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Volume 17, January
 
 

Viruses, Volume 17, Issue 2 (February 2025) – 83 articles

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17 pages, 1425 KiB  
Systematic Review
The Use of Plant Viral Nanoparticles in Cancer Biotherapy—A Review
by Mamorake Donty Komane, Prudence Ngalula Kayoka-Kabongo and Daria Anna Rutkowska
Viruses 2025, 17(2), 218; https://doi.org/10.3390/v17020218 (registering DOI) - 1 Feb 2025
Viewed by 468
Abstract
Cancer is a major global health problem that poses significant challenges. Conventional cancer therapies often have severe side effects, necessitating the development of novel therapeutic approaches that are more effective and less toxic. The utilization of plant viral nanoparticles is one of the [...] Read more.
Cancer is a major global health problem that poses significant challenges. Conventional cancer therapies often have severe side effects, necessitating the development of novel therapeutic approaches that are more effective and less toxic. The utilization of plant viral nanoparticles is one of the more promising strategies for cancer biotherapy. Plant viral nanoparticles exhibit advantageous properties, including safety, high stability, rapid production and scalability, biocompatibility and biodegradability, structural uniformity, inherent immunogenicity, ease of modification and high update efficacy as well as lower cost implications, making them attractive vehicles for health applications. Various studies have demonstrated the efficacy of plant viral nanoparticles in targeted therapeutic drug/molecule delivery, tumor imaging and immunotherapy, highlighting their potential as a versatile platform for cancer biotherapy. The drawbacks of plant viral nanoparticles include their perceived ability to induce a hypersensitive/allergic immune response, non-well-defined regulatory approval processes as well as the reluctance of pharmaceutical companies to adapt their manufacturing processes to facilitate plant-based expression. This review discusses applications of plant virus-derived nanoparticles in cancer therapeutics and prospects for translating these findings into clinical practice. Full article
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27 pages, 923 KiB  
Review
The Temperature-Associated Effects of Rift Valley Fever Virus Infections in Mosquitoes and Climate-Driven Epidemics: A Review
by Faustus A. Azerigyik, Shelby M. Cagle, William C. Wilson, Dana N. Mitzel and Rebekah C. Kading
Viruses 2025, 17(2), 217; https://doi.org/10.3390/v17020217 (registering DOI) - 1 Feb 2025
Viewed by 253
Abstract
Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic disease within the genus Phlebovirus. Symptoms of the disease in animals range from moderate to severe febrile illness, which significantly impacts the livestock industry and causes severe health complications in humans. Similar to [...] Read more.
Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic disease within the genus Phlebovirus. Symptoms of the disease in animals range from moderate to severe febrile illness, which significantly impacts the livestock industry and causes severe health complications in humans. Similar to bunyaviruses in the genus Orthobunyavirus transmitted by mosquitoes, RVFV progression is dependent on the susceptibility of the physical, cellular, microbial, and immune response barriers of the vectors. These barriers, shaped by the genetic makeup of the mosquito species and the surrounding environmental temperature, exert strong selective pressure on the virus, affecting its replication, evolution, and spread. The changing climate coupled with the aforementioned bottlenecks are significant drivers of RVF epidemics and expansion into previously nonendemic areas. Despite the link between microclimatic changes and RVF outbreaks, there is still a dearth of knowledge on how these temperature effects impact RVF transmission and vector competence and virus persistence during interepidemic years. This intricate interdependence between the virus, larval habitat temperatures, and vector competence necessitates increased efforts in addressing RVFV disease burden. This review highlights recent advancements made in response to shifting demographics, weather patterns, and conveyance of RVFV. Additionally, ongoing studies related to temperature-sensitive variations in RVFV–vector interactions and knowledge gaps are discussed. Full article
(This article belongs to the Special Issue Emerging Highlights in the Study of Rift Valley Fever Virus)
18 pages, 2214 KiB  
Article
New Insights into Antiviral Natural Formulations: Biopolymeric Films for the Prevention and Treatment of a Wide Gamma of Viral Infections
by Victoria Belén Ayala-Peña, Ana Karen Jaimes, Ana Lucía Conesa, Cybele Carina García, Claudia Soledad Sepulveda, Fernando Gaspar Dellatorre, Ezequiel Latour, Nora Marta Andrea Ponce, Vera Alejandra Álvarez and Verónica Leticia Lassalle
Viruses 2025, 17(2), 216; https://doi.org/10.3390/v17020216 (registering DOI) - 1 Feb 2025
Viewed by 174
Abstract
Viral infections remain a major concern, as existing treatments often yield inadequate responses or lead to the development of antiviral resistance in some cases. Fucoidan extracted from Undaria pinnatifida (F) is a natural sulphated polysaccharide that exhibits antiviral action. Despite its potential, the [...] Read more.
Viral infections remain a major concern, as existing treatments often yield inadequate responses or lead to the development of antiviral resistance in some cases. Fucoidan extracted from Undaria pinnatifida (F) is a natural sulphated polysaccharide that exhibits antiviral action. Despite its potential, the biomedical application of F is limited due to its difficult administration through trans-mucosal, skin, or oral ingestion. The most effective way to solve these problems is to propose novel methods of administration aiming to ensure better contact between the biopolymers and pathogens, leading to their inactivation. In this work, the synthesis of films based on chitosan (Ch)-coupled F is reported, aiming to generate a synergic effect between both biopolymers in terms of their antiviral and antioxidant capability. Biocomposites were prepared by a sonochemical method. They were characterized to infer structural properties, functionality, and possible F-Ch interactions by using Zeta potential, FTIR, and XRD techniques. The biocomposites showed excellent film-forming ability. They also exhibited improved antioxidant activity with respect to F and Ch individually and proved to be non-cytotoxic. These results demonstrate, for the first time, the antiviral activity of F:Ch biocomposites against bovine coronavirus and human viruses (adenovirus, poliovirus, herpes simplex, and respiratory syncytial virus), which could be applied in film form to prevent or treat viral infections. Full article
7 pages, 765 KiB  
Brief Report
Effectiveness and Immunogenicity of the MMR Vaccine Against SARS-CoV-2 Among Healthcare Workers
by Hyeri Seok, Joon-Yong Bae, Jooyun Kim, Won Suk Choi, Heedo Park, Jungmin Lee, Sohyun Lee, Chulwoo Kim, Man-Seong Park and Dae Won Park
Viruses 2025, 17(2), 215; https://doi.org/10.3390/v17020215 (registering DOI) - 1 Feb 2025
Viewed by 216
Abstract
The purpose of this study was to evaluate the effectiveness and immunogenicity of the measles–mumps–rubella (MMR) vaccine against SARS-CoV-2 in healthcare workers at one medical institution. The effectiveness of the MMR vaccine against SARS-CoV-2 was evaluated in overall healthcare workers (HCWs). In addition, [...] Read more.
The purpose of this study was to evaluate the effectiveness and immunogenicity of the measles–mumps–rubella (MMR) vaccine against SARS-CoV-2 in healthcare workers at one medical institution. The effectiveness of the MMR vaccine against SARS-CoV-2 was evaluated in overall healthcare workers (HCWs). In addition, neutralizing antibodies to SARS-CoV-2 were measured according to the subjects’ measles immunity status with serum samples collected before the coronavirus disease 2019 pandemic period. The effectiveness of the MMR vaccine for SARS-CoV-2 in all HCWs and measles IgG-positive subjects was 34% (adjusted odds ratio [aOR] = 1.20, 95% confidence interval [CI] = 0.53–2.70) and 34% (aOR = 0.66, CI = 0.38–18.4), respectively. The neutralizing antibody levels for SARS-CoV-2 were low in all groups regardless of the measles immune status. The MMR vaccine alone may not provide sufficient protection against SARS-CoV-2. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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37 pages, 1494 KiB  
Review
Tobacco Mosaic Virus Movement: From Capsid Disassembly to Transport Through Plasmodesmata
by Amr Ibrahim, Nobumitsu Sasaki, James E. Schoelz and Richard S. Nelson
Viruses 2025, 17(2), 214; https://doi.org/10.3390/v17020214 (registering DOI) - 31 Jan 2025
Viewed by 350
Abstract
Determining mechanisms to establish an initial infection and form intracellular complexes for accumulation and movement of RNA plant viruses are important areas of study in plant virology. The impact of these findings on the basic understanding of plant molecular virology and its application [...] Read more.
Determining mechanisms to establish an initial infection and form intracellular complexes for accumulation and movement of RNA plant viruses are important areas of study in plant virology. The impact of these findings on the basic understanding of plant molecular virology and its application in agriculture is significant. Studies with tobacco mosaic virus (TMV) and related tobamoviruses often provide important foundational knowledge for studies involving other viruses. Topics discussed here include capsid disassembly, establishment of a virus replication complex (VRC), and transport of the VRCs or virus components within the cell to locations at the plasmodesmata (PD) for intercellular virus RNA (vRNA) movement. Seminal findings with TMV and related tobamoviruses include detecting co-translational disassembly of the vRNA from the virus rod, full sequencing of genomic vRNA, and production of infectious transcript for genetic studies determining virus components necessary for intercellular movement and biochemical and cell biological studies determining the host factors, protein and membrane, needed for replication and movement. This review highlights many of the studies through the years on TMV and selected tobamoviruses that have impacted not only our understanding of tobamovirus accumulation and movement but also that of other plant viruses. Full article
11 pages, 1541 KiB  
Brief Report
Molecular Characterization of the Infectious Laryngotracheitis Virus (ILTV) Involved in Poultry Outbreaks Reveals the Virus Origin and Estimated Spreading Route
by Jorge Luis Chacón, Ruy D. Chacón, Henrique Lage Hagemann, Claudete S. Astolfi-Ferreira, Cesar Nunes, Luiz Sesti, Branko Alva and Antonio J. Piantino Ferreira
Viruses 2025, 17(2), 213; https://doi.org/10.3390/v17020213 (registering DOI) - 31 Jan 2025
Viewed by 294
Abstract
Infectious laryngotracheitis outbreaks have been observed in a short period of time in broiler, layer, and broiler breeder flocks, resulting in clinical signs and high mortality. The affected farms are located in the same geographical area, which is a high-density poultry region of [...] Read more.
Infectious laryngotracheitis outbreaks have been observed in a short period of time in broiler, layer, and broiler breeder flocks, resulting in clinical signs and high mortality. The affected farms are located in the same geographical area, which is a high-density poultry region of Brazil. To estimate the potential origin of the virus or viruses that caused the outbreaks, the ILTVs detected at six companies were molecularly characterized by sequencing two fragments of the ICP4 gene and then compared with previous field and vaccine viruses detected in the country. The sequencing results revealed that all farms investigated were infected with a nonvaccine-origin virus. Phylogenetic analysis revealed that all farms were infected by the same virus classified as genotype VI. In addition, the ILTV detected in the present study was compared with that of viruses previously detected in egg-layer poultry regions in the country. The viruses detected in the recent outbreaks were indistinguishable, with one of them (VI-4) suggesting a possible route of transmission. This study describes for the first time severe ILT outbreaks in meat-type poultry in Brazil that spread quickly, and the phylogenetic analysis suggests the potential origin of the virus and route of transmission. Full article
(This article belongs to the Special Issue Avian Respiratory Viruses, 4th Edition)
19 pages, 991 KiB  
Review
Current Dengue Virus Vaccine Developments and Future Directions
by Govindaraj Anumanthan, Bikash Sahay and Ayalew Mergia
Viruses 2025, 17(2), 212; https://doi.org/10.3390/v17020212 (registering DOI) - 31 Jan 2025
Viewed by 224
Abstract
Dengue fever (DF), a leading arboviral disease globally, is caused by the Dengue virus (DENV) and represents a significant public health concern, with an estimated 390 million cases reported annually. Due to the complexity of the various dengue variants and the severity of [...] Read more.
Dengue fever (DF), a leading arboviral disease globally, is caused by the Dengue virus (DENV) and represents a significant public health concern, with an estimated 390 million cases reported annually. Due to the complexity of the various dengue variants and the severity of the disease, vaccination emerges as the essential strategy for combating this widespread infectious disease. The absence of specific antiviral medications underscores the critical need for developing a Dengue vaccine. This review aims to present the current status and future prospects of Dengue vaccine development. Further, this review elaborates on the various strategies employed in vaccine development, including attenuated, inactivated, subunit, and viral vector vaccines. Each approach is evaluated based on its immunogenicity, safety, and efficacy, drawing on data from preclinical and clinical studies to highlight the strengths and limitations of each candidate vaccine. The current study sheds light on future directions and research priorities in developing Dengue vaccines. In conclusion, the development of a Dengue vaccine holds significant potential for reducing the global burden of DF. However, challenges remain in terms of vaccine safety, efficacy, delivery, and availability. Overcoming these challenges, coupled with advancements in vaccine technology, could lead to better control and prevention of Dengue, thereby enhancing public health and quality of life. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
26 pages, 5920 KiB  
Article
Complete Genome Classification System of Rotavirus alphagastroenteritidis: An Updated Analysis
by Ricardo Gabriel Díaz Alarcón, Karina Salvatierra, Emiliano Gómez Quintero, Domingo Javier Liotta, Viviana Parreño and Samuel Orlando Miño
Viruses 2025, 17(2), 211; https://doi.org/10.3390/v17020211 (registering DOI) - 31 Jan 2025
Viewed by 271
Abstract
Rotavirus alphagastroenteritidis is the major causative agent of acute gastroenteritis in both children under the age of 5 and young mammals and birds globally. RVAs are non-enveloped viruses with a genome comprising 11 double-stranded RNA segments. In 2008, the Rotavirus Classification Working Group [...] Read more.
Rotavirus alphagastroenteritidis is the major causative agent of acute gastroenteritis in both children under the age of 5 and young mammals and birds globally. RVAs are non-enveloped viruses with a genome comprising 11 double-stranded RNA segments. In 2008, the Rotavirus Classification Working Group pioneered a comprehensive and complete RVA genome classification system, establishing a specific threshold, which measures the genetic distances between homologous genes. The aim of this study was to perform an updated systematic analysis of the genetic variability across all RVA genes. Our investigation involved assessing the established cutoff values for each RVA genome segment and determining the need for any updates. To achieve this objective, multiple sequence alignments were constructed for all 11 genes and one for each genotype with discrepancies. Also, pairwise distances along with their cutoff values were evaluated. The analyses provided insights into the current relevance of cutoff values, which remain applicable for the majority of genotypes. In conclusion, this study fortifies the current classification system by highlighting its robustness and accurate genotyping of Rotavirus alphagastroenteritidis. Full article
(This article belongs to the Special Issue Virus Bioinformatics 2024)
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15 pages, 2773 KiB  
Case Report
Novel Oronasal Drainage for Long COVID: Proposed Mechanisms—Case Report
by Claudia Lorenz and Roland Frankenberger
Viruses 2025, 17(2), 210; https://doi.org/10.3390/v17020210 - 31 Jan 2025
Viewed by 1038
Abstract
Long COVID, potentially emerging post COVID-19 infection, involves extreme health challenges. Based on current literature in the field, we propose a novel approach to Long COVID treatment based on epipharyngeal abrasive therapy targeting ostia of the oral and nasal mucosa, having been identified [...] Read more.
Long COVID, potentially emerging post COVID-19 infection, involves extreme health challenges. Based on current literature in the field, we propose a novel approach to Long COVID treatment based on epipharyngeal abrasive therapy targeting ostia of the oral and nasal mucosa, having been identified for the first time. The presented case report documents the application of innovative oronasal drainage (OND), a novel treatment integrating physiological, biochemical, and fluid mechanical components simultaneously. OND led to remarkable improvements and even remissions of various symptoms, along with enhanced hand blood circulation. While the case suggests potential efficacy in Long COVID therapy, acknowledging inherent limitations is essential and its impact needs further validation through clinical trials. Full article
(This article belongs to the Special Issue COVID-19 Complications and Co-infections)
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22 pages, 13356 KiB  
Article
Comparative Genome Sequencing Analysis of Some Novel Feline Infectious Peritonitis Viruses Isolated from Some Feral Cats in Long Island
by Abid Ullah Shah, Blanca Esparza, Oscar Illanes and Maged Gomaa Hemida
Viruses 2025, 17(2), 209; https://doi.org/10.3390/v17020209 - 31 Jan 2025
Viewed by 325
Abstract
Feline infectious peritonitis virus (FIPV) remains as one of the leading causes of morbidity and mortality in young cats from shelters and catteries worldwide. Since little is known about the molecular characteristics of currently circulating FIPV strains in Long Island, New York, samples [...] Read more.
Feline infectious peritonitis virus (FIPV) remains as one of the leading causes of morbidity and mortality in young cats from shelters and catteries worldwide. Since little is known about the molecular characteristics of currently circulating FIPV strains in Long Island, New York, samples from two shelter cats submitted to the Pathology Diagnostic Services of the Long Island University College of Veterinary Medicine, with gross and microscopic lesions consistent with those of FIP were processed for virus isolation, molecular characterization and full-length genome decoding. The younger shelter cat, a 1-year-old male (A15) was found dead without previous signs of illness. Postmortem examination revealed gross and microscopic lesions characterized by vasculitis, necrosis, hemorrhage, and pyogranulomatous inflammation confined to the colon and associated lymph nodes. The second cat, a 7-year-old spayed female (A37) had an identical clinical history and similar but widespread lesions, including fibrinous peritoneal effusion, cecal, colonic, renal, and hepatic involvement. The gross and microscopic diagnosis of FIP in these cats was confirmed by immunohistochemistry (IHC) demonstration of feline coronavirus antigen using mouse anti-FIPV3-70 monoclonal antibody. Virus isolation from saved frozen kidney and colon tissue was performed through several subsequent blind passages in MDCK and Vero cell lines. Confirmation of the FIPV isolation was done through qRT-PCR, IFA, western blot using N protein antibodies, and NGS of the full-length genome sequencing. The full-length genome sequences of the virus isolate from the two cats were decoded using next-generation sequencing (NGS) and deposited in the GenBank as accession numbers PQ192636 and PQ202302. The genome size of these isolates was (29355 and 29321) nucleotides (nt) in length, respectively. While their genome organization was consistent with other FIPV genomes as follows (5’UTR-ORF1ab-S-3abc-M-E-7b-3’UTR-3’), marked differential mutations were observed in the ORF1a/b, S, 3Abc, and 7b protein genes of the two FIPV isolates. One notable deletion of 34 nucleotides was observed in the 7b genes of one of these isolates but was absent in the other. We confirmed the potential recombination events during the evolution of those two FIPV field isolates with the potential parent virus as FECoV-US isolated in 1970 and the potential minor parent as the Canine coronavirus. Our results provide a comprehensive molecular analysis of two novel FIPV isolates causing fatal disease in shelter cats from Long Island. Diagnostic surveillance with molecular characterization and sequencing analysis of circulating FIPV strains within animal shelters may help early detect unique emerging clinical and pathological manifestations of the disease and develop more targeted prophylactic and therapeutic approaches to control it. Full article
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14 pages, 266 KiB  
Article
Neonatal Microcephaly and Central Nervous System Abnormalities During the Zika Outbreak in Rio de Janeiro
by Marlos Melo Martins, Roberto de Andrade Medronho, Carlos Eduardo Raymundo, Arnaldo Prata-Barbosa and Antonio José Ledo Alves da Cunha
Viruses 2025, 17(2), 208; https://doi.org/10.3390/v17020208 - 31 Jan 2025
Viewed by 274
Abstract
This retrospective cohort study analyzed 7870 pregnant women, including 2269 with confirmed Zika virus (ZIKV) infection and 5601 without Zika infection, along with their fetuses and newborns. Data were sourced from multiple databases in the state of Rio de Janeiro, Brazil. A propensity [...] Read more.
This retrospective cohort study analyzed 7870 pregnant women, including 2269 with confirmed Zika virus (ZIKV) infection and 5601 without Zika infection, along with their fetuses and newborns. Data were sourced from multiple databases in the state of Rio de Janeiro, Brazil. A propensity score model was employed to control confounding factors and stratify outcomes by pregnancy trimester. Among ZIKV+ pregnant women, 49 cases of congenital microcephaly or congenital nervous system (CNS) abnormalities were identified (2.16%, or 193.9 cases in 10,000 live births), whereas 44 cases were identified among ZIKV− women (0.78%, or 71.4 cases in 10,000 live births). Multivariable analysis yielded an odds ratio of 2.46 (95% CI 1.30–4.64) overall, with 4.29 (95% CI 1.93–9.53) in the first trimester, 5.29 (95% CI 1.08–25.95) in the second trimester, and 0.68 (95% CI 0.21–2.14) in the third trimester. The most frequent findings among ZIKV+ cases included intracranial calcifications, ventriculomegaly, posterior fossa malformations, reduced brain volume, corpus callosum malformations, cortex dysplasia, lissencephaly, and pachygyria. Ophthalmologic abnormalities were detected in 55.5% of cases, and brainstem auditory evoked potential anomalies were reported in 33.3%. ZIKV infection can result in structural or functional anomalies. Given the absence of specific treatment for congenital Zika syndrome (CZS), clinical care should prioritize monitoring and managing neurological, motor, auditory, visual, and orthopedic disorders in all children with in utero ZIKV exposure, especially during the first and second trimesters of pregnancy. Full article
(This article belongs to the Special Issue Zika Virus and Congenital Zika Syndrome)
17 pages, 382 KiB  
Article
SARS-CoV-2 Infection and Adverse Maternal and Perinatal Outcomes: Time-to-Event Analysis of a Hospital-Based Cohort Study of Pregnant Women in Rio de Janeiro, Brazil
by Michelle Brendolin, Mayumi Duarte Wakimoto, Raquel de Vasconcellos Carvalhaes de Oliveira, Larissa Rangel Mageste, Karin Nielsen-Saines and Patricia Brasil
Viruses 2025, 17(2), 207; https://doi.org/10.3390/v17020207 - 31 Jan 2025
Viewed by 1475
Abstract
Understanding perinatal health outcomes following SARS-CoV-2 infection during pregnancy necessitates large-scale studies of mother-infant dyads. Hospital-based studies of pregnant women and their neonates provide valuable insights within the field of perinatal health research. The aim of this study was to evaluate the effect [...] Read more.
Understanding perinatal health outcomes following SARS-CoV-2 infection during pregnancy necessitates large-scale studies of mother-infant dyads. Hospital-based studies of pregnant women and their neonates provide valuable insights within the field of perinatal health research. The aim of this study was to evaluate the effect of SARS-CoV-2 infection on maternal and perinatal outcomes among hospitalized pregnant women in Rio de Janeiro during the COVID-19 pandemic. Methods: The study consisted of a time-to-event analysis of a hospital-based cohort of 1185 pregnant women ≥ 16 years and their infants from May 2020 to March 2022. Pregnant women were classified as infected if they had a SARS CoV-2 positive RT-PCR or a positive rapid antigen test. An exploratory analysis of qualitative variables was conducted with calculation of absolute and relative frequencies and calculation of 95% confidence intervals. Survival functions were estimated by the Kaplan–Meier method, and the Cox proportional hazards model was employed to interpret the effects of SARS-CoV-2 infection on time to adverse maternal and perinatal outcomes, adjusted for vaccination, comorbidity, and gestational trimester. Results: A total of 21% (249/1185) women were infected with SARS-CoV-2, with a median age of 26 (range: 16–47). Cesarean section deliveries were performed in 57% (135/237) SARS CoV-2+ participants vs. 43% (391/914) of uninfected participants, p < 0.001. Intensive care unit admission and/or death occurred in 68 of 1185 participants (5.7%), 44 of 249 participants (17.7%) infected with SARS CoV-2 vs. 24 of 936 uninfected participants (2.5%). All 21 participants who died were unvaccinated against COVID-19. Women infected with SARS-CoV-2 were at greater risk of adverse maternal outcomes (crude HR: 5.93, 95% CI: 3.58–9.84; adjusted HR: 5.47, 95% CI: 3.16–9.48) than uninfected pregnant women. SARS CoV-2 vertical transmission was observed in 6 of 169 (3.6%) tested neonates. Preterm deliveries occurred more frequently in patients testing positive for SARS-CoV-2 (30.7% vs. 23.6). In the survival analysis, no effect of SARS-CoV-2 infection was observed on prematurity (HR: 0.92, 95% CI: 0.68–1.23) and adverse perinatal outcomes, including fetal distress (HR: 1.29, 95% CI: 0.82–2.05), stillbirth (HR: 1.07, 95% CI: 0.48–2.38), and neonatal death (HR: 0.96, 95% CI: 0.35–2.67), even after adjusting for vaccination, comorbidity, gestational trimester, and periods of time. Conclusion: The risk of maternal death due to COVID-19 highlights the need for adequate preventive measures, particularly vaccination, during the prenatal and postpartum periods. Full article
(This article belongs to the Section Coronaviruses)
18 pages, 856 KiB  
Article
Viral Suppression and HIV Drug Resistance Among Patients on Second-Line Antiretroviral Therapy in Selected Health Facility in Ethiopia
by Kidist Zealiyas, Atsbeha Gebreegziabxier, Yimam Getaneh, Eleni Kidane, Belete Woldesemayat, Ajanaw Yizengaw, Gadisa Gutema, Sisay Adane, Mengistu Yimer, Amelework Yilma, Sisay Tadele, Sviataslau Sasinovich, Patrik Medstrand and Dawit Assefa Arimide
Viruses 2025, 17(2), 206; https://doi.org/10.3390/v17020206 - 31 Jan 2025
Viewed by 267
Abstract
HIV drug resistance (HIVDR) presents a significant challenge to antiretroviral therapy (ART) success, particularly in resource-limited settings like Ethiopia. This cross-sectional study investigated viral suppression rates and resistance patterns among patients on second-line ART across 28 Ethiopian health facilities. Blood samples collected from [...] Read more.
HIV drug resistance (HIVDR) presents a significant challenge to antiretroviral therapy (ART) success, particularly in resource-limited settings like Ethiopia. This cross-sectional study investigated viral suppression rates and resistance patterns among patients on second-line ART across 28 Ethiopian health facilities. Blood samples collected from 586 participants were analyzed to measure CD4 count and viral load and assess HIVDR in patients experiencing virological failure (VF) (viral load ≥ 1000 copies/mL). Demographic and clinical data were analyzed using logistic regression to identify factors associated with VF. Results showed that 13.82% of participants experienced VF, with 67.57% of genotyped samples exhibiting at least one drug resistance mutation. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), and protease inhibitors (PIs) was detected in 48.64%, 64.86%, and 18.92% of cases, respectively. Dual-class resistance was identified in 48.64% of patients, while triple-class resistance was detected in 18.92%. VF was more likely among students and those with CD4 counts below 200 cells/mm³, but less likely in patients on second-line treatment for 12 months or more. Our findings highlight a substantial HIVDR burden among patients on second-line ART with VF, emphasizing the need for comprehensive HIV care, including adherence support, regular viral load monitoring, and HIVDR testing. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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8 pages, 1904 KiB  
Case Report
Mexico’s Laboratory-Confirmed Human Case of Infection with the Influenza A(H5N2) Virus
by Joel Armando Vázquez-Pérez, Claudia Wong-Arámbula, Mario Solís-Hernández, Eduardo Becerril-Vargas, Gisela Barrera-Badillo, Víctor Hugo Ahumada-Topete, Santiago Avila-Rios, Rogelio Pérez-Padilla, Fidencio Mejía-Nepomuceno, Enrique Mendoza-Ramírez, Marisol Karina Rocha-Martinez, Carlos Javier Alcazar-Ramiro, Alfredo Cruz, Joaquin Zúñiga, Karolina Bozena Piekarska, Dayanira Sarith Arellano-Suarez, María Natividad Cruz-Ortiz, Tatiana Ernestina Núñez-García, Eréndira Molina-Gómez, Laura Adriana Flores-Cisneros, Rodrigo Aparicio-Antonio, Abril Rodríguez-Maldonado, Magaly Landa-Flores, Armando García-López, Jorge Membrillo-Hernández, Gabriel García-Rodríguez, Herlinda García-Lozano, Irma López-Martínez, Ruth Purisima González-Sánchez and Carmen Margarita Hernández-Cárdenasadd Show full author list remove Hide full author list
Viruses 2025, 17(2), 205; https://doi.org/10.3390/v17020205 - 31 Jan 2025
Viewed by 2094
Abstract
In April 2024, the Instituto Nacional de Enfermedades Respiratorias of Mexico City identified a case of unsubtypeable Influenza A in a 58-year-old immunocompromised patient with renal failure due to diabetic nephropathy and bacterial peritonitis. Through sequencing the M, NS, NA, NP, and HA [...] Read more.
In April 2024, the Instituto Nacional de Enfermedades Respiratorias of Mexico City identified a case of unsubtypeable Influenza A in a 58-year-old immunocompromised patient with renal failure due to diabetic nephropathy and bacterial peritonitis. Through sequencing the M, NS, NA, NP, and HA complete segments, we identified an H5N2 influenza virus with identity of 99% with avian influenza A(H5N2) from Texcoco, Mexico, in 2024. This case is the first reported with direct evidence of human infection caused by the H5N2 influenza virus; the relationship of the virus with the severity of his condition remains unknown. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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13 pages, 9541 KiB  
Article
Genetic Diversity and Spatiotemporal Distribution of SARS-CoV-2 Variants in Guinea: A Meta-Analysis of Sequence Data (2020–2023)
by Thibaut Armel Chérif Gnimadi, Kadio Jean-Jacques Olivier Kadio, Mano Joseph Mathew, Haby Diallo, Abdoul Karim Soumah, Alpha Kabiné Keita, Castro Gbêmêmali Hounmenou, Nicolas Fernandez-Nuñez, Nicole Vidal, Emilande Guichet, Ahidjo Ayouba, Eric Delaporte, Martine Peeters, Abdoulaye Touré and Alpha Kabinet Keita
Viruses 2025, 17(2), 204; https://doi.org/10.3390/v17020204 - 31 Jan 2025
Viewed by 434
Abstract
In Guinea, genomic surveillance has been established to generate sequences of and to identify locally circulating SARS-CoV-2 variants. This study aims to describe the distributions, genetic diversity, and origins of SARS-CoV-2 lineages circulating in Guinea during the COVID-19 pandemic. A migration analysis was [...] Read more.
In Guinea, genomic surveillance has been established to generate sequences of and to identify locally circulating SARS-CoV-2 variants. This study aims to describe the distributions, genetic diversity, and origins of SARS-CoV-2 lineages circulating in Guinea during the COVID-19 pandemic. A migration analysis was performed by selecting all sequences generated in Guinea for variants of concern and interest. From March 2020 to December 2023, 1038 sequences were generated in Guinea and submitted to the Global Initiative on Sharing All Influenza Data (GISAID) database. Of these, 73.1% corresponded to SARS-CoV-2 variants of concern, which were further grouped into Omicron (69.4%), Delta (21.9%), Alpha (6.6%), and Eta (2.1%). Other variants accounted for 26.9% of the total. Among the total variants analyzed, 75 importations into Guinea from various countries worldwide were identified. Most of the importations (40%) originated from African countries, followed in significance by those from European countries (25.3%) and Asia (18.6%). A significant migratory flow was observed within Guinea. The genomic surveillance reported in this study revealed the diversity of SARS-CoV-2 variants circulating in Guinea, emphasizing the importance of large-scale sequencing analyses in understanding the dynamics of the pandemic. Full article
(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 3rd Edition)
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48 pages, 1297 KiB  
Review
Viruses and the Brain—A Relationship Prone to Trouble
by Matylda Barbara Mielcarska and Barry T. Rouse
Viruses 2025, 17(2), 203; https://doi.org/10.3390/v17020203 - 31 Jan 2025
Viewed by 230
Abstract
Neurological disorders, some of which are associated with viral infections, are growing due to the aging and expanding population. Despite strong defenses of the central nervous system, some viruses have evolved ways to breach them, which often result in dire consequences. In this [...] Read more.
Neurological disorders, some of which are associated with viral infections, are growing due to the aging and expanding population. Despite strong defenses of the central nervous system, some viruses have evolved ways to breach them, which often result in dire consequences. In this review, we recount the various ways by which different viruses can enter the CNS, and we describe the consequences of such invasions. Consequences may manifest as acute disease, such as encephalitis, meningitis, or result in long-term effects, such as neuromuscular dysfunction, as occurs in poliomyelitis. We discuss evidence for viral involvement in the causation of well-known chronic neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis, multiple sclerosis, as well as vascular dementia in the elderly. We also describe the approaches currently available to control a few of the neural viral infections. These include antivirals that are effective against human immunodeficiency virus and herpes simplex virus, as well as vaccines valuable for controlling rabies virus, poliomyelitis virus, and some flavivirus infections. There is an urgent need to better understand, at a molecular level, how viruses contribute to acute and, especially, chronic neurological diseases and to develop more precise and effective vaccines and therapies. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
19 pages, 9669 KiB  
Article
The Genome Sequences of Baculoviruses from the Tufted Apple Bud Moth, Platynota idaeusalis, Reveal Recombination Between an Alphabaculovirus and a Betabaculovirus from the Same Host
by Robert L. Harrison, Michael A. Jansen, Austin N. Fife and Daniel L. Rowley
Viruses 2025, 17(2), 202; https://doi.org/10.3390/v17020202 - 30 Jan 2025
Viewed by 396
Abstract
The USDA-ARS collection of insect viruses at Beltsville, MD, USA, contains samples of an alphabaculovirus from larvae of the tufted apple bud moth, Platynota idaeusalis Walker, as well as a presumptive betabaculovirus from the same host species. The viruses in these samples—Platynota idaeusalis [...] Read more.
The USDA-ARS collection of insect viruses at Beltsville, MD, USA, contains samples of an alphabaculovirus from larvae of the tufted apple bud moth, Platynota idaeusalis Walker, as well as a presumptive betabaculovirus from the same host species. The viruses in these samples—Platynota idaeusalis nucleopolyhedrovirus isolate 2680 (PlidNPV-2680) and Platynota idaeusalis granulovirus isolate 2683 (PlidGV-2683)—were characterized by electron microscopy of their occlusion bodies (OBs) and determination and analysis of their genome sequences. Scanning and transmission electron microscopy of the OBs revealed morphologies typical for alphabaculoviruses and betabaculoviruses. Sequencing viral DNA resulted in circular genomes of 121,881 bp and 106,633 bp for PlidNPV-2680 and PlidGV-2683, respectively. Similar numbers of ORFs (128 for PlidNPV-2680, 125 for PlidGV-2683) were annotated, along with ten homologous regions (hrs) in the PlidNPV-2680 genome and five intergenic regions of tandem direct repeats (drs) in the PlidGV genome. Phylogenetic inference from core gene alignments suggested that PlidMNPV-2680 represents a unique lineage within the genus Alphabaculovirus, while PlidGV-2683 was grouped with clade b betabaculoviruses. A comparison of the PlidNPV-2680 and PlidGV-2683 genomes revealed a 1516 bp region in PlidNPV-2680 that exhibited 97.5% sequence identity to a region of the PlidGV-2683 genome, suggesting that recombination had occurred recently between viruses from these lineages. Full article
(This article belongs to the Section Invertebrate Viruses)
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20 pages, 2965 KiB  
Article
Identification of Diverse Bacteriophages Associated with Bees and Hoverflies
by Rohan A. Bandoo, Simona Kraberger, Cahit Ozturk, Michael C. Lund, Qiyun Zhu, Chelsea Cook, Brian Smith and Arvind Varsani
Viruses 2025, 17(2), 201; https://doi.org/10.3390/v17020201 - 30 Jan 2025
Viewed by 293
Abstract
Bacteriophages are the most numerous, ubiquitous, and diverse biological entities on the planet. Prior studies have identified bacteriophages associated with pathogenic and commensal microbiota of honeybees. In this study we expand on what is known about bacteriophages from the lineages Caudoviricetes, Inoviridae [...] Read more.
Bacteriophages are the most numerous, ubiquitous, and diverse biological entities on the planet. Prior studies have identified bacteriophages associated with pathogenic and commensal microbiota of honeybees. In this study we expand on what is known about bacteriophages from the lineages Caudoviricetes, Inoviridae, and Microviridae, which are associated with honeybees (Apidae, Apis mellifera), solitary bees of the genus Nomia (Halictidae, Nomia), and hoverflies (Syrphidae). The complete genomes of seven caudoviruses, seven inoviruses, and 288 microviruses were assembled from honeybees (n = 286) and hoverflies in Arizona (n = 2). We used bacterial host predictive software and sequence read mapping programs to infer the commensal and transient bacterial hosts of pollinating insects. Lastly, this study explores the phylogenetic relationships of microviruses sampled from bees, opportunistically sampled pollinating insects such as hoverflies, and blackflies. Full article
(This article belongs to the Section Bacterial Viruses)
14 pages, 1227 KiB  
Article
Development of Chimera AMP–Endolysin with Wider Spectra Against Gram-Negative Bacteria Using High-Throughput Assay
by Masato Kogawa, Takuya Yoda, Ayumi Matsuhashi, Ai Matsushita, Yoshiki Otsuka, Shohei Shibagaki, Masahito Hosokawa and Soichiro Tsuda
Viruses 2025, 17(2), 200; https://doi.org/10.3390/v17020200 - 30 Jan 2025
Viewed by 333
Abstract
Bacteriophage-derived endolysins are being developed as an alternative to antimicrobials. The development of endolysins against Gram-negative bacteria requires the discovery of effective endolysins against the target species and the capability to penetrate the outer membrane of bacteria by endolysin. Here, we propose an [...] Read more.
Bacteriophage-derived endolysins are being developed as an alternative to antimicrobials. The development of endolysins against Gram-negative bacteria requires the discovery of effective endolysins against the target species and the capability to penetrate the outer membrane of bacteria by endolysin. Here, we propose an efficient endolysin development approach that combines a data-driven endolysin search utilizing bacterial genomes with high-throughput laboratory assays. As a proof of concept, we analyzed endolysin genes detected in 273 bacterial genomes of Acinetobacter, Pseudomonas, and Escherichia. Firstly, we conducted assays of 192 recombinants of endolysin genes obtained through in silico search from bacterial genomes and identified natural endolysins degrading peptidoglycan of Acinetobacter baumannii. Then, we performed high-throughput screening against Gram-negative bacteria for hundreds of chimera AMP–endolysins, natural endolysin conjugated with antimicrobial peptide. As a result, we obtained four chimera AMP–endolysins against A. baumannii, which demonstrated the minimum inhibitory concentration ranging from 4 to 8 μg/mL. Moreover, we assessed the antimicrobial spectra of these chimera AMP–endolysins, validating that two endolysins exhibited antimicrobial efficacy against Pseudomonas aeruginosa and Escherichia coli with <32 μg/mL of concentration. This endolysin development approach can be applied to other Gram-negative bacterial targets and is expected to facilitate the acquisition of effective novel endolysins. Full article
(This article belongs to the Special Issue Bacteriophage Lytic Proteins)
18 pages, 3056 KiB  
Article
TRIM38 Inhibits Zika Virus by Upregulating RIG-I/MDA5 Pathway and Promoting Ubiquitin-Mediated Degradation of Viral NS3 Protein
by Jing He, Yulian Kuang, Kui Xu, Rong Huang, Xiaoyao Yang, Liyao Deng, Xiaojuan Feng, Yang Ren, Jian Yang and Lei Yuan
Viruses 2025, 17(2), 199; https://doi.org/10.3390/v17020199 - 30 Jan 2025
Viewed by 251
Abstract
Members of the tripartite motif (TRIM)-containing protein family play crucial roles in regulating immune system responses. The TRIM38 protein regulates host innate immunity and directly degrades some viral proteins through its E3 ubiquitin ligase activity. This study demonstrated that Zika virus (ZIKV) infection [...] Read more.
Members of the tripartite motif (TRIM)-containing protein family play crucial roles in regulating immune system responses. The TRIM38 protein regulates host innate immunity and directly degrades some viral proteins through its E3 ubiquitin ligase activity. This study demonstrated that Zika virus (ZIKV) infection can promote the expression of TRIM38 in human glioma cells (U251). TRIM38 overexpression restricted ZIKV replication in U251 cells, while TRIM38 knockout enhanced ZIKV replication. TRIM38 overexpression upregulated the RIG-I/MDA5 pathway and promoted the level of IFN-β early during viral infection, while TRIM38 knockout had the opposite effect. In addition, TRIM38 interacts with ZIKV non-structural protein 3 (NS3) and degrades the NS3 protein through a lysosome-dependent manner via the E3 ligase activity of TRIM38. Deletion of the RING domain of TRIM38 abrogates its interaction with NS3 and impairs the antiviral activity of TRIM38. Our results indicate that TRIM38 is a novel antiviral protein against ZIKV, and it exerts antiviral activity by upregulating the RIG-I/MDA5 pathway, increasing IFN-β levels, and degrading the viral NS3 protein. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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24 pages, 4825 KiB  
Article
Recombination Between Bubaline Alphaherpesvirus 1 and Bovine Alphaherpesvirus 1 as a Possible Origin of Bovine Alphaherpesvirus 5
by Bruna S. Paredes-Galarza, Fabrício S. Campos, Martha T. Oliveira, Bruno A. Prandi, Ueric J. B. de Souza, Dennis M. Junqueira, Darren P. Martin, Fernando R. Spilki, Ana C. Franco and Paulo M. Roehe
Viruses 2025, 17(2), 198; https://doi.org/10.3390/v17020198 - 30 Jan 2025
Viewed by 236
Abstract
Bovine alphaherpesvirus 1 (BoAHV1) is prevalent in cattle throughout the world, whereas bovine alphaherpesvirus 5 (BoAHV5) prevalence seems restricted to some countries in South America, Australia, and other regions, mainly in the Southern Hemisphere. BoAHV5 infections occur where water buffalo (Bubalus bubalis [...] Read more.
Bovine alphaherpesvirus 1 (BoAHV1) is prevalent in cattle throughout the world, whereas bovine alphaherpesvirus 5 (BoAHV5) prevalence seems restricted to some countries in South America, Australia, and other regions, mainly in the Southern Hemisphere. BoAHV5 infections occur where water buffalo (Bubalus bubalis) farming is practiced, often close to cattle (Bos taurus) farms. Bubaline alphaherpesvirus 1 (BuAHV1), a virus whose natural host is believed to be the water buffaloes, usually causes asymptomatic infections in that species. Here, evidence is provided confirming the close relationship between BuAHV1 and BoAHV5. Phylogenetic and recombination analyses were used to reveal the evolutionary relationship between all whole-genome sequences of BoAHV1 (n = 52), BoAHV5 (n = 7), and BuAHV1 (n = 6) available to date. It is proposed here that BoAHV5 most likely resulted from multiple recombination events between a BuAHV1-like ancestor and BoAHV1-like viruses. The BoAHV5 whole unique short (US) region and most of the unique long (UL) genomic regions seem to have been derived from a BuAHV1-like parental genome, whereas at least six small segments of the UL (corresponding to nucleotides 8287 to 8624; 10,658 to 14,496; 48,013 to 48,269; 71,379 to 71,927; 81,426 to 85,003; and 94,012 to 96,841 of the BoAHV5 genome) and two small segments of the US (corresponding to nucleotides 107,039 to 107,581 and 131,267 to 131,810) have been derived from a BoAHV1-like parental genome. The hypothesis that the BoAHV5 species may have originated following a series of recombination events between BuAHV1 and BoAHV1 variants is consistent with the geographical distribution of BoAHV5, which seems to be prevalent in the regions where cattle and water buffalo farming overlap. Full article
(This article belongs to the Section Animal Viruses)
12 pages, 2855 KiB  
Perspective
Evolutionary Mechanisms of the Emergence of the Variants of Concern of SARS-CoV-2
by Igor M. Rouzine
Viruses 2025, 17(2), 197; https://doi.org/10.3390/v17020197 - 30 Jan 2025
Viewed by 352
Abstract
The evolutionary origin of the variants of concern (VOCs) of SARS-CoV-2, characterized by a large number of new substitutions and strong changes in virulence and transmission rate, is intensely debated. The leading explanation in the literature is a chronic infection in immunocompromised individuals, [...] Read more.
The evolutionary origin of the variants of concern (VOCs) of SARS-CoV-2, characterized by a large number of new substitutions and strong changes in virulence and transmission rate, is intensely debated. The leading explanation in the literature is a chronic infection in immunocompromised individuals, where the virus evolves before returning into the main population. The present article reviews less-investigated hypotheses of VOC emergence with transmission between acutely infected hosts, with a focus on the mathematical models of stochastic evolution that have proved to be useful for other viruses, such as HIV and influenza virus. The central message is that understanding the acting factors of VOC evolution requires the framework of stochastic multi-locus evolution models, and that alternative hypotheses can be effectively verified by fitting results of computer simulation to empirical data. Full article
(This article belongs to the Section Animal Viruses)
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20 pages, 1735 KiB  
Article
Perpetuation of Avian Influenza from Molt to Fall Migration in Wild Swan Geese (Anser cygnoides): An Agent-Based Modeling Approach
by John Y. Takekawa, Chang-Yong Choi, Diann J. Prosser, Jeffery D. Sullivan, Nyambayar Batbayar and Xiangming Xiao
Viruses 2025, 17(2), 196; https://doi.org/10.3390/v17020196 - 30 Jan 2025
Viewed by 427
Abstract
Wild waterfowl are considered to be the reservoir of avian influenza, but their distinct annual life cycle stages and their contribution to disease dynamics are not well understood. Studies of the highly pathogenic avian influenza (HPAI) virus have primarily focused on wintering grounds, [...] Read more.
Wild waterfowl are considered to be the reservoir of avian influenza, but their distinct annual life cycle stages and their contribution to disease dynamics are not well understood. Studies of the highly pathogenic avian influenza (HPAI) virus have primarily focused on wintering grounds, where human and poultry densities are high year-round, compared with breeding grounds, where migratory waterfowl are more isolated. Few if any studies of avian influenza have focused on the molting stage where wild waterfowl congregate in a few selected wetlands and undergo the simultaneous molt of wing and tail feathers during a vulnerable flightless period. The molting stage may be one of the most important periods for the perpetuation of the disease in waterfowl, since during this stage, immunologically naïve young birds and adults freely intermix prior to the fall migration. Our study incorporated empirical data from virological field samplings and markings of Swan Geese (Anser cygnoides) on their breeding grounds in Mongolia in an integrated agent-based model (ABM) that included susceptible–exposed–infectious–recovered (SEIR) states. Our ABM results provided unique insights and indicated that individual movements between different molting wetlands and the transmission rate were the key predictors of HPAI perpetuation. While wetland extent was not a significant predictor of HPAI perpetuation, it had a large effect on the number of infections and associated death toll. Our results indicate that conserving undisturbed habitats for wild waterfowl during the molting stage of the breeding season could reduce the risk of HPAI transmission. Full article
15 pages, 2006 KiB  
Article
Statistical Distributions of Genome Assemblies Reveal Random Effects in Ancient Viral DNA Reconstructions
by Fernando Antoneli, Cristina M. Peter and Marcelo R. S. Briones
Viruses 2025, 17(2), 195; https://doi.org/10.3390/v17020195 - 30 Jan 2025
Viewed by 334
Abstract
Ancient human viruses have been detected in ancient DNA (aDNA) samples of both Anatomically Modern Humans and Neanderthals. Reconstructing genomes from aDNA using reference mapping presents numerous problems due to the unique nature of ancient samples, their degraded state, smaller read sizes and [...] Read more.
Ancient human viruses have been detected in ancient DNA (aDNA) samples of both Anatomically Modern Humans and Neanderthals. Reconstructing genomes from aDNA using reference mapping presents numerous problems due to the unique nature of ancient samples, their degraded state, smaller read sizes and the limitations of current methodologies. The spurious alignments of reads to reference sequences (mapping) are a main source of false positives in aDNA assemblies and the assessment of signal-to-noise ratios is essential to differentiate bona fide reconstructions from random, noisy assemblies. Here, we analyzed the statistical distributions of viral genome assemblies, ancient and modern, and their respective random “mock” controls used to evaluate the signal-to-noise ratio. We tested if differences between real and random assemblies could be detected from their statistical distributions. Our analysis shows that the coverage distributions of (1) real viral aDNA assemblies of adenovirus (ADV), herpesvirus (HSV) and papillomavirus (HPV) do not follow power laws nor log-normal laws, (2) (ADV) and control aDNA assemblies are well approximated by log-normal laws, (3) negative control parvovirus B19 (real and random) follow a power law with infinite variance and (4) the mapDamage negative control with non-ancient DNA (modern ADV) and the mapDamage positive control (human mtDNA) are well approximated by the negative binomial distribution, consistent with the Lander–Waterman model. Our results show that the tails of the distributions of aDNA and their controls reveal the weight of random effects and can differentiate spurious assemblies, or false positives, from bona fide assemblies. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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27 pages, 4876 KiB  
Article
A Mutant of Africa Swine Fever Virus Protein p72 Enhances Antibody Production and Regulates the Production of Cytokines
by Mingzhi Li, Yihao Wang, Quansheng Wang, Lingdi Yang, Shiguo Liu, Guangzhi Li, Ziqi Song, Chulu Huang, Lumei Kang, Yanni Zhang, Ting Wang, Lingbao Kong and Sha Li
Viruses 2025, 17(2), 194; https://doi.org/10.3390/v17020194 - 30 Jan 2025
Viewed by 365
Abstract
African swine fever virus (ASFV) is a severe threat to the global pig industry, and domestic pigs mostly develop severe clinical manifestations upon viral invasion. Currently, there is no available vaccine against ASFV. Its capsid structural protein p72 is one of the immuno-dominant [...] Read more.
African swine fever virus (ASFV) is a severe threat to the global pig industry, and domestic pigs mostly develop severe clinical manifestations upon viral invasion. Currently, there is no available vaccine against ASFV. Its capsid structural protein p72 is one of the immuno-dominant proteins. In this study, we unexpectedly obtained a p72 mutant protein (p72∆377–428) which deleted the aa 377–428 within p72 and had stable and high expression in E. coli. Using SWISS-MODEL software, the prediction showed that p72∆377–428 was quite distinct from the wild-type p72 protein in structure. p72∆377–428 induced stronger antibody production in mice on day 42 and 56 post immunization and could recognize ASFV-infected swine sera. p72∆377–428 reduced IFN-γ production in the splenocytes from p72∆377–428-immunized mice and p72∆377–428-treated swine macrophages compared to p72. p72∆377–428 also decreased the production of pro-inflammatory cytokine genes, including IL-1β, IL-6, and IL-12, compared to p72 in mice. Further, we found that p72∆377–428 reduced the induction of pro-inflammatory cytokine genes by inhibiting AKT phosphorylation and HIF1α expression. Taken together, these findings have implications for immunological function and the corresponding mechanism of ASFV p72, and our study indicates that p72∆377–428 could serve as a novel candidate for ASFV vaccines and diagnostic reagents. Full article
(This article belongs to the Section Animal Viruses)
28 pages, 4914 KiB  
Article
Multiple Co-Infecting Caliciviruses in Oral Fluid and Enteric Samples of Swine Detected by a Novel RT-qPCR Assay and a 3′RACE-PCR-NGS Method
by Zoltán László, Péter Pankovics, Péter Urbán, Róbert Herczeg, Gyula Balka, Barbara Igriczi, Attila Cságola, Mihály Albert, Fruzsina Tóth, Gábor Reuter and Ákos Boros
Viruses 2025, 17(2), 193; https://doi.org/10.3390/v17020193 - 30 Jan 2025
Viewed by 247
Abstract
Caliciviruses including noro- and sapoviruses of family Caliciviridae are important enteric human and swine pathogens, while others, like valoviruses, are less known. In this study, we developed a detection and typing pipeline for the most prevalent swine enteric caliciviruses—sapovirus GIII (Sw-SaV), norovirus GII [...] Read more.
Caliciviruses including noro- and sapoviruses of family Caliciviridae are important enteric human and swine pathogens, while others, like valoviruses, are less known. In this study, we developed a detection and typing pipeline for the most prevalent swine enteric caliciviruses—sapovirus GIII (Sw-SaV), norovirus GII (Sw-NoV), and valovirus GI (Sw-VaV). The pipeline integrates triplex RT-qPCR, 3′RACE semi-nested PCR, and next-generation sequencing (NovaSeq, Illumina) techniques. A small-scale epidemiological investigation was conducted on archived enteric and, for the first time, on oral fluid/saliva samples of diarrheic and asymptomatic swine of varying ages from Hungary and Slovakia. In enteric samples, Sw-SaV was the most prevalent, detected in 26.26% of samples, primarily in diarrheic pigs with low Cq values, followed by Sw-NoV (2.53%) in nursery pigs. In oral fluid samples, Sw-NoV predominated (7.46%), followed by Sw-SaV (4.39%). Sw-VaVs were sporadically found in both sample types. A natural, asymptomatic Sw-SaV outbreak was retrospectively detected where the transient shedding of the virus was <2 weeks. Complete capsid sequences (n = 59; 43 Sw-SaV, 13 Sw-NoV, and 3 Sw-VaV) including multiple (up to five) co-infecting variants were identified. Sw-SaV sequences belong to seven genotypes, while Sw-NoV and Sw-VaV strains clustered into distinct sub-clades, highlighting the complex diversity of these enteric caliciviruses in swine. Full article
(This article belongs to the Special Issue Porcine Viruses 2024)
25 pages, 2026 KiB  
Systematic Review
A Systematic Literature Review of Variables Associated with the Occurrence of African Swine Fever
by Sofie Dhollander, Eleonora Chinchio, Stefania Tampach, Lina Mur, Estelle Méroc, Hans-Hermann Thulke, José Abrahantes Cortiñas, Anette E. Boklund, Karl Stahl and Jan Arend Stegeman
Viruses 2025, 17(2), 192; https://doi.org/10.3390/v17020192 - 30 Jan 2025
Viewed by 312
Abstract
Since African swine fever virus (ASFV) genotype II reached Europe in 2007 and has widely spread, causing important economic losses to the pig production sector. To guide policy and management actions, robust quantitative evidence about possible explanatory variables associated with ASF in domestic [...] Read more.
Since African swine fever virus (ASFV) genotype II reached Europe in 2007 and has widely spread, causing important economic losses to the pig production sector. To guide policy and management actions, robust quantitative evidence about possible explanatory variables associated with ASF in domestic pigs and Eurasian wild boar (Sus scrofa) is needed. To this aim, a systematic literature review of the scientific evidence available on variables analysed through quantitative methods investigating their possible association with ASF occurrence was carried out in 2021 and updated in 2024. Information on article metadata, study settings, and details of the analysed variables were extracted from the identified articles. The variables were structured in categories and subcategories, and their frequencies were evaluated, as well as the proportions of the studied variables that proved significant in each subcategory. The literature search retrieved 569 articles, resulting in 48 inclusions in the review after application of the selection criteria. The categories of variables most often significantly associated with the occurrence of ASF in domestic pigs were related to the ASF virus infection pressure in the area, socio-economic factors (mainly human population density and poverty), the pig farming system (pig or farm density and certain biosecurity practises), and wild boar habitats. For wild boars, these were also variables related to ASFV infection pressure in the area, wild boar habitats (mainly climatic conditions, vegetation, waterbodies), and socio-economic factors (especially human population and poverty-related variables). Despite the many studies of variables possibly associated with ASF occurrence, the review identified a gap in quantitative observational studies focusing on manageable variables, i.e., those related to specific biosecurity measures applied to pig farms and during hunting. To allow for a meta-analysis of the results, these studies should be performed according to standardised protocols using harmonised data collections. Full article
(This article belongs to the Collection African Swine Fever Virus (ASFV))
17 pages, 3042 KiB  
Article
The Chikungunya Virus nsP3 Macro Domain Inhibits Activation of the NF-κB Pathway
by Grace C. Roberts, Nicola J. Stonehouse and Mark Harris
Viruses 2025, 17(2), 191; https://doi.org/10.3390/v17020191 - 29 Jan 2025
Viewed by 495
Abstract
The role of the chikungunya virus (CHIKV) non-structural protein 3 (nsP3) in the virus lifecycle is poorly understood. The protein comprises three domains. At the N-terminus is a macro domain, biochemically characterised to bind both RNA and ADP-ribose and to possess ADP-ribosyl hydrolase [...] Read more.
The role of the chikungunya virus (CHIKV) non-structural protein 3 (nsP3) in the virus lifecycle is poorly understood. The protein comprises three domains. At the N-terminus is a macro domain, biochemically characterised to bind both RNA and ADP-ribose and to possess ADP-ribosyl hydrolase activity—an enzymatic activity that removes ADP-ribose from mono-ADP-ribosylated proteins. As ADP-ribosylation is important in the signalling pathway, leading to activation of the transcription factor NF-κB, we sought to determine whether the macro domain might perturb NF-κB signalling. We first showed that CHIKV infection did not induce NF-κB activation and could not block exogenous activation of the pathway via TNFα, although TNFα treatment did result in a modest reduction in virus titre. In contrast, ectopic expression of nsP3 was able to inhibit both basal and TNFα-mediated NF-κB activation, and this was dependent on the macro domain, as a mutation previously shown to disrupt ADP-ribose binding and hydrolase activity (D10A) eliminated the ability to inhibit NF-κB activation. The macro domain D10A mutant also resulted in a dramatic reduction in virus infectivity, consistent with the notion that the ability of the macro domain to inhibit NF-κB activation plays a role in the virus lifecycle. Full article
(This article belongs to the Special Issue Chikungunya Virus and Emerging Alphaviruses—Volume II)
23 pages, 8693 KiB  
Article
DNA-Binding Activities of KSHV DNA Polymerase Processivity Factor (PF-8) Complexes
by Jennifer Kneas Travis, Megan Martin and Lindsey M. Costantini
Viruses 2025, 17(2), 190; https://doi.org/10.3390/v17020190 - 29 Jan 2025
Viewed by 309
Abstract
Kaposi’s Sarcoma Herpesvirus (KSHV) is the causative agent of several human diseases. There are few effective treatments available to treat infection and KSHV oncogenesis. Disrupting the KSHV infectious cycle would diminish the viral spread. The KSHV lytic phase and production of new virions [...] Read more.
Kaposi’s Sarcoma Herpesvirus (KSHV) is the causative agent of several human diseases. There are few effective treatments available to treat infection and KSHV oncogenesis. Disrupting the KSHV infectious cycle would diminish the viral spread. The KSHV lytic phase and production of new virions require efficient copying and packaging of the KSHV genome. KSHV encodes its own lytic DNA replication machinery, including the processivity factor (PF-8), which presents itself as an attractive target for antiviral development. We characterized PF-8 at the single molecule level using transmission electron microscopy to identify key molecular interactions that mediate viral DNA replication initiation. Our results indicate that PF-8 forms oligomeric ring structures (tetramer, hexamer, and/or dodecamer) similar to the related Epstein–Barr virus processivity factor (BMRF1). Our DNA positional mapping revealed high-frequency binding locations of PF-8 within the lytic origin of replication (OriLyt). A multi-variable analysis of PF-8 DNA-binding activity with three mutant OriLyts provides new insights into the mechanisms that PF-8 associates with viral DNA and complexes to form multi-ring-like structures. Collectively, these data enhance the mechanistic understanding of the molecular interactions (protein–protein and protein-DNA) of an essential KSHV DNA replication protein. Full article
(This article belongs to the Special Issue Molecular and Cellular Biology of Human Oncogenic Viruses)
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23 pages, 7595 KiB  
Article
New Bacteriophage Pseudomonas Phage Ka2 from a Tributary Stream of Lake Baikal
by Valeriya Ilyina, Alina Gatina, Elena Trizna, Maria Siniagina, Liudmila Yadykova, Anastasiya Ivannikova, Georgiy Ozhegov, Daria Zhuravleva, Marina Fedorova, Anna Gorshkova, Peter Evseev, Valentin Drucker, Mikhail Bogachev, Shamil Validov, Maya Kharitonova and Airat Kayumov
Viruses 2025, 17(2), 189; https://doi.org/10.3390/v17020189 - 29 Jan 2025
Viewed by 448
Abstract
Pseudomonas aeruginosa, an opportunistic pathogen, causes various biofilm-associated infections like pneumonia, infections in cystic fibrosis patients, and urinary tract and burn infections with high morbidity and mortality, as well as low treatment efficacy due to the extremely wide spread of isolates with [...] Read more.
Pseudomonas aeruginosa, an opportunistic pathogen, causes various biofilm-associated infections like pneumonia, infections in cystic fibrosis patients, and urinary tract and burn infections with high morbidity and mortality, as well as low treatment efficacy due to the extremely wide spread of isolates with multidrug resistance. Here, we report the new bacteriophage Pseudomonas phage Ka2 isolated from a tributary stream of Lake Baikal and belonging to the Pbunavirus genus. Transmission electron microscopy resolved that Pseudomonas phage Ka2 has a capsid of 57 ± 9 nm and a contractile and inflexible tail of 115 ± 10 nm in the non-contracted state. The genome consists of 66,310 bp with a GC content of 55% and contains 96 coding sequences. Among them, 52 encode proteins have known functions, and none of them are potentially associated with lysogeny. The bacteriophage lyses 21 of 30 P. aeruginosa clinical isolates and decreases the MIC of amikacin, gentamicin, and cefepime up to 16-fold and the MIC of colistin up to 32-fold. When treating the biofilms with Ka2, the biomass was reduced by twice, and up to a 32-fold decrease in the antibiotics MBC against biofilm-embedded cells was achieved by the combination of Ka2 with cefepime for the PAO1 strain, along with a decrease of up to 16-fold with either amikacin or colistin for clinical isolates. Taken together, these data characterize the new Pseudomonas phage Ka2 as a promising tool for the combined treatment of infections associated with P. aeruginosa biofilms. Full article
(This article belongs to the Special Issue Phage-Bacteria Interplay in Health and Disease, Second Edition)
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