Viruses

17 pages, 819 KiB

Open AccessArticle

High-Throughput Sequencing Reveals Apple Virome Diversity and Novel Viruses in the Czech Republic

by Karima Ben Mansour, Igor Koloniuk, Jana Brožová, Marcela Komínková, Jaroslava Přibylová, Tatiana Sarkisova, Jiří Sedlák, Josef Špak and Petr Komínek

Viruses 2025, 17(5), 650; https://doi.org/10.3390/v17050650 (registering DOI) - 29 Apr 2025

Abstract

Apple viruses pose significant threat to global apple production. In this study, HTS technology was used to investigate the apple virome in the Czech Republic. Previously reported viruses, including ACLSV, ASPV, ASGV, ApMV, AGCaV, and CCGaV, were confirmed, and near-complete genomes were assembled. [...] Read more.

Apple viruses pose significant threat to global apple production. In this study, HTS technology was used to investigate the apple virome in the Czech Republic. Previously reported viruses, including ACLSV, ASPV, ASGV, ApMV, AGCaV, and CCGaV, were confirmed, and near-complete genomes were assembled. Additionally, two novel viruses, ARWV1 and ARWV2 were identified for the first time in the Czech Republic. Phylogenetic analyses showed low genetic variability among ARWV2 isolates, suggesting a possible recent introduction or limited diversification. In contrast, ARWV1 isolates displayed distinct clustering in the coat protein coding region, separating symptomatic and asymptomatic samples, indicating a potential involvement of genetic determinants in symptom expression. Mixed infections were prevalent, with multiple molecular variants of ACLSV, ASPV, and AGCaV detected within individual samples, along with co-infections involving viruses from different families. Recombination analysis identified frequent recombination events in ACLSV and ASPV, often involving non-apple parental sequences, suggesting their potential for cross-host infections. Additionally, an interspecific recombination event was detected in an almond ApMV isolate, with PNRSV as a minor parent. These findings highlight the impact of agricultural practices on viral evolution and host adaptation. This study demonstrates the utility of HTS as a powerful tool for uncovering viral diversity, recombination events, and evolutionary dynamics. Full article

(This article belongs to the Special Issue Diversity and Coinfections of Plant or Fungal Viruses, 3rd Edition)

11 pages, 826 KiB

Open AccessBrief Report

Concurrent Circulation of Canine Distemper Virus (South America-4 Lineage) at the Wild–Domestic Canid Interface in Aburrá Valley, Colombia

by Carolina Rios-Usuga, Melissa C. Ortiz-Pineda, Sergio Daniel Aguirre-Catolico, Víctor H. Quiroz and Julian Ruiz-Saenz

Viruses 2025, 17(5), 649; https://doi.org/10.3390/v17050649 (registering DOI) - 29 Apr 2025

Abstract

Canine distemper virus (CDV) is the causative agent of a widespread infectious disease affecting both domestic and wild carnivores. Owing to its ability to cross species barriers and its high fatality rate in unvaccinated animals, CDV poses a significant conservation threat to endangered [...] Read more.

Canine distemper virus (CDV) is the causative agent of a widespread infectious disease affecting both domestic and wild carnivores. Owing to its ability to cross species barriers and its high fatality rate in unvaccinated animals, CDV poses a significant conservation threat to endangered wildlife worldwide. To date, two distinct CDV lineages have been reported in Colombia, with cases documented separately in domestic dogs and wild peri-urban carnivores. This study aimed to detect and characterize the concurrent circulation of CDV in naturally infected domestic dogs and crab-eating foxes (Cerdocyon thous) from the same area in Colombia. Through molecular and phylogenetic analyses, we identified the South America/North America-4 lineage infecting both populations simultaneously. Our findings revealed high genetic variability, multiple virus reintroductions, and a close relationship with CDV strains previously detected in the United States. These results confirm the simultaneous circulation of CDV in the domestic and wildlife interface and underscore the urgent need for an integrated approach to CDV prevention and control involving both domestic and wildlife health interventions. Full article

(This article belongs to the Special Issue Canine Distemper Virus)

13 pages, 2432 KiB

Open AccessArticle

PKM2 Facilitates Classical Swine Fever Virus Replication by Enhancing NS5B Polymerase Function

by Mengzhao Song, Shanchuan Liu, Yan Luo, Tiantian Ji, Yanming Zhang and Wen Deng

Viruses 2025, 17(5), 648; https://doi.org/10.3390/v17050648 (registering DOI) - 29 Apr 2025

Abstract

Host metabolic reprogramming is a critical strategy employed by many viruses to support their replication, and the key metabolic enzyme plays important roles in virus infection. This study investigates the role of pyruvate kinase M2 (PKM2), a glycolytic enzyme with non-canonical functions, in [...] Read more.

Host metabolic reprogramming is a critical strategy employed by many viruses to support their replication, and the key metabolic enzyme plays important roles in virus infection. This study investigates the role of pyruvate kinase M2 (PKM2), a glycolytic enzyme with non-canonical functions, in the replication of classical swine fever virus (CSFV). Using PK-15 cells and piglet models, we demonstrate that CSFV infection upregulates PKM2 expression both in vitro and in vivo, creating a proviral environment. knockdown of PKM2 by siRNA reduced CSFV proliferation, while PKM2 overexpression significantly increased virus propagation, which was evaluated by viral protein synthesis, genome replication, and progeny virion production. A direct interaction between PKM2 and CSFV NS5B protein was identified by co-immunoprecipitation and GST-pulldown assays, and PKM2 affected NS5B polymerase activity in a dual-luciferase reporter assay, with PKM2 depletion reducing RdRp function by 50%. Temporal analysis of the first viral replication cycle confirmed PKM2-dependent enhancement of CSFV RNA synthesis. These findings establish PKM2 as a proviral host factor that directly binds NS5B to potentiate RdRp activity, thereby bridging metabolic adaptation and viral genome replication. This study provides new evidence of a glycolytic enzyme physically interacting and enhancing viral polymerase function, offering new information about CSFV–host interaction. Full article

(This article belongs to the Section Animal Viruses)

13 pages, 2710 KiB

Open AccessArticle

Transcriptomic and Proteomic Profiling of Rabbit Kidney Cells Infected with Equine Herpesvirus 8

by Yanfei Ji, Dandan Xu, Wenxuan Si, Yu Zhang, Muhammad Zahoor Khan, Xia Zhao and Wenqiang Liu

Viruses 2025, 17(5), 647; https://doi.org/10.3390/v17050647 (registering DOI) - 29 Apr 2025

Abstract

The present study investigated the host cell response to EHV-8 infection in rabbit kidney (RK-13) cells through transcriptomic and proteomic approaches. At 24 h post-infection, a total of 2118 differentially expressed genes (DEGs) were identified, with 1338 upregulated and 780 downregulated. At 48 [...] Read more.

The present study investigated the host cell response to EHV-8 infection in rabbit kidney (RK-13) cells through transcriptomic and proteomic approaches. At 24 h post-infection, a total of 2118 differentially expressed genes (DEGs) were identified, with 1338 upregulated and 780 downregulated. At 48 h, 7388 DEGs were detected, with 4342 upregulated and 3046 downregulated genes. Proteomic analysis revealed 932 differentially expressed proteins (DEPs) at 24 h (364 upregulated and 568 downregulated) and 3866 DEPs at 48 h (2285 upregulated and 1581 downregulated). Of these, 237 upregulated and 336 downregulated proteins were common across both time points. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the majority of DEGs and DEPs were enriched in key inflammation-related pathways, notably the TNF and NF-κB signaling pathways. Validation of the transcriptomic and proteomic data was performed using RT-PCR and parallel reaction monitoring (PRM), respectively, and confirmed consistent trends for TNFR1, NF-κB p65, and MAP3K8, as reported in the transcriptomic and proteomic screening. These findings suggest that EHV-8 infection may modulate host immune responses by activating the TNF signaling pathway. However, given that RK-13 cells may not fully replicate viral–host interactions in equine species, further in vivo studies in horses and donkeys are required to provide a more comprehensive understanding of the viral pathogenesis in these animals. Full article

(This article belongs to the Special Issue Herpesvirus Transcriptional Control)

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18 pages, 2664 KiB

Open AccessArticle

Tissue-Specific Transcriptomic Responses to Avian Reovirus Inoculation in Ovo

by Zubair Khalid, Shahna Fathima and Ruediger Hauck

Viruses 2025, 17(5), 646; https://doi.org/10.3390/v17050646 (registering DOI) - 29 Apr 2025

Abstract

Avian reovirus (ARV) infections significantly impact the global poultry industry, but host responses across infection models remain poorly characterized. Using specific-pathogen-free chicken embryos, this study examined tissue-specific transcriptomic changes following in ovo inoculation with two doses of ARV S1133 at embryonic day 18. [...] Read more.

Avian reovirus (ARV) infections significantly impact the global poultry industry, but host responses across infection models remain poorly characterized. Using specific-pathogen-free chicken embryos, this study examined tissue-specific transcriptomic changes following in ovo inoculation with two doses of ARV S1133 at embryonic day 18. Quantitative PCR confirmed dose- and time-dependent viral replication, with the liver exhibiting the highest viral load at 24 h post-inoculation (hpi), whereas the kidneys, intestines, and bursa were only positive at 48 hpi with the higher viral dose. Transcriptomic profiling revealed the intestines mounted an extensive gene expression response, implicating early immune activation. Liver samples demonstrated strong upregulation of antiviral pathways, including interferon signaling and viral replication inhibition, while kidneys and intestines were enriched for coagulation and wound healing pathways. The bursae exhibited minimal immunity-related responses, suggesting insufficient maturation. Functional analyses confirmed tissue-specific immune and metabolic adaptations to infection. These findings indicate that ARV replication efficiency and host molecular responses are dose-, tissue-, and time-dependent. Notably, intestinal responses suggest preemptive immune engagement, while hepatic antiviral mechanisms may play a critical role in restricting viral spread. This study establishes foundational knowledge of host molecular responses to ARV in late-stage embryos, with implications for in ovo vaccination and early immunity. Full article

(This article belongs to the Special Issue Avian Reovirus)

14 pages, 1097 KiB

Open AccessReview

Sequences and Structures of Viral Proteins Linked to the Genomes (VPg) of RNA Viruses

by Catherine H. Schein

Viruses 2025, 17(5), 645; https://doi.org/10.3390/v17050645 (registering DOI) - 29 Apr 2025

Abstract

In the mid-1970s, it was revealed that the 5′ end of the RNA genome of poliovirus (PV) was covalently linked to a peptide called VPg (viral protein, genome-linked). Subsequently, VPgs have been found attached to many other viruses and even phages. This review [...] Read more.

In the mid-1970s, it was revealed that the 5′ end of the RNA genome of poliovirus (PV) was covalently linked to a peptide called VPg (viral protein, genome-linked). Subsequently, VPgs have been found attached to many other viruses and even phages. This review summarizes the patterns of physicochemical properties that are conserved within the VPgs of plus-strand RNA viruses where short-peptide VPgs have been identified. Mutagenesis and structural data indicate the importance of a 5 aa conserved motif at the N-termini of picornaviral VPgs (around the tyrosine 3 residue, which forms a covalent bond to UMP and the RNA). Hidden Markov models have been used to find motifs and VPgs in additional genera of picornaviruses, as well as dicistroviruses in insects and comoviruses in plants. These latter VPgs are bound to the RNA termina through linkages to serine or threonine. The role of free VPg and VPgpU needs clarification, especially in light of multiple genome copies in many of the viruses. Lysine and other positively charged side chains are hallmarks of VPgs. These may contribute to interactions with the viral RNA, polymerase, membranes and cellular proteins. The larger protein VPgs from potyviruses and noroviruses/caliciviruses may also show some areas of similar properties to these small peptides. Full article

(This article belongs to the Section General Virology)

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21 pages, 7879 KiB

Open AccessArticle

Identification of TRIM21 and TRIM14 as Antiviral Factors Against Langat and Zika Viruses

by Pham-Tue-Hung Tran, Mir Himayet Kabir, Naveed Asghar, Matthew R. Hathaway, Assim Hayderi, Roger Karlsson, Anders Karlsson, Travis Taylor, Wessam Melik and Magnus Johansson

Viruses 2025, 17(5), 644; https://doi.org/10.3390/v17050644 (registering DOI) - 29 Apr 2025

Abstract

Flaviviruses are usually transmitted to humans via mosquito or tick bites, whose infections may lead to severe diseases and fatality. During intracellular infection, they remodel the endoplasmic reticulum (ER) membrane to generate compartments scaffolding the replication complex (RC) where replication of the viral [...] Read more.

Flaviviruses are usually transmitted to humans via mosquito or tick bites, whose infections may lead to severe diseases and fatality. During intracellular infection, they remodel the endoplasmic reticulum (ER) membrane to generate compartments scaffolding the replication complex (RC) where replication of the viral genome takes place. In this study, we purified the ER membrane fraction of virus infected cells to identify the proteins that were enriched during flavivirus infection. We found that tripartite motif-containing proteins (TRIMs) including TRIM38, TRIM21, and TRIM14 were significantly enriched during infection with mosquito-borne (West Nile virus strain Kunjin and Zika virus (ZIKV)) and tick-borne (Langat virus (LGTV)) flaviviruses. Further characterizations showed that TRIM21 and TRIM14 act as restriction factors against ZIKV and LGTV, while TRIM38 hinders ZIKV infection. These TRIMs worked as interferon-stimulated genes to mediate IFN-I response against LGTV and ZIKV infections. Restriction of ZIKV by TRIM14 and TRIM38 coincides with their colocalization with ZIKV NS3. TRIM14-mediated LGTV restriction coincides with its colocalization with LGTV NS3 and NS5 proteins. However, TRIM21 did not colocalize with ZIKV and LGTV NS3 or NS5 protein suggesting its antiviral activity is not dependent on direct targeting the viral enzyme. Finally, we demonstrated that overexpression of TRIM21 and TRIM14 restricted LGTV replication. Full article

(This article belongs to the Special Issue Advances in Alphavirus and Flavivirus Research, 2nd Edition)

14 pages, 755 KiB

Open AccessArticle

Changes in Body Composition During Intensive Care Unit Stay and Outcomes in Patients with Severe COVID-19 Pneumonia: A Retrospective Cohort Study

by Hayato Nakabayashi, Junko Yamaguchi, Ken Takahashi, Yasuyoshi Kai and Kosaku Kinoshita

Viruses 2025, 17(5), 643; https://doi.org/10.3390/v17050643 (registering DOI) - 29 Apr 2025

Abstract

This single-center retrospective observational study investigated the association between changes in body composition during hospitalization and outcomes in patients with severe coronavirus disease (COVID-19) pneumonia. Body composition was assessed using chest computed tomography (CT) within 3 days of intensive care unit admission and [...] Read more.

This single-center retrospective observational study investigated the association between changes in body composition during hospitalization and outcomes in patients with severe coronavirus disease (COVID-19) pneumonia. Body composition was assessed using chest computed tomography (CT) within 3 days of intensive care unit admission and follow-up CT within 14 days. The study population comprised 89 adult patients, among whom 57 survived. The median APACHE II score on admission was 16. Initial CT scans showed that the iliopsoas muscle volume, sum of the pectoralis major and minor muscle areas, and erector spinae muscle (ESM) area were significantly larger in survivors than in non-survivors (p = 0.019, 0.011, and 0.001, respectively). Subcutaneous fat tissue (SAT) volume was higher in survivors (p = 0.003), and the rate of change in the SAT volume was lower in survivors (p = 0.043). Multivariate logistic regression analysis revealed that a high APACHE II score (OR: 0.834, 95% CI: 0.741–0.938, p = 0.002) and small ESM area (OR: 1.001, 95% CI: 1.000–1.002, p = 0.031) were independent predictors of mortality. In conclusion, the loss of supporting respiratory muscles, particularly ESM, may play a critical role beyond general acute sarcopenia, and the preserved SAT in non-survivors may reflect abnormal glucose metabolism due to severe inflammation. Full article

(This article belongs to the Special Issue COVID-19 and Pneumonia, 3rd Edition)

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27 pages, 10890 KiB

Open AccessArticle

Integrating Sequence- and Structure-Based Similarity Metrics for the Demarcation of Multiple Viral Taxonomic Levels

by Igor C. dos Santos, Rebecca di Stephano de Souza, Igor Tolstoy, Liliane S. Oliveira and Arthur Gruber

Viruses 2025, 17(5), 642; https://doi.org/10.3390/v17050642 (registering DOI) - 29 Apr 2025

Abstract

Viruses exhibit significantly greater diversity than cellular organisms, posing a complex challenge to their taxonomic classification. While primary sequences may diverge considerably, protein functional domains can maintain conserved 3D structures throughout evolution. Consequently, structural homology of viral proteins can reveal deep taxonomic relationships, [...] Read more.

Viruses exhibit significantly greater diversity than cellular organisms, posing a complex challenge to their taxonomic classification. While primary sequences may diverge considerably, protein functional domains can maintain conserved 3D structures throughout evolution. Consequently, structural homology of viral proteins can reveal deep taxonomic relationships, overcoming limitations inherent in sequence-based methods. In this work, we introduce MPACT (Multimetric Pairwise Comparison Tool), an integrated tool that utilizes both sequence- and structure-based metrics. The program incorporates five metrics: sequence identity, similarity, maximum likelihood distance, TM-score, and 3Di-character similarity. MPACT generates heatmaps and distance trees to visualize viral relationships across multiple levels, enabling users to substantiate viral taxa demarcation. Taxa delineation can be achieved by specifying appropriate score cutoffs for each metric, facilitating the definition of viral groups, and storing their corresponding sequence data. By analyzing diverse viral datasets spanning various levels of divergence, we demonstrate MPACT’s capability to reveal viral relationships, even among distantly related taxa. This tool provides a comprehensive approach to assist viral classification, exceeding the current methods by integrating multiple metrics and uncovering deeper evolutionary connections. Full article

(This article belongs to the Special Issue Bioinformatics and Computational Approaches in Viral Genomics and Evolution 2025)

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11 pages, 298 KiB

Open AccessReview

Human Microglia Models for NeuroHIV

by Priyanka Sarkar, Xu Wang, Wenhui Hu, Jian Zhu and Wen-Zhe Ho

Viruses 2025, 17(5), 641; https://doi.org/10.3390/v17050641 (registering DOI) - 29 Apr 2025

Abstract

Microglia are the primary target and reservoir of HIV infection in the central nervous system (CNS), which contributes to HIV-associated neurocognitive disorder (HAND). However, studying HIV infection of microglia has been challenged by the limited availability of primary human microglial cells. To overcome [...] Read more.

Microglia are the primary target and reservoir of HIV infection in the central nervous system (CNS), which contributes to HIV-associated neurocognitive disorder (HAND). However, studying HIV infection of microglia has been challenged by the limited availability of primary human microglial cells. To overcome this issue, investigators have developed various microglial models for HIV studies, including immortalized human microglial cell lines, HIV latently infected microglial clones, peripheral blood monocyte-derived microglia (MMG), induced pluripotent stem cell (iPSC)-derived microglia (iMg), and microglia-containing cerebral organoids (MCOs) from iPSCs. Though these models have been used in many laboratories, the published data about their expression of the specific human microglia markers and the HIV entry receptors are conflicting. In addition, there is limited information about their feasibility and applicability as a suitable model for acute and/or latent HIV infection. This review provides a concise summary of the currently used human microglial models, with a focus on their suitability for NeuroHIV research. Full article

(This article belongs to the Special Issue Roles of Macrophages in Viral Infections, 2nd Edition)

19 pages, 1306 KiB

Open AccessArticle

Individuals Infected with SARS-CoV-2 Prior to COVID-19 Vaccination Maintain Vaccine-Induced RBD-Specific Antibody Levels and Viral Neutralization Activity for One Year

by Christina S. Mcconney, Devin Kenney, Christina S. Ennis, Erika L. Smith-Mahoney, Maria Jose Ayuso, Jiabao Zhong, Florian Douam, Manish Sagar and Jennifer E. Snyder-Cappione

Viruses 2025, 17(5), 640; https://doi.org/10.3390/v17050640 (registering DOI) - 29 Apr 2025

Abstract

The effectiveness of multiple COVID-19 vaccinations in individuals with a history of SARS-CoV-2 infection remains unclear; specifically, elucidation of the durability of anti-viral antibody responses could provide important insights for epidemiological applications. We utilized the BU ELISA protocol to measure the circulating SARS-CoV-2 [...] Read more.

The effectiveness of multiple COVID-19 vaccinations in individuals with a history of SARS-CoV-2 infection remains unclear; specifically, elucidation of the durability of anti-viral antibody responses could provide important insights for epidemiological applications. We utilized the BU ELISA protocol to measure the circulating SARS-CoV-2 receptor-binding domain (RBD) and nucleocapsid (N) specific IgG and IgA antibody levels in a cohort of individuals infected with SARS-CoV-2 in the spring of 2020, with the sample collection spanning six months to two years post-symptom onset. Further, we interrogated the neutralization activity of these samples against the ancestral SARS-CoV-2 (WA-1) and Delta and Omicron (BA.1) variants. Consistent with previous studies, we found a more rapid waning of anti-N compared to anti-RBD antibodies in months prior to the first vaccinations. Vaccine-induced antibody responses in individuals previously infected with SARS-CoV-2 were elevated and sustained for more than one year post-vaccination. Similarly, neutralization activity against WA-1, Delta, and Omicron increased and remained higher than pre-vaccination levels for one year after the first COVID-19 vaccine dose. Collectively, these results indicate that infection followed by vaccination yields robust antibody responses against SARS-CoV-2 that endure for one year. These results suggest that an annual booster would stably boost anti-SARS-CoV-2 antibody responses, preventing infection and disease. Full article

(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)

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15 pages, 1455 KiB

Open AccessArticle

Successful Inactivation of High-Consequence Pathogens in PrimeStore Molecular Transport Media

by Briana Spruill-Harrell, Gregory Kocher, Maurice Boda, Kristen Akers, Denise Freeburger, Nicole Murphy, Jens H. Kuhn, Gerald Fischer, Irina Maljkovic Berry, Prabha Chandrasekaran and Jerry Torrison

Viruses 2025, 17(5), 639; https://doi.org/10.3390/v17050639 (registering DOI) - 29 Apr 2025

Abstract

Handling cultured isolates and clinical, environmental, or wildlife surveillance samples containing Risk Group 3 and 4 pathogens presents considerable biosafety challenges in minimizing human exposure during processing and transport. Safe handling typically requires high- or maximum-containment facilities, demanding substantial logistical planning and resources. [...] Read more.

Handling cultured isolates and clinical, environmental, or wildlife surveillance samples containing Risk Group 3 and 4 pathogens presents considerable biosafety challenges in minimizing human exposure during processing and transport. Safe handling typically requires high- or maximum-containment facilities, demanding substantial logistical planning and resources. We evaluated PrimeStore Molecular Transport Medium (PS-MTM), a guanidine-based solution created to kill pathogens and preserve nucleic acids at ambient temperatures, for inactivating Crimean-Congo hemorrhagic fever, eastern equine encephalitis, Ebola, Hendra, Japanese encephalitis, Lassa, Marburg, Nipah, Rift Valley fever, and West Nile viruses. To mimic diagnostic conditions, human whole blood spiked with any of these viruses was incubated with PS-MTM for 20-, 30-, or 60-min. Samples with titers up to 10⁷ PFU/mL exposed to PS-MTM at all time points resulted in complete loss of infectivity judged by plaque assays. A 30-min incubation provided a 50% safety margin over the minimum inactivation time and was used for quantification with the tissue culture infectious dose (TCID₅₀) assay, enabling evaluation of PS-MTM’s activity for viruses that do or do not produce well-defined plaques. Results confirmed that PS-MTM inactivated all tested viruses at titers up to 10⁷ TCID₅₀/mL, underscoring its reliability for enhancing biosafety in diagnostics, outbreak management, and surveillance. Full article

(This article belongs to the Special Issue BSL4 Viruses: Understanding and Controlling Highly Infectious Pathogens)

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3 pages, 135 KiB

Open AccessEditorial

Advancements and Perspectives in Nanotechnology and Nanomedicine

by Olga Morozova

Viruses 2025, 17(5), 638; https://doi.org/10.3390/v17050638 (registering DOI) - 29 Apr 2025

Abstract

Progress in atom visualization and miniaturization in microelectronics resulted in the discovery of nanomaterials in the second half of the 20th century [...] Full article

(This article belongs to the Special Issue Viruses and Virus-Like Particles as Nanoplatforms for Vaccines, Diagnostic and Therapeutic Nanomedicine)

20 pages, 1131 KiB

Open AccessReview

Zika Virus: A Review of Biology, Clinical Impacts, and Coinfections

by Lucas Matheus Barreto Santana, Ingrid Andrêssa de Moura, Yuri Mouzinho Ramos Tanaka and Rafael Freitas de Oliveira França

Viruses 2025, 17(5), 637; https://doi.org/10.3390/v17050637 (registering DOI) - 28 Apr 2025

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Abstract

The Zika virus (ZIKV) gained prominence as a significant global pathogen after the 2015–2016 outbreaks associated it with an increase in neurological complications in adults and congenital malformations. Different mechanisms have been proposed by which ZIKV may cross the blood–brain barrier and reach [...] Read more.

The Zika virus (ZIKV) gained prominence as a significant global pathogen after the 2015–2016 outbreaks associated it with an increase in neurological complications in adults and congenital malformations. Different mechanisms have been proposed by which ZIKV may cross the blood–brain barrier and reach the central nervous system to cause neuroinflammation. Although ZIKV infection triggers a robust immune response, the virus has developed different strategies to escape it. Furthermore, although the virus is present in areas with cocirculation of other pathogenic agents, few studies have evaluated the cross-immune reactions and coinfection of ZIKV. Coinfections of ZIKV with other viruses, parasites, and bacteria are described. Such interactions can worsen infections and alter the immune response, imposing new therapeutic challenges and highlighting the need for more studies in the field. In this review, we discuss various aspects of ZIKV biology, focusing on the impacts of coinfections. Full article

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

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7 pages, 2305 KiB

Open AccessBrief Report

Investigation of Natural Resistance to Fostemsavir and Lenacapavir in Naïve Primary Infections by Ultra-Deep Sequencing of near Full-Length HIV-1 Genomes

by Elisabetta Lazzari, Gabriella Rozera, Roberta Gagliardini, Valentina Mazzotta, Lavinia Fabeni, Federica Forbici, Giulia Berno, Cristian Cosentino, Enrico Girardi, Andrea Antinori, Fabrizio Maggi and Isabella Abbate

Viruses 2025, 17(5), 636; https://doi.org/10.3390/v17050636 (registering DOI) - 28 Apr 2025

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Abstract

Next-generation sequencing (NGS) of near full-length HIV genomes was performed to investigate natural resistance to Fostemsavir (FTR) and Lenacapavir (LEN) at the quasispecies level in nine naïve primary HIV infections harboring different HIV subtypes and recombinant forms. Reconstructed genomes provided a median (IQR) [...] Read more.

Next-generation sequencing (NGS) of near full-length HIV genomes was performed to investigate natural resistance to Fostemsavir (FTR) and Lenacapavir (LEN) at the quasispecies level in nine naïve primary HIV infections harboring different HIV subtypes and recombinant forms. Reconstructed genomes provided a median (IQR) coverage for gag and env of 1710 (750–6063) and 1768 (871–5270), respectively. In the gp120 encoding region, the M426R variant was found with a frequency of 100% in two HIV subtypes B: one of these also showed the A204T variant at 100%. In the more conserved capsid coding region no mutations possibly related to LEN natural resistance were observed. Full article

(This article belongs to the Special Issue Antiviral Drugs and Biologics Targeting HIV: Drug Resistance to Newer Treatment and Pre-Exposure Prophylaxis (PrEP) Options)

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12 pages, 763 KiB

Open AccessArticle

Circulation and Spillover of pdmH1N1 Influenza A Virus at an Educational Swine Farm in Chile, 2019–2023

by Soledad Ruiz, Constanza Díaz-Gavidia, María Antonieta González, Pablo Galdames, Cristóbal Oyarzún, Cecilia Baumberger, Camila Rojas, Christopher Hamilton-West, Bridgett Sharp, Shaoyuan Tan, Stacey Schultz-Cherry and Pedro Jimenez-Bluhm

Viruses 2025, 17(5), 635; https://doi.org/10.3390/v17050635 (registering DOI) - 28 Apr 2025

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Abstract

Educational farms provide students with hands-on experience in agricultural and animal practices. However, the close contact between humans and farm animals creates a significant interface for zoonotic disease transmission, yet research on infectious diseases in such settings remains limited. This study investigates the [...] Read more.

Educational farms provide students with hands-on experience in agricultural and animal practices. However, the close contact between humans and farm animals creates a significant interface for zoonotic disease transmission, yet research on infectious diseases in such settings remains limited. This study investigates the ongoing spillovers of human-origin influenza A virus (IAV) into swine at an educational farm in central Chile, describing IAV prevalence, outbreak dynamics, and the genomic characterization of detected strains. The Menesianos educational farm, located in Melipilla, central Chile, houses approximately 40 swine alongside other domestic animals, such as horses and cows. As part of an active IAV surveillance project, monthly nasal swab samples were collected from pigs between June 2019 and September 2023 for IAV detection via RT-qPCR targeting the M gene, with positive samples subsequently sequenced. During the study period, monthly IAV prevalence ranged from 0% to 52.5%, with a notable outbreak detected between May and June 2023. The outbreak lasted 5 weeks, peaking at 52.5% prevalence during week 3. Nine IAV strains were isolated over the study period, eight of which were obtained during weeks 2 and 3 of the outbreak. Phylogenetic analysis revealed that all strains were closely related to the pandemic H1N1 2009 influenza virus, with the closest related strains being those circulating in humans in Chile during the same years. These findings highlight the importance of conducting regular IAV surveillance on educational farms, where close interactions between animals and individuals—particularly children and young people—can facilitate viral spillovers and potential reverse zoonosis events. Full article

(This article belongs to the Section Animal Viruses)

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18 pages, 9413 KiB

Open AccessArticle

Primary Cells from a CD46-Edited Bovine Heifer Have Reduced BVDV Susceptibility Despite Viral Adaptation to Heparan Sulfate

by Alexandria C. Krueger, Brian L. Vander Ley, Michael P. Heaton, Tad S. Sonstegard and Aspen M. Workman

Viruses 2025, 17(5), 634; https://doi.org/10.3390/v17050634 (registering DOI) - 28 Apr 2025

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Abstract

A precision genome edit in the bovine CD46 gene (A₈₂LPTFS₈₇) dramatically reduced bovine viral diarrhea virus (BVDV) susceptibility in a cloned heifer. However, pathogen evolution threatens the long-term efficacy of such interventions. Here, our aim is two-fold: first, to [...] Read more.

A precision genome edit in the bovine CD46 gene (A₈₂LPTFS₈₇) dramatically reduced bovine viral diarrhea virus (BVDV) susceptibility in a cloned heifer. However, pathogen evolution threatens the long-term efficacy of such interventions. Here, our aim is two-fold: first, to determine whether BVDV can adapt in vitro to use the edited CD46 receptor to infect Madin–Darby bovine kidney (MDBK) cells, and second, to evaluate the ex vivo infectivity of culture-adapted viruses in cells from the CD46-edited heifer. Serial passage of BVDV on CD46-edited MDBK cells selected for virus variants capable of CD46-independent infection. Virus genome sequencing revealed mutations in the viral E^RNS gene predicted to enhance HS-mediated entry. HS adaptation was confirmed by inhibiting virus infection with heparin or Heparinase I/III treatment. A naturally occurring HS-adapted field isolate from a persistently infected calf showed similar results. However, when tested on primary cells from the CD46-edited heifer, HS-adapted viruses showed reduced infectivity in skin fibroblasts, monocytes, and lymphocytes in a manner that correlated with HS expression. Thus, although BVDV can adapt to use HS as an alternative entry receptor, HS adaptation does not overcome the protection conferred by the CD46 edit in all relevant cell types. Full article

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27 pages, 326 KiB

Open AccessReview

Improving Influenza Nomenclature Based on Transmission Dynamics

by Jwee Chiek Er

Viruses 2025, 17(5), 633; https://doi.org/10.3390/v17050633 (registering DOI) - 28 Apr 2025

Viewed by 68

Abstract

Influenza A viruses (IAVs) evolve rapidly, exhibit zoonotic potential, and frequently adapt to new hosts, often establishing long-term reservoirs. Despite advancements in genetic sequencing and phylogenetic classification, current influenza nomenclature systems remain static, failing to capture evolving epidemiological patterns. This rigidity has led [...] Read more.

Influenza A viruses (IAVs) evolve rapidly, exhibit zoonotic potential, and frequently adapt to new hosts, often establishing long-term reservoirs. Despite advancements in genetic sequencing and phylogenetic classification, current influenza nomenclature systems remain static, failing to capture evolving epidemiological patterns. This rigidity has led to delays or misinterpretations in public health responses, economic disruptions, and confusion in scientific communication. The existing nomenclature does not adequately reflect real-time transmission dynamics or host adaptations, limiting its usefulness for public health management. The 2009 H1N1 pandemic exemplified these limitations, as it was mischaracterized as “swine flu” despite sustained human-to-human transmission and no direct pig-to-human transmission reported. This review proposes a real-time, transmission-informed nomenclature system that prioritizes host adaptation and sustained transmissibility (R₀ > 1) to align influenza classification with epidemiological realities and risk management. Through case studies of H1N1pdm09, H5N1, and H7N9, alongside a historical overview of influenza naming, we demonstrate the advantages of integrating transmission dynamics into naming conventions. Adopting a real-time, transmission-informed approach will improve pandemic preparedness, strengthen global surveillance, and enhance influenza classification for scientists, policymakers, and public health agencies. Full article

(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses)

30 pages, 7440 KiB

Open AccessArticle

Exploring Avian Influenza Viruses in Yakutia—The Largest Breeding Habitat of Wild Migratory Birds in Northeastern Siberia

by Nikita Kasianov, Kirill Sharshov, Anastasiya Derko, Ivan Sobolev, Nikita Dubovitskiy, Arina Loginova, Evgeniy Shemyakin, Maria Vladimirtseva, Nikolay Egorov, Viacheslav Gabyshev, Yujin Kim, Sun-Hak Lee, Andrew Y. Cho, Deok-Hwan Kim, Tae-Hyeon Kim, Chang-Seon Song, Hyesung Jeong, Weonhwa Jheong, Yoonjee Hong, Junki Mine, Yuko Uchida, Ryota Tsunekuni, Takehiko Saito and Alexander Shestopalov Show full author list Hide full author list

Viruses 2025, 17(5), 632; https://doi.org/10.3390/v17050632 (registering DOI) - 27 Apr 2025

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Abstract

Yakutia, the largest breeding ground for wild migratory birds in Northeastern Siberia, plays a big role in the global ecology of avian influenza viruses (AIVs). In this study, we present the results of virological surveillance conducted between 2018 and 2023, analyzing 1970 cloacal [...] Read more.

Yakutia, the largest breeding ground for wild migratory birds in Northeastern Siberia, plays a big role in the global ecology of avian influenza viruses (AIVs). In this study, we present the results of virological surveillance conducted between 2018 and 2023, analyzing 1970 cloacal swab samples collected from 56 bird species. We identified 74 AIVs of H3N6, H3N8, H4N6, H5N3, H7N7, H10N3, and H11N9 subtypes in Anseriformes order. Phylogenetic analysis showed that the isolates belong to the Eurasian lineage and have genetic similarities with strains from East Asia, Europe, and North America. Cluster analysis has demonstrated the circulation of stable AIV genotypes for several years. We assume that Yakutia is an important territory for viral exchange on the migratory routes of migrating birds. In addition, several amino acid substitutions have been found to be associated with increased virulence and adaptation to mammalian hosts, highlighting the potential risk of interspecific transmission. These results provide a critical insight into the ecology of the AIV and highlight the importance of continued monitoring in this geographically significant region. Full article

(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses)

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18 pages, 4543 KiB

Open AccessReview

Attaining the Promise of Geminivirus-Based Vectors in Plant Genome Editing

by Muhammad Arslan Mahmood, Muhammad Waseem Sajjad, Ifrah Imran, Rubab Zahra Naqvi, Imran Amin, Muhammad Shafiq, Muhammad Qasim Aslam and Shahid Mansoor

Viruses 2025, 17(5), 631; https://doi.org/10.3390/v17050631 (registering DOI) - 27 Apr 2025

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Abstract

Over the last 40 years, several studies have provided evidence demonstrating that viral vectors can result in effective gene targeting/insertions in a host’s genome. The traditional approaches of gene knock-down, -out, or -in involve an intensive transgenesis process that is plagued by extensive [...] Read more.

Over the last 40 years, several studies have provided evidence demonstrating that viral vectors can result in effective gene targeting/insertions in a host’s genome. The traditional approaches of gene knock-down, -out, or -in involve an intensive transgenesis process that is plagued by extensive timescales. Plant viruses have the potential to target specific genes and integrate exogenous DNA molecules at the target locus. Their ability to manipulate a host’s genetic material and become a part of it makes them remarkable agents and helpful for molecular and synthetic biology. In this review, we describe how geminivirus-based vectors can be utilized to overcome traditional transgenesis. We highlight the progress that has been made so far and also discuss the hurdles that hinder the employment of geminivirus-based vectors. Furthermore, we conclude with a comparison of geminivirus-based vectors with other plant-derived vectors. Geminivirus-based vectors stand poised to revolutionize plant genome editing by making nucleic acid manipulation cheaper and easier to deploy, thus lessening the major technical constraints, including homology-directed repair (HDR)-mediated genome editing and time-inefficient tissue culture procedures. The insights given in this review illustrate a broader picture of geminiviral vectors, with an emphasis on engineering plant viruses to ease genome editing practices for crop improvements as well as boost experimental timescales from years to months. Full article

(This article belongs to the Special Issue Application of Genetically Engineered Plant Viruses)

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13 pages, 776 KiB

Open AccessArticle

Dynamics of Clinical, Radiological, and Biological Expression in Hospitalised COVID-19 Patients and Post-Infectious Mortality: Comparison Between 2024 and 2020

by Constantin-Marinel Vlase, Alina Plesea-Condratovici, Anca-Adriana Arbune, Roxana-Elena Goroftei-Bogdan, Cristian Gutu and Manuela Arbune

Viruses 2025, 17(5), 630; https://doi.org/10.3390/v17050630 (registering DOI) - 27 Apr 2025

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Abstract

Clinical manifestations and mortality caused by SARS-CoV-2 change, consistent with circulating viral variants and population immunity. Our retrospective study analyses the hospitalised COVID-19 cases from Romania in 2024 comparative with 2020. The circulation of SARS-CoV-2 in the fourth year of the pandemic led [...] Read more.

Clinical manifestations and mortality caused by SARS-CoV-2 change, consistent with circulating viral variants and population immunity. Our retrospective study analyses the hospitalised COVID-19 cases from Romania in 2024 comparative with 2020. The circulation of SARS-CoV-2 in the fourth year of the pandemic led to changes in the characteristics of the hospitalised population, including clinical, biological, and radiological profiles, as well as an increase in 90-day mortality after hospitalisation. The hospitalised population became predominantly older with multiple comorbidities. Notable changes in symptomatology included an increase in the frequency of rhinorrhoea and syncope, while disturbances in taste and smell were less frequent. The mortality rate within the first 90 days increased in 2024 to 9%. Older age and a higher index of chronic comorbidities were associated with a higher frequency of severe forms and deaths within 90 days post-COVID-19. Hospitalisation for COVID-19 may be an unfavourable prognostic factor for the elderly population. Full article

(This article belongs to the Special Issue COVID-19 and Pneumonia, 3rd Edition)

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12 pages, 6449 KiB

Open AccessArticle

Development and Validation of the CARRA-VID Prognostic Score: C Reactive Protein to Albumin Ratio, Red Blood Cell Distribution Width and Age-Based Score for Prognostication of Hospitalized COVID-19 Patients

by Marko Lucijanic, Nevenka Piskac Zivkovic, Nikolina Busic, Josip Stojic, Armin Atic, Lovorka Derek, Ivan Krecak, Bruno Barsic and Ivica Luksic

Viruses 2025, 17(5), 629; https://doi.org/10.3390/v17050629 (registering DOI) - 27 Apr 2025

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Abstract

Patients hospitalized due to coronavirus disease 2019 (COVID-19) usually present with severe or critical intensity of symptoms, accompanied by a marked systemic inflammatory response. Classical inflammatory biomarkers, C-reactive protein (CRP), albumin, and red blood cell distribution width (RDW) have previously been reported to [...] Read more.

Patients hospitalized due to coronavirus disease 2019 (COVID-19) usually present with severe or critical intensity of symptoms, accompanied by a marked systemic inflammatory response. Classical inflammatory biomarkers, C-reactive protein (CRP), albumin, and red blood cell distribution width (RDW) have previously been reported to be prognostic in hospitalized COVID-19 patients. We performed a retrospective analysis of two large cohorts (2305 and 2328 patients, respectively) of consecutive hospitalized COVID-19 patients with mostly severe and critical symptoms admitted to the tertiary referral center to develop and validate a prognostic score for 30-day mortality based on CRP-to-Albumin-Ratio (CAR), RDW, and age (termed CARRA-VID score). We identified 6 prognostic categories: very low, low, intermediate-1, intermediate-2, high, and very high risk, with corresponding 30-day mortality rates of 2.7%, 10.7%, 30.9%, 47.1%, 61.9%, and 89.7%, respectively. Effective risk stratification was validated in an independent cohort of patients and remained independent of the World Health Organization-defined disease severity and other commonly utilized risk scores. Additional analyses evaluated the score across different time periods dominated by distinct viral variants. We also present a simplified 3-tiered version of the score. A Microsoft Excel Workbook containing the score calculator is provided. Full article

(This article belongs to the Section Coronaviruses)

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18 pages, 6026 KiB

Open AccessArticle

Anthraquinone-2-Carboxylic Acid Is a Potential Antiviral Candidate Against Influenza Viruses In Vitro and In Vivo

by Sichen Ren, Yan Luo, Huimin Tao, Ping Wang, Song Li and Jingjing Yang

Viruses 2025, 17(5), 628; https://doi.org/10.3390/v17050628 (registering DOI) - 27 Apr 2025

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Abstract

Seasonal outbreaks and occasional pandemics triggered by influenza viruses annually impose considerable burdens on public health and finances. The continual evolution of viral strains with drug resistance emphasizes the urgency of discovering novel agents for influenza viruses. This study investigated a set of [...] Read more.

Seasonal outbreaks and occasional pandemics triggered by influenza viruses annually impose considerable burdens on public health and finances. The continual evolution of viral strains with drug resistance emphasizes the urgency of discovering novel agents for influenza viruses. This study investigated a set of innovative substances derived from Morinda officinalis with antiviral potential against influenza virus strains. The top candidate, anthraquinone-2-carboxylic acid (A2CA), presented antiviral activity against diverse influenza virus strains, including those resistant to oseltamivir. In an influenza mouse model, the pre-administration of A2CA dose-dependently ameliorated influenza A virus (IAV)-mediated weight loss as well as protected mice from a lethal IAV infection. In addition, lung injury and cytokine dysregulation were mitigated. Further investigation revealed that IAV-induced activation of the RIG-I/STAT1 signaling pathway did not occur after A2CA treatment. A time-of-addition assay revealed that A2CA targeted the final phase of intracellular replication, which was further determined by molecular docking between A2CA and the IAV RdRp protein. Finally, transcriptome analysis revealed that the TP53TG3C, CFAP57 and SNX30-DT genes may be involved in the antiviral effects of A2CA. These results play a part in achieving a thorough comprehension of the capacity of A2CA to inhibit influenza virus infection. Full article

(This article belongs to the Special Issue Antiviral Agents to Influenza Virus 2025)

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15 pages, 2726 KiB

Open AccessArticle

The Impact of EPAC2-Associated Junction Plakoglobin on Respiratory Syncytial Virus Infection

by Chaitra A. Takle, Eun-Jin Choi, Eun Seok Choi, Devang Deepak, Kashish Khatkar, Jong Min Choi, Ke Zhang, Sung Yun Jung, Tian Wang, Wenzhe Wu and Xiaoyong Bao

Viruses 2025, 17(5), 627; https://doi.org/10.3390/v17050627 (registering DOI) - 26 Apr 2025

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Abstract

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections in infants, young children, and immunocompromised individuals. Currently, FDA-approved monoclonal antibody therapies are limited to infants and young children with severe RSV disease. As a result, there is an urgent [...] Read more.

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections in infants, young children, and immunocompromised individuals. Currently, FDA-approved monoclonal antibody therapies are limited to infants and young children with severe RSV disease. As a result, there is an urgent need for comprehensive studies of RSV pathogenesis to support the development of new therapeutic strategies. Exchange proteins directly activated by cAMP (EPAC) have recently emerged as key regulators in various viral infections. Our previous work identified EPAC isoform 2 (EPAC2) as a critical factor in RSV replication and host innate immune responses. However, the molecular mechanisms underlying EPAC2’s role in RSV infection remain unclear. In this study, we investigated EPAC2-mediated RSV infection by identifying EPAC2-interacting proteins. Proteomics and immunoprecipitation analyses revealed that junction plakoglobin (JUP) interacts with EPAC2 in both mock- and RSV-infected cells, with this interaction notably enhanced during RSV infection. To determine JUP’s role in RSV infection, we compared viral replication in JUP-deficient and control cells. JUP downregulation significantly reduced the production of infectious RSV particles, likely by impairing viral budding and viral gene transcription. Moreover, our findings indicate that JUP is essential for an effective cellular immune response to RSV infection. Together, these results suggest that EPAC2 and JUP may cooperatively regulate RSV replication and dissemination. Full article

(This article belongs to the Special Issue Viral Mechanisms of Immune Evasion)

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9 pages, 406 KiB

Open AccessBrief Report

Evaluation of Humoral and Cell-Mediated Immunity Induced by Quadrivalent Influenza Vaccine in Pre-COVID-19 Japan

by Naruhito Otani, Toshiomi Okuno, Kumiko Yamada, Toshie Tsuchida, Kaori Ishikawa, Kaoru Ichiki, Takashi Ueda, Yoshio Takesue, Satoshi Higasa and Kazuhiko Nakajima

Viruses 2025, 17(5), 626; https://doi.org/10.3390/v17050626 (registering DOI) - 26 Apr 2025

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Abstract

This study aimed to evaluate the humoral and cell-mediated immune responses induced by an inactivated influenza vaccine (IIV4) during the 2019/2020 influenza season in Japan. We collected blood samples from 25 healthy adults before vaccination, 2 weeks post-vaccination, and 5 months post-vaccination. Humoral [...] Read more.

This study aimed to evaluate the humoral and cell-mediated immune responses induced by an inactivated influenza vaccine (IIV4) during the 2019/2020 influenza season in Japan. We collected blood samples from 25 healthy adults before vaccination, 2 weeks post-vaccination, and 5 months post-vaccination. Humoral and cell-mediated immunities were assessed based on hemagglutination inhibition antibody titers and interferon-γ (IFN-γ) levels, respectively. The geometric mean titer ratio for A/H3N2 exceeded 2.5, meeting the criteria outlined by the European Medicines Agency guidelines; other strains did not achieve similar thresholds. IFN-γ responses indicated significant activation for all strains, with 32–36% of participants exhibiting ≥ 1.5-fold increases. Due to the implementation of infection control measures against COVID-19, influenza activity was not observed during the 2020/2021 and 2021/2022 seasons, potentially altering influenza immunity. Our findings highlight the importance of both humoral and cell-mediated immunity in evaluating vaccine immunogenicity. Full article

(This article belongs to the Special Issue Influenza, SARS-CoV-2, RSV and Other Vaccines: Immunogenicity Parameters and Protection, 3rd Edition)

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16 pages, 840 KiB

Open AccessArticle

The COVID-19 Infection Did Not Aggravate the Mortality of Long-Term Care Facility Residents Under Strict Infection Control and with Immediate Anti-Viral Treatment: Real-World Analysis

by Hideyasu Shimizu, Jin Kawase, Yuko Higashi, Hiroyuki Nabeno, Masamichi Hayashi, Kazuyoshi Imaizumi, Yuji Ito, Masaaki Matsunaga and Mitsushi Okazawa

Viruses 2025, 17(5), 625; https://doi.org/10.3390/v17050625 (registering DOI) - 26 Apr 2025

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Abstract

Background: Long-term care facilities (LTCFs) remain highly vulnerable to COVID-19. Despite reduced virulence, Omicron’s high transmissibility poses ongoing risks. The effect of infection under strict control measures and early antiviral treatment remains unclear. Methods: We conducted a retrospective cohort study in a 450-bed [...] Read more.

Background: Long-term care facilities (LTCFs) remain highly vulnerable to COVID-19. Despite reduced virulence, Omicron’s high transmissibility poses ongoing risks. The effect of infection under strict control measures and early antiviral treatment remains unclear. Methods: We conducted a retrospective cohort study in a 450-bed LTCF, which implemented rigorous infection control and early antiviral use, evaluating survival outcomes during repeated Omicron outbreaks from January 2022 to December 2023 using Cox regression with time-dependent covariates, adjusted for age, sex, comorbidities, and vaccination status. Mortality trends were also compared across three periods: pre-COVID-19 (2018–2019), COVID-19 present in Japan but absent in our facility (2020–2021), and the Omicron outbreak period (2022–2023). Results: Among 623 residents, 253 were infected. Mortality was lower in the infected group than in the uninfected group (16% vs. 26%), and infection was not significantly associated with increased mortality (HR = 1.36; 95% CI: 0.91–2.04; p = 0.14). Although stratified analysis showed higher mortality among infected females, overall mortality during the outbreak period was unexpectedly lower than in prior periods. Conclusions: In LTCFs with rigorous infection control and early antiviral use, Omicron infection did not raise mortality. Enhanced protocols may have improved survival, even among uninfected residents. Full article

(This article belongs to the Section Coronaviruses)

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19 pages, 5116 KiB

Open AccessArticle

Theobroma cacao Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance

by Gabriel Victor Pina Rodrigues, João Pedro Nunes Santos, Lucas Yago Melo Ferreira, Lucas Barbosa de Amorim Conceição, Joel Augusto Moura Porto and Eric Roberto Guimarães Rocha Aguiar

Viruses 2025, 17(5), 624; https://doi.org/10.3390/v17050624 (registering DOI) - 26 Apr 2025

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Abstract

Cocoa (Theobroma cacao L.) is a major agricultural commodity, essential for the global chocolate industry and the livelihoods of millions of farmers. However, viral diseases pose a significant threat to cocoa production, with Badnavirus species causing severe losses in Africa. Despite its [...] Read more.

Cocoa (Theobroma cacao L.) is a major agricultural commodity, essential for the global chocolate industry and the livelihoods of millions of farmers. However, viral diseases pose a significant threat to cocoa production, with Badnavirus species causing severe losses in Africa. Despite its economic importance, the overall virome of T. cacao remains poorly characterized, limiting our understanding of viral diversity and potential disease interactions. This study aims to assess the cocoa-associated virome by analyzing 109 publicly available RNA-seq libraries from nine BioProjects, covering diverse conditions and geographic regions. We implemented a comprehensive bioinformatics pipeline integrating multiple viral sequence enrichment steps, a hybrid assembly strategy using different assemblers, and sequence similarity searches against NCBI non-redundant databases. Our approach identified ten putative novel viruses associated with the cocoa microbiome and a novel Badnavirus species. These findings provide new insights into the viral landscape of T. cacao, characterizing the diversity of cacao-associated viruses and their potential ecological roles. Expanding the catalog of viruses associated with cocoa plants not only enhances our understanding of plant–virus–microbiome interactions but also contributes to the development of more effective disease surveillance and management strategies, ultimately supporting sustainable cocoa production. Full article

(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)

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33 pages, 59816 KiB

Open AccessArticle

Acinetobacter baumannii and Klebsiella pneumoniae Isolates Obtained from Intensive Care Unit Patients in 2024: General Characterization, Prophages, Depolymerases and Esterases of Phage Origin

by Nadezhda V. Kolupaeva, Lyubov V. Kolupaeva, Peter V. Evseev, Yuriy P. Skryabin, Elena B. Lazareva, Tatyana V. Chernenkaya, Nikolay V. Volozhantsev and Anastasia V. Popova

Viruses 2025, 17(5), 623; https://doi.org/10.3390/v17050623 (registering DOI) - 26 Apr 2025

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Abstract

Acinetobacter baumannii and Klebsiella pneumoniae are significant nosocomial pathogens worldwide. In this study, the general characterization of A. baumannii and K. pneumoniae isolates obtained from the blood of intensive care unit patients of the multidisciplinary scientific and practical center of emergency medicine from [...] Read more.

Acinetobacter baumannii and Klebsiella pneumoniae are significant nosocomial pathogens worldwide. In this study, the general characterization of A. baumannii and K. pneumoniae isolates obtained from the blood of intensive care unit patients of the multidisciplinary scientific and practical center of emergency medicine from January to September 2024 was performed. Prophage regions and prophage-derived tailspike polysaccharide-depolymerizing or -modifying enzymes within these isolates were identified and characterized in detail using a refined workflow. The protocol, encompassing a comprehensive survey of all predicted bacterial proteins, revealed an average of 6.0 prophage regions per Acinetobacter baumannii genome, including regions putatively derived from filamentous phages, and 4.8 prophage regions per Klebsiella pneumoniae isolate. Analysis of these putative prophage regions indicated that most were related to previously isolated, yet unclassified, temperate phages infecting A. baumannii and K. pneumoniae. However, certain identified sequences likely originated from phages representing novel groups comparatively distant from known phages. Full article

(This article belongs to the Section Bacterial Viruses)

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21 pages, 5031 KiB

Open AccessReview

Orthohantaviruses: An Overview of the Current Status of Diagnostics and Surveillance

by Maria Anele Romeo, Silvia Tofani, Daniele Lapa, Cosmina Mija, Fabrizio Maggi, Maria Teresa Scicluna and Roberto Nardini

Viruses 2025, 17(5), 622; https://doi.org/10.3390/v17050622 (registering DOI) - 26 Apr 2025

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Abstract

Orthohantavirus infection is a rodent-to-human zoonotic disease with a worldwide distribution, resulting in more than 200,000 cases per year. Human infection leads to two diseases, haemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome, with mortality rates ranging from 1% to 38%. Apart [...] Read more.

Orthohantavirus infection is a rodent-to-human zoonotic disease with a worldwide distribution, resulting in more than 200,000 cases per year. Human infection leads to two diseases, haemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome, with mortality rates ranging from 1% to 38%. Apart from the data on cases presenting obvious clinical symptoms, the true prevalence is poorly understood, especially in the occupational groups considered to be at risk of exposure. As there is currently no approved therapy or vaccine, surveillance is essential to locate the presumed site of infection following orthohantavirus outbreaks in order to control the spread of infection. To this end, the use of rapid diagnostic tools is essential to rapidly provide data on viral circulation. This review focuses mainly on the available diagnostic methods, both serological and biomolecular, and the surveillance systems used for orthohantaviruses. The information gathered could provide a valid basis for the implementation of further surveillance systems in a country lacking up-to-date data. Full article

(This article belongs to the Section Animal Viruses)

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17 pages, 2563 KiB

Open AccessArticle

Molecular Epidemiology of Travel-Associated and Locally Acquired Dengue Virus Infections in Catalonia, Spain, 2019

by Jéssica Navero-Castillejos, Adrián Sánchez-Montalvá, Elena Sulleiro, Aroa Silgado, Tomás Montalvo, Laura Barahona, Núria Busquets, José Muñoz, Daniel Camprubí-Ferrer, Manuel Valdivia, Ana Martínez, Maria Assumpció Bou-Monclús, Itziar Martínez-Calleja, Mireia Jané, Cristina Rius, Hernán Vargas-Leguas, Beatriz Escudero-Pérez, Rosa Albarracín, Alexander Navarro, Mireia Navarro, Josep Barrachina and Miguel J. Martínez Show full author list Hide full author list

Viruses 2025, 17(5), 621; https://doi.org/10.3390/v17050621 (registering DOI) - 26 Apr 2025

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Abstract

Dengue virus (DENV) is the most important arbovirus worldwide. In 2019, a significant increase in dengue cases was reported worldwide, resulting in a peak of imported cases in some European countries such as Spain. We aimed to describe travel-associated and locally acquired DENV [...] Read more.

Dengue virus (DENV) is the most important arbovirus worldwide. In 2019, a significant increase in dengue cases was reported worldwide, resulting in a peak of imported cases in some European countries such as Spain. We aimed to describe travel-associated and locally acquired DENV strains detected in 2019 in the Catalonia region (northeastern Spain), a hotspot for dengue introduction in Europe. Through sequencing and phylogenetic analysis of the envelope gene, 75 imported viremic cases and two local strains were described. Autochthonous transmission events included an infection of a local mosquito with an imported dengue strain and a locally acquired human dengue infection from a locally infected mosquito. Overall, all four DENV serotypes and up to 10 different genotypes were detected. Phylogenetic analysis revealed transcontinental circulations associated with DENV-1 and DENV-2 and the presence of DENV-4 genotype I in Indonesia, where few cases had been previously described. A molecular study of the autochthonous events determined that local Ae. albopictus mosquitoes were infected by an African DENV-1 genotype V strain, while the locally acquired human case was caused by a DENV-3 genotype I of Asian origin. These findings underline the wide variability of imported strains and the high risk of DENV introduction into this territory, emphasizing the importance and usefulness of molecular characterization and phylogenetics for both local and global surveillance of the disease. Full article

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

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Viruses, Volume 17, Issue 5 (May 2025) – 62 articles

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