepatitis C virus), and HIV (human immunodeficiency virus) coinfections among HBsAg-positive patients and to determine the severity of liver fibrosis and biochemical markers. Furthermore, the study sought to evaluate the noninvasive fibrosis scores (APRI and FIB4) in predicting the severity of liver disease in patients with hepatitis B. A retrospective analysis of 1434 patients with chronic HBV admitted between January 2020 and December 2024 was conducted at Sincan Tertiary Hospital. The positivity rates of the following antibodies were the focus of the study: anti-HDV, anti-HCV, and anti-HIV. In addition to these, the levels of HIV-RNA, HCV-RNA and HBV-DNA, as well as several biochemical markers (ALT, AST, INR, albumin, bilirubin and platelet count) were also evaluated. The APRI and FIB-4 scores were calculated. Of the 1434 patients, 49 (3.4%) tested positive for anti-HDV, 784 were screened for anti-HCV, and 749 were screened for anti-HIV. The positivity rates were 3.4% (27/784) and 3.4% (26/749), respectively. According to ROC analysis, the FIB-4 score had a statistically significant effect on predicting anti-HDV negativity (AUC = 0.59, p = 0.031). However, the APRI score was not a significant predictor for anti-HDV positivity (AUC = 0.53, p > 0.05). APRI and FIB-4 scores did not have a statistically significant discriminatory power in predicting anti-HCV and anti-HIV positivity (p > 0.05). The cut-off value for the FIB-4 score in predicting anti-HDV positivity was 1.72, with a sensitivity of 61.4% and a specificity of 42.9% (p = 0.031). Among the HCV/RNA-positive patients (n = 5), all were male, and two also had positive anti-HBe results with undetectable HBV/DNA levels. One HIV/RNA-positive patient, a foreign national, was confirmed to have HIV/HBV/HDV infection. All HBsAg-positive patients should undergo routine anti-HDV testing. Vaccination programmes are vital in preventing the spread of HDV. Dual screening strategies are essential for identifying infected individuals and developing prevention and treatment programmes. Anti-HDV positivity indicates advanced liver fibrosis, emphasising the importance of screening and monitoring. However, the limited accuracy of the APRI and FIB-4 scores for detecting coinfections highlights the need to integrate noninvasive methods with molecular diagnostics for precise management. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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23 pages, 2606 KiB

Open AccessArticle

Evaluation of Different Machine Learning Approaches to Predict Antigenic Distance Among Newcastle Disease Virus (NDV) Strains

by Giovanni Franzo, Alice Fusaro, Chantal J. Snoeck, Aleksandar Dodovski, Steven Van Borm, Mieke Steensels, Vasiliki Christodoulou, Iuliana Onita, Raluca Burlacu, Azucena Sánchez Sánchez, Ilya A. Chvala, Mia Kim Torchetti, Ismaila Shittu, Mayowa Olabode, Ambra Pastori, Alessia Schivo, Angela Salomoni, Silvia Maniero, Ilaria Zambon, Francesco Bonfante, Isabella Monne, Mattia Cecchinato and Alessio Bortolami Show full author list Hide full author list

Viruses 2025, 17(4), 567; https://doi.org/10.3390/v17040567 - 14 Apr 2025

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Abstract

Newcastle disease virus (NDV) continues to present a significant challenge for vaccination due to its rapid evolution and the emergence of new variants. Although molecular and sequence data are now quickly and inexpensively produced, genetic distance rarely serves as a good proxy for [...] Read more.

Newcastle disease virus (NDV) continues to present a significant challenge for vaccination due to its rapid evolution and the emergence of new variants. Although molecular and sequence data are now quickly and inexpensively produced, genetic distance rarely serves as a good proxy for cross-protection, while experimental studies to assess antigenic differences are time consuming and resource intensive. In response to these challenges, this study explores and compares several machine learning (ML) methods to predict the antigenic distance between NDV strains as determined by hemagglutination-inhibition (HI) assays. By analyzing F and HN gene sequences alongside corresponding amino acid features, we developed predictive models aimed at estimating antigenic distances. Among the models evaluated, the random forest (RF) approach outperformed traditional linear models, achieving a predictive accuracy with an R² value of 0.723 compared to only 0.051 for linear models based on genetic distance alone. This significant improvement demonstrates the usefulness of applying flexible ML approaches as a rapid and reliable tool for vaccine selection, minimizing the need for labor-intensive experimental trials. Moreover, the flexibility of this ML framework holds promise for application to other infectious diseases in both animals and humans, particularly in scenarios where rapid response and ethical constraints limit conventional experimental approaches. Full article

(This article belongs to the Section Animal Viruses)

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20 pages, 686 KiB

Open AccessReview

Self-Amplifying RNA: Advantages and Challenges of a Versatile Platform for Vaccine Development

by Thomas Vallet and Marco Vignuzzi

Viruses 2025, 17(4), 566; https://doi.org/10.3390/v17040566 - 14 Apr 2025

Viewed by 492

Abstract

Self-amplifying RNA is synthetic nucleic acid engineered to replicate within cells without generating viral particles. Derived from alphavirus genomes, saRNA retains the non-structural elements essential for replication while replacing the structural elements with an antigen of interest. By enabling efficient intracellular amplification, saRNA [...] Read more.

Self-amplifying RNA is synthetic nucleic acid engineered to replicate within cells without generating viral particles. Derived from alphavirus genomes, saRNA retains the non-structural elements essential for replication while replacing the structural elements with an antigen of interest. By enabling efficient intracellular amplification, saRNA offers a promising alternative to conventional mRNA vaccines, enhancing antigen expression while requiring lower doses. However, this advantage comes with challenges. In this review, we highlight the key limitations of saRNA technology and explore potential strategies to overcome them. By identifying these challenges, we aim to provide insights that can guide the future design of saRNA-based therapeutics, extending their potential beyond vaccine applications. Full article

(This article belongs to the Special Issue 15-Year Anniversary of Viruses)

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17 pages, 2493 KiB

Open AccessArticle

Experimental Efficacy of an Alphavirus Vectored RNA Particle Vaccine Against Porcine Parainfluenza Virus-1 in Conventional Weaned Pigs

by Michael Welch, Karen Krueger, Jianqiang Zhang, Pablo Piñeyro, Mark Mogler, Erin Strait and Phillip Gauger

Viruses 2025, 17(4), 565; https://doi.org/10.3390/v17040565 - 14 Apr 2025

Viewed by 182

Abstract

Parainfluenza viruses are a common cause of respiratory illness in many species. In this study, experimental, alphavirus-derived RNA particle vaccines either with or without adjuvant were evaluated against porcine parainfluenza virus 1 (PPIV1) challenge and compared to live virus exposure. Groups of ten, [...] Read more.

Parainfluenza viruses are a common cause of respiratory illness in many species. In this study, experimental, alphavirus-derived RNA particle vaccines either with or without adjuvant were evaluated against porcine parainfluenza virus 1 (PPIV1) challenge and compared to live virus exposure. Groups of ten, three-week-old pigs were vaccinated intramuscularly with an adjuvanted RNA particle (RPAdj/C) or non-adjuvanted RP (RP/C) or administered an intranasal live exposure (LE/C) dose of PPIV1 at 0- and 21-days post vaccination (DPV) followed by challenge with PPIV1 at 40 DPV. In addition, two groups were included as non-vaccinated, non-challenged (NV/NC) and non-vaccinated, challenged (NV/C) controls. Intranasal virus exposure and RP vaccination, regardless of adjuvant, reduced PPIV1 shedding in nasal swabs by 5 days post inoculation (DPI). All vaccinated or exposed pigs seroconverted as shown by enzyme-linked immunosorbent assay and serum virus neutralization. The antibody isotype detected in bronchoalveolar lavage fluid (BALF) LE/C was predominantly IgA while RP vaccination induced an IgG response. Reduced PPIV1 antigen was observed in the LE/C, RP/C and RPAdj/C groups in lung, trachea, or nasal turbinate epithelium. Additionally, the RPAdj vaccine significantly reduced nasal shedding compared to NV/C pigs although not as much as LE/C pigs. These results suggest vaccination could mitigate PPIV1 infection in commercial systems. Full article

(This article belongs to the Special Issue Novel Vaccines for Porcine Viruses)

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21 pages, 1396 KiB

Open AccessReview

Phage Endolysins as an Alternative Biocontrol Strategy for Pathogenic and Spoilage Microorganisms in the Food Industry

by Maryoris E. Soto Lopez, Fernando Mendoza-Corvis, Jose Jorge Salgado-Behaine, Ana M. Hernandez-Arteaga, Víctor González-Peña, Andrés M. Burgos-Rivero, Derrick Cortessi, Pedro M. P. Vidigal and Omar Pérez-Sierra

Viruses 2025, 17(4), 564; https://doi.org/10.3390/v17040564 - 14 Apr 2025

Viewed by 251

Abstract

Food contamination by pathogenic and spoilage bacteria causes approximately 47 million cases of foodborne diseases in the United States and leads to tons of food spoilage, worsening the food loss situation worldwide. In addition, conventional preservation treatments implemented in the food industry decrease [...] Read more.

Food contamination by pathogenic and spoilage bacteria causes approximately 47 million cases of foodborne diseases in the United States and leads to tons of food spoilage, worsening the food loss situation worldwide. In addition, conventional preservation treatments implemented in the food industry decrease food’s nutritional and organoleptic quality. Therefore, there is a need for new alternatives to counteract food contamination without altering its characteristics. Endolysins are a promising strategy due to their unique properties, such as host specificity, synergism with other antibacterial agents, mode of action, and low probability of resistance development. These characteristics differentiate them from other antibacterial agents used in the food industry. Endolysins are enzymes produced by bacteriophages during the process of bacterial infection and lysis. This review describes the advances related to endolysin application systems in food, considering their potential for food safety and an overview of the application conditions according to the type of food and bacteria to be controlled. We also highlight the need for new studies on endolysin encapsulation and prolongation of the action time in cases of outbreaks that allow obtaining key information to improve the application of endolysins in different food matrices during food processing and storage Full article

(This article belongs to the Section Bacterial Viruses)

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29 pages, 4948 KiB

Open AccessSystematic Review

A Scoping Review on Progression Towards Freedom from Peste des Petits Ruminants (PPR) and the Role of the PPR Monitoring and Assessment Tool (PMAT)

by Dinara Imanbayeva, Maria Sol Pérez Aguirreburualde, Whitney Knauer, Azimkhan Tegzhanov, Valeriia Yustyniuk, Jonathan Arzt, Andres Perez, Felix Njeumi and Satya Parida

Viruses 2025, 17(4), 563; https://doi.org/10.3390/v17040563 - 14 Apr 2025

Viewed by 191

Abstract

Peste des Petits Ruminants (PPR) is a highly contagious viral disease of small ruminants that severely threatens rural livelihoods and global food security. Under the Global Framework for the Progressive Control of Transboundary Animal Diseases (GF-TADs), the international animal health community has set [...] Read more.

Peste des Petits Ruminants (PPR) is a highly contagious viral disease of small ruminants that severely threatens rural livelihoods and global food security. Under the Global Framework for the Progressive Control of Transboundary Animal Diseases (GF-TADs), the international animal health community has set the ambitious goal of eradicating PPR by 2030. However, significant disparities persist in the progression of PPR control across regions. This scoping review assesses the setbacks, deviations, and progress of 42 countries in Eastern, Western, and Northern Africa, as well as West Eurasia, toward achieving official freedom-from-PPR status. Progress was evaluated across key areas using the stepwise PPR Global Control and Eradication Strategy (GCES) approach and the PPR Monitoring and Assessment Tool (PMAT). The eligibility criteria included PubMed peer-reviewed studies, FAO/WOAH reports, presentations, guidelines, and country/region-specific PPR control plans from 2014 through 2024. The data are generated using qualitative and quantitative analyses, including spatial mapping and GCES stepwise progress evaluation. The findings reveal that many (31%) countries in the assessed regions remain in Stage 1 of the Progressive Stepwise Approach, whereas 59.5% have reached Stages 2 and 3, and only 4.8% are in Stage 4. Countries in Western Eurasia have achieved significant progress towards PPR control, with countries achieving PPR-free status, whereas, compared to Eastern and Northern Africa, the Western African region remains in the early control stages due to infrastructure gaps and resource constraints. Additionally, the recent suspension of PPR-free status in Romania, Greece and Hungary following disease emergence underscored vulnerabilities in historically free countries. The analysis results reiterate the critical role of regional collaboration, surveillance tools, and the integration of wildlife monitoring in advancing PPR control. These insights provide actionable pathways to addressing persistent barriers, highlighting the importance of adaptable, evidence-based approaches in achieving the global goal of PPR eradication by 2030. Full article

(This article belongs to the Special Issue Peste des Petits Ruminants (PPR) Eradication: Improved Understanding of Epidemiology, Diagnostics and Vaccine Efficacy, Volume II)

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20 pages, 1194 KiB

Open AccessReview

A No-Brainer! The Therapeutic Potential of TRIM Proteins in Viral and Central Nervous System Diseases

by Adam Hage, Mikhaila Janes and Sonja M. Best

Viruses 2025, 17(4), 562; https://doi.org/10.3390/v17040562 - 14 Apr 2025

Viewed by 233

Abstract

Tripartite motif (TRIM) proteins comprise an important class of E3 ubiquitin ligases that regulate numerous biological processes including protein expression, cellular signaling pathways, and innate immunity. This ubiquitous participation in fundamental aspects of biology has made TRIM proteins a focus of study in [...] Read more.

Tripartite motif (TRIM) proteins comprise an important class of E3 ubiquitin ligases that regulate numerous biological processes including protein expression, cellular signaling pathways, and innate immunity. This ubiquitous participation in fundamental aspects of biology has made TRIM proteins a focus of study in many fields and has illuminated the negative impact they exert when functioning improperly. Disruption of TRIM function has been linked to the success of various pathogens and separately to the occurrence and development of several neurodegenerative diseases, making TRIM proteins an appealing candidate to study for novel therapeutic approaches. Here, we review the current findings on TRIM proteins that demonstrate their analogous properties in the distinct fields of viral infection and central nervous system (CNS) disorders. We also examine recent advancements in drug development and targeted protein degradation as potential strategies for TRIM-mediated therapeutic treatments and discuss the implications these technologies have on future research directions. Full article

(This article belongs to the Special Issue TRIM Proteins in Antiviral Immunity and Virus Pathogenesis)

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4 pages, 955 KiB

Open AccessCorrection

Correction: Moonga et al. Application of a Sensitive Capture Sequencing Approach to Reservoir Surveillance Detects Novel Viruses in Zambian Wild Rodents. Viruses 2024, 16, 1754

by Lavel C. Moonga, Jones Chipinga, John P. Collins, Vishal Kapoor, Ngonda Saasa, King S. Nalubamba, Bernard M. Hang’ombe, Boniface Namangala, Tapiwa Lundu, Xiang-Jun Lu, Samuel Yingst, J. Kenneth Wickiser and Thomas Briese

Viruses 2025, 17(4), 561; https://doi.org/10.3390/v17040561 - 14 Apr 2025

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Abstract

The authors wish to make the following correction to this paper [...] Full article

(This article belongs to the Section Animal Viruses)

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30 pages, 4043 KiB

Open AccessReview

Phage Endolysins as Promising and Effective Candidates for Use Against Uropathogenic Escherichia coli

by Wojciech Wesołowski, Aleksandra Łukasiak, Sylwia Bloch, Kaja Kuligowska, Julia Neumann, Natalia Lewandowska, Emilia Węglińska, Grzegorz Węgrzyn and Bożena Nejman-Faleńczyk

Viruses 2025, 17(4), 560; https://doi.org/10.3390/v17040560 - 13 Apr 2025

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Abstract

The presented in silico and phylogenetic analysis of putative endolysins potentially produced by phages infecting uropathogenic Escherichia coli (UPEC) demonstrates their remarkable diversity. These proteins exhibit significant variations in sequence length, molecular weight, isoelectric point, and stability, as well as diverse functional domains [...] Read more.

The presented in silico and phylogenetic analysis of putative endolysins potentially produced by phages infecting uropathogenic Escherichia coli (UPEC) demonstrates their remarkable diversity. These proteins exhibit significant variations in sequence length, molecular weight, isoelectric point, and stability, as well as diverse functional domains determining their enzymatic activity, including lysin, lysozyme, hydrolase, amidase, and peptidase functions. Due to their predicted lytic properties, endolysins hold great promise in combating UPEC bacteria, including those within biofilms, which are often highly resistant to conventional treatments. Despite their potential, several challenges hinder the full utilization of endolysins. These include the relatively small number of identified proteins, challenges in the annotation process, and the scarcity of studies evaluating their efficacy in vitro and in vivo against Gram-negative bacteria. In this work, we emphasize these challenges while also underlining the potential of endolysins as an effective tool against UPEC infections. Their effectiveness could be significantly enhanced when combined with agents that disrupt the outer membrane of these bacteria, making them a promising alternative or complement to existing antimicrobial strategies. Further research is necessary to fully explore their therapeutic potential. Full article

(This article belongs to the Special Issue Bacteriophages and Biofilms 2.0)

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23 pages, 38205 KiB

Open AccessArticle

Screening of Neutralizing Antibodies Targeting Gc Protein of RVFV

by Chuanyi Zhao, Meng Hao, Ting Bian, Xiaofan Zhao, Xiangyang Chi, Zhengshan Chen, Guangcheng Fu, Zheng Zhu, Ting Fang, Changming Yu, Jianmin Li and Wei Chen

Viruses 2025, 17(4), 559; https://doi.org/10.3390/v17040559 - 12 Apr 2025

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Abstract

Rift Valley fever virus (RVFV) is a mosquito-transmitted bunyavirus that can cause substantial morbidity and mortality in livestock and humans, for which there are no currently available licensed human therapeutics or vaccines. Therefore, the development of safe and effective antivirals is both necessary [...] Read more.

Rift Valley fever virus (RVFV) is a mosquito-transmitted bunyavirus that can cause substantial morbidity and mortality in livestock and humans, for which there are no currently available licensed human therapeutics or vaccines. Therefore, the development of safe and effective antivirals is both necessary and urgent. The Gc protein is the primary target of the neutralizing antibody response related to Rift Valley fever virus. Here, we report one Gc-specific neutralizing antibody (NA137) isolated from an alpaca and one bispecific antibody (E2-NA137), the protective efficacies of which we evaluated in A129 mice. In this prophylactic study, the survival rates of the NA137 and E2-NA137 groups were both 80%, and in the treatment study, the survival rates were 20% and 60%, respectively. Altogether, our results emphasize that NA137 and E2-NA137 provide a potential approach for treating RVFV either prophylactically or therapeutically. Full article

(This article belongs to the Special Issue Zoonotic and Vector-Borne Viral Diseases)

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